High yield growth of patterned vertically aligned carbon nanotubes using inkjet-printed catalyst.

PubMed

Beard, James D; Stringer, Jonathan; Ghita, Oana R; Smith, Patrick J

2013-10-09

This study reports on the fabrication of vertically aligned carbon nanotubes localized at specific sites on a growth substrate by deposition of a nanoparticle suspension using inkjet printing. Carbon nanotubes were grown with high yield as vertically aligned forests to a length of approximately 400 μm. The use of inkjet printing for catalyst fabrication considerably improves the production rate of vertically aligned patterned nanotube forests compared with conventional patterning techniques, for example, electron beam lithography or photolithography.

Precise design-based defect characterization and root cause analysis

NASA Astrophysics Data System (ADS)

Xie, Qian; Venkatachalam, Panneerselvam; Lee, Julie; Chen, Zhijin; Zafar, Khurram

2017-03-01

As semiconductor manufacturing continues its march towards more advanced technology nodes, it becomes increasingly important to identify and characterize design weak points, which is typically done using a combination of inline inspection data and the physical layout (or design). However, the employed methodologies have been somewhat imprecise, relying greatly on statistical techniques to signal excursions. For example, defect location error that is inherent to inspection tools prevents them from reporting the true locations of defects. Therefore, common operations such as background-based binning that are designed to identify frequently failing patterns cannot reliably identify specific weak patterns. They can only identify an approximate set of possible weak patterns, but within these sets there are many perfectly good patterns. Additionally, characterizing the failure rate of a known weak pattern based on inline inspection data also has a lot of fuzziness due to coordinate uncertainty. SEM (Scanning Electron Microscope) Review attempts to come to the rescue by capturing high resolution images of the regions surrounding the reported defect locations, but SEM images are reviewed by human operators and the weak patterns revealed in those images must be manually identified and classified. Compounding the problem is the fact that a single Review SEM image may contain multiple defective patterns and several of those patterns might not appear defective to the human eye. In this paper we describe a significantly improved methodology that brings advanced computer image processing and design-overlay techniques to better address the challenges posed by today's leading technology nodes. Specifically, new software techniques allow the computer to analyze Review SEM images in detail, to overlay those images with reference design to detect every defect that might be present in all regions of interest within the overlaid reference design (including several classes of defects that human operators will typically miss), to obtain the exact defect location on design, to compare all defective patterns thus detected against a library of known patterns, and to classify all defective patterns as either new or known. By applying the computer to these tasks, we automate the entire process from defective pattern identification to pattern classification with high precision, and we perform this operation en masse during R & D, ramp, and volume production. By adopting the methodology, whenever a specific weak pattern is identified, we are able to run a series of characterization operations to ultimately arrive at the root cause. These characterization operations can include (a) searching all pre-existing Review SEM images for the presence of the specific weak pattern to determine whether there is any spatial (within die or within wafer) or temporal (within any particular date range, before or after a mask revision, etc.) correlation and (b) understanding the failure rate of the specific weak pattern to prioritize the urgency of the problem, (c) comparing the weak pattern against an OPC (Optical Procimity Correction) Verification report or a PWQ (Process Window Qualification)/FEM (Focus Exposure Matrix) result to assess the likelihood of it being a litho-sensitive pattern, etc. After resolving the specific weak pattern, we will categorize it as known pattern, and the engineer will move forward with discovering new weak patterns.

A Robust and Engineerable Self-Assembling Protein Template for the Synthesis and Patterning of Ordered Nanoparticle Arrays

NASA Technical Reports Server (NTRS)

McMillan, R. Andrew; Howard, Jeanie; Zaluzec, Nestor J.; Kagawa, Hiromi K.; Li, Yi-Fen; Paavola, Chad D.; Trent, Jonathan D.

2004-01-01

Self-assembling biomolecules that form highly ordered structures have attracted interest as potential alternatives to conventional lithographic processes for patterning materials. Here we introduce a general technique for patterning materials on the nanoscale using genetically modified protein cage structures called chaperonins that self-assemble into crystalline templates. Constrained chemical synthesis of transition metal nanoparticles is specific to templates genetically functionalized with poly-Histidine sequences. These arrays of materials are ordered by the nanoscale structure of the crystallized protein. This system may be easily adapted to pattern a variety of materials given the rapidly growing list of peptide sequences selected by screening for specificity for inorganic materials.

The Pattern of Gestational Weight Gain is Associated with Changes in Maternal Body Composition and Neonatal Size.

PubMed

Widen, Elizabeth M; Factor-Litvak, Pam R; Gallagher, Dympna; Paxton, Anne; Pierson, Richard N; Heymsfield, Steven B; Lederman, Sally A

2015-10-01

The pattern of gestational weight gain (GWG) reflects general nutrient availability to support growing fetal and maternal compartments and may contribute to later health, but how it relates to changes in maternal body composition is unknown. We evaluated how the pattern of GWG related to changes in maternal body composition during pregnancy and infant size at birth. A prospective, multi-ethnic cohort of 156 pregnant women and their infants was studied in New York City. Prenatal weights were used to estimate total and rate (kg/week) of GWG by trimester. Linear regression models evaluated the association between trimester-specific GWG group (low, medium, high GWG) [total (low ≤25, high ≥75 percentile) or rate (defined by tertiles)] and infant weight, length and maternal body composition changes from 14 to 37 weeks, adjusting for covariates. Compared to the low gain group, medium/high rate of GWG in the second trimester and high rate of GWG in the third trimester were associated with larger gains in maternal fat mass (β range for fat Δ = 2.86-5.29 kg, all p < 0.01). For infant outcomes, high rate of GWG in the second trimester was associated with higher birth weight (β = 356 g, p = 0.001) and length (β = 0.85 cm, p = 0.002). First and third trimester GWG were not associated with neonatal size. The trimester specific pattern and rate of GWG reflect changes in maternal body fat and body water, and are associated with neonatal size, which supports the importance of monitoring trimester-specific GWG.

Effects of Diet on Sleep Quality12

PubMed Central

Mikic, Anja; Pietrolungo, Cara E

2016-01-01

There is much emerging information surrounding the impact of sleep duration and quality on food choice and consumption in both children and adults. However, less attention has been paid to the effects of dietary patterns and specific foods on nighttime sleep. Early studies have shown that certain dietary patterns may affect not only daytime alertness but also nighttime sleep. In this review, we surveyed the literature to describe the role of food consumption on sleep. Research has focused on the effects of mixed meal patterns, such as high-carbohydrate plus low-fat or low-carbohydrate diets, over the short term on sleep. Such studies highlight a potential effect of macronutrient intakes on sleep variables, particularly alterations in slow wave sleep and rapid eye movement sleep with changes in carbohydrate and fat intakes. Other studies instead examined the intake of specific foods, consumed at a fixed time relative to sleep, on sleep architecture and quality. Those foods, specifically milk, fatty fish, tart cherry juice, and kiwifruit, are reviewed here. Studies provide some evidence for a role of certain dietary patterns and foods in the promotion of high-quality sleep, but more studies are necessary to confirm those preliminary findings. PMID:27633109

Lithographically Defined Three-dimensional Pore-patterned Carbon with Nitrogen Doping for High-Performance Ultrathin Supercapacitor Applications

PubMed Central

Kang, Da-Young; Moon, Jun Hyuk

2014-01-01

Supercapacitors that exhibit long cycle lives and fast charge/discharge rates are a promising energy-storage technology for next-generation mobile or wearable electronic systems. A great challenge facing the fabrication of ultrathin supercapacitor components, specifically their porous electrodes, is whether such components can be integrated with the fabrication of electronic devices, i.e., semiconductor fabrication processes. Here, we introduce the lithographic fabrication of micrometre-thick, submicrometre-pore-patterned carbon for supercapacitor electrodes. The pore patterns designed by multi-beam interference lithography and direct carbonisation of the photoresist pattern produced pore-patterned carbon films. A facile doping process was subsequently employed to introduce nitrogen atoms into the carbon, which was intended to further enhance the carbon's capacitive properties. Specifically, during these fabrication steps, we developed an approach that uses a supporting shell on the surface of the pore patterns to maintain their structural integrity. The nitrogen-doped, pore-patterned carbon electrodes exhibited an areal specific capacitance of 32.7 mF/cm2 at 0.5 mA/cm2 when used as supercapacitor electrodes, which is approximately 20 times greater than that of commercially available MWCNT films measured under the same conditions. PMID:24953307

Patterns of Childhood Abuse and Neglect in a Representative German Population Sample

PubMed Central

Schilling, Christoph; Weidner, Kerstin; Brähler, Elmar; Glaesmer, Heide; Häuser, Winfried; Pöhlmann, Karin

2016-01-01

Background Different types of childhood maltreatment, like emotional abuse, emotional neglect, physical abuse, physical neglect and sexual abuse are interrelated because of their co-occurrence. Different patterns of childhood abuse and neglect are associated with the degree of severity of mental disorders in adulthood. The purpose of this study was (a) to identify different patterns of childhood maltreatment in a representative German community sample, (b) to replicate the patterns of childhood neglect and abuse recently found in a clinical German sample, (c) to examine whether participants reporting exposure to specific patterns of child maltreatment would report different levels of psychological distress, and (d) to compare the results of the typological approach and the results of a cumulative risk model based on our data set. Methods In a cross-sectional survey conducted in 2010, a representative random sample of 2504 German participants aged between 14 and 92 years completed the Childhood Trauma Questionnaire (CTQ). General anxiety and depression were assessed by standardized questionnaires (GAD-2, PHQ-2). Cluster analysis was conducted with the CTQ-subscales to identify different patterns of childhood maltreatment. Results Three different patterns of childhood abuse and neglect could be identified by cluster analysis. Cluster one showed low values on all CTQ-scales. Cluster two showed high values in emotional and physical neglect. Only cluster three showed high values in physical and sexual abuse. The three patterns of childhood maltreatment showed different degrees of depression (PHQ-2) and anxiety (GAD-2). Cluster one showed lowest levels of psychological distress, cluster three showed highest levels of mental distress. Conclusion The results show that different types of childhood maltreatment are interrelated and can be grouped into specific patterns of childhood abuse and neglect, which are associated with differing severity of psychological distress in adulthood. The results correspond to those recently found in a German clinical sample and support a typological approach in the research of maltreatment. While cumulative risk models focus on the number of maltreatment types, the typological approach takes the number as well as the severity of the maltreatment types into account. Thus, specific patterns of maltreatment can be examined with regard to specific long-term psychological consequences. PMID:27442446

Progress in mask replication using jet and flash imprint lithography

NASA Astrophysics Data System (ADS)

Selinidis, Kosta S.; Brooks, Cynthia B.; Doyle, Gary F.; Brown, Laura; Jones, Chris; Imhof, Joseph; LaBrake, Dwayne L.; Resnick, Douglas J.; Sreenivasan, S. V.

2011-04-01

The Jet and Flash Imprint Lithography (J-FILTM) process uses drop dispensing of UV curable resists to assist high resolution patterning for subsequent dry etch pattern transfer. The technology is actively being used to develop solutions for memory markets including Flash memory and patterned media for hard disk drives. It is anticipated that the lifetime of a single template (for patterned media) or mask (for semiconductor) will be on the order of 104 - 105imprints. This suggests that tens of thousands of templates/masks will be required to satisfy the needs of a manufacturing environment. Electron-beam patterning is too slow to feasibly deliver these volumes, but instead can provide a high quality "master" mask which can be replicated many times with an imprint lithography tool. This strategy has the capability to produce the required supply of "working" templates/masks. In this paper, we review the development of the mask form factor, imprint replication tools and processes specifically for semiconductor applications. The requirements needed for semiconductors dictate the need for a well defined form factor for both master and replica masks which is also compatible with the existing mask infrastructure established for the 6025 semi standard, 6" x 6" x 0.25" photomasks. Complying with this standard provides the necessary tooling needed for mask fabrication processes, cleaning, metrology, and inspection. The replica form factor has additional features specific to imprinting such as a pre-patterned mesa. A PerfectaTM MR5000 mask replication tool has been developed specifically to pattern replica masks from an e-beam written master. The system specifications include a throughput of four replicas per hour with an added image placement component of 5nm, 3sigma and a critical dimension uniformity error of less than 1nm, 3sigma. A new process has been developed to fabricate replicas with high contrast alignment marks so that designs for imprint can fit within current device layouts and maximize the usable printed area on the wafer. Initial performance results of this marks are comparable to the baseline fused silica align marks.

DNA Photo Lithography with Cinnamate-based Photo-Bio-Nano-Glue

NASA Astrophysics Data System (ADS)

Feng, Lang; Li, Minfeng; Romulus, Joy; Sha, Ruojie; Royer, John; Wu, Kun-Ta; Xu, Qin; Seeman, Nadrian; Weck, Marcus; Chaikin, Paul

2013-03-01

We present a technique to make patterned functional surfaces, using a cinnamate photo cross-linker and photolithography. We have designed and modified a complementary set of single DNA strands to incorporate a pair of opposing cinnamate molecules. On exposure to 360nm UV, the cinnamate makes a highly specific covalent bond permanently linking only the complementary strands containing the cinnamates. We have studied this specific and efficient crosslinking with cinnamate-containing DNA in solution and on particles. UV addressability allows us to pattern surfaces functionally. The entire surface is coated with a DNA sequence A incorporating cinnamate. DNA strands A'B with one end containing a complementary cinnamated sequence A' attached to another sequence B, are then hybridized to the surface. UV photolithography is used to bind the A'B strand in a specific pattern. The system is heated and the unbound DNA is washed away. The pattern is then observed by thermo-reversibly hybridizing either fluorescently dyed B' strands complementary to B, or colloids coated with B' strands. Our techniques can be used to reversibly and/or permanently bind, via DNA linkers, an assortment of molecules, proteins and nanostructures. Potential applications range from advanced self-assembly, such as templated self-replication schemes recently reported, to designed physical and chemical patterns, to high-resolution multi-functional DNA surfaces for genetic detection or DNA computing.

Engineering High Assurance Distributed Cyber Physical Systems

DTIC Science & Technology

2015-01-15

decisions: number of interacting agents and co-dependent decisions made in real-time without causing interference . To engineer a high assurance DART...environment specification, architecture definition, domain-specific languages, design patterns, code - generation, analysis, test-generation, and simulation...include synchronization between the models and source code , debugging at the model level, expression of the design intent, and quality of service

Separation of sulfated urinary glycosaminoglycans by high-resolution electrophoresis for isotyping of mucopolysaccharidoses in Malaysia.

PubMed

Nor, Azimah; Zabedah, Md Yunus; Norsiah, Md Desa; Ngu, Lock Hock; Suhaila, Abd Rahman

2010-06-01

Mucopolysaccharidoses (MPS) are a group of inherited disorders caused by the deficiency of specific lysosomal enzymes involved in glycosaminoglycans (GAGs) degradation. Currently, there are 11 enzyme deficiencies resulting in seven distinct MPS clinical syndromes and their subtypes. Different MPS syndromes cannot be clearly distinguished clinically due to overlapping signs and symptoms. Measurement of GAGs content in urine and separation of GAGs using high-resolution electrophoresis (HRE) are very useful initial screening tests for isotyping of MPS before specific enzyme diagnostics. In this study, we measured total urinary GAGs by a method using dimethylmethylene blue (DMB), and followed by isolation and separation of GAGs using high resolution electrophoresis (HRE) technique. Of 760 urine samples analyzed, 40 have abnormal GAGs HRE patterns. Thirty-five of these 40 cases have elevated urinary GAGs levels as well. These abnormal HRE patterns could be classified into 4 patterns: Pattern A (elevated DS and HS; suggestive of MPS I, II or VII; 16 cases), Pattern B (elevated HS and CS; suggestive of MPS III; 17 cases), and Pattern C (elevated KS and CS; suggestive of MPS IV, 5 cases), and Pattern D (elevated DS; suggestive of MPS VI; 2 cases). Based on the GAGs HRE pattern and a few discriminating clinical signs, we performed selective enzymatic investigation in 16 cases. In all except one case with MPS VII, the enzymatic diagnosis correlated well with the provisional MPS type as suggested by the abnormal HRE pattern. Our results showed that GAGs HRE is a useful, inexpensive and practical first-line screening test when MPS is suspected clinically, and it provides an important guide to further enzymatic studies on a selective basis.

The Dynamics of Visual Experience, an EEG Study of Subjective Pattern Formation

PubMed Central

Elliott, Mark A.; Twomey, Deirdre; Glennon, Mark

2012-01-01

Background Since the origin of psychological science a number of studies have reported visual pattern formation in the absence of either physiological stimulation or direct visual-spatial references. Subjective patterns range from simple phosphenes to complex patterns but are highly specific and reported reliably across studies. Methodology/Principal Findings Using independent-component analysis (ICA) we report a reduction in amplitude variance consistent with subjective-pattern formation in ventral posterior areas of the electroencephalogram (EEG). The EEG exhibits significantly increased power at delta/theta and gamma-frequencies (point and circle patterns) or a series of high-frequency harmonics of a delta oscillation (spiral patterns). Conclusions/Significance Subjective-pattern formation may be described in a way entirely consistent with identical pattern formation in fluids or granular flows. In this manner, we propose subjective-pattern structure to be represented within a spatio-temporal lattice of harmonic oscillations which bind topographically organized visual-neuronal assemblies by virtue of low frequency modulation. PMID:22292053

A combined high-sugar and high-saturated-fat dietary pattern is associated with more depressive symptoms in a multi-ethnic population: the HELIUS (Healthy Life in an Urban Setting) study.

PubMed

Vermeulen, Esther; Stronks, Karien; Snijder, Marieke B; Schene, Aart H; Lok, Anja; de Vries, Jeanne H; Visser, Marjolein; Brouwer, Ingeborg A; Nicolaou, Mary

2017-09-01

To identify a high-sugar (HS) dietary pattern, a high-saturated-fat (HF) dietary pattern and a combined high-sugar and high-saturated-fat (HSHF) dietary pattern and to explore if these dietary patterns are associated with depressive symptoms. We used data from the HELIUS (Healthy Life in an Urban Setting) study and included 4969 individuals aged 18-70 years. Diet was assessed using four ethnic-specific FFQ. Dietary patterns were derived using reduced rank regression with mono- and disaccharides, saturated fat and total fat as response variables. The nine-item Patient Health Questionnaire (PHQ-9) was used to assess depressive symptoms by using continuous scores and depressed mood (identified using the cut-off point: PHQ-9 sum score ≥10). The Netherlands. Three dietary patterns were identified; an HSHF dietary pattern (including chocolates, red meat, added sugars, high-fat dairy products, fried foods, creamy sauces), an HS dietary pattern (including sugar-sweetened beverages, added sugars, fruit (juices)) and an HF dietary pattern (including high-fat dairy products, butter). When comparing extreme quartiles, consumption of an HSHF dietary pattern was associated with more depressive symptoms (Q1 v. Q4: β=0·18, 95 % CI 0·07, 0·30, P=0·001) and with higher odds of depressed mood (Q1 v. Q4: OR=2·36, 95 % CI 1·19, 4·66, P=0·014). No associations were found between consumption of the remaining dietary patterns and depressive symptoms. Higher consumption of an HSHF dietary pattern is associated with more depressive symptoms and with depressed mood. Our findings reinforce the idea that the focus should be on dietary patterns that are high in both sugar and saturated fat.

Ramadan major dietary patterns.

PubMed

Shadman, Zhaleh; Poorsoltan, Nooshin; Akhoundan, Mahdieh; Larijani, Bagher; Soleymanzadeh, Mozhdeh; Akhgar Zhand, Camelia; Seyed Rohani, Zahra Alsadat; Khoshniat Nikoo, Mohsen

2014-09-01

There has been no data on population based dietary patterns during the Ramadan fasting month. The purpose of this study was to detect Ramadan major dietary patterns among those who fast in Tehran. This cross-sectional study included 600 subjects, aged 18-65 with body mass index (BMI) of 18.5-40, who had decided to fast during Ramadan. Anthropometric measurements, usual physical activity level and educational status were collected two weeks before Ramadan. Information on Ramadan dietary intakes was obtained using a food frequency questionnaire and factor analysis was used to identify major dietary patterns. We identified four major dietary patterns: 1) Western-like pattern; high in fast foods, salty snacks, nuts, potato, fish, poultry, chocolates, juices; 2) high cholesterol and high sweet junk food pattern; high in pickles, sweets and condiments, butter and cream, canned fish, visceral meats and eggs; 3) Mediterranean-like pattern; high in vegetables, olive oil, dates, dairy, dried fruits, fruits, red meats, tea and coffee and 4) Ramadan-style pattern; large consumption of Halim, soups, porridges, legumes and whole grains, soft drinks, Zoolbia and Bamieh. Age was positively and inversely associated with Mediterranean-like (P = 0.003; r = 0.17) and Ramadan style (P = 0.1; r = -0.13) dietary pattern, respectively. Pre-Ramadan physical activity level was associated with a Mediterranean-like dietary pattern (P < 0.0001; r = 0.20). This study showed a Ramadan-specific dietary pattern has unique characteristics, which has not yet been identified as a model of dietary pattern. Also, among identified dietary patterns, Mediterranean-like was the healthiest.

Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns1[OPEN

PubMed Central

Lithio, Andrew

2016-01-01

The adaptability of root system architecture to unevenly distributed mineral nutrients in soil is a key determinant of plant performance. The molecular mechanisms underlying nitrate dependent plasticity of lateral root branching across the different root types of maize are only poorly understood. In this study, detailed morphological and anatomical analyses together with cell type-specific transcriptome profiling experiments combining laser capture microdissection with RNA-seq were performed to unravel the molecular signatures of lateral root formation in primary, seminal, crown, and brace roots of maize (Zea mays) upon local high nitrate stimulation. The four maize root types displayed divergent branching patterns of lateral roots upon local high nitrate stimulation. In particular, brace roots displayed an exceptional architectural plasticity compared to other root types. Transcriptome profiling revealed root type-specific transcriptomic reprogramming of pericycle cells upon local high nitrate stimulation. The alteration of the transcriptomic landscape of brace root pericycle cells in response to local high nitrate stimulation was most significant. Root type-specific transcriptome diversity in response to local high nitrate highlighted differences in the functional adaptability and systemic shoot nitrogen starvation response during development. Integration of morphological, anatomical, and transcriptomic data resulted in a framework underscoring similarity and diversity among root types grown in heterogeneous nitrate environments. PMID:26811190

Social Skills Deficits in Learning Disabilities: The Psychiatric Comorbidity Hypothesis.

ERIC Educational Resources Information Center

San Miguel, Stephanie K.; And Others

1996-01-01

This article explores the hypothesis that social skill deficits among children with learning disabilities are associated with high rates of undetected psychiatric diagnoses. The maladaptive social skills patterns of children with specific subtypes of learning disabilities appear to mimic the symptom patterns of children with attention deficit…

Patterns of Cultural Adjustment among Young Migrants to Australia

ERIC Educational Resources Information Center

Sonderegger, Robi; Barrett, Paula M.

2004-01-01

In response to appeals for empirical data on culture-specific differences and developmental pathways of acculturative stress among young migrants and refugees, the present study examines the cultural adjustment patterns of ethnically diverse migrants to Australia. Two hundred and seventy three primary and high school students (comprised of…

Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard

2008-01-10

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched inmore » bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.« less

Stimulus-specific suppression preserves information in auditory short-term memory.

PubMed

Linke, Annika C; Vicente-Grabovetsky, Alejandro; Cusack, Rhodri

2011-08-02

Philosophers and scientists have puzzled for millennia over how perceptual information is stored in short-term memory. Some have suggested that early sensory representations are involved, but their precise role has remained unclear. The current study asks whether auditory cortex shows sustained frequency-specific activation while sounds are maintained in short-term memory using high-resolution functional MRI (fMRI). Investigating short-term memory representations within regions of human auditory cortex with fMRI has been difficult because of their small size and high anatomical variability between subjects. However, we overcame these constraints by using multivoxel pattern analysis. It clearly revealed frequency-specific activity during the encoding phase of a change detection task, and the degree of this frequency-specific activation was positively related to performance in the task. Although the sounds had to be maintained in memory, activity in auditory cortex was significantly suppressed. Strikingly, patterns of activity in this maintenance period correlated negatively with the patterns evoked by the same frequencies during encoding. Furthermore, individuals who used a rehearsal strategy to remember the sounds showed reduced frequency-specific suppression during the maintenance period. Although negative activations are often disregarded in fMRI research, our findings imply that decreases in blood oxygenation level-dependent response carry important stimulus-specific information and can be related to cognitive processes. We hypothesize that, during auditory change detection, frequency-specific suppression protects short-term memory representations from being overwritten by inhibiting the encoding of interfering sounds.

Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites.

PubMed

Fang, Chun; Noguchi, Tamotsu; Yamana, Hayato

2014-10-01

Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSM-based methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.

Sleep patterns and impulse control among Japanese junior high school students.

PubMed

Abe, Takeru; Hagihara, Akihito; Nobutomo, Koichi

2010-10-01

Adolescents with decreased impulse control exhibit behavioral problems. Lifestyles are related to impulse control. However, the relations of sleep patterns and impulse control among adolescents are unknown. Thus we examined how sleep patterns were associated with impulse control among Japanese junior high school students. Surveys were completed by a nationwide sample of 1934 students. A significant association between decreased impulse control and bedtimes after midnight was revealed. Specific lifestyle factors related to bedtimes after midnight were older age, greater numbers of hours spent watching television, lack of participation in an extracurricular activity, greater use of convenience stores, and increased attendance at cram schools. This study revealed that going to sleep after midnight was significantly related to decreased impulse control among adolescents. Data about specific lifestyle factors related to going to sleep after midnight should be useful in preventing those behaviors demonstrated by school children that derive from decreased impulse control.

EUV via hole pattern fidelity enhancement through novel resist and post-litho plasma treatment

NASA Astrophysics Data System (ADS)

Yaegashi, Hidetami; Koike, Kyohei; Fonseca, Carlos; Yamashita, Fumiko; Kaushik, Kumar; Morikita, Shinya; Ito, Kiyohito; Yoshimura, Shota; Timoshkov, Vadim; Maslow, Mark; Jee, Tae Kwon; Reijnen, Liesbeth; Choi, Peter; Feng, Mu; Spence, Chris; Schoofs, Stijn

2018-03-01

Extreme UV(EUV) technology must be potential solution for sustainable scaling, and its adoption in high volume manufacturing(HVM) is getting realistic more and more. This technology has a wide capability to mitigate various technical problem in Multi-patterning (LELELE) for via hole patterning with 193-i. It induced local pattern fidelity error such like CDU, CER, Pattern placement error. Exactly, EUV must be desirable scaling-driving tool, however, specific technical issue, named RLS (Resolution-LER-Sensitivity) triangle, obvious remaining issue. In this work, we examined hole patterning sensitizing (Lower dose approach) utilizing hole patterning restoration technique named "CD-Healing" as post-Litho. treatment.

Helium beam shadowing for high spatial resolution patterning of antibodies on microstructured diagnostic surfaces

PubMed Central

Cacao, Eliedonna; Sherlock, Tim; Nasrullah, Azeem; Kemper, Steven; Knoop, Jennifer; Kourentzi, Katerina; Ruchhoeft, Paul; Stein, Gila E; Atmar, Robert L; Willson, Richard C

2013-01-01

Abstract We have developed a technique for the high-resolution, self-aligning, and high-throughput patterning of antibody binding functionality on surfaces by selectively changing the reactivity of protein-coated surfaces in specific regions of a workpiece with a beam of energetic helium particles. The exposed areas are passivated with bovine serum albumin (BSA) and no longer bind the antigen. We demonstrate that patterns can be formed (1) by using a stencil mask with etched openings that forms a patterned exposure, or (2) by using angled exposure to cast shadows of existing raised microstructures on the surface to form self-aligned patterns. We demonstrate the efficacy of this process through the patterning of anti-lysozyme, anti-Norwalk virus, and anti-Escherichia coli antibodies and the subsequent detection of each of their targets by the enzyme-mediated formation of colored or silver deposits, and also by binding of gold nanoparticles. The process allows for the patterning of three-dimensional structures by inclining the sample relative to the beam so that the shadowed regions remain unaltered. We demonstrate that the resolution of the patterning process is of the order of hundreds of nanometers, and that the approach is well-suited for high throughput patterning. PMID:24706125

STRONG POSITIVE SELECTION AND HABITAT SPECIFIC AMINO ACID SUBSTITUTION PATTERNS IN A MHC FROM AN ESTUARINE FISH UNDER INTENSE POLLUTION STRESS

EPA Science Inventory

Population-level studies using the major histocompatibility complex (Mhc) have linked specific alleles with specific diseases, but data requirements are high and power to detect disease association is low. A novel use of Mhc population surveys is that they map allelic substituti...

Constructing Patient Specific Clinical Trajectories from Electronic Healthcare Reimbursement Claims using Sequential Pattern Mining

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pullum, Laura L; Hobson, Tanner C

We examine the use of electronic healthcare reimbursement claims (EHRC) for analyzing healthcare delivery and practice patterns across the United States (US). By analyzing over 1 billion EHRCs, we track patterns of clinical procedures administered to patients with heart disease (HD) using sequential pattern mining algorithms. Our analyses reveal that the clinical procedures performed on HD patients are highly varied leading up to and after the primary diagnosis. The discovered clinical procedure sequences reveal significant differences in the overall costs incurred across different parts of the US, indicating significant heterogeneity in treating HD patients. We show that a data-driven approachmore » to understand patient specific clinical trajectories constructed from EHRC can provide quantitative insights into how to better manage and treat patients.« less

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

PubMed Central

Yu, Channing; Mannan, Aristotle M.; Yvone, Griselda Metta; Ross, Kenneth N.; Zhang, Yan-Ling; Marton, Melissa A.; Taylor, Bradley R.; Crenshaw, Andrew; Gould, Joshua Z.; Tamayo, Pablo; Weir, Barbara A.; Tsherniak, Aviad; Wong, Bang; Garraway, Levi A.; Shamji, Alykhan F.; Palmer, Michelle A.; Foley, Michael A.; Winckler, Wendy; Schreiber, Stuart L.; Kung, Andrew L.; Golub, Todd R.

2016-01-01

Hundreds of genetically characterized cell lines are available for the discovery of genotype-specific cancer vulnerabilities. However, screening large numbers of compounds against large numbers of cell lines is currently impractical, and such experiments are often difficult to control1-4. Here, we report a method called PRISM that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes. PRISM displayed the expected patterns of cell killing seen in conventional (unpooled) assays. In a screen of 102 cell lines across 8,400 compounds, PRISM led to the identification of BRD-7880 as a potent and highly specific inhibitor of aurora kinases B and C. Cell line pools also efficiently formed tumors as xenografts, and PRISM recapitulated the expected pattern of erlotinib sensitivity in vivo. PMID:26928769

Patterns and Predictors of Language and Literacy Abilities 4-10 Years in the Longitudinal Study of Australian Children.

PubMed

Zubrick, Stephen R; Taylor, Catherine L; Christensen, Daniel

2015-01-01

Oral language is the foundation of literacy. Naturally, policies and practices to promote children's literacy begin in early childhood and have a strong focus on developing children's oral language, especially for children with known risk factors for low language ability. The underlying assumption is that children's progress along the oral to literate continuum is stable and predictable, such that low language ability foretells low literacy ability. This study investigated patterns and predictors of children's oral language and literacy abilities at 4, 6, 8 and 10 years. The study sample comprised 2,316 to 2,792 children from the first nationally representative Longitudinal Study of Australian Children (LSAC). Six developmental patterns were observed, a stable middle-high pattern, a stable low pattern, an improving pattern, a declining pattern, a fluctuating low pattern, and a fluctuating middle-high pattern. Most children (69%) fit a stable middle-high pattern. By contrast, less than 1% of children fit a stable low pattern. These results challenged the view that children's progress along the oral to literate continuum is stable and predictable. Multivariate logistic regression was used to investigate risks for low literacy ability at 10 years and sensitivity-specificity analysis was used to examine the predictive utility of the multivariate model. Predictors were modelled as risk variables with the lowest level of risk as the reference category. In the multivariate model, substantial risks for low literacy ability at 10 years, in order of descending magnitude, were: low school readiness, Aboriginal and/or Torres Strait Islander status and low language ability at 8 years. Moderate risks were high temperamental reactivity, low language ability at 4 years, and low language ability at 6 years. The following risk factors were not statistically significant in the multivariate model: Low maternal consistency, low family income, health care card, child not read to at home, maternal smoking, maternal education, family structure, temperamental persistence, and socio-economic area disadvantage. The results of the sensitivity-specificity analysis showed that a well-fitted multivariate model featuring risks of substantive magnitude did not do particularly well in predicting low literacy ability at 10 years.

Examining geographic patterns of mortality: the atlas of mortality in small areas in Spain (1987-1995).

PubMed

Benach, Joan; Yasui, Yutaka; Borrell, Carme; Rosa, Elisabeth; Pasarín, M Isabel; Benach, Núria; Español, Esther; Martínez, José Miguel; Daponte, Antonio

2003-06-01

Small-area mortality atlases have been demonstrated to be a useful tool for both showing general geographical patterns in mortality data and identifying specific high-risk locations. In Spain no study has so far systematically examined geographic patterns of small-area mortality for the main causes of death. This paper presents the main features, contents and potential uses of the Spanish Atlas of Mortality in small areas (1987-1995). Population data for 2,218 small areas were drawn from the 1991 Census. Aggregated mortality data for 14 specific causes of death for the period 1987-1995 were obtained for each small area. Empirical Bayes-model-based estimates of age-adjusted relative risk were displayed in small-area maps for each cause/gender/age group (0-64 or 65 and over) combination using the same range of values (i.e. septiles) and colour schemes. The 'Spanish Atlas of Mortality' includes multiple choropleth (area-shaded) small-area maps and graphs to answer different questions about the data. The atlas is divided into three main sections. Section 1 includes the methods and comments on the main maps. Section 2 presents a two-page layout for each leading cause of death by gender including 1) a large map with relative risk estimates, 2) a map that indicates high- and low-risk small areas, 3) a graph with median and interquartile range of relative risk estimates for 17 large regions of Spain, and 4) relative-risk maps for two age groups. Section 3 provides specific information on the geographical units of analysis, statistical methods and other supplemental maps. The 'Spanish Atlas of Mortality' is a useful tool for examining geographical patterns of mortality risk and identifying specific high-risk areas. Mortality patterns displayed in the atlas may have important implications for research and social/health policy planning purposes.

The punctum fixum-punctum mobile model: a neuromuscular principle for efficient movement generation?

PubMed

von Laßberg, Christoph; Rapp, Walter

2015-01-01

According to the "punctum fixum-punctum mobile model" that was introduced in prior studies, for generation of the most effective intentional acceleration of a body part the intersegmental neuromuscular onset succession has to spread successively from the rotation axis (punctum fixum) toward the body part that shall be accelerated (punctum mobile). The aim of the present study was to investigate whether this principle is, indeed, fundamental for any kind of efficient rotational accelerations in general, independent of the kind of movements, type of rotational axis, the current body position, or movement direction. Neuromuscular onset succession was captured by surface electromyography of relevant muscles of the anterior and posterior muscle chain in 16 high-level gymnasts during intentional accelerating movement phases while performing 18 different gymnastics elements (in various body positions to forward and backward, performed on high bar, parallel bars, rings and trampoline), as well as during non-sport specific pivot movements around the longitudinal axis. The succession patterns to generate the acceleration phases during these movements were described and statistically evaluated based on the onset time difference between the muscles of the corresponding muscle chain. In all the analyzed movement phases, the results clearly support the hypothesized succession pattern from punctum fixum to punctum mobile. This principle was further underlined by the finding that the succession patterns do change their direction running through the body when the rotational axis (punctum fixum) has been changed (e.g., high bar or rings [hands] vs. floor or trampoline [feet]). The findings improve our understanding of intersegmental neuromuscular coordination patterns to generate intentional movements most efficiently. This could help to develop more specific methods to facilitate such patterns in particular contexts, thus allowing for shorter motor learning procedures of context-specific key movement sequences in different disciplines of sports, as well as during non-sport specific movements.

The Punctum Fixum-Punctum Mobile Model: A Neuromuscular Principle for Efficient Movement Generation?

PubMed Central

von Laßberg, Christoph; Rapp, Walter

2015-01-01

According to the “punctum fixum–punctum mobile model” that was introduced in prior studies, for generation of the most effective intentional acceleration of a body part the intersegmental neuromuscular onset succession has to spread successively from the rotation axis (punctum fixum) toward the body part that shall be accelerated (punctum mobile). The aim of the present study was to investigate whether this principle is, indeed, fundamental for any kind of efficient rotational accelerations in general, independent of the kind of movements, type of rotational axis, the current body position, or movement direction. Neuromuscular onset succession was captured by surface electromyography of relevant muscles of the anterior and posterior muscle chain in 16 high-level gymnasts during intentional accelerating movement phases while performing 18 different gymnastics elements (in various body positions to forward and backward, performed on high bar, parallel bars, rings and trampoline), as well as during non-sport specific pivot movements around the longitudinal axis. The succession patterns to generate the acceleration phases during these movements were described and statistically evaluated based on the onset time difference between the muscles of the corresponding muscle chain. In all the analyzed movement phases, the results clearly support the hypothesized succession pattern from punctum fixum to punctum mobile. This principle was further underlined by the finding that the succession patterns do change their direction running through the body when the rotational axis (punctum fixum) has been changed (e.g., high bar or rings [hands] vs. floor or trampoline [feet]). The findings improve our understanding of intersegmental neuromuscular coordination patterns to generate intentional movements most efficiently. This could help to develop more specific methods to facilitate such patterns in particular contexts, thus allowing for shorter motor learning procedures of context-specific key movement sequences in different disciplines of sports, as well as during non-sport specific movements. PMID:25822498

Do Pattern-Focused Visuals Improve Skin Self-Examination Performance? Explicating the Visual Skill Acquisition Model

PubMed Central

JOHN, KEVIN K.; JENSEN, JAKOB D.; KING, ANDY J.; RATCLIFF, CHELSEA L.; GROSSMAN, DOUGLAS

2017-01-01

Skin self-examination (SSE) consists of routinely checking the body for atypical moles that might be cancerous. Identifying atypical moles is a visual task; thus, SSE training materials utilize pattern-focused visuals to cultivate this skill. Despite widespread use, researchers have yet to explicate how pattern-focused visuals cultivate visual skill. Using eye tracking to capture the visual scanpaths of a sample of laypersons (N = 92), the current study employed a 2 (pattern: ABCDE vs. ugly duckling sign [UDS]) × 2 (presentation: photorealistic images vs. illustrations) factorial design to assess whether and how pattern-focused visuals can increase layperson accuracy in identifying atypical moles. Overall, illustrations resulted in greater sensitivity, while photos resulted in greater specificity. The UDS × photorealistic condition showed greatest specificity. For those in the photo condition with high self-efficacy, UDS increased specificity directly. For those in the photo condition with self-efficacy levels at the mean or lower, there was a conditional indirect effect such that these individuals spent a larger amount of their viewing time observing the atypical moles, and time on target was positively related to specificity. Illustrations provided significant gains in specificity for those with low-to-moderate self-efficacy by increasing total fixation time on the atypical moles. Findings suggest that maximizing visual processing efficiency could enhance existing SSE training techniques. PMID:28759333

Spatial distribution of 12 class B notifiable infectious diseases in China: A retrospective study.

PubMed

Zhu, Bin; Fu, Yang; Liu, Jinlin; Mao, Ying

2018-01-01

China is the largest developing country with a relatively developed public health system. To further prevent and eliminate the spread of infectious diseases, China has listed 39 notifiable infectious diseases characterized by wide prevalence or great harm, and classified them into classes A, B, and C, with severity decreasing across classes. Class A diseases have been almost eradicated in China, thus making class B diseases a priority in infectious disease prevention and control. In this retrospective study, we analyze the spatial distribution patterns of 12 class B notifiable infectious diseases that remain active all over China. Global and local Moran's I and corresponding graphic tools are adopted to explore and visualize the global and local spatial distribution of the incidence of the selected epidemics, respectively. Inter-correlations of clustering patterns of each pair of diseases and a cumulative summary of the high/low cluster frequency of the provincial units are also provided by means of figures and maps. Of the 12 most commonly notifiable class B infectious diseases, viral hepatitis and tuberculosis show high incidence rates and account for more than half of the reported cases. Almost all the diseases, except pertussis, exhibit positive spatial autocorrelation at the provincial level. All diseases feature varying spatial concentrations. Nevertheless, associations exist between spatial distribution patterns, with some provincial units displaying the same type of cluster features for two or more infectious diseases. Overall, high-low (unit with high incidence surrounded by units with high incidence, the same below) and high-high spatial cluster areas tend to be prevalent in the provincial units located in western and southwest China, whereas low-low and low-high spatial cluster areas abound in provincial units in north and east China. Despite the various distribution patterns of 12 class B notifiable infectious diseases, certain similarities between their spatial distributions are present. Substantial evidence is available to support disease-specific, location-specific, and disease-combined interventions. Regarding provinces that show high-high/high-low patterns of multiple diseases, comprehensive interventions targeting different diseases should be established. As to the adjacent provincial units revealing similar patterns, coordinated actions need to be taken across borders.

Dietary patterns in the French adult population: a study from the second French national cross-sectional dietary survey (INCA2) (2006-2007).

PubMed

Gazan, R; Béchaux, C; Crépet, A; Sirot, V; Drouillet-Pinard, P; Dubuisson, C; Havard, S

2016-07-01

Identification and characterisation of dietary patterns are needed to define public health policies to promote better food behaviours. The aim of this study was to identify the major dietary patterns in the French adult population and to determine their main demographic, socio-economic, nutritional and environmental characteristics. Dietary patterns were defined from food consumption data collected in the second French national cross-sectional dietary survey (2006-2007). Non-negative-matrix factorisation method, followed by a cluster analysis, was implemented to derive the dietary patterns. Logistic regressions were then used to determine their main demographic and socio-economic characteristics. Finally, nutritional profiles and contaminant exposure levels of dietary patterns were compared using ANOVA. Seven dietary patterns, with specific food consumption behaviours, were identified: 'Small eater', 'Health conscious', 'Mediterranean', 'Sweet and processed', 'Traditional', 'Snacker' and 'Basic consumer'. For instance, the Health-conscious pattern was characterised by a high consumption of low-fat and light products. Individuals belonging to this pattern were likely to be older and to have a better nutritional profile than the overall population, but were more exposed to many contaminants. Conversely, individuals of Snacker pattern were likely to be younger, consumed more highly processed foods, had a nutrient-poor profile but were exposed to a limited number of food contaminants. The study identified main dietary patterns in the French adult population with distinct food behaviours and specific demographic, socio-economic, nutritional and environmental features. Paradoxically, for better dietary patterns, potential health risks cannot be ruled out. Therefore, this study demonstrated the need to conduct a risk-benefit analysis to define efficient public health policies regarding diet.

The heparanome--the enigma of encoding and decoding heparan sulfate sulfation.

PubMed

Lamanna, William C; Kalus, Ina; Padva, Michael; Baldwin, Rebecca J; Merry, Catherine L R; Dierks, Thomas

2007-04-30

Heparan sulfate (HS) is a cell surface carbohydrate polymer modified with sulfate moieties whose highly ordered composition is central to directing specific cell signaling events. The ability of the cell to generate these information rich glycans with such specificity has opened up a new field of "heparanomics" which seeks to understand the systems involved in generating these cell type and developmental stage specific HS sulfation patterns. Unlike other instances where biological information is encrypted as linear sequences in molecules such as DNA, HS sulfation patterns are generated through a non-template driven process. Thus, deciphering the sulfation code and the dynamic nature of its generation has posed a new challenge to system biologists. The recent discovery of two sulfatases, Sulf1 and Sulf2, with the unique ability to edit sulfation patterns at the cell surface, has opened up a new dimension as to how we understand the regulation of HS sulfation patterning and pattern-dependent cell signaling events. This review will focus on the functional relationship between HS sulfation patterning and biological processes. Special attention will be given to Sulf1 and Sulf2 and how these key editing enzymes might act in concert with the HS biosynthetic enzymes to generate and regulate specific HS sulfation patterns in vivo. We will further explore the use of knock out mice as biological models for understanding the dynamic systems involved in generating HS sulfation patterns and their biological relevance. A brief overview of new technologies and innovations summarizes advances in the systems biology field for understanding non-template molecular networks and their influence on the "heparanome".

Inferring the Structure of Social Contacts from Demographic Data in the Analysis of Infectious Diseases Spread

PubMed Central

Fumanelli, Laura; Ajelli, Marco; Manfredi, Piero; Vespignani, Alessandro; Merler, Stefano

2012-01-01

Social contact patterns among individuals encode the transmission route of infectious diseases and are a key ingredient in the realistic characterization and modeling of epidemics. Unfortunately, the gathering of high quality experimental data on contact patterns in human populations is a very difficult task even at the coarse level of mixing patterns among age groups. Here we propose an alternative route to the estimation of mixing patterns that relies on the construction of virtual populations parametrized with highly detailed census and demographic data. We present the modeling of the population of 26 European countries and the generation of the corresponding synthetic contact matrices among the population age groups. The method is validated by a detailed comparison with the matrices obtained in six European countries by the most extensive survey study on mixing patterns. The methodology presented here allows a large scale comparison of mixing patterns in Europe, highlighting general common features as well as country-specific differences. We find clear relations between epidemiologically relevant quantities (reproduction number and attack rate) and socio-demographic characteristics of the populations, such as the average age of the population and the duration of primary school cycle. This study provides a numerical approach for the generation of human mixing patterns that can be used to improve the accuracy of mathematical models in the absence of specific experimental data. PMID:23028275

High Carbon Use Efficiency is Not Explained by Production of Storage Compounds

NASA Astrophysics Data System (ADS)

Dijkstra, Paul; van Groenigen, Kees-Jan

2015-04-01

The efficiency with which microbes use substrate to make new microbial biomass (Carbon Use Efficiency or CUE; mol C / mol C) is an important variable in soil and ecosystem C cycling models. Estimates of CUE in soil microbial communities vary widely. It has been hypothesized that high values of CUE are associated with production of storage compounds following a sudden increases in substrate availability during CUE measurements. In that case, these high CUE values would not be representative for balanced microbial growth (i.e. the production of all compounds needed to make new microbial cells). To test this hypothesis, we added position-specific 13C-labeled glucose isotopomers in parallel incubations of a ponderosa pine and piñon-juniper soil. We compared the measured pattern of CO2 release for the six glucose C atoms with patterns of CO2 production expected for balanced growth with a low, medium, or high CUE, and with CO2 production patterns associated with production of storage compounds (glycogen, lipids, or polyhydroxybutyrate). The measured position-specific CO2 production did not match that for production of glycogen, lipids, or polyhydroxybutyrate, but agreed closely with that expected for balanced growth at high CUE and high pentose phosphate pathway activity. We conclude that soil microbial communities utilize glucose substrate for biomass growth with high CUE, and that addition of small amounts of 13C-labeled glucose tracers do not affect CUE or induce storage compounds production. We submit that the measurement of position-specific CO2 production offers a quick and easy way to test biochemically explicit hypotheses concerning microbial growth metabolism.

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

PubMed Central

Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2014-01-01

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. PMID:25222488

Comparative study of three sonoelastographic scores for differentiation between benign and malignant cervical lymph nodes.

PubMed

Lenghel, Lavinia Manuela; Botar Jid, Carolina; Bolboaca, Sorana D; Ciortea, Cristiana; Vasilescu, Dan; Baciut, Grigore; Dudea, Sorin M

2015-06-01

The aim of the study was to explore the diagnostic value of three different sonoelastographic scoring systems (labeled S1-S3) for the differentiation between benign and malignant cervical lymph nodes. The authors propose a six pattern scoring system of the elastographic images with pattern 1 - representing purely soft nodes, pattern 2 - predominantly soft nodes, pattern 3 - predominantly soft nodes with focal had area, pattern 4 - predominantly hard node, pattern 5 - entirely hard node and pattern 6 - node with necrosis. The sonoelastographic images of 50 benign and 70 malignant lymph nodes were assessed. The area under the ROC curve (AUROC) for the differentiation between benign vs. malignant and benign vs. metastatic nodes were analyzed for the three scoring systems. When all the malignant lymph nodes were considered, the S1 score showed an AUROC=0.873 (95%CI [0.805-0.918], where CI=confidence interval; p<0.001), sensibility (Se)=58.57%, and specificity (Sp)=96%. For S2 score the AUROC was 0.890 (95%CI [0.824-0.933], p<0.001), Se=92.86%, and Sp=72%. For S3 score, the AUROC was 0.852 (95%CI [0.778-0.902], p<0.001), Se=64.29%, and Sp=94%). When lymphomatous nodes were excluded, for S1 the AUROC was 0.884 (95%CI [0.809-0.932], p<0.001), Se=64%, and Sp=96%. For S2 the AUROC was 0.894 (95%CI [0.818-0.939], p<0.001), Se=92%, and Sp=72%. For S3, the AUROC was 0.856 (95%CI [0.771-0.911], p<0.001), Se=66%, and Sp=94%. In the S3 scoring system, setting the benign vs. malignant cut off at pattern 3 increases the sensibility (41-65%) with minimal loss of specificity (96-94%). From the gray-scale and Doppler criteria, changes of the nodular margins and the presence of the vessels in the cortical part of the lymph node showed both very high sensibility and specificity, the others criteria taken into account had either very good sensibility with low specificity or high specificity and low sensibility. Our study suggests that there are no significant differences between the three scoring systems in terms of overall diagnostic value. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Assessing Patterns of Alcohol Taxes Produced by Various Types of Excise Tax Methods--A Simulation Study.

PubMed

Sornpaisarn, Bundit; Kaewmungkun, Chuthaporn; Rehm, Jürgen

2015-11-01

To examine patterns of tax burdens produced by specific, ad valorem, and various types of combination taxations. One hundred unique hypothetical alcoholic beverages were mathematically simulated based on the amount of ethanol and perceived-qualities contained. Second, beverages were assigned values of various costs and tax rates, and third, patterns of tax burden were assessed per unit of ethanol produced by each type of tax method. Different tax methods produced different tax burdens per unit of ethanol for different alcoholic beverages. The tax burden produced by the ad valorem tax resulted in a lower tax burden for low perceived-quality alcoholic beverages. The specific tax method showed the same tax burden for both low and high perceived-quality alcoholic beverages. However, high perceived-quality beverages benefited from a lower tax burden per beverage price. Lastly, the combination tax method resulted in a lower tax burden for medium perceived-quality alcoholic beverages. Under the oligopoly market, ad valorem taxation encourages consumption of low perceived-quality beverages; specific taxation encourages consumption of high perceived-quality beverages; and combination tax methods encourage consumption of medium perceived-quality beverages. © The Author 2015. Medical Council on Alcohol and Oxford University Press. All rights reserved.

Deeper than Shallow: Evidence for Structure-Based Parsing Biases in Second-Language Sentence Processing

ERIC Educational Resources Information Center

Witzel, Jeffrey; Witzel, Naoko; Nicol, Janet

2012-01-01

This study examines the reading patterns of native speakers (NSs) and high-level (Chinese) nonnative speakers (NNSs) on three English sentence types involving temporarily ambiguous structural configurations. The reading patterns on each sentence type indicate that both NSs and NNSs were biased toward specific structural interpretations. These…

Virus-based surface patterning of biological molecules, probes, and inorganic materials.

PubMed

Ahn, Suji; Jeon, Seongho; Kwak, Eun-A; Kim, Jong-Man; Jaworski, Justyn

2014-10-01

An essential requirement for continued technological advancement in many areas of biology, physics, chemistry, and materials science is the growing need to generate custom patterned materials. Building from recent achievements in the site-specific modification of virus for covalent surface tethering, we show in this work that stable 2D virus patterns can be generated in custom geometries over large area glass surfaces to yield templates of biological, biochemical, and inorganic materials in high density. As a nanomaterial building block, filamentous viruses have been extensively used in recent years to produce materials with interesting properties, owing to their ease of genetic and chemical modification. By utilizing un-natural amino acids generated at specific locations on the filamentous fd bacteriophage protein coat, surface immobilization is carried out on APTES patterned glass resulting in precise geometries of covalently linked virus material. This technique facilitated the surface display of a high density of virus that were labeled with biomolecules, fluorescent probes, and gold nanoparticles, thereby opening the possibility of integrating virus as functional components for surface engineering. Copyright © 2014 Elsevier B.V. All rights reserved.

Age estimation using cortical surface pattern combining thickness with curvatures

PubMed Central

Wang, Jieqiong; Li, Wenjing; Miao, Wen; Dai, Dai; Hua, Jing; He, Huiguang

2014-01-01

Brain development and healthy aging have been proved to follow a specific pattern, which, in turn, can be applied to help doctors diagnose mental diseases. In this paper, we design a cortical surface pattern (CSP) combining the cortical thickness with curvatures, which constructs an accurate human age estimation model with relevance vector regression. We test our model with two public databases. One is the IXI database (360 healthy subjects aging from 20 to 82 years old were selected), and the other is the INDI database (303 subjects aging from 7 to 22 years old were selected). The results show that our model can achieve as small as 4.57 years deviation in the IXI database and 1.38 years deviation in the INDI database. Furthermore, we employ this surface pattern to age groups classification, and get a remarkably high accuracy (97.77%) and a significantly high sensitivity/specificity (97.30%/98.10%). These results suggest that our designed CSP combining thickness with curvatures is stable and sensitive to brain development, and it is much more powerful than voxel-based morphometry used in previous methods for age estimation. PMID:24395657

The differential impact of job isostrain and home-work interference on indicators of physical and mental health in women and men.

PubMed

Casini, Annalisa; Clays, Els; Godin, Isabelle; De Backer, Guy; Kornitzer, Marcel; Kittel, France

2010-12-01

To evaluate (1) whether the physical and mental health of male workers differs from that of female workers, and, if so, whether (2) this is affected by the interplay between work and nonwork burden. We pooled two large Belgian databases (BELSTRESS III, SOMSTRESS) comprising data on 4810 (2847 women). Gender-specific logistic regressions were performed using a four-level variable as predictor. This combined two predictors: isolated job strain (isostrain) and home-work interference (HWI). Male workers are at greater risk of chronic fatigue when they experience high isostrain but not high HWI. Although accumulated high isostrain and high HWI affect women mainly via chronic fatigue, the same pattern has a greater impact on men's perceived health. There was no difference for the other patterns. To improve workers' well-being, organizations should develop work and nonwork balance policies specific for men and women.

Detecting Biological Warfare Agents

PubMed Central

Song, Linan; Ahn, Soohyoun

2005-01-01

We developed a fiber-optic, microsphere-based, high-density array composed of 18 species-specific probe microsensors to identify biological warfare agents. We simultaneously identified multiple biological warfare agents in environmental samples by looking at specific probe responses after hybridization and response patterns of the multiplexed array. PMID:16318712

A Comparison of Women’s Collegiate and Girls’ High School Volleyball Injury Data Collected Prospectively Over a 4-Year Period

PubMed Central

Reeser, Jonathan C.; Gregory, Andrew; Berg, Richard L.; Comstock, R. Dawn

2015-01-01

Background: There is a relative paucity of research examining the sport-specific injury epidemiology of high school and collegiate volleyball athletes. Moreover, differences in study methodology frequently limit our ability to compare and contrast injury data collected from selected populations. Hypothesis: There are differences between the injury patterns characteristic of high school and collegiate female volleyball athletes. Study Design: Retrospective clinical review. Level of Evidence: Level 3. Methods: We statistically analyzed injury incidence and outcome data collected over a 4-year interval (2005-2006 to 2008-2009) by 2 similar injury surveillance systems, the National Collegiate Athletic Association’s Injury Surveillance System (NCAA ISS) and the High School Reporting Injuries Online (HS RIO). We compared diagnoses, anatomic distribution of injuries, mechanisms of injury, and time lost from training or competition between high school and collegiate volleyball athletes. Results: The overall volleyball-related injury rate was significantly greater among collegiate athletes than among high school athletes during both competition (injury rate ratio, 2.9; 95% CI, 2.5-3.4) and practice (injury rate ratio, 3.5; 95% CI, 3.1-3.9). Collegiate athletes had a higher rate of ankle sprain, knee injury, and shoulder injury. Concussions represented a relatively high percentage of injuries in both populations (5.0% of total NCAA ISS injuries vs 4.8% of total HS RIO injuries, respectively). Conclusion: The data suggest that although similar, there were distinct differences between the injury patterns of the 2 populations. Compared with high school volleyball players, collegiate athletes have a higher rate of acute time loss injury as well as overuse time loss injury (particularly patellar tendinosis). Concussions represented a significant and worrisome component of the injury pattern for both study populations. Clinical Relevance: The injury data suggest that important differences exist in the injury patterns of female high school compared with collegiate volleyball athletes. Consideration of the specific injury patterns may be helpful in future prevention efforts. PMID:26502443

A Comparison of Women's Collegiate and Girls' High School Volleyball Injury Data Collected Prospectively Over a 4-Year Period.

PubMed

Reeser, Jonathan C; Gregory, Andrew; Berg, Richard L; Comstock, R Dawn

2015-01-01

There is a relative paucity of research examining the sport-specific injury epidemiology of high school and collegiate volleyball athletes. Moreover, differences in study methodology frequently limit our ability to compare and contrast injury data collected from selected populations. There are differences between the injury patterns characteristic of high school and collegiate female volleyball athletes. Retrospective clinical review. Level 3. We statistically analyzed injury incidence and outcome data collected over a 4-year interval (2005-2006 to 2008-2009) by 2 similar injury surveillance systems, the National Collegiate Athletic Association's Injury Surveillance System (NCAA ISS) and the High School Reporting Injuries Online (HS RIO). We compared diagnoses, anatomic distribution of injuries, mechanisms of injury, and time lost from training or competition between high school and collegiate volleyball athletes. The overall volleyball-related injury rate was significantly greater among collegiate athletes than among high school athletes during both competition (injury rate ratio, 2.9; 95% CI, 2.5-3.4) and practice (injury rate ratio, 3.5; 95% CI, 3.1-3.9). Collegiate athletes had a higher rate of ankle sprain, knee injury, and shoulder injury. Concussions represented a relatively high percentage of injuries in both populations (5.0% of total NCAA ISS injuries vs 4.8% of total HS RIO injuries, respectively). The data suggest that although similar, there were distinct differences between the injury patterns of the 2 populations. Compared with high school volleyball players, collegiate athletes have a higher rate of acute time loss injury as well as overuse time loss injury (particularly patellar tendinosis). Concussions represented a significant and worrisome component of the injury pattern for both study populations. The injury data suggest that important differences exist in the injury patterns of female high school compared with collegiate volleyball athletes. Consideration of the specific injury patterns may be helpful in future prevention efforts. © 2015 The Author(s).

Infant feeding patterns over the first year of life: influence of family characteristics

PubMed Central

Betoko, Aisha; Charles, Marie-Aline; Hankard, Régis; Forhan, Anne; Bonet, Mercedes; Saurel-Cubizolles, Marie-Josephe; Heude, Barbara; De Lauzon-Guillain, Blandine

2013-01-01

Background/Objectives Early eating patterns and behaviors can determine later eating habits and food preferences and they have been related to the development of childhood overweight and obesity. We aimed to identify patterns of feeding in the first year of life and to examine their associations with family characteristics. Subjects/Methods Our analysis included 1004 infants from the EDEN mother-child cohort. Feeding practices were assessed through maternal self-report at birth, 4, 8 and 12 months. Principal component analysis was applied to derive patterns from breastfeeding duration, age at complementary food (CF) introduction and type of food used at 1y. Associations between patterns and family characteristics were analyzed by linear regressions. Results The main source of variability in infant feeding was characterized by a pattern labeled ‘Late CF introduction and use of ready-prepared baby foods’. Older, more educated, primiparous women with high monthly income ranked high on this pattern. The second pattern, labeled ‘Longer breastfeeding, late CF introduction and use of home-made foods’ was the closest to infant feeding guidelines. Mothers ranking high on this pattern were older and more educated. The third pattern, labeled ‘Use of adults’ foods’ suggests a less age-specific diet for the infants. Mothers ranking high on this pattern were often younger and multiparous. Recruitment center was related to all patterns. Conclusion Not only maternal education level and age but also parity and region are important contributors to the variability in patterns. Further studies are needed to describe associations between these patterns and infant growth and later food preferences. PMID:23299715

Infant feeding patterns over the first year of life: influence of family characteristics.

PubMed

Betoko, A; Charles, M-A; Hankard, R; Forhan, A; Bonet, M; Saurel-Cubizolles, M-J; Heude, B; de Lauzon-Guillain, B

2013-06-01

Early eating patterns and behaviors can determine later eating habits and food preferences and they have been related to the development of childhood overweight and obesity. We aimed to identify patterns of feeding in the first year of life and to examine their associations with family characteristics. Our analysis included 1004 infants from the EDEN mother-child cohort. Feeding practices were assessed through maternal self-report at birth, 4, 8 and 12 months. Principal component analysis was applied to derive patterns from breastfeeding duration, age at complementary food (CF) introduction and type of food used at 1 year. Associations between patterns and family characteristics were analyzed by linear regressions. The main source of variability in infant feeding was characterized by a pattern labeled 'late CF introduction and use of ready-prepared baby foods'. Older, more educated, primiparous women with high monthly income ranked high on this pattern. The second pattern, labeled 'longer breastfeeding, late CF introduction and use of home-made foods' was the closest to infant feeding guidelines. Mothers ranking high on this pattern were older and more educated. The third pattern, labeled 'use of adults' foods' suggests a less age-specific diet for the infants. Mothers ranking high on this pattern were often younger and multiparous. Recruitment center was related to all patterns. Not only maternal education level and age, but also parity and region are important contributors to the variability in patterns. Further studies are needed to describe associations between these patterns and infant growth and later food preferences.

Photothermal nanoblade for patterned cell membrane cutting

PubMed Central

Wu, Ting-Hsiang; Teslaa, Tara; Teitell, Michael A.; Chiou, Pei-Yu

2010-01-01

We report a photothermal nanoblade that utilizes a metallic nanostructure to harvest short laser pulse energy and convert it into a highly localized and specifically shaped explosive vapor bubble. Rapid bubble expansion and collapse punctures a lightly-contacting cell membrane via high-speed fluidic flows and induced transient shear stress. The membrane cutting pattern is controlled by the metallic nanostructure configuration, laser pulse polarization, and energy. Highly controllable, sub-micron sized circular hole pairs to half moon-like, or cat-door shaped, membrane cuts were realized in glutaraldehyde treated HeLa cells. PMID:21164656

The pattern of gestational weight gain is associated with changes in maternal body composition and neonatal size

PubMed Central

Widen, Elizabeth M.; Factor-Litvak, Pam R.; Gallagher, Dympna; Paxton, Anne; Pierson, Richard N.; Heymsfield, Steven B.; Lederman, Sally A.

2015-01-01

Objectives The pattern of gestational weight gain (GWG) reflects general nutrient availability to support growing fetal and maternal compartments and may contribute to later health; but how it relates to changes in maternal body composition is unknown. We evaluated how the pattern of gestational weight gain (GWG) related to changes in maternal body composition during pregnancy and infant size at birth. Methods A prospective, multi-ethnic cohort of 156 pregnant women and their infants was studied in New York City. Prenatal weights were used to estimate total and rate (kg/wk) of GWG by trimester. Linear regression models evaluated the association between trimester-specific GWG group (low, medium, high GWG) [total (low≤25%ile, high≥75%ile) or rate (defined by tertiles)] and infant weight, length and maternal body composition changes from 14–37 weeks, adjusting for covariates. Results Compared to the low gain group, medium/high rate of GWG in the second trimester and high rate of GWG in the third trimester was associated with larger gains in maternal fat mass (β range for fat Δ=2.86–5.29 kg, all p<0.01) For infant outcomes, high rate of GWG in the second trimester was associated with higher birth weight (β=356 g, p=0.001) and length (β=0.85 cm, p=0.002). First and third trimester GWG were not associated with neonatal size. Conclusions The trimester specific pattern and rate of GWG reflect changes in maternal body fat and body water, and are associated with neonatal size, which supports the importance of monitoring trimester-specific GWG. PMID:26179720

The role of negative urgency and expectancies in problem drinking and disordered eating: testing a model of comorbidity in pathological and at-risk samples.

PubMed

Fischer, Sarah; Settles, Regan; Collins, Brittany; Gunn, Rachel; Smith, Gregory T

2012-03-01

The aim of this study was to test hypotheses derived from a model that explains both the comorbidity of problem drinking and eating disorder symptoms and the difference in risk process between the two disorders. In Study One, the authors examined four personality constructs typically associated with rash action (sensation seeking, lack of planning, lack of persistence, and negative urgency) and disorder-specific expectancies in samples of women with eating disorders, substance dependence disorders, comorbid conditions, and no symptoms (N = 104). Negative urgency, the tendency to act rashly when distressed, differentiated the disordered groups from the control group. In contrast, learned expectancies differentiated among clinical groups. Women with eating disorders endorsed high levels of eating and dieting expectancies and women with substance use disorders endorsed high levels of alcohol expectancies, while comorbid women endorsed high levels of both. In Study Two, this pattern of findings was replicated in a sample of fifth grade girls (N = 905). Girls who had engaged in binge eating, alcohol use, or both had higher levels of negative urgency than asymptomatic girls, and the pattern of outcome expectancy endorsement was disorder specific. Negative urgency may represent a general, personality influence on both eating disordered behaviors and symptoms of alcohol dependence, which, when combined with learned, behavior-specific expectancies, leads to specific addictive behavior patterns. PsycINFO Database Record (c) 2012 APA, all rights reserved.

A high-resolution method for the localization of proanthocyanidins in plant tissues

PubMed Central

2011-01-01

Background Histochemical staining of plant tissues with 4-dimethylaminocinnamaldehyde (DMACA) or vanillin-HCl is widely used to characterize spatial patterns of proanthocyanidin accumulation in plant tissues. These methods are limited in their ability to allow high-resolution imaging of proanthocyanidin deposits. Results Tissue embedding techniques were used in combination with DMACA staining to analyze the accumulation of proanthocyanidins in Lotus corniculatus (L.) and Trifolium repens (L.) tissues. Embedding of plant tissues in LR White or paraffin matrices, with or without DMACA staining, preserved the physical integrity of the plant tissues, allowing high-resolution imaging that facilitated cell-specific localization of proanthocyanidins. A brown coloration was seen in proanthocyanidin-producing cells when plant tissues were embedded without DMACA staining and this was likely to have been due to non-enzymatic oxidation of proanthocyanidins and the formation of colored semiquinones and quinones. Conclusions This paper presents a simple, high-resolution method for analysis of proanthocyanidin accumulation in organs, tissues and cells of two plant species with different patterns of proanthocyanidin accumulation, namely Lotus corniculatus (birdsfoot trefoil) and Trifolium repens (white clover). This technique was used to characterize cell type-specific patterns of proanthocyanidin accumulation in white clover flowers at different stages of development. PMID:21595992

Dietary patterns and whole grain cereals in the Scandinavian countries--differences and similarities. The HELGA project.

PubMed

Engeset, Dagrun; Hofoss, Dag; Nilsson, Lena M; Olsen, Anja; Tjønneland, Anne; Skeie, Guri

2015-04-01

To identify dietary patterns with whole grains as a main focus to see if there is a similar whole grain pattern in the three Scandinavian countries; Denmark, Sweden and Norway. Another objective is to see if items suggested for a Nordic Food Index will form a typical Nordic pattern when using factor analysis. The HELGA study population is based on samples of existing cohorts: the Norwegian Women and Cancer Study, the Swedish Västerbotten cohort and the Danish Diet, Cancer and Health study. The HELGA study aims to generate knowledge about the health effects of whole grain foods. The study included a total of 119 913 participants. The associations among food variables from FFQ were investigated by principal component analysis. Only food groups common for all three cohorts were included. High factor loading of a food item shows high correlation of the item to the specific diet pattern. The main whole grain for Denmark and Sweden was rye, while Norway had highest consumption of wheat. Three similar patterns were found: a cereal pattern, a meat pattern and a bread pattern. However, even if the patterns look similar, the food items belonging to the patterns differ between countries. High loadings on breakfast cereals and whole grain oat were common in the cereal patterns for all three countries. Thus, the cereal pattern may be considered a common Scandinavian whole grain pattern. Food items belonging to a Nordic Food Index were distributed between different patterns.

Segregation or aggregation? Sex-specific patterns in the seasonal occurrence of white sharks Carcharodon carcharias at the Neptune Islands, South Australia.

PubMed

Bruce, B; Bradford, R

2015-12-01

The seasonal patterns of occurrence of male and female white sharks Carcharodon carcharias at the Neptune Islands in South Australia were reviewed. Analyses of a 14 year data series indicate that females seasonally aggregate in late autumn and winter coinciding with the maximum in-water availability of lactating female long-nose fur seals and seal pups. During this period, observed male:female sex ratios were similar; whereas during late spring and summer, males continued to visit, but females were rarely recorded. There was no evidence for segregation by sex or size at the Neptunes, but the highly focused seasonal pattern of occurrence of females compared with the year-round records of males suggests that there are likely to be differences between the sexes in overall distribution and movement patterns across southern Australia. It is suggested that foraging strategies and prey selection differ between sexes in C. carcharias across the life-history stages represented and that sex-specific foraging strategies may play an important role in structuring movement patterns and the sex ratios observed at such aggregation sites. Differences between sexes in distribution, movement patterns and foraging strategies are likely to have implications for modelling the consequences of fisheries by-catch between regions or jurisdictions and other spatially or temporally discrete anthropogenic effects on C. carcharias populations. Such differences urge for caution when estimating the size of C. carcharias populations based on observations at pinniped colonies due to the likelihood of sex-specific differences in movements and patterns of residency. These differences also suggest a need to account for sex-specific movement patterns and distribution in population and movement models as well as under conservation actions. © 2015 The Fisheries Society of the British Isles.

Distribution patterns of microcalcifications in suspected thyroid carcinoma: a classification method helpful for diagnosis.

PubMed

Ning, Chun-Ping; Ji, Qing-Lian; Fang, Shi-Bao; Wang, Hong-Qiao; Zhong, Yan-Mi; Niu, Hai-Tao

2018-06-01

The aim of this study was to compare the distribution patterns of microcalcifications in thyroid cancers with benign cases. In total, 358 patients having microcalcifications on ultrasonography were analysed. Microcalcifications were categorised according to the distribution patterns: (I) microcalcifications inside one (a) or more (b) suspected nodules, (II) microcalcifications not only inside but also surrounding a suspected single (a) or multiple (b) nodules, and (III) focal (a) or diffuse (b) microcalcifications in the absence of any suspected nodule. Differences in distribution patterns of microcalcifications in benign and malignant thyroid lesions were compared. We found that the distribution patterns of microcalcifications differed between malignant (n = 325) and benign lesions (n = 117) (X 2 = 9.926, p < 0.01). Benign lesions were classified as type Ia (66.7%), type Ib (29.1%) or type IIIa (4.3%). The specificity of type II and type IIIb in diagnosing malignant cases was 100%. Among malignant lesions, 172 locations were classified as type Ia, 106 as type Ib, 12 as type IIa, 7 as IIb, 7 as type IIIa and 19 as type IIIb. Accompanying Hashimoto thyroiditis was most frequent in type III (51.6%). Types II and IIIb are highly specific for cancer detection. Microcalcifications outside a nodule and those detected in the absence of any nodule should therefore be reviewed carefully in clinical practice. • A method to classify distribution patterns of thyroid microcalcifications is presented. • Distribution features of microcalcifications are useful for diagnosing thyroid cancers. • Microcalcifications outside a suspicious nodule are highly specific for thyroid cancers. • Microcalcifications without suspicious nodules should also alert the physician to thyroid cancers.

Peer Victimization Trajectories from Kindergarten through High School: Differential Pathways for Children's School Engagement and Achievement?

ERIC Educational Resources Information Center

Ladd, Gary W.; Ettekal, Idean; Kochenderfer-Ladd, Becky

2017-01-01

This investigation's aims were to map prevalence, normative trends, and patterns of continuity or change in school-based peer victimization throughout formal schooling (i.e., Grades K-12), and determine whether specific victimization patterns (i.e., differential trajectories) were associated with children's academic performance. A sample of 383…

Testing of DRAINMOD for Forested Watersheds with Non-Pattern Drainage

Treesearch

Devendra M. Amatya; Ge Sun; R. Wayne Skaggs; Carl C. Trettin

2003-01-01

Models like DRAINMOD and its forestry version, DRAINLOB, have been specifically developed as a field scale model for evaluating hydrologic effects of crops (trees), soil, and water management practices for lands with pattern drainage (i.e. with parallel ditches) on relatively flat, high water table soils. These models conduct a water balance between the ditches to...

Polymerizable Supramolecular Approach to Highly Conductive PEDOT:PSS Patterns.

PubMed

Kim, Tae Geun; Ha, Su Ryong; Choi, Hyosung; Uh, Kyungchan; Kundapur, Umesha; Park, Sumin; Lee, Chan Woo; Lee, Sang-Hwa; Kim, Jaeyong; Kim, Jong-Man

2017-06-07

Owing to its high conductivity, solution processability, mechanical flexibility, and transparency, poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) has been extensively explored for use in functional devices including solar cells, sensors, light-emitting diodes, and supercapacitors. The ability to fabricate patterned PEDOT:PSS on a solid substrate is of significant importance to develop practical applications of this conducting polymer. Herein, we describe a new approach to obtain PEDOT:PSS patterns that are based on a polymerizable supramolecular concept. Specifically, we found that UV irradiation of a photopolymerizable diacetylene containing PEDOT:PSS film followed by development in deionized water and subsequent treatment with sulfuric acid (glass and silicon wafer) or formic acid (PET) produces micron-sized PEDOT:PSS patterns on solid substrates. The newly designed photolithographic method, which can be employed to generate highly conductive (>1000 S/cm) PEDOT:PSS patterns, has many advantages including the use of aqueous process conditions, a reduced number of process steps, and no requirement for plasma etching procedures.

Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions.

PubMed

Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Edge, Thomas; Topp, Edward; Neumann, Norman F

2015-11-01

Host specificity in E. coli is widely debated. Herein, we used supervised learning logic-regression-based analysis of intergenic DNA sequence variability in E. coli in an attempt to identify single nucleotide polymorphism (SNP) biomarkers of E. coli that are associated with natural selection and evolution toward host specificity. Seven-hundred and eighty strains of E. coli were isolated from 15 different animal hosts. We utilized logic regression for analyzing DNA sequence data of three intergenic regions (flanked by the genes uspC-flhDC, csgBAC-csgDEFG, and asnS-ompF) to identify genetic biomarkers that could potentially discriminate E. coli based on host sources. Across 15 different animal hosts, logic regression successfully discriminated E. coli based on animal host source with relatively high specificity (i.e., among the samples of the non-target animal host, the proportion that correctly did not have the host-specific marker pattern) and sensitivity (i.e., among the samples from a given animal host, the proportion that correctly had the host-specific marker pattern), even after fivefold cross validation. Permutation tests confirmed that for most animals, host specific intergenic biomarkers identified by logic regression in E. coli were significantly associated with animal host source. The highest level of biomarker sensitivity was observed in deer isolates, with 82% of all deer E. coli isolates displaying a unique SNP pattern that was 98% specific to deer. Fifty-three percent of human isolates displayed a unique biomarker pattern that was 98% specific to humans. Twenty-nine percent of cattle isolates displayed a unique biomarker that was 97% specific to cattle. Interestingly, even within a related host group (i.e., Family: Canidae [domestic dogs and coyotes]), highly specific SNP biomarkers (98% and 99% specificity for dog and coyotes, respectively) were observed, with 21% of dog E. coli isolates displaying a unique dog biomarker and 61% of coyote isolates displaying a unique coyote biomarker. Application of a supervised learning method, such as logic regression, to DNA sequence analysis at certain intergenic regions demonstrates that some E. coli strains may evolve to become host-specific. Copyright © 2015 Elsevier Inc. All rights reserved.

Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

PubMed Central

Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93–96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13–89%)/functional allelic diversity (18–77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54–0.68) and extended LD decay (400–500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating important complex quantitative agronomic traits in chickpea. The numerous informative genome-wide SNPs, natural allelic diversity-led domestication pattern, and LD-based information generated in our study have got multidimensional applicability with respect to chickpea genomics-assisted breeding. PMID:25873920

High performance embedded system for real-time pattern matching

NASA Astrophysics Data System (ADS)

Sotiropoulou, C.-L.; Luciano, P.; Gkaitatzis, S.; Citraro, S.; Giannetti, P.; Dell'Orso, M.

2017-02-01

In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device.

Source location of the smooth high-frequency radio emissions from Uranus

NASA Technical Reports Server (NTRS)

Farrell, W. M.; Calvert, W.

1989-01-01

The source location of the smooth high-frequency radio emissions from Uranus has been determined. Specifically, by fitting the signal dropouts which occurred as Voyager traversed the hollow center of the emission pattern to a symmetrical cone centered on the source magnetic field direction at the cyclotron frequency, a southern-hemisphere (nightside) source was found at approximately 56 deg S, 219 deg W. The half-angle for the hollow portion of the emission pattern was found to be 13 deg.

Prognostic interaction patterns in diabetes mellitus II: A random-matrix-theory relation

NASA Astrophysics Data System (ADS)

Rai, Aparna; Pawar, Amit Kumar; Jalan, Sarika

2015-08-01

We analyze protein-protein interactions in diabetes mellitus II and its normal counterpart under the combined framework of random matrix theory and network biology. This disease is the fifth-leading cause of death in high-income countries and an epidemic in developing countries, affecting around 8 % of the total adult population in the world. Treatment at the advanced stage is difficult and challenging, making early detection a high priority in the cure of the disease. Our investigation reveals specific structural patterns important for the occurrence of the disease. In addition to the structural parameters, the spectral properties reveal the top contributing nodes from localized eigenvectors, which turn out to be significant for the occurrence of the disease. Our analysis is time-efficient and cost-effective, bringing a new horizon in the field of medicine by highlighting major pathways involved in the disease. The analysis provides a direction for the development of novel drugs and therapies in curing the disease by targeting specific interaction patterns instead of a single protein.

Guidance of vascular development: lessons from the nervous system.

PubMed

Larrivée, Bruno; Freitas, Catarina; Suchting, Steven; Brunet, Isabelle; Eichmann, Anne

2009-02-27

The vascular system of vertebrates consists of an organized, branched network of arteries, veins, and capillaries that penetrates all the tissues of the body. One of the most striking features of the vascular system is that its branching pattern is highly stereotyped, with major and secondary branches forming at specific sites and developing highly conserved organ-specific vascular patterns. The factors controlling vascular patterning are not yet completely understood. Recent studies have highlighted the anatomic and structural similarities between blood vessels and nerves. The 2 networks are often aligned, with nerve fibers and blood vessels following parallel routes. Furthermore, both systems require precise control over their guidance and growth. Several molecules with attractive and repulsive properties have been found to modulate the proper guidance of both nerves and blood vessels. These include the Semaphorins, the Slits, and the Netrins and their receptors. In this review, we describe the molecular mechanisms by which blood vessels and axons achieve proper path finding and the molecular cues that are involved in their guidance.

Integration of wings and their eyespots in the speckled wood butterfly Pararge aegeria.

PubMed

Breuker, Casper J; Gibbs, Melanie; Van Dyck, Hans; Brakefield, Paul M; Klingenberg, Christian Peter; Van Dongen, Stefan

2007-07-15

We investigated both the phenotypic and developmental integration of eyespots on the fore- and hindwings of speckled wood butterflies Pararge aegeria. Eyespots develop within a framework of wing veins, which may not only separate eyespots developmentally, but may at the same time also integrate them by virtue of being both signalling sources and barriers during eyespot development. We therefore specifically investigated the interaction between wing venation patterns and eyespot integration. Phenotypic covariation among eyespots was very high, but only eyespots in neighbouring wing cells and in homologous wing cells on different wing surfaces were developmentally integrated. This can be explained by the fact that the wing cells of these eyespots share one or more wing veins. The wing venation patterns of fore- and hindwings were highly integrated, both phenotypically and developmentally. This did not affect overall developmental integration of the eyespots. The adaptive significance of integration patterns is discussed and more specifically we stress the need to conduct studies on phenotypic plasticity of integration.

Shared memories reveal shared structure in neural activity across individuals

PubMed Central

Chen, J.; Leong, Y.C.; Honey, C.J.; Yong, C.H.; Norman, K.A.; Hasson, U.

2016-01-01

Our lives revolve around sharing experiences and memories with others. When different people recount the same events, how similar are their underlying neural representations? Participants viewed a fifty-minute movie, then verbally described the events during functional MRI, producing unguided detailed descriptions lasting up to forty minutes. As each person spoke, event-specific spatial patterns were reinstated in default-network, medial-temporal, and high-level visual areas. Individual event patterns were both highly discriminable from one another and similar between people, suggesting consistent spatial organization. In many high-order areas, patterns were more similar between people recalling the same event than between recall and perception, indicating systematic reshaping of percept into memory. These results reveal the existence of a common spatial organization for memories in high-level cortical areas, where encoded information is largely abstracted beyond sensory constraints; and that neural patterns during perception are altered systematically across people into shared memory representations for real-life events. PMID:27918531

Patterns and Predictors of Language and Literacy Abilities 4-10 Years in the Longitudinal Study of Australian Children

PubMed Central

Zubrick, Stephen R.; Taylor, Catherine L.; Christensen, Daniel

2015-01-01

Aims Oral language is the foundation of literacy. Naturally, policies and practices to promote children’s literacy begin in early childhood and have a strong focus on developing children’s oral language, especially for children with known risk factors for low language ability. The underlying assumption is that children’s progress along the oral to literate continuum is stable and predictable, such that low language ability foretells low literacy ability. This study investigated patterns and predictors of children’s oral language and literacy abilities at 4, 6, 8 and 10 years. The study sample comprised 2,316 to 2,792 children from the first nationally representative Longitudinal Study of Australian Children (LSAC). Six developmental patterns were observed, a stable middle-high pattern, a stable low pattern, an improving pattern, a declining pattern, a fluctuating low pattern, and a fluctuating middle-high pattern. Most children (69%) fit a stable middle-high pattern. By contrast, less than 1% of children fit a stable low pattern. These results challenged the view that children’s progress along the oral to literate continuum is stable and predictable. Findings Multivariate logistic regression was used to investigate risks for low literacy ability at 10 years and sensitivity-specificity analysis was used to examine the predictive utility of the multivariate model. Predictors were modelled as risk variables with the lowest level of risk as the reference category. In the multivariate model, substantial risks for low literacy ability at 10 years, in order of descending magnitude, were: low school readiness, Aboriginal and/or Torres Strait Islander status and low language ability at 8 years. Moderate risks were high temperamental reactivity, low language ability at 4 years, and low language ability at 6 years. The following risk factors were not statistically significant in the multivariate model: Low maternal consistency, low family income, health care card, child not read to at home, maternal smoking, maternal education, family structure, temperamental persistence, and socio-economic area disadvantage. The results of the sensitivity-specificity analysis showed that a well-fitted multivariate model featuring risks of substantive magnitude did not do particularly well in predicting low literacy ability at 10 years. PMID:26352436

Deaf-And-Mute Sign Language Generation System

NASA Astrophysics Data System (ADS)

Kawai, Hideo; Tamura, Shinichi

1984-08-01

We have developed a system which can recognize speech and generate the corresponding animation-like sign language sequence. The system is implemented in a popular personal computer. This has three video-RAM's and a voice recognition board which can recognize only registered voice of a specific speaker. Presently, fourty sign language patterns and fifty finger spellings are stored in two floppy disks. Each sign pattern is composed of one to four sub-patterns. That is, if the pattern is composed of one sub-pattern, it is displayed as a still pattern. If not, it is displayed as a motion pattern. This system will help communications between deaf-and-mute persons and healthy persons. In order to display in high speed, almost programs are written in a machine language.

Prediction of isometric motor tasks and effort levels based on high-density EMG in patients with incomplete spinal cord injury

NASA Astrophysics Data System (ADS)

Jordanić, Mislav; Rojas-Martínez, Mónica; Mañanas, Miguel Angel; Francesc Alonso, Joan

2016-08-01

Objective. The development of modern assistive and rehabilitation devices requires reliable and easy-to-use methods to extract neural information for control of devices. Group-specific pattern recognition identifiers are influenced by inter-subject variability. Based on high-density EMG (HD-EMG) maps, our research group has already shown that inter-subject muscle activation patterns exist in a population of healthy subjects. The aim of this paper is to analyze muscle activation patterns associated with four tasks (flexion/extension of the elbow, and supination/pronation of the forearm) at three different effort levels in a group of patients with incomplete Spinal Cord Injury (iSCI). Approach. Muscle activation patterns were evaluated by the automatic identification of these four isometric tasks along with the identification of levels of voluntary contractions. Two types of classifiers were considered in the identification: linear discriminant analysis and support vector machine. Main results. Results show that performance of classification increases when combining features extracted from intensity and spatial information of HD-EMG maps (accuracy = 97.5%). Moreover, when compared to a population with injuries at different levels, a lower variability between activation maps was obtained within a group of patients with similar injury suggesting stronger task-specific and effort-level-specific co-activation patterns, which enable better prediction results. Significance. Despite the challenge of identifying both the four tasks and the three effort levels in patients with iSCI, promising results were obtained which support the use of HD-EMG features for providing useful information regarding motion and force intention.

Recent advances in the imaging of hepatocellular carcinoma. From ultrasound to positron emission tomography scan.

PubMed

Camaggi, Valeria; Piscaglia, Fabio; Bolondi, Luigi

2007-07-01

Recent advances in imaging techniques for hepatocellular carcinoma (HCC) offer the possibility of investigating contrast perfusion of liver nodules in cirrhosis. It is now accepted that a non-invasive diagnosis of HCC can be established based on the vascular pattern obtained with pure blood pool contrast agents. The diagnostic pattern consists of contrast enhancement in the arterial phase, indicative of arterial hypervascularization, followed by contrast wash out in the portal and late phases, which leads the nodule to show the same, or, more specifically, a lower contrast signal than the surrounding parenchyma. Such patterns can be obtained by CT, MRI and, more recently, by real time Contrast Enhanced Ultrasonography with second-generation ultrasound contrast agents. A typical vascular pattern in a nodule perceptible also without contrast is highly specific for HCC, so that non-invasive diagnostic algorithms have been developed and recently updated.

Association between dietary patterns and low bone mineral density among adults aged 50 years and above: findings from the North West Adelaide Health Study (NWAHS).

PubMed

Melaku, Yohannes Adama; Gill, Tiffany K; Adams, Robert; Shi, Zumin

2016-10-01

Studies on the association between dietary patterns and bone mineral density (BMD) have reported inconsistent findings. Data from the North West Adelaide Health Study, a population-based cohort study undertaken in Australia, were used to assess this association among adults aged 50 years and above. In this specific study, 1182 adults (545 males, 45·9 %) had dietary data collected using a FFQ and also had BMD measurements taken using dual-energy X-ray absorptiometry. Factor analysis with principal component method was applied to ascertain dietary patterns. Two distinct dietary patterns were identified. Pattern 1 ('prudent pattern') was characterised by high intake of fruits, vegetables, sugar, nut-based milk, fish, legumes and high-fibre bread. In contrast, pattern 2 ('Western pattern') was characterised by high levels of processed and red meat, snacks, takeaway foods, jam, beer, soft drinks, white bread, poultry, potato with fat, high-fat dairy products and eggs. Compared with the study participants in the first tertile (T1, lowest consumption) of the prudent pattern, participants in the third tertile (T3) had a lower prevalence of low BMD (prevalence ratio (PR)=0·52; 95 % CI 0·33, 0·83) after adjusting for socio-demographic, lifestyle and behavioural characteristics, chronic conditions and energy intake. Participants in T3 of the Western pattern had a higher prevalence of low BMD (PR=1·68; 95 % CI 1·02, 2·77) compared with those in T1. In contrast to the Western diet, a dietary pattern characterised by high intake of fruits, vegetables and dairy products is positively associated with BMD.

Orbitofrontal sulcogyral patterns are related to temperamental risk for psychopathology.

PubMed

Whittle, Sarah; Bartholomeusz, Cali; Yücel, Murat; Dennison, Meg; Vijayakumar, Nandita; Allen, Nicholas B

2014-02-01

There are marked individual differences in the pattern of cortical (sulcogyral) folding in the orbitofrontal cortex (OFC), and there is a growing literature suggesting that these individual differences are associated with risk for psychotic disorders. To date, however, no study has investigated whether OFC folding patterns are associated with broader risk factors relevant to a range of psychopathology. This study helps address this knowledge gap by examining whether OFC sulcogyral folding patterns are associated with putative risk factors, specifically affective temperament and psychiatric symptoms, in a large community sample (N = 152) of adolescents. Results showed that the most common pattern of folding ('Type I', marked by discontinuity of the medial orbital sulcus and continuity of the lateral orbital sulcus) was associated with low levels of Surgency, high levels of Negative Affectivity (in girls) and higher depressive symptoms. This pattern was also associated with reduced thickness of OFC gray matter. Overall, the findings, combined with previous work, suggest some specificity of neurodevelopmental risk for different types of psychopathology. Thus, these results have the potential to inform the early identification of at-risk individuals.

High-purity capture and release of circulating exosomes using an exosome-specific dual-patterned immunofiltration (ExoDIF) device.

PubMed

Kang, Yoon-Tae; Kim, Young Jun; Bu, Jiyoon; Cho, Young-Ho; Han, Sae-Won; Moon, Byung-In

2017-09-21

We present a microfluidic device for the capture and release of circulating exosomes from human blood. The exosome-specific dual-patterned immunofiltration (ExoDIF) device is composed of two distinct immuno-patterned layers, and is capable of enhancing the chance of binding between the antibody and exosomes by generating mechanical whirling, thus achieving high-throughput exosome isolation with high specificity. Moreover, follow-up recovery after the immuno-affinity based isolation, via cleavage of a linker, enables further downstream analysis. We verified the performance of the present device using MCF-7 secreted exosomes and found that both the concentration and proportion of exosome-sized vesicles were higher than in the samples obtained from the conventional exosome isolation kit. We then isolated exosomes from the human blood samples with our device to compare the exosome level between cancer patients and healthy donors. Cancer patients show a significantly higher exosome level with higher selectivity when validating the exosome-sized vesicles using both electron microscopy and nanoparticle tracking analysis. The captured exosomes from cancer patients also express abundant cancer-associated antigens, the epithelial cell adhesion molecule (EpCAM) on their surface. Our simple and rapid exosome recovery technique has huge potential to elucidate the function of exosomes in cancer patients and can thus be applied for various exosome-based cancer research studies.

Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

PubMed Central

Aanen, Duur K; Ros, Vera ID; de Fine Licht, Henrik H; Mitchell, Jannette; de Beer, Z Wilhelm; Slippers, Bernard; Rouland-LeFèvre, Corinne; Boomsma, Jacobus J

2007-01-01

Background Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species divided over three genera. Knowledge of interaction specificity is important to test the hypothesis that inhabitants (symbionts) are taxonomically less diverse than 'exhabitants' (hosts) and to test the hypothesis that transmission mode is an important determinant for interaction specificity. Results Analysis of Molecular Variance among symbiont ITS sequences across termite hosts at three hierarchical levels showed that 47 % of the variation occurred between genera, 18 % between species, and the remaining 35 % between colonies within species. Different patterns of specificity were evident. High mutual specificity was found for the single Macrotermes species studied, as M. natalensis was associated with a single unique fungal haplotype. The three species of the genus Odontotermes showed low symbiont specificity: they were all associated with a genetically diverse set of fungal symbionts, but their fungal symbionts showed some host specificity, as none of the fungal haplotypes were shared between the studied Odontotermes species. Finally, bilaterally low specificity was found for the four tentatively recognized species of the genus Microtermes, which shared and apparently freely exchanged a common pool of divergent fungal symbionts. Conclusion Interaction specificity was high at the genus level and generally much lower at the species level. A comparison of the observed diversity among fungal symbionts with the diversity among termite hosts, indicated that the fungal symbiont does not follow the general pattern of an endosymbiont, as we found either similar diversity at both sides or higher diversity in the symbiont. Our results further challenge the hypothesis that transmission-mode is a general key-determinant of interaction specificity in fungus-growing termites. PMID:17629911

Task-specific reorganization of the auditory cortex in deaf humans

PubMed Central

Bola, Łukasz; Zimmermann, Maria; Mostowski, Piotr; Jednoróg, Katarzyna; Marchewka, Artur; Rutkowski, Paweł; Szwed, Marcin

2017-01-01

The principles that guide large-scale cortical reorganization remain unclear. In the blind, several visual regions preserve their task specificity; ventral visual areas, for example, become engaged in auditory and tactile object-recognition tasks. It remains open whether task-specific reorganization is unique to the visual cortex or, alternatively, whether this kind of plasticity is a general principle applying to other cortical areas. Auditory areas can become recruited for visual and tactile input in the deaf. Although nonhuman data suggest that this reorganization might be task specific, human evidence has been lacking. Here we enrolled 15 deaf and 15 hearing adults into an functional MRI experiment during which they discriminated between temporally complex sequences of stimuli (rhythms). Both deaf and hearing subjects performed the task visually, in the central visual field. In addition, hearing subjects performed the same task in the auditory modality. We found that the visual task robustly activated the auditory cortex in deaf subjects, peaking in the posterior–lateral part of high-level auditory areas. This activation pattern was strikingly similar to the pattern found in hearing subjects performing the auditory version of the task. Although performing the visual task in deaf subjects induced an increase in functional connectivity between the auditory cortex and the dorsal visual cortex, no such effect was found in hearing subjects. We conclude that in deaf humans the high-level auditory cortex switches its input modality from sound to vision but preserves its task-specific activation pattern independent of input modality. Task-specific reorganization thus might be a general principle that guides cortical plasticity in the brain. PMID:28069964

Converging evidence for control of color-word Stroop interference at the item level.

PubMed

Bugg, Julie M; Hutchison, Keith A

2013-04-01

Prior studies have shown that cognitive control is implemented at the list and context levels in the color-word Stroop task. At first blush, the finding that Stroop interference is reduced for mostly incongruent items as compared with mostly congruent items (i.e., the item-specific proportion congruence [ISPC] effect) appears to provide evidence for yet a third level of control, which modulates word reading at the item level. However, evidence to date favors the view that ISPC effects reflect the rapid prediction of high-contingency responses and not item-specific control. In Experiment 1, we first show that an ISPC effect is obtained when the relevant dimension (i.e., color) signals proportion congruency, a problematic pattern for theories based on differential response contingencies. In Experiment 2, we replicate and extend this pattern by showing that item-specific control settings transfer to new stimuli, ruling out alternative frequency-based accounts. In Experiment 3, we revert to the traditional design in which the irrelevant dimension (i.e., word) signals proportion congruency. Evidence for item-specific control, including transfer of the ISPC effect to new stimuli, is apparent when 4-item sets are employed but not when 2-item sets are employed. We attribute this pattern to the absence of high-contingency responses on incongruent trials in the 4-item set. These novel findings provide converging evidence for reactive control of color-word Stroop interference at the item level, reveal theoretically important factors that modulate reliance on item-specific control versus contingency learning, and suggest an update to the item-specific control account (Bugg, Jacoby, & Chanani, 2011).

Task-specific reorganization of the auditory cortex in deaf humans.

PubMed

Bola, Łukasz; Zimmermann, Maria; Mostowski, Piotr; Jednoróg, Katarzyna; Marchewka, Artur; Rutkowski, Paweł; Szwed, Marcin

2017-01-24

The principles that guide large-scale cortical reorganization remain unclear. In the blind, several visual regions preserve their task specificity; ventral visual areas, for example, become engaged in auditory and tactile object-recognition tasks. It remains open whether task-specific reorganization is unique to the visual cortex or, alternatively, whether this kind of plasticity is a general principle applying to other cortical areas. Auditory areas can become recruited for visual and tactile input in the deaf. Although nonhuman data suggest that this reorganization might be task specific, human evidence has been lacking. Here we enrolled 15 deaf and 15 hearing adults into an functional MRI experiment during which they discriminated between temporally complex sequences of stimuli (rhythms). Both deaf and hearing subjects performed the task visually, in the central visual field. In addition, hearing subjects performed the same task in the auditory modality. We found that the visual task robustly activated the auditory cortex in deaf subjects, peaking in the posterior-lateral part of high-level auditory areas. This activation pattern was strikingly similar to the pattern found in hearing subjects performing the auditory version of the task. Although performing the visual task in deaf subjects induced an increase in functional connectivity between the auditory cortex and the dorsal visual cortex, no such effect was found in hearing subjects. We conclude that in deaf humans the high-level auditory cortex switches its input modality from sound to vision but preserves its task-specific activation pattern independent of input modality. Task-specific reorganization thus might be a general principle that guides cortical plasticity in the brain.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

NASA Astrophysics Data System (ADS)

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

PubMed Central

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-01-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. PMID:21974603

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.

PubMed

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. © 2011 American Institute of Physics

Nonparametric Multiple Imputation for Questionnaires with Individual Skip Patterns and Constraints: The Case of Income Imputation in The National Educational Panel Study

ERIC Educational Resources Information Center

Aßmann, Christian; Würbach, Ariane; Goßmann, Solange; Geissler, Ferdinand; Bela, Anika

2017-01-01

Large-scale surveys typically exhibit data structures characterized by rich mutual dependencies between surveyed variables and individual-specific skip patterns. Despite high efforts in fieldwork and questionnaire design, missing values inevitably occur. One approach for handling missing values is to provide multiply imputed data sets, thus…

Pattern Specificity in the Effect of Prior [delta]f on Auditory Stream Segregation

ERIC Educational Resources Information Center

Snyder, Joel S.; Weintraub, David M.

2011-01-01

During repeating sequences of low (A) and high (B) tones, perception of two separate streams ("streaming") increases with greater frequency separation ([delta]f) between the A and B tones; in contrast, a prior context with large [delta]f results in less streaming during a subsequent test pattern. The purpose of the present study was to…

Phase-shift/transmittance measurements in a micro pattern using MPM193EX

NASA Astrophysics Data System (ADS)

Nozawa, Hiroto; Ishida, Takayuki; Kato, Satoru; Sato, Osamu; Miyazaki, Koji; Takehisa, Kiwamu; Awamura, Naoki; Takizawa, Hideo; Kusunose, Hal

2009-04-01

A new direct Phase-shift/Transmittance measurement tool "MPM193EX" has been developed to respond to the growing demand for higher precision measurements of finer patterns in ArF Lithography. Specifications of MPM193EX are listed below along with corresponding specifications of the conventional tool MPM193. 1) Phase-shift [3 Sigma]: 0.5 deg. (MPM193) => 0.2 deg. (MPM193EX) 2) Transmittance [3 Sigma]: 0.20 % (MPM193) => 0.04 % (MPM193EX) 3) Minimum measurement pattern width: 7.5 μm (MPM193) => 1.0 μm (MPM193EX) Furthermore, new design optics using an ArF Laser and an objective lens with long working distance allows measurements of masks with pellicles. The new method for improving the measurement repeatability is based on elimination of influence from instantaneous fluctuation in interferometer fringes by scanning two adjacent areas simultaneously. Also, MPM193EX is equipped with high-resolution and stable optics. The newly employed auto-focus system in MPM193EX accurately adjusts, by a new image processing method using high-resolution optics, the focus height that is one of the most important factors for measurements in a micro pattern.

Boechera Species Exhibit Species-Specific Responses to Combined Heat and High Light Stress

PubMed Central

Gallas, Genna; Waters, Elizabeth R.

2015-01-01

As sessile organisms, plants must be able to complete their life cycle in place and therefore tolerance to abiotic stress has had a major role in shaping biogeographical patterns. However, much of what we know about plant tolerance to abiotic stresses is based on studies of just a few plant species, most notably the model species Arabidopsis thaliana. In this study we examine natural variation in the stress responses of five diverse Boechera (Brassicaceae) species. Boechera plants were exposed to basal and acquired combined heat and high light stress. Plant response to these stresses was evaluated based on chlorophyll fluorescence measurements, induction of leaf chlorosis, and gene expression. Many of the Boechera species were more tolerant to heat and high light stress than A. thaliana. Gene expression data indicates that two important marker genes for stress responses: APX2 (Ascorbate peroxidase 2) and HsfA2 (Heat shock transcription factor A2) have distinct species-specific expression patterns. The findings of species-specific responses and tolerance to stress indicate that stress pathways are evolutionarily labile even among closely related species. PMID:26030823

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

PubMed Central

Shinbrot, Eve; Henninger, Erin E.; Weinhold, Nils; Covington, Kyle R.; Göksenin, A. Yasemin; Schultz, Nikolaus; Chao, Hsu; Doddapaneni, HarshaVardhan; Muzny, Donna M.; Gibbs, Richard A.; Sander, Chris; Pursell, Zachary F.

2014-01-01

Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication. PMID:25228659

Etching-free patterning method for electrical characterization of atomically thin MoSe2 films grown by chemical vapor deposition

NASA Astrophysics Data System (ADS)

Utama, M. Iqbal Bakti; Lu, Xin; Zhan, Da; Ha, Son Tung; Yuan, Yanwen; Shen, Zexiang; Xiong, Qihua

2014-10-01

Patterning two-dimensional materials into specific spatial arrangements and geometries is essential for both fundamental studies of materials and practical applications in electronics. However, the currently available patterning methods generally require etching steps that rely on complicated and expensive procedures. We report here a facile patterning method for atomically thin MoSe2 films using stripping with an SU-8 negative resist layer exposed to electron beam lithography. Additional steps of chemical and physical etching were not necessary in this SU-8 patterning method. The SU-8 patterning was used to define a ribbon channel from a field effect transistor of MoSe2 film, which was grown by chemical vapor deposition. The narrowing of the conduction channel area with SU-8 patterning was crucial in suppressing the leakage current within the device, thereby allowing a more accurate interpretation of the electrical characterization results from the sample. An electrical transport study, enabled by the SU-8 patterning, showed a variable range hopping behavior at high temperatures.Patterning two-dimensional materials into specific spatial arrangements and geometries is essential for both fundamental studies of materials and practical applications in electronics. However, the currently available patterning methods generally require etching steps that rely on complicated and expensive procedures. We report here a facile patterning method for atomically thin MoSe2 films using stripping with an SU-8 negative resist layer exposed to electron beam lithography. Additional steps of chemical and physical etching were not necessary in this SU-8 patterning method. The SU-8 patterning was used to define a ribbon channel from a field effect transistor of MoSe2 film, which was grown by chemical vapor deposition. The narrowing of the conduction channel area with SU-8 patterning was crucial in suppressing the leakage current within the device, thereby allowing a more accurate interpretation of the electrical characterization results from the sample. An electrical transport study, enabled by the SU-8 patterning, showed a variable range hopping behavior at high temperatures. Electronic supplementary information (ESI) available: Further experiments on patterning and additional electrical characterizations data. See DOI: 10.1039/c4nr03817g

On Expression Patterns and Developmental Origin of Human Brain Regions.

PubMed

Kirsch, Lior; Chechik, Gal

2016-08-01

Anatomical substructures of the human brain have characteristic cell-types, connectivity and local circuitry, which are reflected in area-specific transcriptome signatures, but the principles governing area-specific transcription and their relation to brain development are still being studied. In adult rodents, areal transcriptome patterns agree with the embryonic origin of brain regions, but the processes and genes that preserve an embryonic signature in regional expression profiles were not quantified. Furthermore, it is not clear how embryonic-origin signatures of adult-brain expression interplay with changes in expression patterns during development. Here we first quantify which genes have regional expression-patterns related to the developmental origin of brain regions, using genome-wide mRNA expression from post-mortem adult human brains. We find that almost all human genes (92%) exhibit an expression pattern that agrees with developmental brain-region ontology, but that this agreement changes at multiple phases during development. Agreement is particularly strong in neuron-specific genes, but also in genes that are not spatially correlated with neuron-specific or glia-specific markers. Surprisingly, agreement is also stronger in early-evolved genes. We further find that pairs of similar genes having high agreement to developmental region ontology tend to be more strongly correlated or anti-correlated, and that the strength of spatial correlation changes more strongly in gene pairs with stronger embryonic signatures. These results suggest that transcription regulation of most genes in the adult human brain is spatially tuned in a way that changes through life, but in agreement with development-determined brain regions.

On Expression Patterns and Developmental Origin of Human Brain Regions

PubMed Central

Kirsch, Lior; Chechik, Gal

2016-01-01

Anatomical substructures of the human brain have characteristic cell-types, connectivity and local circuitry, which are reflected in area-specific transcriptome signatures, but the principles governing area-specific transcription and their relation to brain development are still being studied. In adult rodents, areal transcriptome patterns agree with the embryonic origin of brain regions, but the processes and genes that preserve an embryonic signature in regional expression profiles were not quantified. Furthermore, it is not clear how embryonic-origin signatures of adult-brain expression interplay with changes in expression patterns during development. Here we first quantify which genes have regional expression-patterns related to the developmental origin of brain regions, using genome-wide mRNA expression from post-mortem adult human brains. We find that almost all human genes (92%) exhibit an expression pattern that agrees with developmental brain-region ontology, but that this agreement changes at multiple phases during development. Agreement is particularly strong in neuron-specific genes, but also in genes that are not spatially correlated with neuron-specific or glia-specific markers. Surprisingly, agreement is also stronger in early-evolved genes. We further find that pairs of similar genes having high agreement to developmental region ontology tend to be more strongly correlated or anti-correlated, and that the strength of spatial correlation changes more strongly in gene pairs with stronger embryonic signatures. These results suggest that transcription regulation of most genes in the adult human brain is spatially tuned in a way that changes through life, but in agreement with development-determined brain regions. PMID:27564987

Intact Spectral but Abnormal Temporal Processing of Auditory Stimuli in Autism

ERIC Educational Resources Information Center

Groen, Wouter B.; van Orsouw, Linda; ter Huurne, Niels; Swinkels, Sophie; van der Gaag, Rutger-Jan; Buitelaar, Jan K.; Zwiers, Marcel P.

2009-01-01

The perceptual pattern in autism has been related to either a specific localized processing deficit or a pathway-independent, complexity-specific anomaly. We examined auditory perception in autism using an auditory disembedding task that required spectral and temporal integration. 23 children with high-functioning-autism and 23 matched controls…

Conserved and divergent functions of Pax6 underlie species-specific neurogenic patterns in the developing amniote brain.

PubMed

Yamashita, Wataru; Takahashi, Masanori; Kikkawa, Takako; Gotoh, Hitoshi; Osumi, Noriko; Ono, Katsuhiko; Nomura, Tadashi

2018-04-16

The evolution of unique organ structures is associated with changes in conserved developmental programs. However, characterizing the functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics has remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that the neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, whereas stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, consistent with Pax6-dependent temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium is highly divergent in these species. Our results suggest that spatiotemporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie the morphological divergence of the amniote pallial architectures. © 2018. Published by The Company of Biologists Ltd.

A Holarctic Biogeographical Analysis of the Collembola (Arthropoda, Hexapoda) Unravels Recent Post-Glacial Colonization Patterns

PubMed Central

Ávila-Jiménez, María Luisa; Coulson, Stephen James

2011-01-01

We aimed to describe the main Arctic biogeographical patterns of the Collembola, and analyze historical factors and current climatic regimes determining Arctic collembolan species distribution. Furthermore, we aimed to identify possible dispersal routes, colonization sources and glacial refugia for Arctic collembola. We implemented a Gaussian Mixture Clustering method on species distribution ranges and applied a distance- based parametric bootstrap test on presence-absence collembolan species distribution data. Additionally, multivariate analysis was performed considering species distributions, biodiversity, cluster distribution and environmental factors (temperature and precipitation). No clear relation was found between current climatic regimes and species distribution in the Arctic. Gaussian Mixture Clustering found common elements within Siberian areas, Atlantic areas, the Canadian Arctic, a mid-Siberian cluster and specific Beringian elements, following the same pattern previously described, using a variety of molecular methods, for Arctic plants. Species distribution hence indicate the influence of recent glacial history, as LGM glacial refugia (mid-Siberia, and Beringia) and major dispersal routes to high Arctic island groups can be identified. Endemic species are found in the high Arctic, but no specific biogeographical pattern can be clearly identified as a sign of high Arctic glacial refugia. Ocean currents patterns are suggested as being an important factor shaping the distribution of Arctic Collembola, which is consistent with Antarctic studies in collembolan biogeography. The clear relations between cluster distribution and geographical areas considering their recent glacial history, lack of relationship of species distribution with current climatic regimes, and consistency with previously described Arctic patterns in a series of organisms inferred using a variety of methods, suggest that historical phenomena shaping contemporary collembolan distribution can be inferred through biogeographical analysis. PMID:26467728

Laying-sequence-specific variation in yolk oestrogen levels, and relationship to plasma oestrogen in female zebra finches (Taeniopygia guttata)

PubMed Central

Williams, Tony D.; Ames, Caroline E.; Kiparissis, Yiannis; Wynne-Edwards, Katherine E.

2005-01-01

We investigated the relationship between plasma and yolk oestrogens in laying female zebra finches (Taeniopygia guttata) by manipulating plasma oestradiol (E2) levels, via injection of oestradiol-17β, in a sequence-specific manner to maintain chronically high plasma levels for later-developing eggs (contrasting with the endogenous pattern of decreasing plasma E2 concentrations during laying). We report systematic variation in yolk oestrogen concentrations, in relation to laying sequence, similar to that widely reported for androgenic steroids. In sham-manipulated females, yolk E2 concentrations decreased with laying sequence. However, in E2-treated females plasma E2 levels were higher during the period of rapid yolk development of later-laid eggs, compared with control females. As a consequence, we reversed the laying-sequence-specific pattern of yolk E2: in E2-treated females, yolk E2 concentrations increased with laying-sequence. In general therefore, yolk E2 levels were a direct reflection of plasma E2 levels. However, in control females there was some inter-individual variability in the endogenous pattern of plasma E2 levels through the laying cycle which could generate variation in sequence-specific patterns of yolk hormone levels even if these primarily reflect circulating steroid levels. PMID:15695208

Dietary patterns explaining differences in bone mineral density and hip structure in the elderly: the Rotterdam Study.

PubMed

de Jonge, Ester Al; Kiefte-de Jong, Jessica C; Hofman, Albert; Uitterlinden, André G; Kieboom, Brenda Ct; Voortman, Trudy; Franco, Oscar H; Rivadeneira, Fernando

2017-01-01

Evidence on the association between dietary patterns, measures of hip bone geometry, and subsequent fracture risk are scarce. The objective of this study was to evaluate whether dietary patterns that explain most variation in bone mineral density (BMD) and hip bone geometry are associated with fracture risk. We included 4028 subjects aged ≥55 y from the Rotterdam study. Intake of 28 food groups was assessed with the use of food-frequency questionnaires. BMD, bone width, section modulus (SM; reflecting bending strength) and cortical buckling ratio (BR; reflecting bone instability) were measured with the use of dual-energy X-ray absorptiometry. BMD and geometry-specific dietary patterns were identified with the use of reduced rank regression. Fracture data were reported by general practitioners (median follow-up 14.8 y). We identified 4 dietary patterns. Of the 4, we named 2 patterns "fruit, vegetables, and dairy" and "sweets, animal fat, and low meat," respectively. These 2 patterns were used for further analysis. Independently of confounders, adherence to the fruit, vegetables, and dairy pattern was associated with high BMD, high SM, low BR, and low risk of fractures [HR (95% CI) for osteoporotic fractures: 0.90 (0.83, 0.96); for hip fractures: 0.85 (0.81, 0.89) per z score of dietary pattern adherence]. Adherence to the sweets, animal fat, and low meat pattern was associated with high bone width, high SM, high BR, and high risk of fractures [HR (95% CI) for osteoporotic fractures: 1.08 (1.00, 1.06); for hip fractures: 1.06 (1.02, 1.12) per z score]. The fruit, vegetables, and dairy pattern might be associated with lower fracture risk because of high BMD, high bending strength, and more stable bones. The sweets, animal fat, and low meat pattern might be associated with higher fracture risk because of widened, unstable bones, independently of BMD. Dietary recommendations associated with bone geometry in addition to BMD might influence risk of fractures. © 2017 American Society for Nutrition.

Dermoscopy of pigmented lesions on mucocutaneous junction and mucous membrane.

PubMed

Lin, J; Koga, H; Takata, M; Saida, T

2009-12-01

The dermoscopic features of pigmented lesions on the mucocutaneous junction and mucous membrane are different from those on hairy skin. Differentiation between benign lesions and malignant melanomas of these sites is often difficult. To define the dermoscopic patterns of lesions on the mucocutaneous junction and mucous membrane, and assess the applicability of standard dermoscopic algorithms to these lesions. An unselected consecutive series of 40 lesions on the mucocutaneous junction and mucous membrane was studied. All the lesions were imaged using dermoscopy devices, analysed for dermoscopic patterns and scored with algorithms including the ABCD rule, Menzies method, 7-point checklist, 3-point checklist and the CASH algorithm. Benign pigmented lesions of the mucocutaneous junction and mucous membrane frequently presented a dotted-globular pattern (25%), a homogeneous pattern (25%), a fish scale-like pattern (18.8%) and a hyphal pattern (18.8%), while melanomas of these sites showed a multicomponent pattern (75%) and a homogeneous pattern (25%). The fish scale-like pattern and hyphal pattern were considered to be variants of the ring-like pattern. The sensitivities of the ABCD rule, Menzies method, 7-point checklist, 3-point checklist and CASH algorithm in diagnosing mucosal melanomas were 100%, 100%, 63%, 88% and 100%; and the specificities were 100%, 94%, 100%, 94% and 100%, respectively. The ring-like pattern and its variants (fish scale-like pattern and hyphal pattern) are frequently observed as well as the dotted-globular pattern and homogeneous pattern in mucosal melanotic macules. The algorithms for pigmented lesions on hairy skin also apply to those on the mucocutaneous junction and mucous membrane with high sensitivity and specificity.

Patterns of recurrence and outcomes in surgically treated women with endometrial cancer according to ESMO-ESGO-ESTRO Consensus Conference risk groups: Results from the FRANCOGYN study Group.

PubMed

Bendifallah, Sofiane; Ouldamer, Lobna; Lavoue, Vincent; Canlorbe, Geoffroy; Raimond, Emilie; Coutant, Charles; Graesslin, Olivier; Touboul, Cyril; Collinet, Pierre; Daraï, Emile; Ballester, Marcos

2017-01-01

The purpose of this study was to analyse the endometrial cancer (EC) patterns of recurrence based on a large French multicentre database according to ESMO-ESGO-ESTRO classification. Data of women with histologically proven EC who received primary surgical treatment between January 2001 and December 2012 were retrospectively abstracted from seven institutions with prospectively maintained databases. The endpoints were recurrence, recurrence free survival (RFS) and overall survival (OS). Time to the first EC recurrence in a specific site was evaluated by using cumulative incidence analysis (Gray's test). Data from 829 women were analysed in whom recurrences were observed in 176 (21%) with a median and mean time to recurrence of 13 and 19.5months, respectively. High (35%) and high-intermediate risk groups (16%) were associated with higher recurrence rates compared with low (9%) and intermediate (9%) risk patients (p<0.0001). Women with high risk EC had a higher 5-year cumulative incidence of distant recurrence (20.7%) than women with high-intermediate, intermediate and low risk EC (5.6%, 3.5%, 3.3%), (p<0.001), respectively. Women with high risk and high-intermediate risk EC had a higher 5-year cumulative incidence of loco-regional recurrence (24.3% and 16.6%, respectively) than women with intermediate and low risk EC (6.6% and 6.5%, respectively), (p<0.001). We report specific time and site patterns of first recurrence according to the ESMO/ESGO/ESTRO classification. Sites and hazard rates for recurrence differ widely between subgroups over time. Defining patterns of EC recurrence may provide useful information for developing follow-up recommendations and designing therapeutic approaches. Copyright © 2016 Elsevier Inc. All rights reserved.

High-Latitude Ionospheric Dynamics During Conditions of Northward IMF

NASA Technical Reports Server (NTRS)

Sharber, J. R.

1996-01-01

In order to better understand the physical processes operating during conditions of northward interplanetary magnetic field (IMF), in situ measurements from the Dynamics Explorer-2 (low altitude) polar satellite and simultaneous observations from the auroral imager on the Dynamics Explorer-1 (high altitude) satellite were used to investigate the relationships between optical emissions, particle precipitation, and convective flows in the high-latitude ionosphere. Field aligned current and convective flow patterns during IMF north include polar cap arcs, the theta aurora or transpolar arc, and the 'horse-collar' aurora. The initial part of the study concentrated on the electrodynamics of auroral features in the horse-collar aurora, a contracted but thickened emission region in which the dawn and dusk portions can spread to very high latitudes, while the latter part focused on the evolution of one type of IMF north auroral pattern to another, specifically the quiet-time horse-collar pattern to a theta aurora.

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

PubMed Central

Lutsik, Pavlo; Feuerbach, Lars; Arand, Julia; Lengauer, Thomas; Walter, Jörn; Bock, Christoph

2011-01-01

Bisulfite sequencing is a widely used method for measuring DNA methylation in eukaryotic genomes. The assay provides single-base pair resolution and, given sufficient sequencing depth, its quantitative accuracy is excellent. High-throughput sequencing of bisulfite-converted DNA can be applied either genome wide or targeted to a defined set of genomic loci (e.g. using locus-specific PCR primers or DNA capture probes). Here, we describe BiQ Analyzer HT (http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/), a user-friendly software tool that supports locus-specific analysis and visualization of high-throughput bisulfite sequencing data. The software facilitates the shift from time-consuming clonal bisulfite sequencing to the more quantitative and cost-efficient use of high-throughput sequencing for studying locus-specific DNA methylation patterns. In addition, it is useful for locus-specific visualization of genome-wide bisulfite sequencing data. PMID:21565797

Specific Eph receptor-cytoplasmic effector signaling mediated by SAM-SAM domain interactions.

PubMed

Wang, Yue; Shang, Yuan; Li, Jianchao; Chen, Weidi; Li, Gang; Wan, Jun; Liu, Wei; Zhang, Mingjie

2018-05-11

The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain many Eph SAM mutations identified in patients suffering from cancers and other diseases. © 2018, Wang et al.

Full-length Transcriptome Sequencing and Modular Organization Analysis of Naringin/Neoeriocitrin Related Gene Expression Pattern in Drynaria roosii.

PubMed

Sun, Mei-Yu; Li, Jing-Yi; Li, Dong; Huang, Feng-Jie; Wang, Di; Li, Hui; Xing, Quan; Zhu, Hui-Bin; Shi, Lei

2018-04-12

Drynaria roosii (Nakaike) is a traditional Chinese medicinal fern, known as 'GuSuiBu'. The corresponding effective components of naringin/neoeriocitrin share highly similar chemical structure and medicinal function. Our HPLC-MS/MS results showed that the accumulation of naringin/neoeriocitrin depended on specific tissues or ages. However, little was known about the expression patterns of naringin/neoeriocitrin related genes involved in their regulatory pathways. For lack of the basic genetic information, we applied a combination of SMRT sequencing and SGS to generate the complete and full-length transcriptome of D. roosii. According to the SGS data, the DEG-based heat map analysis revealed the naringin/neoeriocitrin related gene expression exhibited obvious tissue- and time-specific transcriptomic differences. Using the systems biology method of modular organization analysis, we clustered 16,472 DEGs into 17 gene modules and studied the relationships between modules and tissue/time point samples, as well as modules and naringin/neoeriocitrin contents. Hereinto, naringin/neoeriocitrin related DEGs distributed in nine distinct modules, and DEGs in these modules showed significant different patterns of transcript abundance to be linked with specific tissues or ages. Moreover, WGCNA results further identified that PAL, 4CL, C4H and C3H, HCT acted as the major hub genes involved in naringin and neoeriocitrin synthesis respectively and exhibited high co-expression with MYB- and bHLH-regulated genes. In this work, modular organization and co-expression networks elucidated the tissue- and time-specificity of gene expression pattern, as well as hub genes associated with naringin/neoeriocitrin synthesis in D. roosii. Simultaneously, the comprehensive transcriptome dataset provided the important genetic information for further research on D. roosii.

Will He Take Over? A Longitudinal, Five County Study of Patterns of Establishment in Farming by Wisconsin's Farm Youth.

ERIC Educational Resources Information Center

Bjoraker, W. T.; And Others

The main purpose of this investigation was to determine patterns of establishment in farming followed by youth in five Wisconsin counties. Specific objectives were: (1) to determine who among the 1957 high-school graduates had ever farmed and were actually farming in 1968; (2) to determine the similarities and differences of those who stayed in…

Sports-specific concerns in the young athlete: football.

PubMed

Metzl, J D

1999-10-01

There are over 1.5 million males playing American football at all levels in the United States. American football is the most common participant sport among high-school-aged males. Owing to its high rate of injury per exposure hour, American football injuries are commonly treated in the emergency department during the autumn sports season. This article will review the history, epidemiology, and specific injury patterns seen in American football, with a focus on head and shoulder injuries.

Directed self-assembly of high-chi block copolymer for nano fabrication of bit patterned media via solvent annealing

NASA Astrophysics Data System (ADS)

Xiong, Shisheng; Chapuis, Yves-Andre; Wan, Lei; Gao, He; Li, Xiao; Ruiz, Ricardo; Nealey, Paul F.

2016-10-01

We report the formation of nanoimprint master templates that can be used for the fabrication of bit patterned media (BPM). The template was formed by directed self-assembly, with solvent annealing, of a symmetric ABA triblock copolymer to form perpendicularly oriented lamellae on chemical patterns. We used a high-χ block copolymer, poly(2-vinyl pyridine)-block-polystyrene-block-poly(2-vinyl pyridine) to achieve smaller feature sizes than are possible with polystyrene-block-poly(methyl methacrylate). The work shows that triblock copolymers can provide a large processing window in terms of pitch commensurability. Using block-selective infiltration (atomic layer deposition with sequential long soaking/purge cycles), an alumina composite with high etch resistance was specifically incorporated into the polar and hydrophilic P2VP domains. Subsequently, the surface pattern was successfully transferred into underlying Si substrates by etching with a fluorine-containing plasma to create a nanoimprint master. The line/space pattern of the nanoimprint master met the BPM fabrication requirement of defectivity <10-3. For demonstration purposes, the nanoimprint master was used to imprint a replica pattern of photoresist on a quartz wafer.

Brain-based decoding of mentally imagined film clips and sounds reveals experience-based information patterns in film professionals.

PubMed

de Borst, Aline W; Valente, Giancarlo; Jääskeläinen, Iiro P; Tikka, Pia

2016-04-01

In the perceptual domain, it has been shown that the human brain is strongly shaped through experience, leading to expertise in highly-skilled professionals. What has remained unclear is whether specialization also shapes brain networks underlying mental imagery. In our fMRI study, we aimed to uncover modality-specific mental imagery specialization of film experts. Using multi-voxel pattern analysis we decoded from brain activity of professional cinematographers and sound designers whether they were imagining sounds or images of particular film clips. In each expert group distinct multi-voxel patterns, specific for the modality of their expertise, were found during classification of imagery modality. These patterns were mainly localized in the occipito-temporal and parietal cortex for cinematographers and in the auditory cortex for sound designers. We also found generalized patterns across perception and imagery that were distinct for the two expert groups: they involved frontal cortex for the cinematographers and temporal cortex for the sound designers. Notably, the mental representations of film clips and sounds of cinematographers contained information that went beyond modality-specificity. We were able to successfully decode the implicit presence of film genre from brain activity during mental imagery in cinematographers. The results extend existing neuroimaging literature on expertise into the domain of mental imagery and show that experience in visual versus auditory imagery can alter the representation of information in modality-specific association cortices. Copyright © 2016 Elsevier Inc. All rights reserved.

Automated classification of neurological disorders of gait using spatio-temporal gait parameters.

PubMed

Pradhan, Cauchy; Wuehr, Max; Akrami, Farhoud; Neuhaeusser, Maximilian; Huth, Sabrina; Brandt, Thomas; Jahn, Klaus; Schniepp, Roman

2015-04-01

Automated pattern recognition systems have been used for accurate identification of neurological conditions as well as the evaluation of the treatment outcomes. This study aims to determine the accuracy of diagnoses of (oto-)neurological gait disorders using different types of automated pattern recognition techniques. Clinically confirmed cases of phobic postural vertigo (N = 30), cerebellar ataxia (N = 30), progressive supranuclear palsy (N = 30), bilateral vestibulopathy (N = 30), as well as healthy subjects (N = 30) were recruited for the study. 8 measurements with 136 variables using a GAITRite(®) sensor carpet were obtained from each subject. Subjects were randomly divided into two groups (training cases and validation cases). Sensitivity and specificity of k-nearest neighbor (KNN), naive-bayes classifier (NB), artificial neural network (ANN), and support vector machine (SVM) in classifying the validation cases were calculated. ANN and SVM had the highest overall sensitivity with 90.6% and 92.0% respectively, followed by NB (76.0%) and KNN (73.3%). SVM and ANN showed high false negative rates for bilateral vestibulopathy cases (20.0% and 26.0%); while KNN and NB had high false negative rates for progressive supranuclear palsy cases (76.7% and 40.0%). Automated pattern recognition systems are able to identify pathological gait patterns and establish clinical diagnosis with good accuracy. SVM and ANN in particular differentiate gait patterns of several distinct oto-neurological disorders of gait with high sensitivity and specificity compared to KNN and NB. Both SVM and ANN appear to be a reliable diagnostic and management tool for disorders of gait. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Heat Vulnerability Index: Spatial Patterns of Exposure, Sensitivity and Adaptive Capacity for Santiago de Chile.

PubMed

Inostroza, Luis; Palme, Massimo; de la Barrera, Francisco

2016-01-01

Climate change will worsen the high levels of urban vulnerability in Latin American cities due to specific environmental stressors. Some impacts of climate change, such as high temperatures in urban environments, have not yet been addressed through adaptation strategies, which are based on poorly supported data. These impacts remain outside the scope of urban planning. New spatially explicit approaches that identify highly vulnerable urban areas and include specific adaptation requirements are needed in current urban planning practices to cope with heat hazards. In this paper, a heat vulnerability index is proposed for Santiago, Chile. The index was created using a GIS-based spatial information system and was constructed from spatially explicit indexes for exposure, sensitivity and adaptive capacity levels derived from remote sensing data and socio-economic information assessed via principal component analysis (PCA). The objective of this study is to determine the levels of heat vulnerability at local scales by providing insights into these indexes at the intra city scale. The results reveal a spatial pattern of heat vulnerability with strong variations among individual spatial indexes. While exposure and adaptive capacities depict a clear spatial pattern, sensitivity follows a complex spatial distribution. These conditions change when examining PCA results, showing that sensitivity is more robust than exposure and adaptive capacity. These indexes can be used both for urban planning purposes and for proposing specific policies and measures that can help minimize heat hazards in highly dynamic urban areas. The proposed methodology can be applied to other Latin American cities to support policy making.

A Heat Vulnerability Index: Spatial Patterns of Exposure, Sensitivity and Adaptive Capacity for Santiago de Chile

PubMed Central

Palme, Massimo; de la Barrera, Francisco

2016-01-01

Climate change will worsen the high levels of urban vulnerability in Latin American cities due to specific environmental stressors. Some impacts of climate change, such as high temperatures in urban environments, have not yet been addressed through adaptation strategies, which are based on poorly supported data. These impacts remain outside the scope of urban planning. New spatially explicit approaches that identify highly vulnerable urban areas and include specific adaptation requirements are needed in current urban planning practices to cope with heat hazards. In this paper, a heat vulnerability index is proposed for Santiago, Chile. The index was created using a GIS-based spatial information system and was constructed from spatially explicit indexes for exposure, sensitivity and adaptive capacity levels derived from remote sensing data and socio-economic information assessed via principal component analysis (PCA). The objective of this study is to determine the levels of heat vulnerability at local scales by providing insights into these indexes at the intra city scale. The results reveal a spatial pattern of heat vulnerability with strong variations among individual spatial indexes. While exposure and adaptive capacities depict a clear spatial pattern, sensitivity follows a complex spatial distribution. These conditions change when examining PCA results, showing that sensitivity is more robust than exposure and adaptive capacity. These indexes can be used both for urban planning purposes and for proposing specific policies and measures that can help minimize heat hazards in highly dynamic urban areas. The proposed methodology can be applied to other Latin American cities to support policy making. PMID:27606592

Poly(acrylic acid) brushes pattern as a 3D functional biosensor surface for microchips

NASA Astrophysics Data System (ADS)

Wang, Yan-Mei; Cui, Yi; Cheng, Zhi-Qiang; Song, Lu-Sheng; Wang, Zhi-You; Han, Bao-Hang; Zhu, Jin-Song

2013-02-01

Poly(acrylic acid) (PAA) brushes, a novel three dimensional (3D) precursor layer of biosensor or protein microarrays, possess high protein loading level and low non-specific protein adsorption. In this article, we describe a simple and convenient way to fabricate 3D PAA brushes pattern by microcontact printing (μCP) and characterize it with FT-IR and optical microscopy. The carboxyl groups of PAA brushes can be applied to covalently immobilize protein for immunoassay. Thriving 3D space made by patterning PAA brushes thin film is available to enhance protein immobilization, which is confirmed by measuring model protein interaction between human immunoglobulin G (H-IgG) and goat anti-H-IgG (G-H-IgG) with fluorescence microscopy and surface plasmon resonance imaging (SPRi). As expected, the SPRi signals of H-IgG coating on 3D PAA brushes pattern and further measuring specific binding with G-H-IgG are all larger than that of 3D PAA brushes without pattern and 2D bare gold surface. We further revealed that this surface can be used for high-throughput screening and clinical diagnosis by label-free assaying of Hepatitis-B-Virus surface antibody (HBsAb) with Hepatitis-B-Virus surface antigen (HBsAg) concentration array chip. The linearity range for HBsAb assay is wider than that of conventional ELISA method.

Evaluation of a novel risk assessment method for self-harm associated with Borderline Personality Disorder.

PubMed

Rao, Sathya; Broadbear, Jillian H; Thompson, Katherine; Correia, Anna; Preston, Martin; Katz, Paul; Trett, Robert

2017-10-01

Borderline personality disorder (BPD) is associated with frequent self-harm and suicidal behaviours. This study compared physician-assessed self-harm risk and intervention choice according to a (i) standard risk assessment and (ii) BPD-specific risk assessment methods. Forty-five junior and senior mental health physicians were assigned to standard or BPD-specific risk training groups. The assessment utilized a BPD case vignette containing four scenarios describing high/low lethality self-harm and chronic/new patterns of self-harm behaviour. Participants chose from among four interventions, each corresponding to a risk category. Standard and BPD-specific groups were alike in their assessment of self-harm risk. Divergence occurred on intervention choice for assessments of low lethality, chronic risk ( p<.01) and high lethality, chronic risk ( p<.005). Overall, psychiatrists were more likely than their junior colleagues to correctly assess risk and management options. Although standard and BPD-specific methods are well aligned for assessing self harm-associated risk, BPD-specific training raised awareness of BPD-appropriate interventions, particularly in the context of chronic patterns of self-harm behaviour. Wider dissemination of BPD-specific risk training may enhance the confidence of mental health clinicians in identifying the nature of self-harm risk as well as the most clinically appropriate interventions for clients with BPD.

Comparison of glomerular activity patterns by fMRI and wide-field calcium imaging: implications for principles underlying odor mapping

PubMed Central

Sanganahalli, Basavaraju G.; Rebello, Michelle R.; Herman, Peter; Papademetris, Xenophon; Shepherd, Gordon M.; Verhagen, Justus V.; Hyder, Fahmeed

2015-01-01

Functional imaging signals arise from distinct metabolic and hemodynamic events at the neuropil, but how these processes are influenced by pre- and post-synaptic activities need to be understood for quantitative interpretation of stimulus-evoked mapping data. The olfactory bulb (OB) glomeruli, spherical neuropil regions with well-defined neuronal circuitry, can provide insights into this issue. Optical calcium-sensitive fluorescent dye imaging (OICa2+) reflects dynamics of pre-synaptic input to glomeruli, whereas high-resolution functional magnetic resonance imaging (fMRI) using deoxyhemoglobin contrast reveals neuropil function within the glomerular layer where both pre- and post-synaptic activities contribute. We imaged odor-specific activity patterns of the dorsal OB in the same anesthetized rats with fMRI and OICa2+ and then co-registered the respective maps to compare patterns in the same space. Maps by each modality were very reproducible as trial-to-trial patterns for a given odor, overlapping by ~80%. Maps evoked by ethyl butyrate and methyl valerate for a given modality overlapped by ~80%, suggesting activation of similar dorsal glomerular networks by these odors. Comparison of maps generated by both methods for a given odor showed ~70% overlap, indicating similar odor-specific maps by each method. These results suggest that odor-specific glomerular patterns by high-resolution fMRI primarily tracks pre-synaptic input to the OB. Thus combining OICa2+ and fMRI lays the framework for studies of OB processing over a range of spatiotemporal scales, where OICa2+ can feature the fast dynamics of dorsal glomerular clusters and fMRI can map the entire glomerular sheet in the OB. PMID:26631819

Directional patterns of cross frequency phase and amplitude coupling within the resting state mimic patterns of fMRI functional connectivity

PubMed Central

Weaver, Kurt E.; Wander, Jeremiah D.; Ko, Andrew L.; Casimo, Kaitlyn; Grabowski, Thomas J.; Ojemann, Jeffrey G.; Darvas, Felix

2016-01-01

Functional imaging investigations into the brain's resting state interactions have yielded a wealth of insight into the intrinsic and dynamic neural architecture supporting cognition and behavior. Electrophysiological studies however have highlighted the fact that synchrony across large-scale cortical systems is composed of spontaneous interactions occurring at timescales beyond the traditional resolution of fMRI, a feature that limits the capacity of fMRI to draw inference on the true directional relationship between network nodes. To approach the question of directionality in resting state signals, we recorded resting state functional MRI (rsfMRI) and electrocorticography (ECoG) from four human subjects undergoing invasive epilepsy monitoring. Using a seed-point based approach, we employed phase-amplitude coupling (PAC) and biPhase Locking Values (bPLV), two measures of cross-frequency coupling (CFC) to explore both outgoing and incoming connections between the seed and all non-seed, site electrodes. We observed robust PAC between a wide range of low-frequency phase and high frequency amplitude estimates. However, significant bPLV, a CFC measure of phase-phase synchrony, was only observed at specific narrow low and high frequency bandwidths. Furthermore, the spatial patterns of outgoing PAC connectivity were most closely associated with the rsfMRI connectivity maps. Our results support the hypothesis that PAC is relatively ubiquitous phenomenon serving as a mechanism for coordinating high-frequency amplitudes across distant neuronal assemblies even in absence of overt task structure. Additionally, we demonstrate that the spatial distribution of a seed-point rsfMRI sensorimotor network is strikingly similar to specific patterns of directional PAC. Specifically, the high frequency activities of distal patches of cortex owning membership in a rsfMRI sensorimotor network were most likely to be entrained to the phase of a low frequency rhythm engendered from the neural populations at the seed-point, suggestive of greater directional coupling from the seed out to the site electrodes. PMID:26747745

R-spondin 1 is required for specification of hematopoietic stem cells through Wnt16 and Vegfa signaling pathways

PubMed Central

2017-01-01

Hematopoietic stem cells (HSCs) are the therapeutic component of bone marrow transplants, but finding immune-compatible donors limits treatment availability and efficacy. Recapitulation of endogenous specification during development is a promising approach to directing HSC specification in vitro, but current protocols are not capable of generating authentic HSCs with high efficiency. Across phyla, HSCs arise from hemogenic endothelium in the ventral floor of the dorsal aorta concurrent with arteriovenous specification and intersegmental vessel (ISV) sprouting, processes regulated by Notch and Wnt. We hypothesized that coordination of HSC specification with vessel patterning might involve modulatory regulatory factors such as R-spondin 1 (Rspo1), an extracellular protein that enhances β-catenin-dependent Wnt signaling and has previously been shown to regulate ISV patterning. We find that Rspo1 is required for HSC specification through control of parallel signaling pathways controlling HSC specification: Wnt16/DeltaC/DeltaD and Vegfa/Tgfβ1. Our results define Rspo1 as a key upstream regulator of two crucial pathways necessary for HSC specification. PMID:28087636

Element-specific behaviour and sediment properties modulate transfer and bioaccumulation of trace elements in a highly-contaminated area (Augusta Bay, Central Mediterranean Sea).

PubMed

Signa, Geraldina; Mazzola, Antonio; Di Leonardo, Rossella; Vizzini, Salvatrice

2017-11-01

High sediment contamination in the coastal area of Priolo Bay, adjacent to the highly-polluted Augusta Harbour, poses serious risks for the benthic communities inhabiting the area. Nevertheless, the transfer of trace elements and consequent bioaccumulation in the biota is an overlooked issue. This study aimed to assess the transfer and bioaccumulation patterns of As, Cd, Ni and Hg to the dominant macroalgae and benthic invertebrates of Priolo Bay. Results revealed different patterns among trace elements (TEs), not driven by sediment contamination but rather by element-specific behaviour coupled with sediment physicochemical properties. Specifically, As accumulated in macroalgae but not in invertebrates, indicating bioavailability of dissolved As only, and a lack of effective trophic transfer. Ni was confined to surface sediment and transfer to biota was not highlighted. Cd and Hg showed the highest concentrations in invertebrates and bioaccumulated especially in filter feeders and carnivores, revealing the importance of suspended particulate and diet as transfer pathways. Total organic carbon (TOC), fine-grained sediments and redox potential were the most important sediment features in shaping the sediment contamination spatial patterns as well as those of TE transfer and bioaccumulation. In particular, As and Cd transfer to macroalgae, and especially Hg bioaccumulation in benthic invertebrates was controlled by sediment properties, resulting in limited transfer and accumulation in the most contaminated stations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pattern centric design based sensitive patterns and process monitor in manufacturing

NASA Astrophysics Data System (ADS)

Hsiang, Chingyun; Cheng, Guojie; Wu, Kechih

2017-03-01

When design rule is mitigating to smaller dimension, process variation requirement is tighter than ever and challenges the limits of device yield. Masks, lithography, etching and other processes have to meet very tight specifications in order to keep defect and CD within the margins of the process window. Conventionally, Inspection and metrology equipments are utilized to monitor and control wafer quality in-line. In high throughput optical inspection, nuisance and review-classification become a tedious labor intensive job in manufacturing. Certain high-resolution SEM images are taken to validate defects after optical inspection. These high resolution SEM images catch not only optical inspection highlighted point, also its surrounding patterns. However, this pattern information is not well utilized in conventional quality control method. Using this complementary design based pattern monitor not only monitors and analyzes the variation of patterns sensitivity but also reduce nuisance and highlight defective patterns or killer defects. After grouping in either single or multiple layers, systematic defects can be identified quickly in this flow. In this paper, we applied design based pattern monitor in different layers to monitor process variation impacts on all kinds of patterns. First, the contour of high resolutions SEM image is extracted and aligned to design with offset adjustment and fine alignment [1]. Second, specified pattern rules can be applied on design clip area, the same size as SEM image, and form POI (pattern of interest) areas. Third, the discrepancy of contour and design measurement at different pattern types in measurement blocks. Fourth, defective patterns are reported by discrepancy detection criteria and pattern grouping [4]. Meanwhile, reported pattern defects are ranked by number and severity by discrepancy. In this step, process sensitive high repeatable systematic defects can be identified quickly Through this design based process pattern monitor method, most of optical inspection nuisances can be filtered out at contour to design discrepancy measurement. Daily analysis results are stored at database as reference to compare with incoming data. Defective pattern library contains existing and known systematic defect patterns which help to catch and identify new pattern defects or process impacts. On the other hand, this defect pattern library provides extra valuable information for mask, pattern and defects verification, inspection care area generation, further OPC fix and process enhancement and investigation.

Real-Time Pattern Recognition - An Industrial Example

NASA Astrophysics Data System (ADS)

Fitton, Gary M.

1981-11-01

Rapid advancements in cost effective sensors and micro computers are now making practical the on-line implementation of pattern recognition based systems for a variety of industrial applications requiring high processing speeds. One major application area for real time pattern recognition is in the sorting of packaged/cartoned goods at high speed for automated warehousing and return goods cataloging. While there are many OCR and bar code readers available to perform these functions, it is often impractical to use such codes (package too small, adverse esthetics, poor print quality) and an approach which recognizes an item by its graphic content alone is desirable. This paper describes a specific application within the tobacco industry, that of sorting returned cigarette goods by brand and size.

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi

2009-05-15

BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. RESULTS: Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of functionmore » and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. CONCLUSIONS: It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.« less

Phyllostomid Bat Occurrence in Successional Stages of Neotropical Dry Forests

PubMed Central

Avila-Cabadilla, Luis Daniel; Stoner, Kathryn Elizabeth; Nassar, Jafet M.; Espírito-Santo, Mario M.; Alvarez-Añorve, Mariana Yolotl; Aranguren, Carla I.; Henry, Mickael; González-Carcacía, José A.; Dolabela Falcão, Luiz A.; Sanchez-Azofeifa, Gerardo Arturo

2014-01-01

Tropical dry forests (TDFs) are highly endangered tropical ecosystems being replaced by a complex mosaic of patches of different successional stages, agricultural fields and pasturelands. In this context, it is urgent to understand how taxa playing critical ecosystem roles respond to habitat modification. Because Phyllostomid bats provide important ecosystem services (e.g. facilitate gene flow among plant populations and promote forest regeneration), in this study we aimed to identify potential patterns on their response to TDF transformation in sites representing four different successional stages (initial, early, intermediate and late) in three Neotropical regions: México, Venezuela and Brazil. We evaluated bat occurrence at the species, ensemble (abundance) and assemblage level (species richness and composition, guild composition). We also evaluated how bat occurrence was modulated by the marked seasonality of TDFs. In general, we found high seasonal and regional specificities in phyllostomid occurrence, driven by specificities at species and guild levels. For example, highest frugivore abundance occurred in the early stage of the moistest TDF, while highest nectarivore abundance occurred in the same stage of the driest TDF. The high regional specificity of phyllostomid responses could arise from: (1) the distinctive environmental conditions of each region, (2) the specific behavior and ecological requirements of the regional bat species, (3) the composition, structure and phenological patterns of plant assemblages in the different stages, and (4) the regional landscape composition and configuration. We conclude that, in tropical seasonal environments, it is imperative to perform long-term studies considering seasonal variations in environmental conditions and plant phenology, as well as the role of landscape attributes. This approach will allow us to identify potential patterns in bat responses to habitat modification, which constitute an invaluable tool for not only bat biodiversity conservation but also for the conservation of the key ecological processes they provide. PMID:24404175

DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming.

PubMed

Couldrey, Christine; Lee, Rita Sf

2010-03-07

Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI). Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not.

DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

PubMed Central

2010-01-01

Background Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI). Results Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. Conclusion These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not. PMID:20205951

Sea Urchin Morphogenesis.

PubMed

McClay, David R

2016-01-01

In the sea urchin morphogenesis follows extensive molecular specification. The specification controls the many morphogenetic events and these, in turn, precede patterning steps that establish the larval body plan. To understand how the embryo is built it was necessary to understand those series of molecular steps. Here an example of the historical sequence of those discoveries is presented as it unfolded over the last 50 years, the years during which major progress in understanding development of many animals and plants was documented by CTDB. In sea urchin development a rich series of experimental studies first established many of the phenomenological components of skeletal morphogenesis and patterning without knowledge of the molecular components. The many discoveries of transcription factors, signals, and structural proteins that contribute to the shape of the endoskeleton of the sea urchin larva then followed as molecular tools became available. A number of transcription factors and signals were discovered that were necessary for specification, morphogenesis, and patterning. Perturbation of the transcription factors and signals provided the means for assembling models of the gene regulatory networks used for specification and controlled the subsequent morphogenetic events. The earlier experimental information informed perturbation experiments that asked how patterning worked. As a consequence it was learned that ectoderm provides a series of patterning signals to the skeletogenic cells and as a consequence the skeletogenic cells secrete a highly patterned skeleton based on their ability to genotypically decode the localized reception of several signals. We still do not understand the complexity of the signals received by the skeletogenic cells, nor do we understand in detail how the genotypic information shapes the secreted skeletal biomineral, but the current knowledge at least outlines the sequence of events and provides a useful template for future discoveries. © 2016 Elsevier Inc. All rights reserved.

Progressive massive fibrosis in patients with pneumoconiosis: utility of MRI in differentiating from lung cancer.

PubMed

Ogihara, Yukihiro; Ashizawa, Kazuto; Hayashi, Hideyuki; Nagayasu, Takeshi; Hayashi, Tomayoshi; Honda, Sumihisa; Uetani, Masataka

2018-01-01

Background It is occasionally difficult to distinguish progressive massive fibrosis (PMF) from lung cancer on computed tomography (CT) in patients with pneumoconiosis. Purpose To evaluate the magnetic resonance imaging (MRI) features of PMF and to assess its ability to differentiate PMF from lung cancer. Material and Methods Between 2000 and 2014, 40 pulmonary lesions suspected to be lung cancer on the basis of CT in 28 patients with known pneumoconiosis were evaluated. Twenty-four of the 40 lesions were pathologically or clinically diagnosed as PMF. The signal pattern on T2-weighted (T2W) images, post-contrast enhancement pattern on T1-weighted (T1W) images, and the pattern of the time intensity curve (TIC) on contrast-enhanced dynamic studies were evaluated. All images were analyzed independently by two chest radiologists. Results All 24 PMF lesions showed low signal intensity (SI) on T2W images (sensitivity, 100%), while 15 of 16 lung cancer lesions showed intermediate or high SI on T2W images (specificity, 94%) when PMF was regarded as a positive result. Six of 17 PMF lesions showed a homogeneous enhancement pattern (sensitivity, 35%), and 4/9 lung cancer lesions showed an inhomogeneous or a ring-like enhancement pattern (specificity, 44%). Six of 16 PMF lesions showed a gradually increasing enhancement pattern (sensitivity, 38%), and 7/9 lung cancer lesions showed rapid enhancement pattern (specificity, 78%). Conclusion When differentiation between PMF and lung cancer in patients with pneumoconiosis is difficult on CT, an additional MRI study, particularly the T2W imaging sequence, may help differentiate between the two.

Cytometer on a chip

NASA Technical Reports Server (NTRS)

Lynes, Michael A. (Inventor); Fernandez, Salvador M. (Inventor)

2010-01-01

An assay technique for label-free, highly parallel, qualitative and quantitative detection of specific cell populations in a sample and for assessing cell functional status, cell-cell interactions and cellular responses to drugs, environmental toxins, bacteria, viruses and other factors that may affect cell function. The technique includes a) creating a first array of binding regions in a predetermined spatial pattern on a sensor surface capable of specifically binding the cells to be assayed; b) creating a second set of binding regions in specific spatial patterns relative to the first set designed to efficiently capture potential secreted or released products from cells captured on the first set of binding regions; c) contacting the sensor surface with the sample, and d) simultaneously monitoring the optical properties of all the binding regions of the sensor surface to determine the presence and concentration of specific cell populations in the sample and their functional status by detecting released or secreted bioproducts.

Assessment of local variability by high-throughput e-beam metrology for prediction of patterning defect probabilities

NASA Astrophysics Data System (ADS)

Wang, Fuming; Hunsche, Stefan; Anunciado, Roy; Corradi, Antonio; Tien, Hung Yu; Tang, Peng; Wei, Junwei; Wang, Yongjun; Fang, Wei; Wong, Patrick; van Oosten, Anton; van Ingen Schenau, Koen; Slachter, Bram

2018-03-01

We present an experimental study of pattern variability and defectivity, based on a large data set with more than 112 million SEM measurements from an HMI high-throughput e-beam tool. The test case is a 10nm node SRAM via array patterned with a DUV immersion LELE process, where we see a variation in mean size and litho sensitivities between different unique via patterns that leads to a seemingly qualitative differences in defectivity. The large available data volume enables further analysis to reliably distinguish global and local CDU variations, including a breakdown into local systematics and stochastics. A closer inspection of the tail end of the distributions and estimation of defect probabilities concludes that there is a common defect mechanism and defect threshold despite the observed differences of specific pattern characteristics. We expect that the analysis methodology can be applied for defect probability modeling as well as general process qualification in the future.

Nonlinear gamma correction via normed bicoherence minimization in optical fringe projection metrology

NASA Astrophysics Data System (ADS)

Kamagara, Abel; Wang, Xiangzhao; Li, Sikun

2018-03-01

We propose a method to compensate for the projector intensity nonlinearity induced by gamma effect in three-dimensional (3-D) fringe projection metrology by extending high-order spectra analysis and bispectral norm minimization to digital sinusoidal fringe pattern analysis. The bispectrum estimate allows extraction of vital signal information features such as spectral component correlation relationships in fringe pattern images. Our approach exploits the fact that gamma introduces high-order harmonic correlations in the affected fringe pattern image. Estimation and compensation of projector nonlinearity is realized by detecting and minimizing the normed bispectral coherence of these correlations. The proposed technique does not require calibration information and technical knowledge or specification of fringe projection unit. This is promising for developing a modular and calibration-invariant model for intensity nonlinear gamma compensation in digital fringe pattern projection profilometry. Experimental and numerical simulation results demonstrate this method to be efficient and effective in improving the phase measuring accuracies with phase-shifting fringe pattern projection profilometry.

Dietary patterns and breast cancer risk in the California Teachers Study cohort.

PubMed

Link, Lilli B; Canchola, Alison J; Bernstein, Leslie; Clarke, Christina A; Stram, Daniel O; Ursin, Giske; Horn-Ross, Pamela L

2013-12-01

Evidence that diet is associated with breast cancer risk is inconsistent. Most studies have examined risks associated with specific foods and nutrients, rather than measures of overall diet. This study aimed to evaluate dietary patterns and their relation to breast cancer risk in a large cohort of women. Data from 91,779 women in the California Teachers Study cohort were analyzed, including data from 4140 women with a diagnosis of invasive breast cancer made between 1995 and 2009. Five predominant dietary patterns were identified by using principal components factor analysis: a plant-based diet, high in fruit and vegetables; a high-protein, high-fat diet, high in meats, eggs, fried foods, and high-fat condiments; a high-carbohydrate diet, high in convenience foods, pasta, and bread products; an ethnic diet, high in legumes, soy-based foods, rice, and dark-green leafy vegetables; and a salad and wine diet, high in lettuce, fish, wine, low-fat salad dressing, and coffee and tea. The plant-based pattern was associated with a reduction in breast cancer risk (RR: 0.85; 95% CI: 0.76, 0.95 for the highest compared with the lowest consumption quintile; P-trend = 0.003); risk reduction was greater for estrogen receptor-negative progesterone receptor-negative (ER-PR-) tumors (RR: 0.66; 95% CI: 0.48, 0.91; P-trend = 0.03). The salad and wine pattern was associated with an increased risk of estrogen receptor-positive progesterone receptor-positive tumors (RR: 1.29; 95% CI: 1.12, 1.49); this effect was only slightly attenuated after adjustment for alcohol consumption. The finding that greater consumption of a plant-based dietary pattern is associated with a reduced breast cancer risk, particularly for ER-PR- tumors, offers a potential avenue for prevention.

LOLA: a 40.000 km optical link between an aircraft and a geostationary satellite

NASA Astrophysics Data System (ADS)

Cazaubiel, Vincent; Planche, Gilles; Chorvalli, Vincent; Le Hors, Lénaïc.; Roy, Bernard; Giraud, Emmanuel; Vaillon, Ludovic; Carre, Francois; Decourbey, Eric

2017-11-01

The LOLA program aims at characterising a 40.000 km optical link through the atmosphere between a high altitude aircraft and a geostationary platform. It opens a new area in the field of optical communications with moving platforms. A complete new optical terminal has been designed and manufactured for this program. The optical terminal architecture includes a specific pointing subsystem to acquire and stabilize the line of sight despite the induced vibrations from the aircraft and the moving pattern from the received laser signal. The optical configuration features a silicon carbide telescope and optical bench to ensure a high thermoelastic angular stability between receive and transmit beams. The communications subsystem includes fibered laser diodes developed in Europe and high performance avalanche photo detectors. Specific encoding patterns are used to maintain the performance of the link despite potential strong fading of the signal. A specific optical link model through the atmosphere has been developed and has been validated thanks to the optical link measurements performed between ARTEMIS and the Optical Ground Station located in the Canarian islands. This model will be used during the flight tests campaign that is to start this summer.

Spectral pattern of urinary water as a biomarker of estrus in the giant panda

NASA Astrophysics Data System (ADS)

Kinoshita, Kodzue; Miyazaki, Mari; Morita, Hiroyuki; Vassileva, Maria; Tang, Chunxiang; Li, Desheng; Ishikawa, Osamu; Kusunoki, Hiroshi; Tsenkova, Roumiana

2012-11-01

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection.

Spectral pattern of urinary water as a biomarker of estrus in the giant panda.

PubMed

Kinoshita, Kodzue; Miyazaki, Mari; Morita, Hiroyuki; Vassileva, Maria; Tang, Chunxiang; Li, Desheng; Ishikawa, Osamu; Kusunoki, Hiroshi; Tsenkova, Roumiana

2012-01-01

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection.

Spectral pattern of urinary water as a biomarker of estrus in the giant panda

PubMed Central

Kinoshita, Kodzue; Miyazaki, Mari; Morita, Hiroyuki; Vassileva, Maria; Tang, Chunxiang; Li, Desheng; Ishikawa, Osamu; Kusunoki, Hiroshi; Tsenkova, Roumiana

2012-01-01

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection. PMID:23181188

Spatial distribution of 12 class B notifiable infectious diseases in China: A retrospective study

PubMed Central

Zhu, Bin; Fu, Yang; Liu, Jinlin

2018-01-01

Background China is the largest developing country with a relatively developed public health system. To further prevent and eliminate the spread of infectious diseases, China has listed 39 notifiable infectious diseases characterized by wide prevalence or great harm, and classified them into classes A, B, and C, with severity decreasing across classes. Class A diseases have been almost eradicated in China, thus making class B diseases a priority in infectious disease prevention and control. In this retrospective study, we analyze the spatial distribution patterns of 12 class B notifiable infectious diseases that remain active all over China. Methods Global and local Moran’s I and corresponding graphic tools are adopted to explore and visualize the global and local spatial distribution of the incidence of the selected epidemics, respectively. Inter-correlations of clustering patterns of each pair of diseases and a cumulative summary of the high/low cluster frequency of the provincial units are also provided by means of figures and maps. Results Of the 12 most commonly notifiable class B infectious diseases, viral hepatitis and tuberculosis show high incidence rates and account for more than half of the reported cases. Almost all the diseases, except pertussis, exhibit positive spatial autocorrelation at the provincial level. All diseases feature varying spatial concentrations. Nevertheless, associations exist between spatial distribution patterns, with some provincial units displaying the same type of cluster features for two or more infectious diseases. Overall, high–low (unit with high incidence surrounded by units with high incidence, the same below) and high–high spatial cluster areas tend to be prevalent in the provincial units located in western and southwest China, whereas low–low and low–high spatial cluster areas abound in provincial units in north and east China. Conclusion Despite the various distribution patterns of 12 class B notifiable infectious diseases, certain similarities between their spatial distributions are present. Substantial evidence is available to support disease-specific, location-specific, and disease-combined interventions. Regarding provinces that show high–high/high–low patterns of multiple diseases, comprehensive interventions targeting different diseases should be established. As to the adjacent provincial units revealing similar patterns, coordinated actions need to be taken across borders. PMID:29621351

Effect of sex on ethanol consumption and conditioned taste aversion in adolescent and adult rats.

PubMed

Schramm-Sapyta, Nicole L; Francis, Reynold; MacDonald, Andrea; Keistler, Colby; O'Neill, Lauren; Kuhn, Cynthia M

2014-04-01

Vulnerability to alcoholism is determined by many factors, including the balance of pleasurable vs. aversive alcohol-induced sensations: pleasurable sensations increase intake, while aversive sensations decrease it. Female sex and adolescent age are associated with lower sensitivity to intake-reducing effects and more rapid development of alcohol abuse. This study assessed voluntary drinking and the aversive effects of alcohol to determine whether these measures are inversely related across the sexes and development. Voluntary drinking of 20 % ethanol in an every-other-day (EOD) availability pattern and the dose-response relationship of ethanol conditioned taste aversion (CTA) were assessed in male and female adolescent and adult rats. CTA was sex specific in adult but not adolescent rats, with adult females exhibiting less aversion. Voluntary ethanol consumption varied according to age and individual differences but was not sex specific. Adolescents initially drank more than adults, exhibited greater day-to-day variation in consumption, were more susceptible to the alcohol deprivation effect, and took longer to establish individual differences in consumption patterns. These results show that the emergence of intake patterns differs between adolescents and adults. Adolescents as a group initiate drinking at high levels but decrease intake as they mature. A subset of adolescents maintained high drinking levels into adulthood. In contrast, most adults consumed at steady, low levels, but a small subset quickly established and maintained high-consumption patterns. Adolescents also showed marked deprivation-induced increases. Sex differences were not observed in EOD drinking during either adolescence or adulthood.

Somatic and vicarious pain are represented by dissociable multivariate brain patterns

PubMed Central

Krishnan, Anjali; Woo, Choong-Wan; Chang, Luke J; Ruzic, Luka; Gu, Xiaosi; López-Solà, Marina; Jackson, Philip L; Pujol, Jesús; Fan, Jin; Wager, Tor D

2016-01-01

Understanding how humans represent others’ pain is critical for understanding pro-social behavior. ‘Shared experience’ theories propose common brain representations for somatic and vicarious pain, but other evidence suggests that specialized circuits are required to experience others’ suffering. Combining functional neuroimaging with multivariate pattern analyses, we identified dissociable patterns that predicted somatic (high versus low: 100%) and vicarious (high versus low: 100%) pain intensity in out-of-sample individuals. Critically, each pattern was at chance in predicting the other experience, demonstrating separate modifiability of both patterns. Somatotopy (upper versus lower limb: 93% accuracy for both conditions) was also distinct, located in somatosensory versus mentalizing-related circuits for somatic and vicarious pain, respectively. Two additional studies demonstrated the generalizability of the somatic pain pattern (which was originally developed on thermal pain) to mechanical and electrical pain, and also demonstrated the replicability of the somatic/vicarious dissociation. These findings suggest possible mechanisms underlying limitations in feeling others’ pain, and present new, more specific, brain targets for studying pain empathy. DOI: http://dx.doi.org/10.7554/eLife.15166.001 PMID:27296895

The effect of high temperature on cause-specific mortality: A multi-county analysis in China.

PubMed

Ban, Jie; Xu, Dandan; He, Mike Z; Sun, Qinghua; Chen, Chen; Wang, Wentao; Zhu, Pengfei; Li, Tiantian

2017-09-01

Although existing studies have linked high temperature to mortality in a small number of regions, less evidence is available on the variation in the associations between high temperature exposure and cause-specific mortality of multiple regions in China. Our study focused on the use of time series analysis to quantify the association between high temperature and different cause-specific mortalities for susceptible populations for 43 counties in China. Two-stage analyses adopting a distributed lag non-linear model (DLNM) and a meta-analysis allowed us to obtain county-specific estimates and national-scale pooled estimates of the nonlinear temperature-mortality relationship. We also considered different populations stratified by age and sex, causes of death, absolute and relative temperature patterns, and potential confounding from air pollutants. All of the observed cause-specific mortalities are significantly associated with higher temperature. The estimated effects of high temperature on mortality varied by spatial distribution and temperature patterns. Compared with the 90th percentile temperature, the overall relative risk (RR) at the 99th percentile temperature for non-accidental mortality is 1.105 (95%CI: 1.089, 1.122), for circulatory disease is 1.107 (95%CI: 1.081, 1.133), for respiratory disease is 1.095 (95%CI: 1.050, 1.142), for coronary heart disease is 1.073 (95%CI: 1.047, 1.099), for acute myocardial infarction is 1.072 (95%CI: 1.042, 1.104), and for stroke is 1.095 (95%CI: 1.052, 1.138). Based on our findings, we believe that heat-related health effect in China is a significant issue that requires more attention and allocation of existing resources. Copyright © 2017 Elsevier Ltd. All rights reserved.

Contrasted patterns of age-specific reproduction in long-lived seabirds.

PubMed

Berman, M; Gaillard, J-M; Weimerskirch, H

2009-01-22

While the number of studies providing evidence of actuarial senescence is increasing, and covers a wide range of taxa, the process of reproductive senescence remains poorly understood. In fact, quite high reproductive output until the last years of life has been reported in several vertebrate species, so that whether or not reproductive senescence is widespread remains unknown. We compared age-specific changes of reproductive parameters between two closely related species of long-lived seabirds: the small-sized snow petrel Pagodroma nivea, and the medium-sized southern fulmar Fulmarus glacialoides. Both are sympatric in Antarctica. We used an exceptional dataset collected over more than 40 years to assess age-specific variations of both breeding probability and breeding success. We found contrasted age-specific reproductive patterns between the two species. Reproductive senescence clearly occurred from 21 years of age onwards in the southern fulmar, in both breeding probability and success, whereas we did not report any decline in the breeding success of the snow petrel, although a very late decrease in the proportion of breeders occurred at 34 years. Such a contrasted age-specific reproductive pattern was rather unexpected. Differences in life history including size or migratory behaviour are the most likely candidates to account for the difference we reported in reproductive senescence between these sympatric seabird species.

Detection of artifacts from high energy bursts in neonatal EEG.

PubMed

Bhattacharyya, Sourya; Biswas, Arunava; Mukherjee, Jayanta; Majumdar, Arun Kumar; Majumdar, Bandana; Mukherjee, Suchandra; Singh, Arun Kumar

2013-11-01

Detection of non-cerebral activities or artifacts, intermixed within the background EEG, is essential to discard them from subsequent pattern analysis. The problem is much harder in neonatal EEG, where the background EEG contains spikes, waves, and rapid fluctuations in amplitude and frequency. Existing artifact detection methods are mostly limited to detect only a subset of artifacts such as ocular, muscle or power line artifacts. Few methods integrate different modules, each for detection of one specific category of artifact. Furthermore, most of the reference approaches are implemented and tested on adult EEG recordings. Direct application of those methods on neonatal EEG causes performance deterioration, due to greater pattern variation and inherent complexity. A method for detection of a wide range of artifact categories in neonatal EEG is thus required. At the same time, the method should be specific enough to preserve the background EEG information. The current study describes a feature based classification approach to detect both repetitive (generated from ECG, EMG, pulse, respiration, etc.) and transient (generated from eye blinking, eye movement, patient movement, etc.) artifacts. It focuses on artifact detection within high energy burst patterns, instead of detecting artifacts within the complete background EEG with wide pattern variation. The objective is to find true burst patterns, which can later be used to identify the Burst-Suppression (BS) pattern, which is commonly observed during newborn seizure. Such selective artifact detection is proven to be more sensitive to artifacts and specific to bursts, compared to the existing artifact detection approaches applied on the complete background EEG. Several time domain, frequency domain, statistical features, and features generated by wavelet decomposition are analyzed to model the proposed bi-classification between burst and artifact segments. A feature selection method is also applied to select the feature subset producing highest classification accuracy. The suggested feature based classification method is executed using our recorded neonatal EEG dataset, consisting of burst and artifact segments. We obtain 78% sensitivity and 72% specificity as the accuracy measures. The accuracy obtained using the proposed method is found to be about 20% higher than that of the reference approaches. Joint use of the proposed method with our previous work on burst detection outperforms reference methods on simultaneous burst and artifact detection. As the proposed method supports detection of a wide range of artifact patterns, it can be improved to incorporate the detection of artifacts within other seizure patterns and background EEG information as well. © 2013 Elsevier Ltd. All rights reserved.

Interactions between concentric form-from-structure and face perception revealed by visual masking but not adaptation

PubMed Central

Feczko, Eric; Shulman, Gordon L.; Petersen, Steven E.; Pruett, John R.

2014-01-01

Findings from diverse subfields of vision research suggest a potential link between high-level aspects of face perception and concentric form-from-structure perception. To explore this relationship, typical adults performed two adaptation experiments and two masking experiments to test whether concentric, but not nonconcentric, Glass patterns (a type of form-from-structure stimulus) utilize a processing mechanism shared by face perception. For the adaptation experiments, subjects were presented with an adaptor for 5 or 20 s, prior to discriminating a target. In the masking experiments, subjects saw a mask, then a target, and then a second mask. Measures of discriminability and bias were derived and repeated measures analysis of variance tested for pattern-specific masking and adaptation effects. Results from Experiment 1 show no Glass pattern-specific effect of adaptation to faces; results from Experiment 2 show concentric Glass pattern masking, but not adaptation, may impair upright/inverted face discrimination; results from Experiment 3 show concentric and radial Glass pattern masking impaired subsequent upright/inverted face discrimination more than translational Glass pattern masking; and results from Experiment 4 show concentric and radial Glass pattern masking impaired subsequent face gender discrimination more than translational Glass pattern masking. Taken together, these findings demonstrate interactions between concentric form-from-structure and face processing, suggesting a possible common processing pathway. PMID:24563526

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning

PubMed Central

Fakhro, Khalid A.; Choi, Murim; Ware, Stephanie M.; Belmont, John W.; Towbin, Jeffrey A.; Lifton, Richard P.; Khokha, Mustafa K.; Brueckner, Martina

2011-01-01

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10−4). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10−6). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning. PMID:21282601

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning.

PubMed

Fakhro, Khalid A; Choi, Murim; Ware, Stephanie M; Belmont, John W; Towbin, Jeffrey A; Lifton, Richard P; Khokha, Mustafa K; Brueckner, Martina

2011-02-15

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10(-4)). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10(-6)). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning.

Patient-specific connectivity pattern of epileptic network in frontal lobe epilepsy

PubMed Central

Luo, Cheng; An, Dongmei; Yao, Dezhong; Gotman, Jean

2014-01-01

There is evidence that focal epilepsy may involve the dysfunction of a brain network in addition to the focal region. To delineate the characteristics of this epileptic network, we collected EEG/fMRI data from 23 patients with frontal lobe epilepsy. For each patient, EEG/fMRI analysis was first performed to determine the BOLD response to epileptic spikes. The maximum activation cluster in the frontal lobe was then chosen as the seed to identify the epileptic network in fMRI data. Functional connectivity analysis seeded at the same region was also performed in 63 healthy control subjects. Nine features were used to evaluate the differences of epileptic network patterns in three connection levels between patients and controls. Compared with control subjects, patients showed overall more functional connections between the epileptogenic region and the rest of the brain and higher laterality. However, the significantly increased connections were located in the neighborhood of the seed, but the connections between the seed and remote regions actually decreased. Comparing fMRI runs with interictal epileptic discharges (IEDs) and without IEDs, the patient-specific connectivity pattern was not changed significantly. These findings regarding patient-specific connectivity patterns of epileptic networks in FLE reflect local high connectivity and connections with distant regions differing from those of healthy controls. Moreover, the difference between the two groups in most features was observed in the strictest of the three connection levels. The abnormally high connectivity might reflect a predominant attribute of the epileptic network, which may facilitate propagation of epileptic activity among regions in the network. PMID:24936418

Results of a Two-Year Longitudinal Study of Beverage-Specific Alcohol Use among Adolescents

ERIC Educational Resources Information Center

Moore, Michele Johnson; Werch, Chudley

2007-01-01

This study explored beverage-specific alcohol consumption patterns among a sample of high school students over a two-year period. Four hundred fifty-five students completed the validated questionnaire at all three time points (2002, 2003, 2004). Variables of interest included five use measures (past year use, 30-day frequency, quantity, heavy use,…

Floral scent contributes to interaction specificity in coevolving plants and their insect pollinators.

PubMed

Friberg, Magne; Schwind, Christopher; Roark, Lindsey C; Raguso, Robert A; Thompson, John N

2014-09-01

Chemical defenses, repellents, and attractants are important shapers of species interactions. Chemical attractants could contribute to the divergence of coevolving plant-insect interactions, if pollinators are especially responsive to signals from the local plant species. We experimentally investigated patterns of daily floral scent production in three Lithophragma species (Saxifragaceae) that are geographically isolated and tested how scent divergence affects attraction of their major pollinator-the floral parasitic moth Greya politella (Prodoxidae). These moths oviposit through the corolla while simultaneously pollinating the flower with pollen adhering to the abdomen. The complex and species-specific floral scent profiles were emitted in higher amounts during the day, when these day-flying moths are active. There was minimal divergence found in petal color, which is another potential floral attractant. Female moths responded most strongly to scent from their local host species in olfactometer bioassays, and were more likely to oviposit in, and thereby pollinate, their local host species in no-choice trials. The results suggest that floral scent is an important attractant in this interaction. Local specialization in the pollinator response to a highly specific plant chemistry, thus, has the potential to contribute importantly to patterns of interaction specificity among coevolving plants and highly specialized pollinators.

Dynamic interneuron-principal cell interplay leads to a specific pattern of in vitro ictogenesis.

PubMed

Lévesque, Maxime; Chen, Li-Yuan; Hamidi, Shabnam; Avoli, Massimo

2018-07-01

Ictal discharges induced by 4-aminopyridine in the in vitro rodent entorhinal cortex present with either low-voltage fast or sudden onset patterns. The role of interneurons in initiating low-voltage fast onset ictal discharges is well established but the processes leading to sudden onset ictal discharges remain unclear. We analysed here the participation of interneurons (n = 75) and principal cells (n = 13) in the sudden onset pattern by employing in vitro tetrode wire recordings in the entorhinal cortex of brain slices from Sprague-Dawley rats. Ictal discharges emerged from a background of frequently occurring interictal spikes that were associated to a specific interneuron/principal cell interplay. High rates of interneuron firing occurred 12 ms before interictal spike onset while principal cells fired later during low interneuron firing. In contrast, the onset of sudden ictal discharges was characterized by increased firing from principal cells 627 ms before ictal onset whereas interneurons increased their firing rates 161 ms before ictal onset. Our data show that sudden onset ictogenesis is associated with frequently occurring interictal spikes resting on the interplay between interneurons and principal cells while ictal discharges stem from enhanced principal cell firing leading to increased interneuron activity. These findings indicate that specific patterns of interactions between interneurons and principal cells shape interictal and ictal discharges with sudden onset in the rodent entorhinal cortex. We propose that specific neuronal interactions lead to the generation of distinct onset patterns in focal epileptic disorders. Copyright © 2018 Elsevier Inc. All rights reserved.

Phenotype-specific CpG island methylation events in a murine model of prostate cancer.

PubMed

Camoriano, Marta; Kinney, Shannon R Morey; Moser, Michael T; Foster, Barbara A; Mohler, James L; Trump, Donald L; Karpf, Adam R; Smiraglia, Dominic J

2008-06-01

Aberrant DNA methylation plays a significant role in nearly all human cancers and may contribute to disease progression to advanced phenotypes. Study of advanced prostate cancer phenotypes in the human disease is hampered by limited availability of tissues. We therefore took advantage of the Transgenic Adenocarcinoma of Mouse Prostate (TRAMP) model to study whether three different phenotypes of TRAMP tumors (PRIM, late-stage primary tumors; AIP, androgen-independent primary tumors; and MET, metastases) displayed specific patterns of CpG island hypermethylation using Restriction Landmark Genomic Scanning. Each tumor phenotype displayed numerous hypermethylation events, with the most homogeneous methylation pattern in AIP and the most heterogeneous pattern in MET. Several loci displayed a phenotype-specific methylation pattern; the most striking pattern being loci methylated at high frequency in PRIM and AIP but rarely in MET. Examination of the mRNA expression of three genes, BC058385, Goosecoid, and Neurexin 2, which exhibited nonpromoter methylation, revealed increased expression associated with downstream methylation. Only methylated samples showed mRNA expression, in which tumor phenotype was a key factor determining the level of expression. The CpG island in the human orthologue of BC058385 was methylated in human AIP but not in primary androgen-stimulated prostate cancer or benign prostate. The clinical data show a proof-of-principle that the TRAMP model can be used to identify targets of aberrant CpG island methylation relevant to human disease. In conclusion, phenotype-specific hypermethylation events were associated with the overexpression of different genes and may provide new markers of prostate tumorigenesis.

Recognition of pigment network pattern in dermoscopy images based on fuzzy classification of pixels.

PubMed

Garcia-Arroyo, Jose Luis; Garcia-Zapirain, Begonya

2018-01-01

One of the most relevant dermoscopic patterns is the pigment network. An innovative method of pattern recognition is presented for its detection in dermoscopy images. It consists of two steps. In the first one, by means of a supervised machine learning process and after performing the extraction of different colour and texture features, a fuzzy classification of pixels into the three categories present in the pattern's definition ("net", "hole" and "other") is carried out. This enables the three corresponding fuzzy sets to be created and, as a result, the three probability images that map them out are generated. In the second step, the pigment network pattern is characterised from a parameterisation process -derived from the system specification- and the subsequent extraction of different features calculated from the combinations of image masks extracted from the probability images, corresponding to the alpha-cuts obtained from the fuzzy sets. The method was tested on a database of 875 images -by far the largest used in the state of the art to detect pigment network- extracted from a public Atlas of Dermoscopy, obtaining AUC results of 0.912 and 88%% accuracy, with 90.71%% sensitivity and 83.44%% specificity. The main contribution of this method is the very design of the algorithm, highly innovative, which could also be used to deal with other pattern recognition problems of a similar nature. Other contributions are: 1. The good performance in discriminating between the pattern and the disturbing artefacts -which means that no prior preprocessing is required in this method- and between the pattern and other dermoscopic patterns; 2. It puts forward a new methodological approach for work of this kind, introducing the system specification as a required step prior to algorithm design and development, being this specification the basis for a required parameterisation -in the form of configurable parameters (with their value ranges) and set threshold values- of the algorithm and the subsequent conducting of the experiments. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

[Phylo- and ontogenetic aspects of erect posture and walking in developmental neurology].

PubMed

Berényi, Marianne; Katona, Ferenc; Sanchez, Carmen; Mandujano, Mario

2011-07-30

The group or profile of elementary neuromotor patterns is different from the primitive reflex group which is now called the "primitive reflex profile." All these elementary neuromotor patterns are characterized by a high degree of organization, persistence, and stereotypy. In many regards, these patterns are predecessors or precursors of from them the specific human motor patterns which appear spontaneously later as crawling, creeping, sitting, and walking with erect posture. On the basis of our experiences it can be stated that the elementary neuromotor patterns can be activated in all neonates and young infants as congenital motor functions. With regards to their main properties and functional forms, the normal patterns can be divided into two main groups: (1) One group is characterized by lifting of the head and complex chains of movements which are directed to the verticalization of the body; (2) The other group is characterized by complex movements directed to locomotion and change of body position. The neuromotor patterns can be activated by placing the human infant in specific body positions that trigger the vestibulospinal and the reticulospinal systems, the archicerebellum and the basal gangliae. Most of these systems display early myelinisation and are functioning very soon. Many of the elementary neuromotor patterns reflect the most important - spontaneously developing forms of human movements such as sitting upright in space and head elevation crawling and walking. The majority of the human neuromotor patterns are human specific. When the infant is put in an activating position, crawling, sitting up, and walking begin and last as long as the activating position is maintained. Each elementary neuromotor pattern is a repeated, continuous train of complex movements in response to a special activating position. The brainstem is not sufficient to organize these complex movements, the integrity of the basal ganglia is also necessary. Elementary sensorimotor patterns during human ontogenesis reflect phylogenetic develpoment of species specific human functions. During ontogenesis spontaneous motor development gradually arises from these early specific sensorimotor predecessors.. The regular use of the elementary neuromotor patterns for diagnostic puposes has several distinct advantages. The neuromotor patterns have a natural stereotypy in normal infants and, therefore, deflections from this regular pattern may be detected easily, thus, the activation of the elementary neuromotor pattern is a more suitable method for identifying defects in the motor activity of the neonate or young infant than the assessment of the primitive reflexes. The "stiumulus positions," which activate specific movements according to how the human neonate or young infant is positioned, do not activate such motor patterns in neonate or young primates including apes. The characteristic locomotor pattern in these adult primates, including the apes, is swinging and involves brachiation with an extreme prehensility. This species specific motor activity is reflected in the orangutan and gibbon neonates by an early extensive grasp. However, according to our investigations, no crawling, creeping, elementary walk, or sitting up can be activated in them. Neonates grasp the hair of the mother, a vital function for the survival of the young. In contemporary nonhuman primates including apes, the neonate brain is more mature. Thus, pronounced differences can be observed between early motor ontogenesis in the human and all other primates. The earliest human movements are complex performances rather than simple reflexes. The distinction between primitive reflexes and elementary neuromotor patterns is essential. Primitive reflexes are controlled by the brainstem. All can be activated in primates. These reflexes have short durations and contrary to elementary sensorimotor patterns occur only once in response to one stimulus, e.g., one head drop elicits one abduction-adduction of the upper extremities correlated to adduction and flexion of the lower extremities to a lesser degree with the Moro reflex. Elementary neuromotor patterns are much more complex and most of them including elementary walk may be elicited as early as the 19th-20th gestational week, though less perfectly than later.

Inflammatory Dietary Pattern, IL-17F Genetic Variant, and the Risk of Colorectal Cancer.

PubMed

Cho, Young Ae; Lee, Jeonghee; Oh, Jae Hwan; Chang, Hee Jin; Sohn, Dae Kyung; Shin, Aesun; Kim, Jeongseon

2018-06-05

A proinflammatory diet may increase the risk of colorectal cancer, but its role may differ according to individuals' genetic variants. We aimed to examine whether a specific dietary pattern reflecting inflammation was associated with a risk of colorectal cancer and whether IL-17F genetic variant altered this association. In a study of 695 colorectal cancer cases and 1846 controls, we derived a reduced rank regression dietary pattern using 32 food groups as predictors and the plasma C-reactive protein (CRP) concentration as the response. High CRP levels were associated with a high risk of colorectal cancer (OR (95% CI) = 3.58 (2.65⁻4.82) for the highest quartile vs. lowest quartile). After adjusting for potential confounding factors, high pattern scores were associated with a high risk of colorectal cancer (OR (95% CI) = 9.98 (6.81⁻14.62) for the highest quartile vs. lowest quartile). When stratified by the IL-17F rs763780 genotype, this association was stronger for individuals carrying the C allele ( p for interaction = 0.034), particularly for individuals with rectal cancer ( p for interaction = 0.011). In conclusion, a dietary pattern reflecting inflammation was significantly associated with colorectal cancer risk. Moreover, this association could be modified according to the IL-17F rs763780 genotype and anatomic site.

Vertical transmission explains the specific Burkholderia pattern in Sphagnum mosses at multi-geographic scale

PubMed Central

Bragina, Anastasia; Cardinale, Massimiliano; Berg, Christian; Berg, Gabriele

2013-01-01

The betaproteobacterial genus Burkholderia is known for its versatile interactions with its hosts that can range from beneficial to pathogenic. A plant-beneficial-environmental (PBE) Burkholderia cluster was recently separated from the pathogen cluster, yet still little is known about burkholderial diversity, distribution, colonization, and transmission patterns on plants. In our study, we applied a combination of high-throughput molecular and microscopic methods to examine the aforementioned factors for Burkholderia communities associated with Sphagnum mosses – model plants for long-term associations – in Austrian and Russian bogs. Analysis of 16S rRNA gene amplicons libraries revealed that most of the Burkholderia are part of the PBE group, but a minor fraction was closely related to B. glathei and B. andropogonis from the pathogen cluster. Notably, Burkholderia showed highly similar composition patterns for each moss species independent of the geographic region, and Burkholderia-specific fluorescent in situ hybridization of Sphagnum gametophytes exhibited similar colonization patterns in different Sphagnum species at multi-geographic scales. To explain these patterns, we compared the compositions of the surrounding water, gametophyte-, and sporophyte-associated microbiome at genus level and discovered that Burkholderia were present in the Sphagnum sporophyte and gametophyte, but were absent in the flark water. Therefore, Burkholderia is a part of the core microbiome transmitted from the moss sporophyte to the gametophyte. This suggests a vertical transmission of Burkholderia strains, and thus underlines their importance for the plants themselves. PMID:24391630

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns.

PubMed

Kirby, Marie K; Ramaker, Ryne C; Roberts, Brian S; Lasseigne, Brittany N; Gunther, David S; Burwell, Todd C; Davis, Nicholas S; Gulzar, Zulfiqar G; Absher, Devin M; Cooper, Sara J; Brooks, James D; Myers, Richard M

2017-04-17

Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids such as urine and blood plasma that could serve as a non-invasive diagnostic biomarker for prostate cancer. We measured genome-wide DNA methylation patterns in 73 clinically annotated fresh-frozen prostate cancers and 63 benign-adjacent prostate tissues using the Illumina Infinium HumanMethylation450 BeadChip array. We overlaid the most significantly differentially methylated sites in the genome with transcription factor binding sites measured by the Encyclopedia of DNA Elements consortium. We used logistic regression and receiver operating characteristic curves to assess the performance of candidate diagnostic models. We identified methylation patterns that have a high predictive power for distinguishing malignant prostate tissue from benign-adjacent prostate tissue, and these methylation signatures were validated using data from The Cancer Genome Atlas Project. Furthermore, by overlaying ENCODE transcription factor binding data, we observed an enrichment of enhancer of zeste homolog 2 binding in gene regulatory regions with higher DNA methylation in malignant prostate tissues. DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.

A Priori and a Posteriori Dietary Patterns during Pregnancy and Gestational Weight Gain: The Generation R Study

PubMed Central

Tielemans, Myrte J.; Erler, Nicole S.; Leermakers, Elisabeth T. M.; van den Broek, Marion; Jaddoe, Vincent W. V.; Steegers, Eric A. P.; Kiefte-de Jong, Jessica C.; Franco, Oscar H.

2015-01-01

Abnormal gestational weight gain (GWG) is associated with adverse pregnancy outcomes. We examined whether dietary patterns are associated with GWG. Participants included 3374 pregnant women from a population-based cohort in the Netherlands. Dietary intake during pregnancy was assessed with food-frequency questionnaires. Three a posteriori-derived dietary patterns were identified using principal component analysis: a “Vegetable, oil and fish”, a “Nuts, high-fiber cereals and soy”, and a “Margarine, sugar and snacks” pattern. The a priori-defined dietary pattern was based on national dietary recommendations. Weight was repeatedly measured around 13, 20 and 30 weeks of pregnancy; pre-pregnancy and maximum weight were self-reported. Normal weight women with high adherence to the “Vegetable, oil and fish” pattern had higher early-pregnancy GWG than those with low adherence (43 g/week (95% CI 16; 69) for highest vs. lowest quartile (Q)). Adherence to the “Margarine, sugar and snacks” pattern was associated with a higher prevalence of excessive GWG (OR 1.45 (95% CI 1.06; 1.99) Q4 vs. Q1). Normal weight women with higher scores on the “Nuts, high-fiber cereals and soy” pattern had more moderate GWG than women with lower scores (−0.01 (95% CI −0.02; −0.00) per SD). The a priori-defined pattern was not associated with GWG. To conclude, specific dietary patterns may play a role in early pregnancy but are not consistently associated with GWG. PMID:26569303

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

PubMed

Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

2015-04-01

Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

Patterning of supported lipid bilayers and proteins using material selective nitrodopamine-mPEG.

PubMed

Spycher, Philipp R; Hall, Heike; Vogel, Viola; Reimhult, Erik

2015-01-01

We present a generic patterning process by which biomolecules in a passivated background are patterned directly from physiological buffer to microfabricated surfaces without the need for further processing. First, nitrodopamine-mPEG is self-assembled to selectively render TiO2 patterns non-fouling to biomolecule adsorption on hydrophilic and adhesive glass surfaces. After the controlled TiO2 passivation, the biomolecules can be directly adsorbed from solution in a single step creating large scale micropatterned and highly homogeneous arrays of biomolecules with very high pattern definition. We demonstrate the formation of fluid supported lipid bilayers (SLBs) down to the single μm-level limited only by the photolithographic process. Non-specific adsorption of lipid vesicles to the TiO2 background was found to be almost completely suppressed. The SLB patterns can be further selectively functionalized with retained mobility, which we demonstrate through biotin-streptavidin coupling. We envision this single step patterning approach to be very beneficial for membrane-based biosensors and for pattering of cells on a passivated background with complex, sub-cellular geometries; in each application the adherent areas have a tunable mobility of interaction sites controlled by the fluidity of the membrane.

Facile Fabrication of Hierarchically Thermoresponsive Binary Polymer Pattern for Controlled Cell Adhesion.

PubMed

Hou, Jianwen; Cui, Lele; Chen, Runhai; Xu, Xiaodong; Chen, Jiayue; Yin, Ligang; Liu, Jingchuan; Shi, Qiang; Yin, Jinghua

2018-03-01

A versatile platform allowing capture and detection of normal and dysfunctional cells on the same patterned surface is important for accessing the cellular mechanism, developing diagnostic assays, and implementing therapy. Here, an original and effective method for fabricating binary polymer brushes pattern is developed for controlled cell adhesion. The binary polymer brushes pattern, composed of poly(N-isopropylacrylamide) (PNIPAAm) and poly[poly(ethylene glycol) methyl ether methacrylate] (POEGMA) chains, is simply obtained via a combination of surface-initiated photopolymerization and surface-activated free radical polymerization. This method is unique in that it does not utilize any protecting groups or procedures of backfilling with immobilized initiator. It is demonstrated that the precise and well-defined binary polymer patterns with high resolution are fabricated using this facile method. PNIPAAm chains capture and release cells by thermoresponsiveness, while POEGMA chains possess high capability to capture dysfunctional cells specifically, inducing a switch of normal red blood cells (RBCs) arrays to hemolytic RBCs arrays on the pattern with temperature. This novel platform composed of binary polymer brush pattern is smart and versatile, which opens up pathways to potential applications as microsensors, biochips, and bioassays. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mask replication using jet and flash imprint lithography

NASA Astrophysics Data System (ADS)

Selinidis, Kosta S.; Jones, Chris; Doyle, Gary F.; Brown, Laura; Imhof, Joseph; LaBrake, Dwayne L.; Resnick, Douglas J.; Sreenivasan, S. V.

2011-11-01

The Jet and Flash Imprint Lithography (J-FILTM) process uses drop dispensing of UV curable resists to assist high resolution patterning for subsequent dry etch pattern transfer. The technology is actively being used to develop solutions for memory markets including Flash memory and patterned media for hard disk drives. It is anticipated that the lifetime of a single template (for patterned media) or mask (for semiconductor) will be on the order of 104 - 105imprints. This suggests that tens of thousands of templates/masks will be required to satisfy the needs of a manufacturing environment. Electron-beam patterning is too slow to feasibly deliver these volumes, but instead can provide a high quality "master" mask which can be replicated many times with an imprint lithography tool. This strategy has the capability to produce the required supply of "working" templates/masks. In this paper, we review the development of the mask form factor, imprint replication tools and the semiconductor mask replication process. A PerfectaTM MR5000 mask replication tool has been developed specifically to pattern replica masks from an ebeam written master. Performance results, including image placement, critical dimension uniformity, and pattern transfer are covered in detail.

Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus

PubMed Central

2012-01-01

Background Body coloration is an ecologically important trait that is often involved in prey-predator interactions through mimicry and crypsis. Although this subject has attracted the interest of biologists and the general public, our scientific knowledge on the subject remains fragmentary. In the caterpillar of the swallowtail butterfly Papilio xuthus, spectacular changes in the color pattern are observed; the insect mimics bird droppings (mimetic pattern) as a young larva, and switches to a green camouflage coloration (cryptic pattern) in the final instar. Despite the wide variety and significance of larval color patterns, few studies have been conducted at a molecular level compared with the number of studies on adult butterfly wing patterns. Results To obtain a catalog of genes involved in larval mimetic and cryptic pattern formation, we constructed expressed sequence tag (EST) libraries of larval epidermis for P. xuthus, and P. polytes that contained 20,736 and 5,376 clones, respectively, representing one of the largest collections available in butterflies. A comparison with silkworm epidermal EST information revealed the high expression of putative blue and yellow pigment-binding proteins in Papilio species. We also designed a microarray from the EST dataset information, analyzed more than five stages each for six markings, and confirmed spatial expression patterns by whole-mount in situ hybridization. Hence, we succeeded in elucidating many novel marking-specific genes for mimetic and cryptic pattern formation, including pigment-binding protein genes, the melanin-associated gene yellow-h3, the ecdysteroid synthesis enzyme gene 3-dehydroecdysone 3b-reductase, and Papilio-specific genes. We also found many cuticular protein genes with marking specificity that may be associated with the unique surface nanostructure of the markings. Furthermore, we identified two transcription factors, spalt and ecdysteroid signal-related E75, as genes expressed in larval eyespot markings. This finding suggests that E75 is a strong candidate mediator of the hormone-dependent coordination of larval pattern formation. Conclusions This study is one of the most comprehensive molecular analyses of complicated morphological features, and it will serve as a new resource for studying insect mimetic and cryptic pattern formation in general. The wide variety of marking-associated genes (both regulatory and structural genes) identified by our screening indicates that a similar strategy will be effective for understanding other complex traits. PMID:22651552

Property Specification Patterns for intelligence building software

NASA Astrophysics Data System (ADS)

Chun, Seungsu

2018-03-01

In this paper, through the property specification pattern research for Modal MU(μ) logical aspects present a single framework based on the pattern of intelligence building software. In this study, broken down by state property specification pattern classification of Dwyer (S) and action (A) and was subdivided into it again strong (A) and weaknesses (E). Through these means based on a hierarchical pattern classification of the property specification pattern analysis of logical aspects Mu(μ) was applied to the pattern classification of the examples used in the actual model checker. As a result, not only can a more accurate classification than the existing classification systems were easy to create and understand the attributes specified.

Patterned Colloidal Photonic Crystals.

PubMed

Hou, Jue; Li, Mingzhu; Song, Yanlin

2018-03-01

Colloidal photonic crystals (PCs) have been well developed because they are easy to prepare, cost-effective, and versatile with regards to modification and functionalization. Patterned colloidal PCs contribute a novel approach to constructing high-performance PC devices with unique structures and specific functions. In this review, an overview of the strategies for fabricating patterned colloidal PCs, including patterned substrate-induced assembly, inkjet printing, and selective immobilization and modification, is presented. The advantages of patterned PC devices are also discussed in detail, for example, improved detection sensitivity and response speed of the sensors, control over the flow direction and wicking rate of microfluidic channels, recognition of cross-reactive molecules through an array-patterned microchip, fabrication of display devices with tunable patterns, well-arranged RGB units, and wide viewing-angles, and the ability to construct anti-counterfeiting devices with different security strategies. Finally, the perspective of future developments and challenges is presented. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear emulsions for the detection of micrometric-scale fringe patterns: an application to positron interferometry

NASA Astrophysics Data System (ADS)

Aghion, S.; Ariga, A.; Bollani, M.; Ereditato, A.; Ferragut, R.; Giammarchi, M.; Lodari, M.; Pistillo, C.; Sala, S.; Scampoli, P.; Vladymyrov, M.

2018-05-01

Nuclear emulsions are capable of very high position resolution in the detection of ionizing particles. This feature can be exploited to directly resolve the micrometric-scale fringe pattern produced by a matter-wave interferometer for low energy positrons (in the 10–20 keV range). We have tested the performance of emulsion films in this specific scenario. Exploiting silicon nitride diffraction gratings as absorption masks, we produced periodic patterns with features comparable to the expected interferometer signal. Test samples with periodicities of 6, 7 and 20 μ m were exposed to the positron beam, and the patterns clearly reconstructed. Our results support the feasibility of matter-wave interferometry experiments with positrons.

Learning Cue Phrase Patterns from Radiology Reports Using a Genetic Algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patton, Robert M; Beckerman, Barbara G; Potok, Thomas E

2009-01-01

Various computer-assisted technologies have been developed to assist radiologists in detecting cancer; however, the algorithms still lack high degrees of sensitivity and specificity, and must undergo machine learning against a training set with known pathologies in order to further refine the algorithms with higher validity of truth. This work describes an approach to learning cue phrase patterns in radiology reports that utilizes a genetic algorithm (GA) as the learning method. The approach described here successfully learned cue phrase patterns for two distinct classes of radiology reports. These patterns can then be used as a basis for automatically categorizing, clustering, ormore » retrieving relevant data for the user.« less

Novel fabrication of flexible graphene-based chemical sensors with heaters using soft lithographic patterning method.

PubMed

Jung, Min Wook; Myung, Sung; Song, Wooseok; Kang, Min-A; Kim, Sung Ho; Yang, Cheol-Soo; Lee, Sun Sook; Lim, Jongsun; Park, Chong-Yun; Lee, Jeong-O; An, Ki-Seok

2014-08-27

We have fabricated graphene-based chemical sensors with flexible heaters for the highly sensitive detection of specific gases. We believe that increasing the temperature of the graphene surface significantly enhanced the electrical signal change of the graphene-based channel, and reduced the recovery time needed to obtain a normal state of equilibrium. In addition, a simple and efficient soft lithographic patterning process was developed via surface energy modification for advanced, graphene-based flexible devices, such as gas sensors. As a proof of concept, we demonstrated the high sensitivity of NO2 gas sensors based on graphene nanosheets. These devices were fabricated using a simple soft-lithographic patterning method, where flexible graphene heaters adjacent to the channel of sensing graphene were utilized to control graphene temperature.

Exploring patterns enriched in a dataset with contrastive principal component analysis.

PubMed

Abid, Abubakar; Zhang, Martin J; Bagaria, Vivek K; Zou, James

2018-05-30

Visualization and exploration of high-dimensional data is a ubiquitous challenge across disciplines. Widely used techniques such as principal component analysis (PCA) aim to identify dominant trends in one dataset. However, in many settings we have datasets collected under different conditions, e.g., a treatment and a control experiment, and we are interested in visualizing and exploring patterns that are specific to one dataset. This paper proposes a method, contrastive principal component analysis (cPCA), which identifies low-dimensional structures that are enriched in a dataset relative to comparison data. In a wide variety of experiments, we demonstrate that cPCA with a background dataset enables us to visualize dataset-specific patterns missed by PCA and other standard methods. We further provide a geometric interpretation of cPCA and strong mathematical guarantees. An implementation of cPCA is publicly available, and can be used for exploratory data analysis in many applications where PCA is currently used.

3D Printed, Microgroove Pattern-Driven Generation of Oriented Ligamentous Architectures.

PubMed

Park, Chan Ho; Kim, Kyoung-Hwa; Lee, Yong-Moo; Giannobile, William V; Seol, Yang-Jo

2017-09-08

Specific orientations of regenerated ligaments are crucially required for mechanoresponsive properties and various biomechanical adaptations, which are the key interplay to support mineralized tissues. Although various 2D platforms or 3D printing systems can guide cellular activities or aligned organizations, it remains a challenge to develop ligament-guided, 3D architectures with the angular controllability for parallel, oblique or perpendicular orientations of cells required for biomechanical support of organs. Here, we show the use of scaffold design by additive manufacturing for specific topographies or angulated microgroove patterns to control cell orientations such as parallel (0°), oblique (45°) and perpendicular (90°) angulations. These results demonstrate that ligament cells displayed highly predictable and controllable orientations along microgroove patterns on 3D biopolymeric scaffolds. Our findings demonstrate that 3D printed topographical approaches can regulate spatiotemporal cell organizations that offer strong potential for adaptation to complex tissue defects to regenerate ligament-bone complexes.

Vertebrate homologues of Frodo are dynamically expressed during embryonic development in tissues undergoing extensive morphogenetic movements.

PubMed

Hunter, Nina L; Hikasa, Hiroki; Dymecki, Susan M; Sokol, Sergei Y

2006-01-01

Frodo has been identified as a protein interacting with Dishevelled, an essential mediator of the Wnt signaling pathway, critical for the determination of cell fate and polarity in embryonic development. In this study, we use specific gene probes to characterize stage- and tissue-specific expression patterns of the mouse Frodo homologue and compare them with Frodo expression patterns in Xenopus embryos. In situ hybridization analysis of mouse Frodo transcripts demonstrates that, similar to Xenopus Frodo, mouse Frodo is expressed in primitive streak mesoderm, neuroectoderm, neural crest, presomitic mesoderm, and somites. In many cases, Frodo expression is confined to tissues undergoing extensive morphogenesis, suggesting that Frodo may be involved in the regulation of cell shape and motility. Highly conserved dynamic expression patterns of Frodo homologues indicate a similar function for these proteins in different vertebrates. 2005 Wiley-Liss, Inc.

Evaluation of photomask flatness compensation for extreme ultraviolet lithography

NASA Astrophysics Data System (ADS)

Ballman, Katherine; Lee, Christopher; Zimmerman, John; Dunn, Thomas; Bean, Alexander

2016-10-01

As the semiconductor industry continues to strive towards high volume manufacturing for EUV, flatness specifications for photomasks have decreased to below 10nm for 2018 production, however the current champion masks being produced report P-V flatness values of roughly 50nm. Write compensation presents the promising opportunity to mitigate pattern placement errors through the use of geometrically adjusted target patterns which counteract the reticle's flatness induced distortions and address the differences in chucking mechanisms between e-beam write and electrostatic clamping during scan. Compensation relies on high accuracy flatness data which provides the critical topographical components of the reticle to the write tool. Any errors included in the flatness data file are translated to the pattern during the write process, which has now driven flatness measurement tools to target a 6σ reproducibility <1nm. Using data collected from a 2011 Sematech study on the Alpha Demo Tool, the proposed methodology for write compensation is validated against printed wafer results. Topographic features which lack compensation capability must then be held to stringent specifications in order to limit their contributions to the final image placement error (IPE) at wafer. By understanding the capabilities and limitations of write compensation, it is then possible to shift flatness requirements towards the "non-correctable" portion of the reticle's profile, potentially relieving polishers from having to adhere to the current single digit flatness specifications.

Ultrasonography of ovarian masses using a pattern recognition approach

PubMed Central

Jung, Sung Il

2015-01-01

As a primary imaging modality, ultrasonography (US) can provide diagnostic information for evaluating ovarian masses. Using a pattern recognition approach through gray-scale transvaginal US, ovarian masses can be diagnosed with high specificity and sensitivity. Doppler US may allow ovarian masses to be diagnosed as benign or malignant with even greater confidence. In order to differentiate benign and malignant ovarian masses, it is necessary to categorize ovarian masses into unilocular cyst, unilocular solid cyst, multilocular cyst, multilocular solid cyst, and solid tumor, and then to detect typical US features that demonstrate malignancy based on pattern recognition approach. PMID:25797108

Dynamic high-resolution patterning for biomedical, materials, and semiconductor research

NASA Astrophysics Data System (ADS)

Garner, Harold R.; Joshi, Amruta; Mitnala, Sandhya N.; Huebschman, Michael L.; Shandy, Surya; Wallek, Brandi; Wong, Season

2009-02-01

By combining unique light sources, a Texas Instruments DLP system and a microscope, a submicron dynamic patterning system has been created. This system has a resolution of 0.5 microns, and can illuminate with rapidly changing patterns of visible, UV or pulsed laser light. This system has been used to create digital masks for the production of micron scale electronic test circuits and has been used in biological applications. Specifically we have directed light on a sub-organelle scale to cells to control their morphology and motility with applications to tissue engineering, cell biology, drug discovery and neurology.

Proliferation-dependent positioning of individual centromeres in the interphase nucleus of human lymphoblastoid cell lines

PubMed Central

Ollion, Jean; Loll, François; Cochennec, Julien; Boudier, Thomas; Escudé, Christophe

2015-01-01

The cell nucleus is a highly organized structure and plays an important role in gene regulation. Understanding the mechanisms that sustain this organization is therefore essential for understanding genome function. Centromeric regions (CRs) of chromosomes have been known for years to adopt specific nuclear positioning patterns, but the significance of this observation is not yet completely understood. Here, using a combination of fluorescence in situ hybridization and immunochemistry on fixed human cells and high-throughput imaging, we directly and quantitatively investigated the nuclear positioning of specific human CRs. We observe differential attraction of individual CRs toward both the nuclear border and the nucleoli, the former being enhanced in nonproliferating cells and the latter being enhanced in proliferating cells. Similar positioning patterns are observed in two different lymphoblastoid cell lines. Moreover, the positioning of CRs differs from that of noncentromeric regions, and CRs display specific orientations within chromosome territories. These results suggest the existence of not-yet-characterized mechanisms that drive the nuclear positioning of CRs and therefore pave the way toward a better understanding of how CRs affect nuclear organization. PMID:25947134

Mapping lexical-semantic networks and determining hemispheric language dominance: Do task design, sex, age, and language performance make a difference?

PubMed

Chang, Yu-Hsuan A; Javadi, Sogol S; Bahrami, Naeim; Uttarwar, Vedang S; Reyes, Anny; McDonald, Carrie R

2018-04-01

Blocked and event-related fMRI designs are both commonly used to localize language networks and determine hemispheric dominance in research and clinical settings. We compared activation profiles on a semantic monitoring task using one of the two designs in a total of 43 healthy individual to determine whether task design or subject-specific factors (i.e., age, sex, or language performance) influence activation patterns. We found high concordance between the two designs within core language regions, including the inferior frontal, posterior temporal, and basal temporal region. However, differences emerged within inferior parietal cortex. Subject-specific factors did not influence activation patterns, nor did they interact with task design. These results suggest that despite high concordance within perisylvian regions that are robust to subject-specific factors, methodological differences between blocked and event-related designs may contribute to parietal activations. These findings provide important information for researchers incorporating fMRI results into meta-analytic studies, as well as for clinicians using fMRI to guide pre-surgical planning. Copyright © 2018 Elsevier Inc. All rights reserved.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens

PubMed Central

Glinsky, Gennadi V.

2016-01-01

Abstract Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8–10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. PMID:27503290

Assessment of hemodynamics of intracranial aneurysms using Doppler optical coherence tomography in patient specific phantoms: preliminary results (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ramjist, Joel M.; Jivraj, Jamil; Barrows, Dexter; Vuong, Barry; Wong, Ronnie; Yang, Victor X. D.

2017-02-01

Intracranial aneurysms affect a large number of individuals every year. Changes to hemodynamics are thought to be a crucial factor in the initial formation and enlargement of intracranial aneurysms. Previously, surgical clipping - an open an invasive procedure, was the standard of care. More recently, minimally invasive, catheter based therapies, specifically stenting and coiling, has been employed for treatment as it is less invasive and poses fewer overall risks. However, these treatments can further alter hemodynamic patterns of patients, affecting efficacy and prognosis. Doppler optical coherence tomography (DOCT) has shown to be useful for the evaluation of changes to hemodynamic patterns in various vascular pathologies, and intravascular DOCT may provide useful insight in the evaluation and changes to hemodynamic patterns before and during the treatment of aneurysms. In this study, we present preliminary results of DOCT imaging used in three patient-specific aneurysm phantoms located within the Circle of Willis both pre and post-treatment. These results are compared with computational fluid dynamics (CFD) simulations and high-speed camera imaging for further interpretation and validation of results.

Conservation of small RNA pathways in platypus

PubMed Central

Murchison, Elizabeth P.; Kheradpour, Pouya; Sachidanandam, Ravi; Smith, Carly; Hodges, Emily; Xuan, Zhenyu; Kellis, Manolis; Grützner, Frank; Stark, Alexander; Hannon, Gregory J.

2008-01-01

Small RNA pathways play evolutionarily conserved roles in gene regulation and defense from parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find a large rapidly evolving cluster of microRNAs on platypus chromosome X1, which is unique to monotremes. Platypus and echidna testes contain a robust Piwi-interacting (piRNA) system, which appears to be participating in ongoing transposon defense. PMID:18463306

Conservation of small RNA pathways in platypus.

PubMed

Murchison, Elizabeth P; Kheradpour, Pouya; Sachidanandam, Ravi; Smith, Carly; Hodges, Emily; Xuan, Zhenyu; Kellis, Manolis; Grützner, Frank; Stark, Alexander; Hannon, Gregory J

2008-06-01

Small RNA pathways play evolutionarily conserved roles in gene regulation and defense from parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find a large rapidly evolving cluster of microRNAs on platypus chromosome X1, which is unique to monotremes. Platypus and echidna testes contain a robust Piwi-interacting (piRNA) system, which appears to be participating in ongoing transposon defense.

Sparse Feature Selection Identifies H2A.Z as a Novel, Pattern-Specific Biomarker for Asymmetrically Self-Renewing Distributed Stem Cells

PubMed Central

Huh, Yang Hoon; Noh, Minsoo; Burden, Frank R.; Chen, Jennifer C.; Winkler, David A.; Sherley, James L.

2015-01-01

There is a long-standing unmet clinical need for biomarkers with high specificity for distributed stem cells (DSCs) in tissues, or for use in diagnostic and therapeutic cell preparations (e.g., bone marrow). Although DSCs are essential for tissue maintenance and repair, accurate determination of their numbers for medical applications has been problematic. Previous searches for biomarkers expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and by the challenges in mining complex molecular expression data. To identify DSC such useful and specific biomarkers, we combined a novel sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a conspicuous property of DSCs. The analysis identified reduced expression of the histone H2A variant H2A.Z as a superior molecular discriminator for DSC asymmetric self-renewal. Subsequent molecular expression studies showed H2A.Z to be a novel “pattern-specific biomarker” for asymmetrically self-renewing cells with sufficient specificity to count asymmetrically self-renewing DSCs in vitro and potentially in situ. PMID:25636161

Application-specific coarse-grained reconfigurable array: architecture and design methodology

NASA Astrophysics Data System (ADS)

Zhou, Li; Liu, Dongpei; Zhang, Jianfeng; Liu, Hengzhu

2015-06-01

Coarse-grained reconfigurable arrays (CGRAs) have shown potential for application in embedded systems in recent years. Numerous reconfigurable processing elements (PEs) in CGRAs provide flexibility while maintaining high performance by exploring different levels of parallelism. However, a difference remains between the CGRA and the application-specific integrated circuit (ASIC). Some application domains, such as software-defined radios (SDRs), require flexibility with performance demand increases. More effective CGRA architectures are expected to be developed. Customisation of a CGRA according to its application can improve performance and efficiency. This study proposes an application-specific CGRA architecture template composed of generic PEs (GPEs) and special PEs (SPEs). The hardware of the SPE can be customised to accelerate specific computational patterns. An automatic design methodology that includes pattern identification and application-specific function unit generation is also presented. A mapping algorithm based on ant colony optimisation is provided. Experimental results on the SDR target domain show that compared with other ordinary and application-specific reconfigurable architectures, the CGRA generated by the proposed method performs more efficiently for given applications.

National Collegiate Athletic Association Division I athletic trainers' concussion-management practice patterns.

PubMed

Kelly, Kassandra C; Jordan, Erin M; Joyner, A Barry; Burdette, G Trey; Buckley, Thomas A

2014-01-01

A cornerstone of the recent consensus statements on concussion is a multifaceted concussion-assessment program at baseline and postinjury and when tracking recovery. Earlier studies of athletic trainers' (ATs') practice patterns found limited use of multifaceted protocols; however, these authors typically grouped diverse athletic training settings together. To (1) describe the concussion-management practice patterns of National Collegiate Athletic Association (NCAA) Division I ATs, (2) compare these practice patterns to earlier studies, and (3) objectively characterize the clinical examination. Cross-sectional study. Online survey. A total of 610 ATs from NCAA Division I institutions, for a response rate of 34.4%. The survey had 3 subsections: demographic questions related to the participant's experiences, concussion-assessment practice patterns, and concussion-recovery and return-to-participation practice patterns. Specific practice-pattern questions addressed balance, cognitive and mental status, neuropsychological testing, and self-reported symptoms. Finally, specific components of the clinical examination were examined. We identified high rates of multifaceted assessments (i.e., assessments using at least 3 techniques) during testing at baseline (71.2%), acute concussion assessment (79.2%), and return to participation (66.9%). The specific techniques used are provided along with their adherence with evidence-based practice findings. Respondents endorsed a diverse array of clinical examination techniques that often overlapped objective concussion-assessment protocols or were likely used to rule out associated potential conditions. Respondents were cognizant of the Third International Consensus Statement, the National Athletic Trainers' Association position statement, and the revised NCAA Sports Medicine Handbook recommendations. Athletic trainers in NCAA Division I demonstrated widespread use of multifaceted concussion-assessment techniques and appeared compliant with recent consensus statements and the NCAA Sports Medicine Handbook.

Toward Abstracting the Communication Intent in Applications to Improve Portability and Productivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mintz, Tiffany M; Hernandez, Oscar R; Kartsaklis, Christos

Programming with communication libraries such as the Message Passing Interface (MPI) obscures the high-level intent of the communication in an application and makes static communication analysis difficult to do. Compilers are unaware of communication libraries specifics, leading to the exclusion of communication patterns from any automated analysis and optimizations. To overcome this, communication patterns can be expressed at higher-levels of abstraction and incrementally added to existing MPI applications. In this paper, we propose the use of directives to clearly express the communication intent of an application in a way that is not specific to a given communication library. Our communicationmore » directives allow programmers to express communication among processes in a portable way, giving hints to the compiler on regions of computations that can be overlapped with communication and relaxing communication constraints on the ordering, completion and synchronization of the communication imposed by specific libraries such as MPI. The directives can then be translated by the compiler into message passing calls that efficiently implement the intended pattern and be targeted to multiple communication libraries. Thus far, we have used the directives to express point-to-point communication patterns in C, C++ and Fortran applications, and have translated them to MPI and SHMEM.« less

Hox gene control of segment-specific bristle patterns in Drosophila

PubMed Central

Rozowski, Marion; Akam, Michael

2002-01-01

Hox genes specify the different morphologies of segments along the anteroposterior axis of animals. How they control complex segment morphologies is not well understood. We have studied how the Hox gene Ultrabithorax (Ubx) controls specific differences between the bristle patterns of the second and third thoracic segments (T2 and T3) of Drosophila melanogaster. We find that Ubx blocks the development of two particular bristles on T3 at different points in sensory organ development. For the apical bristle, a precursor is singled out and undergoes a first division in both the second and third legs, but in the third leg further differentiation of the second-order precursors is blocked. For the posterior sternopleural bristle, development on T3 ceases after proneural cluster initiation. Analysis of the temporal requirement for Ubx shows that in both cases Ubx function is required shortly before bristle development is blocked. We suggest that interactions between Ubx and the bristle patterning hierarchy have evolved independently on many occasions, affecting different molecular steps. The effects of Ubx on bristle development are highly dependent on the context of other patterning information. Suppression of bristle development or changes in bristle morphology in response to endogenous and ectopic Ubx expression are limited to bristles at specific locations. PMID:12000797

The use of dendrograms to describe the electrical activity of motoneurons underlying behaviors in leeches

PubMed Central

Juárez-Hernández, León J.; Bisson, Giacomo; Torre, Vincent

2013-01-01

The present manuscript aims at identifying patterns of electrical activity recorded from neurons of the leech nervous system, characterizing specific behaviors. When leeches are at rest, the electrical activity of neurons and motoneurons is poorly correlated. When leeches move their head and/or tail, in contrast, action potential (AP) firing becomes highly correlated. When the head or tail suckers detach, specific patterns of electrical activity are detected. During elongation and contraction the electrical activity of motoneurons in the Medial Anterior and Dorsal Posterior nerves increase, respectively, and several motoneurons are activated both during elongation and contraction. During crawling, swimming, and pseudo-swimming patterns of electrical activity are better described by the dendrograms of cross-correlations of motoneurons pairs. Dendrograms obtained from different animals exhibiting the same behavior are similar and by averaging these dendrograms we obtained a template underlying a given behavior. By using this template, the corresponding behavior is reliably identified from the recorded electrical activity. The analysis of dendrograms during different leech behavior reveals the fine orchestration of motoneurons firing specific to each stereotyped behavior. Therefore, dendrograms capture the subtle changes in the correlation pattern of neuronal networks when they become involved in different tasks or functions. PMID:24098274

Patterns of Protein Food Intake Are Associated with Nutrient Adequacy in the General French Adult Population.

PubMed

Gavelle, Erwan de; Huneau, Jean-François; Mariotti, François

2018-02-17

Protein food intake appears to partially structure dietary patterns, as most current emergent diets (e.g., vegetarian and flexitarian) can be described according to their levels of specific protein sources. However, few data are available on dietary protein patterns in the general population and their association with nutrient adequacy. Based on protein food intake data concerning 1678 adults from a representative French national dietary survey, and non-negative-matrix factorization followed by cluster analysis, we were able to identify distinctive dietary protein patterns and compare their nutrient adequacy (using PANDiet probabilistic scoring). The findings revealed eight patterns that clearly discriminate protein intakes and were characterized by the intakes of one or more specific protein foods: 'Processed meat', 'Poultry', 'Pork', 'Traditional', 'Milk', 'Take-away', 'Beef' and 'Fish'. 'Fish eaters' and 'Milk drinkers' had the highest overall nutrient adequacy, whereas that of 'Pork' and 'Take-away eaters' was the lowest. Nutrient adequacy could often be accounted for by the characteristics of the food contributing to protein intake: 'Meat eaters' had high probability of adequacy for iron and zinc, for example. We concluded that protein patterns constitute strong elements in the background structure of the dietary intake and are associated with the nutrient profile that they convey.

E6-associated transcription patterns in human papilloma virus 16-positive cervical tissues.

PubMed

Lin, Kezhi; Lu, Xulian; Chen, Jun; Zou, Ruanmin; Zhang, Lifang; Xue, Xiangyang

2015-01-01

The change in transcription pattern induced by post-transcriptional RNA splicing is an important mechanism in the regulation of the early gene expression of human papilloma virus (HPV). The present study was conducted to establish a method to specifically amplify HPV-16 E6-associated transcripts. The E6-related transcripts from 63 HPV-16-positive cervical tumor tissue samples were amplified, consisting of eight cases of low-risk intraepithelial lesions, 38 cases of high-risk intraepithelial lesions and 17 cases of cervical cancer (CxCa). The appropriate amplified segments were recovered following agarose gel electrophoresis, and subjected to further sequencing and sequence alignment analysis. Six groups of E6 transcription patterns were identified from HPV-16-positive cervical tumor tissue, including five newly-discovered transcripts. Different HPV-16 E6-associated transcription patterns were detected during the development of CxCa. Over the course of the progression of the low-grade squamous intraepithelial lesions to CxCa, the specific HPV-16 E6-associated transcription patterns and the dominant transcripts were all different. As indicated by this study, the transcription pattern of the E6 early gene of HPV-16 was closely associated with the stages of cervical carcinogenesis, and may also be involved in the development of CxCa.

Describing the brain in autism in five dimensions--magnetic resonance imaging-assisted diagnosis of autism spectrum disorder using a multiparameter classification approach.

PubMed

Ecker, Christine; Marquand, Andre; Mourão-Miranda, Janaina; Johnston, Patrick; Daly, Eileen M; Brammer, Michael J; Maltezos, Stefanos; Murphy, Clodagh M; Robertson, Dene; Williams, Steven C; Murphy, Declan G M

2010-08-11

Autism spectrum disorder (ASD) is a neurodevelopmental condition with multiple causes, comorbid conditions, and a wide range in the type and severity of symptoms expressed by different individuals. This makes the neuroanatomy of autism inherently difficult to describe. Here, we demonstrate how a multiparameter classification approach can be used to characterize the complex and subtle structural pattern of gray matter anatomy implicated in adults with ASD, and to reveal spatially distributed patterns of discriminating regions for a variety of parameters describing brain anatomy. A set of five morphological parameters including volumetric and geometric features at each spatial location on the cortical surface was used to discriminate between people with ASD and controls using a support vector machine (SVM) analytic approach, and to find a spatially distributed pattern of regions with maximal classification weights. On the basis of these patterns, SVM was able to identify individuals with ASD at a sensitivity and specificity of up to 90% and 80%, respectively. However, the ability of individual cortical features to discriminate between groups was highly variable, and the discriminating patterns of regions varied across parameters. The classification was specific to ASD rather than neurodevelopmental conditions in general (e.g., attention deficit hyperactivity disorder). Our results confirm the hypothesis that the neuroanatomy of autism is truly multidimensional, and affects multiple and most likely independent cortical features. The spatial patterns detected using SVM may help further exploration of the specific genetic and neuropathological underpinnings of ASD, and provide new insights into the most likely multifactorial etiology of the condition.

An evaluation of time-series MODIS 250-meter vegetation index data for crop mapping in the United States Central Great Plains

NASA Astrophysics Data System (ADS)

Wardlow, Brian Douglas

The objectives of this research were to: (1) investigate time-series MODIS (Moderate Resolution Imaging Spectroradiometer) 250-meter EVI (Enhanced Vegetation Index) and NDVI (Normalized Difference Vegetation Index) data for regional-scale crop-related land use/land cover characterization in the U.S. Central Great Plains and (2) develop and test a MODIS-based crop mapping protocol. A pixel-level analysis of the time-series MODIS 250-m VIs for 2,000+ field sites across Kansas found that unique spectral-temporal signatures were detected for the region's major crop types, consistent with the crops' phenology. Intra-class variations were detected in VI data associated with different land use practices, climatic conditions, and planting dates for the crops. The VIs depicted similar seasonal variations and were highly correlated. A pilot study in southwest Kansas found that accurate and detailed cropping patterns could be mapped using the MODIS 250-m VI data. Overall and class-specific accuracies were generally greater than 90% for mapping crop/non-crop, general crops (alfalfa, summer crops, winter wheat, and fallow), summer crops (corn, sorghum, and soybeans), and irrigated/non-irrigated crops using either VI dataset. The classified crop areas also had a high level of agreement (<5% difference) with the USDA reported crop areas. Both VIs produced comparable crop maps with only a 1-2% difference between their classification accuracies and a high level of pixel-level agreement (>90%) between their classified crop patterns. This hierarchical crop mapping protocol was tested for Kansas and produced similar classification results over a larger and more diverse area. Overall and class-specific accuracies were typically between 85% and 95% for the crop maps. At the state level, the maps had a high level of areal agreement (<5% difference) with the USDA crop area figures and their classified patterns were consistent with the state's cropping practices. In general, the protocol's performance was relatively consistent across the state's range of environmental conditions, landscape patterns, and cropping practices. The largest areal differences occurred in eastern Kansas due to the omission of many small cropland areas that were not resolvable at MODIS' 250-m resolution. Notable regional deviations in classified areas also occurred for selected classes due to localized precipitation patterns and specific cropping practices.

Dermoscopic patterns of Melanoma Metastases: inter-observer consistency and accuracy for metastases recognition

PubMed Central

Costa, J.; Ortiz-Ibañez, K.; Salerni, G.; Borges, V.; Carrera, C.; Puig, S.; Malvehy, J.

2013-01-01

Background Cutaneous metastases of malignant melanoma (CMMM) can be confused with other skin lesions. Dermoscopy could be helpful in the differential diagnosis. Objective To describe distinctive dermoscopic patterns that are reproducible and accurate in the identification of CMMM Methods A retrospective study of 146 dermoscopic images of CMMM from 42 patients attending a Melanoma Unit between 2002 and 2009 was performed. Firstly, two investigators established six dermoscopic patterns for CMMM. The correlation of 73 dermoscopic images with their distinctive patterns was assessed by four independent dermatologists to evaluate the reproducibility in the identification of the patterns. Finally, 163 dermoscopic images, including CMMM and non-metastatic lesions, were evaluated by the same four dermatologists to calculate the accuracy of the patterns in the recognition of CMMM. Results Five CMMM dermoscopic patterns had a good inter-observer agreement (blue nevus-like, nevus-like, angioma like, vascular and unspecific). When CMMM were classified according to these patterns, correlation between the investigators and the four dermatologists ranged from κ = 0.56 to 0.7. 71 CMMM, 16 angiomas, 22 blue nevus, 15 malignant melanoma, 11 seborrheic keratosis, 15 melanocytic nevus with globular pattern and 13 pink lesions with vascular pattern were evaluated according to the previously described CMMM dermoscopy patterns, showing an overall sensitivity of 68% (between 54.9–76%) and a specificity of 81% (between 68.6–93.5) for the diagnosis of CMMM. Conclusion Five dermoscopic patterns of CMMM with good inter-observer agreement obtained a high sensitivity and specificity in the diagnosis of metastasis, the accuracy varying according to the experience of the observer. PMID:23495915

The Influence of Wheelchair Propulsion Hand Pattern on Upper Extremity Muscle Power and Stress

PubMed Central

Slowik, Jonathan S.; Requejo, Philip S.; Mulroy, Sara J.; Neptune, Richard R.

2016-01-01

The hand pattern (i.e., full-cycle hand path) used during manual wheelchair propulsion is frequently classified as one of four distinct hand pattern types: arc, single loop, double loop and semicircular. Current clinical guidelines recommend the use of the semicircular pattern, which is based on advantageous levels of broad biomechanical metrics implicitly related to the demand placed on the upper extremity (e.g., lower cadence). However, an understanding of the influence of hand pattern on specific measures of upper extremity muscle demand (e.g., muscle power and stress) is needed to help make such recommendations, but these quantities are difficult and impractical to measure experimentally. The purpose of this study was to use musculoskeletal modeling and forward dynamics simulations to investigate the influence of the hand pattern used on specific measures of upper extremity muscle demand. The simulation results suggest that the double loop and semicircular patterns produce the most favorable levels of overall muscle stress and total muscle power. The double loop pattern had the lowest full-cycle and recovery-phase upper extremity demand but required high levels of muscle power during the relatively short contact phase. The semicircular pattern had the second-lowest full-cycle levels of overall muscle stress and total muscle power, and demand was more evenly distributed between the contact and recovery phases. These results suggest that in order to decrease upper extremity demand, manual wheelchair users should use either the double loop or semicircular pattern when propelling their wheelchairs at a self-selected speed on level ground. PMID:27062591

A selection criterion for patterns in reaction–diffusion systems

PubMed Central

2014-01-01

Background Alan Turing’s work in Morphogenesis has received wide attention during the past 60 years. The central idea behind his theory is that two chemically interacting diffusible substances are able to generate stable spatial patterns, provided certain conditions are met. Ever since, extensive work on several kinds of pattern-generating reaction diffusion systems has been done. Nevertheless, prediction of specific patterns is far from being straightforward, and a great deal of interest in deciphering how to generate specific patterns under controlled conditions prevails. Results Techniques allowing one to predict what kind of spatial structure will emerge from reaction–diffusion systems remain unknown. In response to this need, we consider a generalized reaction diffusion system on a planar domain and provide an analytic criterion to determine whether spots or stripes will be formed. Our criterion is motivated by the existence of an associated energy function that allows bringing in the intuition provided by phase transitions phenomena. Conclusions Our criterion is proved rigorously in some situations, generalizing well-known results for the scalar equation where the pattern selection process can be understood in terms of a potential. In more complex settings it is investigated numerically. Our work constitutes a first step towards rigorous pattern prediction in arbitrary geometries/conditions. Advances in this direction are highly applicable to the efficient design of Biotechnology and Developmental Biology experiments, as well as in simplifying the analysis of morphogenetic models. PMID:24476200

Callous-Unemotional Features, Behavioral Inhibition, and Parenting: Independent Predictors of Aggression in a High-Risk Preschool Sample

ERIC Educational Resources Information Center

Kimonis, Eva R.; Frick, Paul J.; Boris, Neil W.; Smyke, Anna T.; Cornell, Amy H.; Farrell, Jamie M.; Zeanah, Charles H.

2006-01-01

A behaviorally-uninhibited temperament, callous-unemotional (CU) features, and harsh parenting have been associated with specific patterns of aggressive behavior in older children and adolescents. We tested the additive and interactive effects of these factors in predicting different types of aggressive behavior in a high-risk preschool sample.…

An Investigation into Physics Teaching in Senior High Schools

ERIC Educational Resources Information Center

Buabeng, Isaac; Ossei-Anto, Theophilus Aquinas; Ampiah, Joseph Ghartey

2014-01-01

This study sought to examine the activities that go on in physics classrooms in Senior High Schools in Ghana. Specifically, the study sought to investigate the pattern of interaction and instructional methods used for teaching physics and level of coverage of physics syllabus. The survey design was employed for the study in which questionnaire was…

Teacher argumentation in the secondary science classroom: Images of two modes of scientific inquiry

NASA Astrophysics Data System (ADS)

Gray, Ron E.

The purpose of this exploratory study was to examine scientific arguments constructed by secondary science teachers during instruction. The analysis focused on how arguments constructed by teachers differed based on the mode of inquiry underlying the topic. Specifically, how did the structure and content of arguments differ between experimentally and historically based topics? In addition, what factors mediate these differences? Four highly experienced high school science teachers were observed daily during instructional units for both experimental and historical science topics. Data sources include classroom observations, field notes, reflective memos, classroom artifacts, a nature of science survey, and teacher interviews. The arguments were analyzed for structure and content using Toulmin's argumentation pattern and Walton's schemes for presumptive reasoning revealing specific patterns of use between the two modes of inquiry. Interview data was analyzed to determine possible factors mediating these patterns. The results of this study reveal that highly experienced teachers present arguments to their students that, while simple in structure, reveal authentic images of science based on experimental and historical modes of inquiry. Structural analysis of the data revealed a common trend toward a greater amount of scientific data used to evidence knowledge claims in the historical science units. The presumptive reasoning analysis revealed that, while some presumptive reasoning schemes remained stable across the two units (e.g. 'causal inferences' and 'sign' schemes), others revealed different patterns of use including the 'analogy', 'evidence to hypothesis', 'example', and 'expert opinion' schemes. Finally, examination of the interview and survey data revealed five specific factors mediating the arguments constructed by the teachers: view of the nature of science, nature of the topic, teacher personal factors, view of students, and pedagogical decisions. These factors influenced both the structure and use of presumptive reasoning in the arguments. The results have implications for classroom practice, teacher education, and further research.

Strategic enzyme patterning for microfluidic biofuel cells

NASA Astrophysics Data System (ADS)

Kjeang, E.; Sinton, D.; Harrington, D. A.

The specific character of biological enzyme catalysts enables combined fuel and oxidant channels and simplified non-compartmentalized fuel cell assemblies. In this work, a microstructured enzymatic biofuel cell architecture is proposed, and species transport phenomena combined with consecutive chemical reactions are studied computationally in order to provide guidelines for optimization. This is the first computational study of this technology, and a 2D CFD model for species transport coupled with laminar fluid flow and Michaelis-Menten enzyme kinetics is established. It is shown that the system is reaction rate limited, indicating that enzyme specific turnover numbers are key parameters for biofuel cell performance. Separated and mixed enzyme patterns in different proportions are analyzed for various Peclet numbers. High fuel utilization is achieved in the diffusion dominated and mixed species transport regimes with separated enzymes arranged in relation to individual turnover rates. However, the Peclet number has to be above a certain threshold value to obtain satisfying current densities. The mixed transport regime is particularly attractive while current densities are maintained close to maximum levels. Optimum performance is achieved by mixed enzyme patterning tailored with respect to individual turnover rates, enabling high current densities combined with nearly complete fuel utilization.

Mild Dermatoglyphic Deviations in Adolescents with Autism Spectrum Disorders and Average Intellectual Abilities as Compared to Typically Developing Boys

PubMed Central

de Bruin, Esther I.; Graham, John H.; Huizink, Anja C.

2014-01-01

Dermatoglyphics, ridge constellations on the hands and feet, are permanently formed by the second trimester of pregnancy. Consequently, they are considered “fossilized” evidence of a specific prenatal period. A high frequency of dermatoglyphic anomalies, or a high rate of dermatoglyphic asymmetry (discordance), is an indication of developmental instability (prenatal disturbances) prior to 24-week gestation. Most dermatoglyphic studies in psychiatry focus on adult schizophrenia. Studies on dermatoglyphic deviances and autism are sparse, include severely disturbed and intellectually retarded patients with autism, and are carried out mainly in non-Western European populations. In this study, finger print patterns, atd-angles, and palmar flexion crease patterns (PFCs) are compared between Western European adolescent teenage males, of average intellect, with Autism Spectrum Disorders (ASD; n = 46) and typically developing adolescent teenage males (TD; n = 49). Boys with ASD had a higher rate of discordance in their finger print patterns than TD boys. Thus, the hypothesized prenatal disturbances that play a role in the etiology of schizophrenia and severe autism might not be specific to these severe psychiatric disorders but might also be involved in the etiology of varying degrees of ASD. PMID:25478224

Photomask repeater strategy for high-quality and low-cost reticle fabrication

NASA Astrophysics Data System (ADS)

Kyoh, Suigen; Inoue, Soichi; Ikenaga, Osamu; Higaki, Tomotaka; Shigemitsu, Fumiaki; Mori, Ichiro; Kokubo, Haruo; Hayashi, Naoya; Irie, Nobuyuki; Ishii, Yuki; Umatate, Toshikazu

2003-08-01

The severe mask specification makes mask cost increase drastically. Especially, the increase in the mask cost deals ASIC businesses a fatal blow due to its small chip volume per product. Pattern writing cost has always occupied the main part of the prime mask cost and the emphasis of this is still increasing. This paper reports on a Photomask Repeater strategy to be a solution for reducing mask cost in pattern writing, comparing with conventional EB system.

[Psychopathological and comorbid disorders of incarcerated adolescents in Austria].

PubMed

Plattner, Belinda; Aebi, Marcel; Steinhausen, Hans-Christoph; Bessler, Cornelia

2011-07-01

Incarcerated adolescents show a high prevalence rate of psychopathology and comorbid psychiatric conditions. Child and adolescent psychiatrists working in the penal system are confronted with the need to provide care and to develop specific treatment plans. The data gathered from incarcerated juveniles were analyzed with a special focus on gender-specific treatment aspects. The Mini-International Neuropsychiatric Interview for children and adolescents was used to assess psychopathology in detained juveniles in Austria. The final study sample consisted of 333 juveniles (58 girls and 275 boys). 90 % of the juveniles in our sample suffered from at least one psychiatric disorder, and more than 60 % were diagnosed with two or more simultaneous psychiatric disorders. Using factor analyses we found three clinically relevant disorder patterns according to psychopathological characteristics for males: ADHD/conduct disorder and drug abuse; anxiety and depression; separation anxiety disorder/PTSD and alcohol abuse. In females, we found four disorder patterns: separation anxiety disorder/social phobia/dysthymia; PTSD and drug abuse in combination with either ADHD or conduct disorder; depression and alcohol abuse. Considering that juvenile detainees are burdened by high rates of psychopathology and comorbidity, it is essential to develop a substantiated diagnostic procedure in order when making treatment decisions; different disorder patterns must be considered in conjunction with detained juveniles. The patterns of psychopathology observed might be related to different characteristics in the development of delinquent behavior, in treatment needs, and legal prognosis.

Integrating data from multiple time-location measurement methods for use in exposure assessment: the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air).

PubMed

Hazlehurst, Marnie F; Spalt, Elizabeth W; Curl, Cynthia L; Davey, Mark E; Vedal, Sverre; Burke, Gregory L; Kaufman, Joel D

2017-11-01

Tools to assess time-location patterns related to environmental exposures have expanded from reliance on time-location diaries (TLDs) and questionnaires to use of geospatial location devices such as data-logging Global Positioning System (GPS) equipment. The Multi-Ethnic Study of Atherosclerosis and Air Pollution obtained typical time-location patterns via questionnaire for 6424 adults in six US cities. At a later time (mean 4.6 years after questionnaire), a subset (n=128) participated in high-resolution data collection for specific 2-week periods resulting in concurrent GPS and detailed TLD data, which were aggregated to estimate time spent in various microenvironments. During these 2-week periods, participants were observed to spend the most time at home indoors (mean of 78%) and a small proportion of time in-vehicle (mean of 4%). Similar overall patterns were reported by these participants on the prior questionnaire (mean home indoors: 75%; mean in-vehicle: 4%). However, individual micro-environmental time estimates measured over specific 2-week periods were not highly correlated with an individual's questionnaire report of typical behavior (Spearman's ρ of 0.43 for home indoors and 0.39 for in-vehicle). Although questionnaire data about typical time-location patterns can inform interpretation of long-term epidemiological analyses and risk assessment, they may not reliably represent an individual's short-term experience.

Thyroid Ultrasonography in Differentiation between Graves' Disease and Hashimoto's Thyroiditis.

PubMed

Pishdad, P; Pishdad, G R; Tavanaa, S; Pishdad, R; Jalli, R

2017-03-01

Graves' disease and Hashimoto's thyroiditis are the most common causes of hyper and hypothyroidism, respectively. Differentiation of these 2 diseases, if the patient is euthyroid, may sometimes be extremely difficult on the basis of clinical and laboratory findings. The purpose of this study was to determine the sensitivity and specificity of gray scale sonography in differentiation of Graves' disease from Hashimoto's thyroiditis. This study included 149 patients divided into three groups, patients with Graves' disease (34 patients, mean age = 36.8 ± 10.17 years), Patients with Hashimoto's thyroiditis (62 patients, mean age = 33.4 ± 12.16 years) and control group (53 healthy people, mean age = 34.74 ± 16.87 years). Members of all groups were referred to a single radiologist for thyroid sonography for evaluation of thyroid echogenicity pattern. A total of 117 women and 32 men were examined by sonography. The most common sonographic pattern in Hashimoto and Graves' was homogenous hypo-echogenicity which was observed in 45.2% and 47.1% of cases, respectively. Peripheral hypo-echogenicity pattern was seen in 40.3% of Hashimoto's group with 100% specificity and 40.3% sensitivity. Central-hypoechogenic pattern was observed in 17.6% of Graves' group with 100% and 17.6% specificity and sensitivity, respectively. Our findings indicate that sonography has high specificity but low sensitivity in the diagnosis of either Graves' disease or Hashimoto's thyroiditis. It is therefore not possible to differentiate between these two diseases using sonography alone. Confirmation by laboratory data is also needed.

Topography and Radiative Forcing Patterns on Glaciers in the Karakoram Himalaya

NASA Astrophysics Data System (ADS)

Dobreva, I. D.; Bishop, M. P.; Liu, J. C.; Liang, D.

2015-12-01

Glaciers in the western Himalaya exhibit significant spatial variations in morphology and dynamics. Climate, topography and debris cover variations are thought to significantly affect glacier fluctuations and glacier sensitivity to climate change, although the role of topography and radiative forcing have not been adequately characterized and related to glacier fluctuations and dynamics. Consequently, we examined the glaciers in the Karakoram Himalaya, as they exhibit high spatial variability in glacier fluctuation rates and ice dynamics including flow velocity and surging. Specifically, we wanted to examine the relationships between these glacier characteristics and temporal patterns of surface irradiance over the ablation season. To accomplish this, we developed and used a rigorous GIS-based solar radiative transfer model that accounts for the direct and diffuse-skylight irradiance components. The model accounts for multiple topographic effects on the magnitude of irradiance reaching glacier surfaces. We specifically used the ASTER GDEM digital elevation model for irradiance simulations. We then examined temporal patterns of irradiance at the grid-cell level to identify the dominant patterns that were used to train a 3-layer artificial neural network. Our results demonstrate that there are unique spatial and temporal patterns associated with downwasting and surging glaciers, and that these patterns partially account for the spatial distribution of advancing and retreating glaciers. Lower-altitude terminus regions of surging glaciers exhibited relatively low surface irradiance values that decreased in magnitude with time, demonstrating that high-velocity surging glaciers facilitate relief production and exhibit steeper surface irradiance gradients with altitude. Collectively, these results demonstrate the important role that local and regional topography play in governing climate-glacier dynamics in the Himalaya.

Effects of Sport-Specific Training Intensity on Sleep Patterns and Psychomotor Performance in Adolescent Athletes.

PubMed

Suppiah, Haresh T; Low, Chee Yong; Chia, Michael

2016-11-01

Adolescent student-athletes face time constraints due to athletic and scholastic commitments, resulting in habitually shortened nocturnal sleep durations. However, there is a dearth of research on the effects of sleep debt on student-athlete performance. The study aimed to (i) examine the habitual sleep patterns (actigraphy) of high-level student-athletes during a week of training and academic activities, (ii) ascertain the effects of habitual sleep durations experienced by high-level student-athletes on psychomotor performance, and (iii) examine the impact of sport training intensities on the sleep patterns of high-level student-athletes that participate in low and high intensity sports. Sleep patterns of 29 high-level student-athletes (14.7 ± 1.3 yrs) were monitored over 7 days. A psychomotor vigilance task was administered on weekdays to ascertain the effects of habitual sleep durations. Weekend total sleep time was longer than weekdays along with a delay in bedtime, and waketimes. Psychomotor vigilance reaction times on Monday were faster than on Thursday and Friday, with reaction times on Tuesday also faster than on Friday. False starts and lapses were greater on Friday compared with Monday. There was a negative impact of sleep debt on student-athletes' psychomotor performance.

Epidemiology of moderate-to-severe injury patterns observed in rollover crashes.

PubMed

McMurry, Timothy L; Bose, Dipan; Ridella, Stephen A; Eigen, Ana M; Crandall, Jeff R; Kerrigan, Jason R

2016-05-01

Previous epidemiological studies have highlighted the high risk of injury to the head, thorax, and cervical spine in rollover crashes. However, such results provide limited information on whole-body injury distribution and multiple region injury patterns necessary for the improvement and prioritization of rollover-focused injury countermeasures. Sampled cases representing approximately 133,000 U.S. adult occupants involved in rollover crashes (between 1995 and 2013) sustaining moderate-to-severe injuries were selected from the National Automotive Sampling System Crashworthiness Data System database. A retrospective cohort study, based on a survey of population-based data, was used to identify relevant whole body injury patterns. Among belted occupants injured in rollover crashes, 79.2% sustained injuries to only one body region. The three most frequently injured (AIS2+) body regions were head (42.1%), upper extremity (28.0%), and thorax (27.1%). The most frequent multi-region injury pattern involved the head and upper extremity, but this pattern only accounted for 2.3% of all of occupants with moderate or worse injuries. The results indicated that for rollover-dominated crashes, the frequently observed injury patterns involved isolated body regions. In contrast, multi-region injury patterns are more frequently observed in rollovers with significant planar impacts. Identification of region-specific injury patterns in pure rollover crashes is essential for clarifying injury mitigation targets and developing whole-body injury metrics specifically applicable to rollovers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complex auditory behaviour emerges from simple reactive steering

NASA Astrophysics Data System (ADS)

Hedwig, Berthold; Poulet, James F. A.

2004-08-01

The recognition and localization of sound signals is fundamental to acoustic communication. Complex neural mechanisms are thought to underlie the processing of species-specific sound patterns even in animals with simple auditory pathways. In female crickets, which orient towards the male's calling song, current models propose pattern recognition mechanisms based on the temporal structure of the song. Furthermore, it is thought that localization is achieved by comparing the output of the left and right recognition networks, which then directs the female to the pattern that most closely resembles the species-specific song. Here we show, using a highly sensitive method for measuring the movements of female crickets, that when walking and flying each sound pulse of the communication signal releases a rapid steering response. Thus auditory orientation emerges from reactive motor responses to individual sound pulses. Although the reactive motor responses are not based on the song structure, a pattern recognition process may modulate the gain of the responses on a longer timescale. These findings are relevant to concepts of insect auditory behaviour and to the development of biologically inspired robots performing cricket-like auditory orientation.

The Maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID Gene Family: Phylogeny, Synteny, and Unique Root-Type and Tissue-Specific Expression Patterns during Development

PubMed Central

Ludwig, Yvonne; Zhang, Yanxiang; Hochholdinger, Frank

2013-01-01

The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues. PMID:24223858

The maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID gene family: phylogeny, synteny, and unique root-type and tissue-specific expression patterns during development.

PubMed

Ludwig, Yvonne; Zhang, Yanxiang; Hochholdinger, Frank

2013-01-01

The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

A cytoarchitecture-driven myelin model reveals area-specific signatures in human primary and secondary areas using ultra-high resolution in-vivo brain MRI.

PubMed

Dinse, J; Härtwich, N; Waehnert, M D; Tardif, C L; Schäfer, A; Geyer, S; Preim, B; Turner, R; Bazin, P-L

2015-07-01

This work presents a novel approach for modelling laminar myelin patterns in the human cortex in brain MR images on the basis of known cytoarchitecture. For the first time, it is possible to estimate intracortical contrast visible in quantitative ultra-high resolution MR images in specific primary and secondary cytoarchitectonic areas. The presented technique reveals different area-specific signatures which may help to study the spatial distribution of cortical T1 values and the distribution of cortical myelin in general. It may lead to a new discussion on the concordance of cyto- and myeloarchitectonic boundaries, given the absence of such concordance atlases. The modelled myelin patterns are quantitatively compared with data from human ultra-high resolution in-vivo 7T brain MR images (9 subjects). In the validation, the results are compared to one post-mortem brain sample and its ex-vivo MRI and histological data. Details of the analysis pipeline are provided. In the context of the increasing interest in advanced methods in brain segmentation and cortical architectural studies, the presented model helps to bridge the gap between the microanatomy revealed by classical histology and the macroanatomy visible in MRI. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Nonrandom community assembly and high temporal turnover promote regional coexistence in tropics but not temperate zone.

PubMed

Freestone, Amy L; Inouye, Brian D

2015-01-01

A persistent challenge for ecologists is understanding the ecological mechanisms that maintain global patterns of biodiversity, particularly the latitudinal diversity gradient of peak species richness in the tropics. Spatial and temporal variation in community composition contribute to these patterns of biodiversity, but how this variation and its underlying processes change across latitude remains unresolved. Using a model system of sessile marine invertebrates across 25 degrees of latitude, from the temperate zone to the tropics, we tested the prediction that spatial and temporal patterns of taxonomic richness and composition, and the community assembly processes underlying these patterns, will differ across latitude. Specifically, we predicted that high beta diversity (spatial variation in composition) and high temporal turnover contribute to the high species richness of the tropics. Using a standardized experimental approach that controls for several confounding factors that hinder interpretation of prior studies, we present results that support our predictions. In the temperate zone, communities were more similar across spatial scales from centimeters to tens of kilometers and temporal scales up to one year than at lower latitudes. Since the patterns at northern latitudes were congruent with a null model, stochastic assembly processes are implicated. In contrast, the communities in the tropics were a dynamic spatial and temporal mosaic, with low similarity even across small spatial scales and high temporal turnover at both local and regional scales. Unlike the temperate zone, deterministic community assembly processes such as predation likely contributed to the high beta diversity in the tropics. Our results suggest that community assembly processes and temporal dynamics vary across latitude and help structure and maintain latitudinal patterns of diversity.

Asymmetric hindwing foldings in rove beetles.

PubMed

Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

2014-11-18

Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

Clinicopathologic Association and Prognostic Value of Microcystic, Elongated, and Fragmented (MELF) Pattern in Endometrial Endometrioid Carcinoma.

PubMed

Kihara, Atsushi; Yoshida, Hiroshi; Watanabe, Reiko; Takahashi, Kenta; Kato, Tomoyasu; Ino, Yoshinori; Kitagawa, Masanobu; Hiraoka, Nobuyoshi

2017-07-01

Microcystic, elongated, and fragmented (MELF) pattern is seen in the invasive front of some endometrial endometrioid carcinomas. Although MELF pattern can be expected as an indicator of patient outcomes, its prognostic significance remains unclear. This study was conducted to elucidate clinicopathologic features and the prognostic impact of MELF pattern in patients with endometrial endometrioid carcinoma. We retrospectively analyzed data of 479 consecutive patients with endometrial endometrioid carcinoma that had been surgically resected. In 45 of 427 patients (11%) with low-grade endometrioid carcinoma, MELF pattern was found, but it was found in none of the 52 patients with high-grade endometrioid carcinoma. Among the patients with low-grade endometrioid carcinoma, MELF pattern was associated significantly with larger tumor size, myometrial invasion of more than 50%, advanced International Federation of Gynecology and Obstetrics stages, lymphovascular space invasion, lymph node metastasis, papillary architecture, and mucinous differentiation. However, survival analysis revealed that the patients with MELF pattern showed no significantly worse prognosis than those without MELF pattern either in disease-specific survival or in recurrence-free survival. MELF was not a significant prognosticator after adjustment for International Federation of Gynecology and Obstetrics stage (disease-specific survival [hazard ratio, 1.47; 95% confidence interval, 0.28-7.67; P=0.64], recurrence-free survival [hazard ratio, 0.98, 95% confidence interval, 0.32-2.99, P=0.98]). Immunohistochemical analysis revealed that MELF pattern was positive for p16 and p21 and almost negative for Ki-67 labeling, which suggested that tumor cells in MELF pattern were involved in growth arrest or cellular senescence. We conclude that MELF pattern could have little impact on outcomes of patients with low-grade endometrial endometrioid carcinoma.

The type of carbohydrates specifically selects microbial community structures and fermentation patterns.

PubMed

Chatellard, Lucile; Trably, Eric; Carrère, Hélène

2016-12-01

The impact on dark fermentation of seven carbohydrates as model substrates of lignocellulosic fractions (glucose, cellobiose, microcrystalline cellulose, arabinose, xylose, xylan and wheat straw) was investigated. Metabolic patterns and bacterial communities were characterized at the end of batch tests inoculated with manure digestate. It was found that hydrogen production was linked to the sugar type (pentose or hexose) and the degree of polymerisation. Hexoses produced less hydrogen, with a specific selection of lactate-producing bacterial community structures. Maximal hydrogen production was five times higher on pentose-based substrates, with specific bacterial community structures producing acetate and butyrate as main metabolites. Low hydrogen amounts accumulated from complex sugars (cellulose, xylan and wheat straw). A relatively high proportion of the reads was affiliated to Ruminococcaceae suggesting an efficient hydrolytic activity. Knowing that the bacterial community structure is very specific to a particular substrate offers new possibilities to design more efficient H 2 -producing biological systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns.

PubMed

Sack, Laura Magill; Davoli, Teresa; Li, Mamie Z; Li, Yuyang; Xu, Qikai; Naxerova, Kamila; Wooten, Eric C; Bernardi, Ronald J; Martin, Timothy D; Chen, Ting; Leng, Yumei; Liang, Anthony C; Scorsone, Kathleen A; Westbrook, Thomas F; Wong, Kwok-Kin; Elledge, Stephen J

2018-04-05

Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors. Copyright © 2018 Elsevier Inc. All rights reserved.

Design of a variable-line-spacing grating pattern for spectrometers based on a grating Fresnel device.

PubMed

Li, Xinghui; Zhang, Jinchao; Zhou, Qian; Ni, Kai; Pang, Jinchao; Tian, Rui

2016-04-01

In this Letter, we propose a variable-line-spacing (VLS) grating pattern for a hybrid diffractive device termed a grating Fresnel (G-Fresnel) lens, which is used in spectrometers to improve spectral resolution over a wide spectral range. The VLS grating pattern disperses light of specific wavelengths with a different angle and position such that the aberration caused by the Fresnel surface can be compensated for. In this manner, high resolution can be achieved over a relatively wide spectral range. The VLS grating pattern is designed based on the least wave-change principle and simulated by ZEMAX. Results reveal that the VLS G-Fresnel device allows a subnanometer resolution over a spectral range of 200 nm.

Ultrastructure and wear patterns of the ventral epidermis of four snake species (Squamata, Serpentes).

PubMed

Klein, Marie-Christin G; Gorb, Stanislav N

2014-10-01

Snakes are limbless tetrapods highly specialized for sliding locomotion. This locomotion leads to the skin being exposed to friction loads, especially on the ventral body side, which leads to wear. It is presumed that snakes therefore have specific optimizations for minimizing abrasion. Scales from snakes with habitat, locomotor and/or behavior specializations have specific gradients in material properties that may be due to different epidermal architecture. To approach this issue we examined the skin of Lampropeltis getula californiae (terrestrial), Epicrates cenchria cenchria (generalist), Morelia viridis (arboreal), and Gongylophis colubrinus (burrowing) with a focus on (i) the ultrastructure of the ventral epidermis and (ii) the qualitative abrasion pattern of the ventral scales. Scanning and transmission electron microscopy revealed variations in the structure, thickness, layering, and material composition of the epidermis between the species. Furthermore, SEM and white light interferometer images of the scale surface showed that the abrasion patterns differed, even when the snakes were reared on the same substrate. These data support the idea that (i) a specific gradient in material properties may be due to a variation in epidermis architecture (thickness/ultrastructure) and (ii) this variation may be an optimization of material properties for specific ways of life. Copyright © 2014 Elsevier GmbH. All rights reserved.

Peripheral Blood Signatures of Lead Exposure

PubMed Central

LaBreche, Heather G.; Meadows, Sarah K.; Nevins, Joseph R.; Chute, John P.

2011-01-01

Background Current evidence indicates that even low-level lead (Pb) exposure can have detrimental effects, especially in children. We tested the hypothesis that Pb exposure alters gene expression patterns in peripheral blood cells and that these changes reflect dose-specific alterations in the activity of particular pathways. Methodology/Principal Finding Using Affymetrix Mouse Genome 430 2.0 arrays, we examined gene expression changes in the peripheral blood of female Balb/c mice following exposure to per os lead acetate trihydrate or plain drinking water for two weeks and after a two-week recovery period. Data sets were RMA-normalized and dose-specific signatures were generated using established methods of supervised classification and binary regression. Pathway activity was analyzed using the ScoreSignatures module from GenePattern. Conclusions/Significance The low-level Pb signature was 93% sensitive and 100% specific in classifying samples a leave-one-out crossvalidation. The high-level Pb signature demonstrated 100% sensitivity and specificity in the leave-one-out crossvalidation. These two signatures exhibited dose-specificity in their ability to predict Pb exposure and had little overlap in terms of constituent genes. The signatures also seemed to reflect current levels of Pb exposure rather than past exposure. Finally, the two doses showed differential activation of cellular pathways. Low-level Pb exposure increased activity of the interferon-gamma pathway, whereas high-level Pb exposure increased activity of the E2F1 pathway. PMID:21829687

Usual interstitial pneumonia: typical, possible, and “inconsistent” patterns

PubMed Central

Torres, Pedro Paulo Teixeira e Silva; Rabahi, Marcelo Fouad; Moreira, Maria Auxiliadora Carmo; Meirelles, Gustavo de Souza Portes; Marchiori, Edson

2017-01-01

ABSTRACT Idiopathic pulmonary fibrosis is a severe and progressive chronic fibrosing interstitial lung disease, a definitive diagnosis being established by specific combinations of clinical, radiological, and pathological findings. According to current international guidelines, HRCT plays a key role in establishing a diagnosis of usual interstitial pneumonia (UIP). Current guidelines describe three UIP patterns based on HRCT findings: a typical UIP pattern; a pattern designated “possible UIP”; and a pattern designated “inconsistent with UIP”, each pattern having important diagnostic implications. A typical UIP pattern on HRCT is highly accurate for the presence of histopathological UIP, being currently considered to be diagnostic of UIP. The remaining patterns require further diagnostic investigation. Other known causes of a UIP pattern include drug-induced interstitial lung disease, chronic hypersensitivity pneumonitis, occupational diseases (e.g., asbestosis), and connective tissue diseases, all of which should be included in the clinical differential diagnosis. Given the importance of CT studies in establishing a diagnosis and the possibility of interobserver variability, the objective of this pictorial essay was to illustrate all three UIP patterns on HRCT. PMID:29160385

Experimental analysis for fabrication of high-aspect-ratio piezoelectric ceramic structure by micro-powder injection molding process

NASA Astrophysics Data System (ADS)

Han, Jun Sae; Gal, Chang Woo; Park, Jae Man; Kim, Jong Hyun; Park, Seong Jin

2018-04-01

Aspect ratio effects in the micro-powder injection molding process were experimentally analyzed for fabrication of high-aspect-ratio piezoelectric ceramic structure. The mechanisms of critical defects have been studied according to individual manufacturing steps. In the molding process, incomplete filling phenomenon determines the critical aspect ratios of a micro pattern. According to mold temperature, an incomplete filling phenomenon has been analyzed with respect to different pattern sizes and aspect ratio. In demolding and drying process, the capillary behavior of sacrificial polymeric mold insert determines the critical aspect ratio of a micro pattern. With respect to pattern dimensions, slumping behavior has been analyzed. Based on our current systems, micro PZT feature has stability when it has lower aspect ratio than 5. Under optimized processing conditions, 20 μm and 40 μm ceramic rod array feature which has 5 of aspect ratio were successfully fabricated by the developed process. Further modification points to fabricate the smaller and higher feature were specifically addressed.

Characterization of Disease-Related Covariance Topographies with SSMPCA Toolbox: Effects of Spatial Normalization and PET Scanners

PubMed Central

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2013-01-01

In order to generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [18F]fluorodeoxyglucose PET scans from PD patients and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5 and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in PD patients imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. PMID:23671030

Characterization of disease-related covariance topographies with SSMPCA toolbox: effects of spatial normalization and PET scanners.

PubMed

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2014-05-01

To generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [(18) F]fluorodeoxyglucose PET scans from patients with PD and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5, and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in patients with PD imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. Copyright © 2013 Wiley Periodicals, Inc.

Patterns of Information-Seeking for Cancer on the Internet: An Analysis of Real World Data

PubMed Central

Ofran, Yishai; Paltiel, Ora; Pelleg, Dan; Rowe, Jacob M.; Yom-Tov, Elad

2012-01-01

Although traditionally the primary information sources for cancer patients have been the treating medical team, patients and their relatives increasingly turn to the Internet, though this source may be misleading and confusing. We assess Internet searching patterns to understand the information needs of cancer patients and their acquaintances, as well as to discern their underlying psychological states. We screened 232,681 anonymous users who initiated cancer-specific queries on the Yahoo Web search engine over three months, and selected for study users with high levels of interest in this topic. Searches were partitioned by expected survival for the disease being searched. We compared the search patterns of anonymous users and their contacts. Users seeking information on aggressive malignancies exhibited shorter search periods, focusing on disease- and treatment-related information. Users seeking knowledge regarding more indolent tumors searched for longer periods, alternated between different subjects, and demonstrated a high interest in topics such as support groups. Acquaintances searched for longer periods than the proband user when seeking information on aggressive (compared to indolent) cancers. Information needs can be modeled as transitioning between five discrete states, each with a unique signature representing the type of information of interest to the user. Thus, early phases of information-seeking for cancer follow a specific dynamic pattern. Areas of interest are disease dependent and vary between probands and their contacts. These patterns can be used by physicians and medical Web site authors to tailor information to the needs of patients and family members. PMID:23029317

Differentiation of specific ripple patterns helps to identify epileptogenic areas for surgical procedures.

PubMed

Kerber, Karolin; Dümpelmann, Matthias; Schelter, Björn; Le Van, Pierre; Korinthenberg, Rudolf; Schulze-Bonhage, Andreas; Jacobs, Julia

2014-07-01

High frequency oscillations (HFOs) at 80-500 Hz are promising markers of epileptic areas. Several retrospective studies reported that surgical removal of areas generating HFOs was associated with a good seizure outcome. Recent reports suggested that ripple (80-200 Hz) HFO patterns co-existed with different background EEG activities. We hypothesized that the coexisting background EEG pattern may distinguish physiological from epileptic ripples. Rates of HFOs were analyzed in intracranial EEG recordings of 22 patients. Additionally, ripple patterns were classified for each channel depending either as coexisting with a flat or oscillatory background activity. A multi-variate analysis was performed to determine whether removal of areas showing the above EEG markers correlated with seizure outcome. Removal of areas generating high rates of 'fast ripples (>200 Hz)' and 'ripples on a flat background activity' showed a significant correlation with a seizure-free outcome. In contrast, removal of high rates of 'ripples' or 'ripple patterns in a continuously oscillating background' was not significantly associated with seizure outcome. Ripples occurring in an oscillatory background activity may be suggestive of physiological activity, while those on a flat background reflect epileptic activity. Consideration of coexisting background patterns may improve the delineation of the epileptogenic areas using ripple oscillations. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Equine recurrent uveitis: classification, etiology, and pathogenesis.

PubMed

Curling, Amanda

2011-06-01

Equine recurrent uveitis is a cyclical disease that affects the eye and often leads to high management costs and unfavorable results, such as blindness. Research has improved understanding of the roles of various etiologies, especially leptospirosis, in initiating and perpetuating the pathogenesis of equine recurrent uveitis. Research has also led to the discovery that specific breeds and horses with specific coat color patterns may be predisposed to developing recurrent uveitis.

Phospholipase C-β1 and β4 Contribute to Non-Genetic Cell-to-Cell Variability in Histamine-Induced Calcium Signals in HeLa Cells

PubMed Central

Ishida, Sachiko; Matsu-ura, Toru; Fukami, Kiyoko; Michikawa, Takayuki; Mikoshiba, Katsuhiko

2014-01-01

A uniform extracellular stimulus triggers cell-specific patterns of Ca2+ signals, even in genetically identical cell populations. However, the underlying mechanism that generates the cell-to-cell variability remains unknown. We monitored cytosolic inositol 1,4,5-trisphosphate (IP3) concentration changes using a fluorescent IP3 sensor in single HeLa cells showing different patterns of histamine-induced Ca2+ oscillations in terms of the time constant of Ca2+ spike amplitude decay and the Ca2+ oscillation frequency. HeLa cells stimulated with histamine exhibited a considerable variation in the temporal pattern of Ca2+ signals and we found that there were cell-specific IP3 dynamics depending on the patterns of Ca2+ signals. RT-PCR and western blot analyses showed that phospholipase C (PLC)-β1, -β3, -β4, -γ1, -δ3 and -ε were expressed at relatively high levels in HeLa cells. Small interfering RNA-mediated silencing of PLC isozymes revealed that PLC-β1 and PLC-β4 were specifically involved in the histamine-induced IP3 increases in HeLa cells. Modulation of IP3 dynamics by knockdown or overexpression of the isozymes PLC-β1 and PLC-β4 resulted in specific changes in the characteristics of Ca2+ oscillations, such as the time constant of the temporal changes in the Ca2+ spike amplitude and the Ca2+ oscillation frequency, within the range of the cell-to-cell variability found in wild-type cell populations. These findings indicate that the heterogeneity in the process of IP3 production, rather than IP3-induced Ca2+ release, can cause cell-to-cell variability in the patterns of Ca2+ signals and that PLC-β1 and PLC-β4 contribute to generate cell-specific Ca2+ signals evoked by G protein-coupled receptor stimulation. PMID:24475116

ChIP-less analysis of chromatin states.

PubMed

Su, Zhangli; Boersma, Melissa D; Lee, Jin-Hee; Oliver, Samuel S; Liu, Shichong; Garcia, Benjamin A; Denu, John M

2014-01-01

Histone post-translational modifications (PTMs) are key epigenetic regulators in chromatin-based processes. Increasing evidence suggests that vast combinations of PTMs exist within chromatin histones. These complex patterns, rather than individual PTMs, are thought to define functional chromatin states. However, the ability to interrogate combinatorial histone PTM patterns at the nucleosome level has been limited by the lack of direct molecular tools. Here we demonstrate an efficient, quantitative, antibody-free, chromatin immunoprecipitation-less (ChIP-less) method for interrogating diverse epigenetic states. At the heart of the workflow are recombinant chromatin reader domains, which target distinct chromatin states with combinatorial PTM patterns. Utilizing a newly designed combinatorial histone peptide microarray, we showed that three reader domains (ATRX-ADD, ING2-PHD and AIRE-PHD) displayed greater specificity towards combinatorial PTM patterns than corresponding commercial histone antibodies. Such specific recognitions were employed to develop a chromatin reader-based affinity enrichment platform (matrix-assisted reader chromatin capture, or MARCC). We successfully applied the reader-based platform to capture unique chromatin states, which were quantitatively profiled by mass spectrometry to reveal interconnections between nucleosomal histone PTMs. Specifically, a highly enriched signature that harbored H3K4me0, H3K9me2/3, H3K79me0 and H4K20me2/3 within the same nucleosome was identified from chromatin enriched by ATRX-ADD. This newly reported PTM combination was enriched in heterochromatin, as revealed by the associated DNA. Our results suggest the broad utility of recombinant reader domains as an enrichment tool specific to combinatorial PTM patterns, which are difficult to probe directly by antibody-based approaches. The reader affinity platform is compatible with several downstream analyses to investigate the physical coexistence of nucleosomal PTM states associated with specific genomic loci. Collectively, the reader-based workflow will greatly facilitate our understanding of how distinct chromatin states and reader domains function in gene regulatory mechanisms.

Transformed Neural Pattern Reinstatement during Episodic Memory Retrieval.

PubMed

Xiao, Xiaoqian; Dong, Qi; Gao, Jiahong; Men, Weiwei; Poldrack, Russell A; Xue, Gui

2017-03-15

Contemporary models of episodic memory posit that remembering involves the reenactment of encoding processes. Although encoding-retrieval similarity has been consistently reported and linked to memory success, the nature of neural pattern reinstatement is poorly understood. Using high-resolution fMRI on human subjects, our results obtained clear evidence for item-specific pattern reinstatement in the frontoparietal cortex, even when the encoding-retrieval pairs shared no perceptual similarity. No item-specific pattern reinstatement was found in the ventral visual cortex. Importantly, the brain regions and voxels carrying item-specific representation differed significantly between encoding and retrieval, and the item specificity for encoding-retrieval similarity was smaller than that for encoding or retrieval, suggesting different nature of representations between encoding and retrieval. Moreover, cross-region representational similarity analysis suggests that the encoded representation in the ventral visual cortex was reinstated in the frontoparietal cortex during retrieval. Together, these results suggest that, in addition to reinstatement of the originally encoded pattern in the brain regions that perform encoding processes, retrieval may also involve the reinstatement of a transformed representation of the encoded information. These results emphasize the constructive nature of memory retrieval that helps to serve important adaptive functions. SIGNIFICANCE STATEMENT Episodic memory enables humans to vividly reexperience past events, yet how this is achieved at the neural level is barely understood. A long-standing hypothesis posits that memory retrieval involves the faithful reinstatement of encoding-related activity. We tested this hypothesis by comparing the neural representations during encoding and retrieval. We found strong pattern reinstatement in the frontoparietal cortex, but not in the ventral visual cortex, that represents visual details. Critically, even within the same brain regions, the nature of representation during retrieval was qualitatively different from that during encoding. These results suggest that memory retrieval is not a faithful replay of past event but rather involves additional constructive processes to serve adaptive functions. Copyright © 2017 the authors 0270-6474/17/372986-13$15.00/0.

Dietary patterns and breast cancer risk in the California Teachers Study cohort12345

PubMed Central

Link, Lilli B; Canchola, Alison J; Bernstein, Leslie; Clarke, Christina A; Stram, Daniel O; Ursin, Giske

2013-01-01

Background: Evidence that diet is associated with breast cancer risk is inconsistent. Most studies have examined risks associated with specific foods and nutrients, rather than measures of overall diet. Objective: This study aimed to evaluate dietary patterns and their relation to breast cancer risk in a large cohort of women. Design: Data from 91,779 women in the California Teachers Study cohort were analyzed, including data from 4140 women with a diagnosis of invasive breast cancer made between 1995 and 2009. Five predominant dietary patterns were identified by using principal components factor analysis: a plant-based diet, high in fruit and vegetables; a high-protein, high-fat diet, high in meats, eggs, fried foods, and high-fat condiments; a high-carbohydrate diet, high in convenience foods, pasta, and bread products; an ethnic diet, high in legumes, soy-based foods, rice, and dark-green leafy vegetables; and a salad and wine diet, high in lettuce, fish, wine, low-fat salad dressing, and coffee and tea. Results: The plant-based pattern was associated with a reduction in breast cancer risk (RR: 0.85; 95% CI: 0.76, 0.95 for the highest compared with the lowest consumption quintile; P-trend = 0.003); risk reduction was greater for estrogen receptor–negative progesterone receptor–negative (ER–PR–) tumors (RR: 0.66; 95% CI: 0.48, 0.91; P-trend = 0.03). The salad and wine pattern was associated with an increased risk of estrogen receptor–positive progesterone receptor–positive tumors (RR: 1.29; 95% CI: 1.12, 1.49); this effect was only slightly attenuated after adjustment for alcohol consumption. Conclusion: The finding that greater consumption of a plant-based dietary pattern is associated with a reduced breast cancer risk, particularly for ER−PR− tumors, offers a potential avenue for prevention. PMID:24108781

Hot pen and laser writable photonic polymer films

NASA Astrophysics Data System (ADS)

Moirangthem, Monali; Stumpel, Jelle E.; Alp, Baran; Teunissen, Pit; Bastiaansen, Cees W. M.; Schenning, Albertus P. H. J.

2016-03-01

An orange-reflecting photonic polymer film has been fabricated based on a hydrogen-bonded cholesteric liquid crystalline (CLC) polymer consisting of non-reactive (R)-(+)-3-methyladipic acid as the chiral dopant. This polymer film can be patterned easily by evaporating the chiral dopant at specific locations with a hot pen or a laser beam. Removal of chiral dopant leads to a decrease in the helical pitch at the heat treated areas leading to a change in color from orange to green revealing a high contrast pattern. The photonic patterns are irreversible and stable at ambient conditions. This makes such a CLC polymer film interesting as writable photonic paper.

An investigation of short haul air transportation in the southeastern United States

NASA Technical Reports Server (NTRS)

Kanafani, A.; Yuan, H. S.

1977-01-01

The specific objectives of this stage of the study are numerous. First, an attempt is made to characterize the travel patterns in the study region, both in terms of origin destination patterns, and connecting and through trip patterns. Second, the structure of the air service in the region is characterized in an attempt to develop an understanding of the evolution of the short haul air transportation network. Finally, a look is taken at the socioeconomic environment of Atlanta and the region in order to seek an explanation for the historic evolution of short haul air travel activities and the rather high growth rates experienced in recent years.

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets

PubMed Central

2012-01-01

Background ChIP-seq provides new opportunities to study allele-specific protein-DNA binding (ASB). However, detecting allelic imbalance from a single ChIP-seq dataset often has low statistical power since only sequence reads mapped to heterozygote SNPs are informative for discriminating two alleles. Results We develop a new method iASeq to address this issue by jointly analyzing multiple ChIP-seq datasets. iASeq uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. Using the discovered correlation patterns, the model allows one to borrow information across datasets to improve detection of allelic imbalance. Application of iASeq to 77 ChIP-seq samples from 40 ENCODE datasets and 1 genomic DNA sample in GM12878 cells reveals that allele-specificity of multiple proteins are highly correlated, and demonstrates the ability of iASeq to improve allelic inference compared to analyzing each individual dataset separately. Conclusions iASeq illustrates the value of integrating multiple datasets in the allele-specificity inference and offers a new tool to better analyze ASB. PMID:23194258

Self-organizing human cardiac microchambers mediated by geometric confinement

NASA Astrophysics Data System (ADS)

Ma, Zhen; Wang, Jason; Loskill, Peter; Huebsch, Nathaniel; Koo, Sangmo; Svedlund, Felicia L.; Marks, Natalie C.; Hua, Ethan W.; Grigoropoulos, Costas P.; Conklin, Bruce R.; Healy, Kevin E.

2015-07-01

Tissue morphogenesis and organ formation are the consequences of biochemical and biophysical cues that lead to cellular spatial patterning in development. To model such events in vitro, we use PEG-patterned substrates to geometrically confine human pluripotent stem cell colonies and spatially present mechanical stress. Modulation of the WNT/β-catenin pathway promotes spatial patterning via geometric confinement of the cell condensation process during epithelial-mesenchymal transition, forcing cells at the perimeter to express an OCT4+ annulus, which is coincident with a region of higher cell density and E-cadherin expression. The biochemical and biophysical cues synergistically induce self-organizing lineage specification and creation of a beating human cardiac microchamber confined by the pattern geometry. These highly defined human cardiac microchambers can be used to study aspects of embryonic spatial patterning, early cardiac development and drug-induced developmental toxicity.

Fluorine-containing composition for forming anti-reflection film on resist surface and pattern formation method

DOEpatents

Nishi, Mineo; Makishima, Hideo

1996-01-01

A composition for forming anti-reflection film on resist surface which comprises an aqueous solution of a water soluble fluorine compound, and a pattern formation method which comprises the steps of coating a photoresist composition on a substrate; coating the above-mentioned composition for forming anti-reflection film; exposing the coated film to form a specific pattern; and developing the photoresist, are provided. Since the composition for forming anti-reflection film can be coated on the photoresist in the form of an aqueous solution, not only the anti-reflection film can be formed easily, but also, the film can be removed easily by rinsing with water or alkali development. Therefore, by the pattern formation method according to the present invention, it is possible to form a pattern easily with a high dimensional accuracy.

Structural Pattern Recognition Techniques for Data Retrieval in Massive Fusion Databases

NASA Astrophysics Data System (ADS)

Vega, J.; Murari, A.; Rattá, G. A.; Castro, P.; Pereira, A.; Portas, A.

2008-03-01

Diagnostics of present day reactor class fusion experiments, like the Joint European Torus (JET), generate thousands of signals (time series and video images) in each discharge. There is a direct correspondence between the physical phenomena taking place in the plasma and the set of structural shapes (patterns) that they form in the signals: bumps, unexpected amplitude changes, abrupt peaks, periodic components, high intensity zones or specific edge contours. A major difficulty related to data analysis is the identification, in a rapid and automated way, of a set of discharges with comparable behavior, i.e. discharges with "similar" patterns. Pattern recognition techniques are efficient tools to search for similar structural forms within the database in a fast an intelligent way. To this end, classification systems must be developed to be used as indexation methods to directly fetch the more similar patterns.

Metaphor Comprehension in Autistic Spectrum Disorders: Case Studies of Two High-Functioning Children

ERIC Educational Resources Information Center

Melogno, Sergio; D'Ardia, Caterina; Pinto, Maria Antonietta; Levi, Gabriel

2012-01-01

This article presents case studies on metaphor comprehension in two boys with high-functioning autistic spectrum disorder, aged 9;1 (9 years, 1 month) and 8;11. The participants were assessed twice, before and after an intervention program aimed at improving their social skills. The focus of the article is on the specific patterns exhibited by…

Landscape-level movement patterns by lions in western Serengeti: comparing the influence of inter-specific competitors, habitat attributes and prey availability.

PubMed

Kittle, Andrew M; Bukombe, John K; Sinclair, Anthony R E; Mduma, Simon A R; Fryxell, John M

2016-01-01

Where apex predators move on the landscape influences ecosystem structure and function and is therefore key to effective landscape-level management and species-specific conservation. However the factors underlying predator distribution patterns within functional ecosystems are poorly understood. Predator movement should be sensitive to the spatial patterns of inter-specific competitors, spatial variation in prey density, and landscape attributes that increase individual prey vulnerability. We investigated the relative role of these fundamental factors on seasonal resource utilization by a globally endangered apex carnivore, the African lion (Panthera leo) in Tanzania's Serengeti National Park. Lion space use was represented by novel landscape-level, modified utilization distributions (termed "localized density distributions") created from telemetry relocations of individual lions from multiple neighbouring prides. Spatial patterns of inter-specific competitors were similarly determined from telemetry re-locations of spotted hyenas (Crocuta crocuta), this system's primary competitor for lions; prey distribution was derived from 18 months of detailed census data; and remote sensing data was used to represent relevant habitat attributes. Lion space use was consistently influenced by landscape attributes that increase individual prey vulnerability to predation. Wet season activity, when available prey were scarce, was concentrated near embankments, which provide ambush opportunities, and dry season activity, when available prey were abundant, near remaining water sources where prey occurrence is predictable. Lion space use patterns were positively associated with areas of high prey biomass, but only in the prey abundant dry season. Finally, at the broad scale of this analysis, lion and hyena space use was positively correlated in the comparatively prey-rich dry season and unrelated in the wet season, suggesting lion movement was unconstrained by the spatial patterns of their main inter-specific competitors. The availability of potential prey and vulnerability of that prey to predation both motivate lion movement decisions, with their relative importance apparently mediated by overall prey abundance. With practical and theoretical implications, these results suggest that while top carnivores are consistently cognizant of how landscape features influence individual prey vulnerability, they also adopt a flexible approach to range use by adjusting spatial behaviour according to fluctuations in local prey abundance.

Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins.

PubMed

Pombo, Marina A; Zheng, Yi; Fernandez-Pozo, Noe; Dunham, Diane M; Fei, Zhangjun; Martin, Gregory B

2014-01-01

Plants have two related immune systems to defend themselves against pathogen attack. Initially,pattern-triggered immunity is activated upon recognition of microbe-associated molecular patterns by pattern recognition receptors. Pathogenic bacteria deliver effector proteins into the plant cell that interfere with this immune response and promote disease. However, some plants express resistance proteins that detect the presence of specific effectors leading to a robust defense response referred to as effector-triggered immunity. The interaction of tomato with Pseudomonas syringae pv. tomato is an established model system for understanding the molecular basis of these plant immune responses. We apply high-throughput RNA sequencing to this pathosystem to identify genes whose expression changes specifically during pattern-triggered or effector-triggered immunity. We then develop reporter genes for each of these responses that will enable characterization of the host response to the large collection of P. s. pv. tomato strains that express different combinations of effectors. Virus-induced gene silencing of 30 of the effector-triggered immunity-specific genes identifies Epk1 which encodes a predicted protein kinase from a family previously unknown to be involved in immunity. Knocked-down expression of Epk1 compromises effector-triggered immunity triggered by three bacterial effectors but not by effectors from non-bacterial pathogens. Epistasis experiments indicate that Epk1 acts upstream of effector-triggered immunity-associated MAP kinase signaling. Using RNA-seq technology we identify genes involved in specific immune responses. A functional genomics screen led to the discovery of Epk1, a novel predicted protein kinase required for plant defense activation upon recognition of three different bacterial effectors.

The diagnostic value and histologic correlate of distinct patterns of shiny white streaks for the diagnosis of melanoma: A retrospective, case-control study.

PubMed

Verzi, Anna Eliza; Quan, Victor L; Walton, Kara E; Martini, Mary C; Marghoob, Ashfaq A; Garfield, Erin M; Kong, Betty Y; Isales, Maria Cristina; VandenBoom, Timothy; Zhang, Bin; West, Dennis P; Gerami, Pedram

2018-05-01

Shiny white streaks (SWSs) are best visualized with polarized dermoscopy and correlate with dermal fibroplasia histopathologically. SWSs have been described at higher frequencies in melanomas than in benign nevi. We assessed the diagnostic value of different patterns of SWSs and their histologic correlate in melanocytic lesions. Polarized dermoscopic images of 1507 histopathologically diagnosed melanocytic neoplasms were analyzed for presence and pattern of SWSs. Histology was also reviewed for correlation. Among 1507 melanocytic neoplasms, SWSs were observed in 31 of 144 melanomas (22%) and 22 of 1363 benign neoplasms (1.6%) (P < .001). The sensitivity and specificity of SWSs for melanoma were 22% and 98%, respectively. Diffuse SWSs exhibited the greatest diagnostic value for melanoma, with sensitivity of 11.8% and specificity of 99.5%. Focal central and peripheral SWSs were comparable in diagnostic significance. The presence of SWSs was highly uncommon in dysplastic nevi, whereas in certain benign subgroups of nevi such as Spitz nevi and atypical genital special site nevi, SWSs were not uncommon. Diffuse SWSs correlated with greater breadth of deep fibroplasia than focal SWSs (P = .009), and SWSs correlated with greater Breslow depth among melanomas (P = .007). This study was retrospective. Polarized dermoscopy is a valuable diagnostic tool in the identification of SWSs, a feature that is highly specific for melanoma. Copyright © 2017 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Heterogeneous genetic diversity pattern in Plasmodium vivax genes encoding merozoite surface proteins (MSP) -7E, -7F and -7L.

PubMed

Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A

2014-12-13

The msp-7 gene has become differentially expanded in the Plasmodium genus; Plasmodium vivax has the highest copy number of this gene, several of which encode antigenic proteins in merozoites. DNA sequences from thirty-six Colombian clinical isolates from P. vivax (pv) msp-7E, -7F and -7L genes were analysed for characterizing and studying the genetic diversity of these pvmsp-7 members which are expressed during the intra-erythrocyte stage; natural selection signals producing the variation pattern so observed were evaluated. The pvmsp-7E gene was highly polymorphic compared to pvmsp-7F and pvmsp-7L which were seen to have limited genetic diversity; pvmsp-7E polymorphism was seen to have been maintained by different types of positive selection. Even though these copies seemed to be species-specific duplications, a search in the Plasmodium cynomolgi genome (P. vivax sister taxon) showed that both species shared the whole msp-7 repertoire. This led to exploring the long-term effect of natural selection by comparing the orthologous sequences which led to finding signatures for lineage-specific positive selection. The results confirmed that the P. vivax msp-7 family has a heterogeneous genetic diversity pattern; some members are highly conserved whilst others are highly diverse. The results suggested that the 3'-end of these genes encode MSP-7 proteins' functional region whilst the central region of pvmsp-7E has evolved rapidly. The lineage-specific positive selection signals found suggested that mutations occurring in msp-7s genes during host switch may have succeeded in adapting the ancestral P. vivax parasite population to humans.

Degree of suppression of associations to stages of addiction by the response of "high".

PubMed

Haertzen, C A; Ross, F E

1980-05-01

Male heroin or opiate addicts (N = 78) had a great inclination to give the association "to be high" to the names of nine drugs of abuse in a multiple-forced-choice association test irrespective of whether they had weak or strong habits for the drugs used as stimulus words. The tendency to give the "high" response was so great that other responses indicative of stages of addiction, steps in drug-taking, or drug effects were suppressed below the chance level. When scales were scored so that the response of "high" had no effect, the habit status of the sample revealed by associations with a specific set of words became clearer. A pattern of a strong habit for opiates evoked by opiate names became more evident after elimination of the effect of the response to "high," as did the strong habit pattern in response to drug relevant words. However, the pattern of responses characteristic of a nonaddictive status evoked by clean words remained relatively stable even including the effect of the response of "high." The study suggests that more meaningful responses are found when the response options are multiple rather than fixed.

Adherence to predefined dietary patterns and incident type 2 diabetes in European populations: EPIC-InterAct Study.

PubMed

2014-02-01

Few studies have investigated the relationship between predefined dietary patterns and type 2 diabetes incidence; little is known about the generalisability of these associations. We aimed to assess the association between predefined dietary patterns and type 2 diabetes risk in European populations. From among a case-cohort of 12,403 incident diabetes cases and 16,154 subcohort members nested within the prospective European Prospective Investigation into Cancer and Nutrition study, we used data on 9,682 cases and 12,595 subcohort participants from seven countries. Habitual dietary intake was assessed at baseline with country-specific dietary questionnaires. Two diet-quality scores (alternative Healthy Eating Index [aHEI], Dietary Approaches to Stop Hypertension [DASH] score) and three reduced rank regression (RRR)-derived dietary-pattern scores were constructed. Country-specific HRs were calculated and combined using a random-effects meta-analysis. After multivariable adjustment, including body size, the aHEI and DASH scores were not significantly associated with diabetes, although for the aHEI there was a tendency towards an inverse association in countries with higher mean age. We observed inverse associations of the three RRR-derived dietary-pattern scores with diabetes: HRs (95% CIs) for a 1-SD difference were 0.91 (0.86, 0.96), 0.92 (0.84, 1.01) and 0.87 (0.82, 0.92). Random-effects meta-analyses revealed heterogeneity between countries that was explainable by differences in the age of participants or the distribution of dietary intake. Adherence to specific RRR-derived dietary patterns, commonly characterised by high intake of fruits or vegetables and low intake of processed meat, sugar-sweetened beverages and refined grains, may lower type 2 diabetes risk.

Clinical application of qualitative assessment for breast masses in shear-wave elastography.

PubMed

Gweon, Hye Mi; Youk, Ji Hyun; Son, Eun Ju; Kim, Jeong-Ah

2013-11-01

To evaluate the interobserver agreement and the diagnostic performance of various qualitative features in shear-wave elastography (SWE) for breast masses. A total of 153 breast lesions in 152 women who underwent B-mode ultrasound and SWE before biopsy were included. Qualitative analysis in SWE was performed using two different classifications: E values (Ecol; 6-point color score, Ehomo; homogeneity score and Esha; shape score) and a four-color pattern classification. Two radiologists reviewed five data sets: B-mode ultrasound, SWE, and combination of both for E values and four-color pattern. The BI-RADS categories were assessed B-mode and combined sets. Interobserver agreement was assessed using weighted κ statistics. Areas under the receiver operating characteristic curve (AUC), sensitivity, and specificity were analyzed. Interobserver agreement was substantial for Ecol (κ=0.79), Ehomo (κ=0.77) and four-color pattern (κ=0.64), and moderate for Esha (κ=0.56). Better-performing qualitative features were Ecol and four-color pattern (AUCs, 0.932 and 0.925) compared with Ehomo and Esha (AUCs, 0.857 and 0.864; P<0.05). The diagnostic performance of B-mode ultrasound (AUC, 0.950) was not significantly different from combined sets with E value and with four color pattern (AUCs, 0.962 and 0.954). When all qualitative values were negative, leading to downgrade the BI-RADS category, the specificity increased significantly from 16.5% to 56.1% (E value) and 57.0% (four-color pattern) (P<0.001) without improvement in sensitivity. The qualitative SWE features were highly reproducible and showed good diagnostic performance in suspicious breast masses. Adding qualitative SWE to B-mode ultrasound increased specificity in decision making for biopsy recommendation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Soft lithographic functionalization and patterning oxide-free silicon and germanium.

PubMed

Bowers, Carleen M; Toone, Eric J; Clark, Robert L; Shestopalov, Alexander A

2011-12-16

The development of hybrid electronic devices relies in large part on the integration of (bio)organic materials and inorganic semiconductors through a stable interface that permits efficient electron transport and protects underlying substrates from oxidative degradation. Group IV semiconductors can be effectively protected with highly-ordered self-assembled monolayers (SAMs) composed of simple alkyl chains that act as impervious barriers to both organic and aqueous solutions. Simple alkyl SAMs, however, are inert and not amenable to traditional patterning techniques. The motivation for immobilizing organic molecular systems on semiconductors is to impart new functionality to the surface that can provide optical, electronic, and mechanical function, as well as chemical and biological activity. Microcontact printing (μCP) is a soft-lithographic technique for patterning SAMs on myriad surfaces. Despite its simplicity and versatility, the approach has been largely limited to noble metal surfaces and has not been well developed for pattern transfer to technologically important substrates such as oxide-free silicon and germanium. Furthermore, because this technique relies on the ink diffusion to transfer pattern from the elastomer to substrate, the resolution of such traditional printing is essentially limited to near 1 μm. In contrast to traditional printing, inkless μCP patterning relies on a specific reaction between a surface-immobilized substrate and a stamp-bound catalyst. Because the technique does not rely on diffusive SAM formation, it significantly expands the diversity of patternable surfaces. In addition, the inkless technique obviates the feature size limitations imposed by molecular diffusion, facilitating replication of very small (<200 nm) features. However, up till now, inkless μCP has been mainly used for patterning relatively disordered molecular systems, which do not protect underlying surfaces from degradation. Here, we report a simple, reliable high-throughput method for patterning passivated silicon and germanium with reactive organic monolayers and demonstrate selective functionalization of the patterned substrates with both small molecules and proteins. The technique utilizes a preformed NHS-reactive bilayered system on oxide-free silicon and germanium. The NHS moiety is hydrolyzed in a pattern-specific manner with a sulfonic acid-modified acrylate stamp to produce chemically distinct patterns of NHS-activated and free carboxylic acids. A significant limitation to the resolution of many μCP techniques is the use of PDMS material which lacks the mechanical rigidity necessary for high fidelity transfer. To alleviate this limitation we utilized a polyurethane acrylate polymer, a relatively rigid material that can be easily functionalized with different organic moieties. Our patterning approach completely protects both silicon and germanium from chemical oxidation, provides precise control over the shape and size of the patterned features, and gives ready access to chemically discriminated patterns that can be further functionalized with both organic and biological molecules. The approach is general and applicable to other technologically-relevant surfaces.

Cross-Cultural Communication Patterns in Computer Mediated Communication

ERIC Educational Resources Information Center

Panina, Daria; Kroumova, Maya

2015-01-01

There are important cultural differences in attitudes towards and use of electronic text communication. Consistent with Hall's high-context/low-context conceptualization of culture, electronic inter-cultural communication, just as verbal inter-cultural communication, is affected by the culturally-specific assumptions and preferences of message…

Self-Perception in Late Adolescence: An Interactive Perspective.

ERIC Educational Resources Information Center

Klein, Helen Altman

1995-01-01

Examined self-perception during late adolescence as a correlate of individual temperament. Found that positive self-perception correlated with approaching, flexible, and positive mood patterns, and with high task orientation. Different aspects of self-perception showed distinct relationships with specific temperament dimensions. Noted men's and…

Proneness to Suicide: Does It Exist?

ERIC Educational Resources Information Center

Ovuga, Emilio B. L.; Mugisha, Xavier R.

Although no specific personality disorder seems responsible for suicide behavior, it has been suggested that hysterical personality could predispose to suicide behavior. Schizoid, anti-social and obsessoid rigid personalities have been linked to high risk suicide attempts. This study elicited response patterns and attitudes of South African…

Chemometrics Methods for Specificity, Authenticity and Traceability Analysis of Olive Oils: Principles, Classifications and Applications.

PubMed

Messai, Habib; Farman, Muhammad; Sarraj-Laabidi, Abir; Hammami-Semmar, Asma; Semmar, Nabil

2016-11-17

Olive oils (OOs) show high chemical variability due to several factors of genetic, environmental and anthropic types. Genetic and environmental factors are responsible for natural compositions and polymorphic diversification resulting in different varietal patterns and phenotypes. Anthropic factors, however, are at the origin of different blends' preparation leading to normative, labelled or adulterated commercial products. Control of complex OO samples requires their (i) characterization by specific markers; (ii) authentication by fingerprint patterns; and (iii) monitoring by traceability analysis. These quality control and management aims require the use of several multivariate statistical tools: specificity highlighting requires ordination methods; authentication checking calls for classification and pattern recognition methods; traceability analysis implies the use of network-based approaches able to separate or extract mixed information and memorized signals from complex matrices. This chapter presents a review of different chemometrics methods applied for the control of OO variability from metabolic and physical-chemical measured characteristics. The different chemometrics methods are illustrated by different study cases on monovarietal and blended OO originated from different countries. Chemometrics tools offer multiple ways for quantitative evaluations and qualitative control of complex chemical variability of OO in relation to several intrinsic and extrinsic factors.

Correct Hox gene expression established independently of position in Caenorhabditis elegans.

PubMed

Cowing, D; Kenyon, C

1996-07-25

The Hox genes are expressed in a conserved sequence of spatial domains along the anteroposterior (A/P) body axes of many organisms. In Drosophila, position-specific signals located along the A/P axis establish the pattern of Hox gene expression. In the nematode Caenorhabditis elegans, it is not known how the pattern of Hox gene expression is established. C. elegans uses lineal control mechanisms and local cell interactions to specify early blastomere identities. However, many cells expressing the same Hox gene are unrelated by lineage, suggesting that, as in Drosophila, domains of Hox gene expression may be defined by cell-extrinsic A/P positional signals. To test this, we have investigated whether posterior mesodermal and ectodermal cells will express their normal posterior Hox gene when they are mispositioned in the anterior. Surprisingly, we find that correct Hox gene expression does not depend on cell position, but is highly correlated with cell lineage. Thus, although the most striking feature of Hox gene expression is its positional specificity, in C. elegans the pattern is achieved, at least in part, by a lineage-specific control system that operates without regard to A/P position.

Pattern Genes Suggest Functional Connectivity of Organs

NASA Astrophysics Data System (ADS)

Qin, Yangmei; Pan, Jianbo; Cai, Meichun; Yao, Lixia; Ji, Zhiliang

2016-05-01

Human organ, as the basic structural and functional unit in human body, is made of a large community of different cell types that organically bound together. Each organ usually exerts highly specified physiological function; while several related organs work smartly together to perform complicated body functions. In this study, we present a computational effort to understand the roles of genes in building functional connection between organs. More specifically, we mined multiple transcriptome datasets sampled from 36 human organs and tissues, and quantitatively identified 3,149 genes whose expressions showed consensus modularly patterns: specific to one organ/tissue, selectively expressed in several functionally related tissues and ubiquitously expressed. These pattern genes imply intrinsic connections between organs. According to the expression abundance of the 766 selective genes, we consistently cluster the 36 human organs/tissues into seven functional groups: adipose & gland, brain, muscle, immune, metabolism, mucoid and nerve conduction. The organs and tissues in each group either work together to form organ systems or coordinate to perform particular body functions. The particular roles of specific genes and selective genes suggest that they could not only be used to mechanistically explore organ functions, but also be designed for selective biomarkers and therapeutic targets.

Contact Patterns among High School Students

PubMed Central

Fournet, Julie; Barrat, Alain

2014-01-01

Face-to-face contacts between individuals contribute to shape social networks and play an important role in determining how infectious diseases can spread within a population. It is thus important to obtain accurate and reliable descriptions of human contact patterns occurring in various day-to-day life contexts. Recent technological advances and the development of wearable sensors able to sense proximity patterns have made it possible to gather data giving access to time-varying contact networks of individuals in specific environments. Here we present and analyze two such data sets describing with high temporal resolution the contact patterns of students in a high school. We define contact matrices describing the contact patterns between students of different classes and show the importance of the class structure. We take advantage of the fact that the two data sets were collected in the same setting during several days in two successive years to perform a longitudinal analysis on two very different timescales. We show the high stability of the contact patterns across days and across years: the statistical distributions of numbers and durations of contacts are the same in different periods, and we observe a very high similarity of the contact matrices measured in different days or different years. The rate of change of the contacts of each individual from one day to the next is also similar in different years. We discuss the interest of the present analysis and data sets for various fields, including in social sciences in order to better understand and model human behavior and interactions in different contexts, and in epidemiology in order to inform models describing the spread of infectious diseases and design targeted containment strategies. PMID:25226026

Investigating Patterns for Self-Induced Emotion Recognition from EEG Signals.

PubMed

Zhuang, Ning; Zeng, Ying; Yang, Kai; Zhang, Chi; Tong, Li; Yan, Bin

2018-03-12

Most current approaches to emotion recognition are based on neural signals elicited by affective materials such as images, sounds and videos. However, the application of neural patterns in the recognition of self-induced emotions remains uninvestigated. In this study we inferred the patterns and neural signatures of self-induced emotions from electroencephalogram (EEG) signals. The EEG signals of 30 participants were recorded while they watched 18 Chinese movie clips which were intended to elicit six discrete emotions, including joy, neutrality, sadness, disgust, anger and fear. After watching each movie clip the participants were asked to self-induce emotions by recalling a specific scene from each movie. We analyzed the important features, electrode distribution and average neural patterns of different self-induced emotions. Results demonstrated that features related to high-frequency rhythm of EEG signals from electrodes distributed in the bilateral temporal, prefrontal and occipital lobes have outstanding performance in the discrimination of emotions. Moreover, the six discrete categories of self-induced emotion exhibit specific neural patterns and brain topography distributions. We achieved an average accuracy of 87.36% in the discrimination of positive from negative self-induced emotions and 54.52% in the classification of emotions into six discrete categories. Our research will help promote the development of comprehensive endogenous emotion recognition methods.

Investigating Patterns for Self-Induced Emotion Recognition from EEG Signals

PubMed Central

Zeng, Ying; Yang, Kai; Tong, Li; Yan, Bin

2018-01-01

Most current approaches to emotion recognition are based on neural signals elicited by affective materials such as images, sounds and videos. However, the application of neural patterns in the recognition of self-induced emotions remains uninvestigated. In this study we inferred the patterns and neural signatures of self-induced emotions from electroencephalogram (EEG) signals. The EEG signals of 30 participants were recorded while they watched 18 Chinese movie clips which were intended to elicit six discrete emotions, including joy, neutrality, sadness, disgust, anger and fear. After watching each movie clip the participants were asked to self-induce emotions by recalling a specific scene from each movie. We analyzed the important features, electrode distribution and average neural patterns of different self-induced emotions. Results demonstrated that features related to high-frequency rhythm of EEG signals from electrodes distributed in the bilateral temporal, prefrontal and occipital lobes have outstanding performance in the discrimination of emotions. Moreover, the six discrete categories of self-induced emotion exhibit specific neural patterns and brain topography distributions. We achieved an average accuracy of 87.36% in the discrimination of positive from negative self-induced emotions and 54.52% in the classification of emotions into six discrete categories. Our research will help promote the development of comprehensive endogenous emotion recognition methods. PMID:29534515

Membrane Driven Spatial Organization of GPCRs

NASA Astrophysics Data System (ADS)

Mondal, Sayan; Johnston, Jennifer M.; Wang, Hao; Khelashvili, George; Filizola, Marta; Weinstein, Harel

2013-10-01

Spatial organization of G-protein coupled receptors (GPCRs) into dimers and higher order oligomers has been demonstrated in vitro and in vivo. The pharmacological readout was shown to depend on the specific interfaces, but why particular regions of the GPCR structure are involved, and how ligand-determined states change them remains unknown. Here we show why protein-membrane hydrophobic matching is attained upon oligomerization at specific interfaces from an analysis of coarse-grained molecular dynamics simulations of the spontaneous diffusion-interaction of the prototypical beta2-adrenergic (β2AR) receptors in a POPC lipid bilayer. The energy penalty from mismatch is significantly reduced in the spontaneously emerging oligomeric arrays, making the spatial organization of the GPCRs dependent on the pattern of mismatch in the monomer. This mismatch pattern is very different for β2AR compared to the highly homologous and structurally similar β1AR, consonant with experimentally observed oligomerization patterns of β2AR and β1AR. The results provide a mechanistic understanding of the structural context of oligomerization.

Preliminary demonstration using localized skin temperature elevation as observed with thermal imaging as an indicator of fat-specific absorption during focused-field radiofrequency therapy.

PubMed

Key, Douglas J

2014-07-01

This study incorporates concurrent thermal camera imaging as a means of both safely extending the length of each treatment session within skin surface temperature tolerances and to demonstrate not only the homogeneous nature of skin surface temperature heating but the distribution of that heating pattern as a reflection of localization of subcutaneous fat distribution. Five subjects were selected because of a desire to reduce abdomen and flank fullness. Full treatment field thermal camera imaging was captured at 15 minute intervals, specifically at 15, 30, and 45 minutes into active treatment with the purpose of monitoring skin temperature and avoiding any patterns of skin temperature excess. Peak areas of heating corresponded anatomically to the patients' areas of greatest fat excess ie, visible "pinchable" fat. Preliminary observation of high-resolution thermal camera imaging used concurrently with focused field RF therapy show peak skin heating patterns overlying the areas of greatest fat excess.

Illuminating the multifaceted roles of neurotransmission in shaping neuronal circuitry.

PubMed

Okawa, Haruhisa; Hoon, Mrinalini; Yoshimatsu, Takeshi; Della Santina, Luca; Wong, Rachel O L

2014-09-17

Across the nervous system, neurons form highly stereotypic patterns of synaptic connections that are designed to serve specific functions. Mature wiring patterns are often attained upon the refinement of early, less precise connectivity. Much work has led to the prevailing view that many developing circuits are sculpted by activity-dependent competition among converging afferents, which results in the elimination of unwanted synapses and the maintenance and strengthening of desired connections. Studies of the vertebrate retina, however, have recently revealed that activity can play a role in shaping developing circuits without engaging competition among converging inputs that differ in their activity levels. Such neurotransmission-mediated processes can produce stereotypic wiring patterns by promoting selective synapse formation rather than elimination. We discuss how the influence of transmission may also be limited by circuit design and further highlight the importance of transmission beyond development in maintaining wiring specificity and synaptic organization of neural circuits. Copyright © 2014 Elsevier Inc. All rights reserved.

The RS4939827 polymorphism in the SMAD7 GENE and its association with Mediterranean diet in colorectal carcinogenesis.

PubMed

Alonso-Molero, Jéssica; González-Donquiles, Carmen; Palazuelos, Camilo; Fernández-Villa, Tania; Ramos, Elena; Pollán, Marina; Aragonés, Nuria; Llorca, Javier; Henar Alonso, M; Tardón, Adonina; Amiano, Pilar; Moleon, José Juan Jiménez; Pérez, Rosana Peiró; Capelo, Rocío; Molina, Antonio J; Acebo, Inés Gómez; Guevara, Marcela; Perez-Gomez, Beatriz; Lope, Virginia; Huerta, José María; Castaño-Vinyals, Gemma; Kogevinas, Manolis; Moreno, Victor; Martín, Vicente

2017-10-30

The objective of our investigation is to study the relationship between the rs4939827 SNP in the SMAD7 gene, Mediterranean diet pattern and the risk of colorectal cancer. We examined 1087 cases of colorectal cancer and 2409 population controls with available DNA samples from the MCC-Spain study, 2008-2012. Descriptive statistical analyses, and multivariate logistic mixed models were performed. The potential synergistic effect of rs4939827 and the Mediterranean diet pattern was evaluated with logistic regression in different strata of of adherence to the Mediterranean diet and the genotype. High adherence to Mediterrenean diet was statistically significantly associated with colorectal cancer risk. A decreased risk for CRC cancer was observed for the CC compared to the TT genotype (OR = 0.65 and 95% CI = 0.51-0.81) of the rs4939827 SNP Also, we could show an association between the Mediterranean diet pattern (protective factor) and rs4939827. Although the decreased risk for the CC genotype was slightly more pronounced in subjects with high adherence to Mediterrenean diet, there was no statistically significant synergistic effect between genotype CC and adherence to the Mediterranean dietary pattern factors. The SMAD7 gene and specifically the allele C could be protective for colorectal cancer. An independent protective association was also observed between high adherence Mediterranean diet pattern and CRC risk. Findings form this study indicate that high adherence to Mediterranean diet pattern has a protective role for CRC cancer probably involving the Tumor Growth Factor- β pathway in this cancer.

Thyroid Ultrasonography in Differentiation between Graves’ Disease and Hashimoto’s Thyroiditis

PubMed Central

Pishdad, P.; Pishdad, G.R.; Tavanaa, S.; Pishdad, R.; Jalli, R.

2017-01-01

Objective: Graves’ disease and Hashimoto’s thyroiditis are the most common causes of hyper and hypothyroidism, respectively. Differentiation of these 2 diseases, if the patient is euthyroid, may sometimes be extremely difficult on the basis of clinical and laboratory findings. The purpose of this study was to determine the sensitivity and specificity of gray scale sonography in differentiation of Graves’ disease from Hashimoto’s thyroiditis. Methods: This study included 149 patients divided into three groups, patients with Graves’ disease (34 patients, mean age = 36.8 ± 10.17 years), Patients with Hashimoto’s thyroiditis (62 patients, mean age = 33.4 ± 12.16 years) and control group (53 healthy people, mean age = 34.74 ± 16.87 years). Members of all groups were referred to a single radiologist for thyroid sonography for evaluation of thyroid echogenicity pattern. Results: A total of 117 women and 32 men were examined by sonography. The most common sonographic pattern in Hashimoto and Graves’ was homogenous hypo-echogenicity which was observed in 45.2% and 47.1% of cases, respectively. Peripheral hypo-echogenicity pattern was seen in 40.3% of Hashimoto’s group with 100% specificity and 40.3% sensitivity. Central-hypoechogenic pattern was observed in 17.6% of Graves’ group with 100% and 17.6% specificity and sensitivity, respectively. Conclusion: Our findings indicate that sonography has high specificity but low sensitivity in the diagnosis of either Graves’ disease or Hashimoto’s thyroiditis. It is therefore not possible to differentiate between these two diseases using sonography alone. Confirmation by laboratory data is also needed. PMID:28451576

Examining Solutions to Missing Data in Longitudinal Nursing Research

PubMed Central

Roberts, Mary B.; Sullivan, Mary C.; Winchester, Suzy B.

2017-01-01

Purpose Longitudinal studies are highly valuable in pediatrics because they provide useful data about developmental patterns of child health and behavior over time. When data are missing, the value of the research is impacted. The study’s purpose was to: (1) introduce a 3-step approach to assess and address missing data; (2) illustrate this approach using categorical and continuous level variables from a longitudinal study of premature infants. Methods A three-step approach with simulations was followed to assess the amount and pattern of missing data and to determine the most appropriate imputation method for the missing data. Patterns of missingness were Missing Completely at Random, Missing at Random, and Not Missing at Random. Missing continuous-level data were imputed using mean replacement, stochastic regression, multiple imputation, and fully conditional specification. Missing categorical-level data were imputed using last value carried forward, hot-decking, stochastic regression, and fully conditional specification. Simulations were used to evaluate these imputation methods under different patterns of missingness at different levels of missing data. Results The rate of missingness was 16–23% for continuous variables and 1–28% for categorical variables. Fully conditional specification imputation provided the least difference in mean and standard deviation estimates for continuous measures. Fully conditional specification imputation was acceptable for categorical measures. Results obtained through simulation reinforced and confirmed these findings. Practice Implications Significant investments are made in the collection of longitudinal data. The prudent handling of missing data can protect these investments and potentially improve the scientific information contained in pediatric longitudinal studies. PMID:28425202

Search for Patterns of Functional Specificity in the Brain: A Nonparametric Hierarchical Bayesian Model for Group fMRI Data

PubMed Central

Sridharan, Ramesh; Vul, Edward; Hsieh, Po-Jang; Kanwisher, Nancy; Golland, Polina

2012-01-01

Functional MRI studies have uncovered a number of brain areas that demonstrate highly specific functional patterns. In the case of visual object recognition, small, focal regions have been characterized with selectivity for visual categories such as human faces. In this paper, we develop an algorithm that automatically learns patterns of functional specificity from fMRI data in a group of subjects. The method does not require spatial alignment of functional images from different subjects. The algorithm is based on a generative model that comprises two main layers. At the lower level, we express the functional brain response to each stimulus as a binary activation variable. At the next level, we define a prior over sets of activation variables in all subjects. We use a Hierarchical Dirichlet Process as the prior in order to learn the patterns of functional specificity shared across the group, which we call functional systems, and estimate the number of these systems. Inference based on our model enables automatic discovery and characterization of dominant and consistent functional systems. We apply the method to data from a visual fMRI study comprised of 69 distinct stimulus images. The discovered system activation profiles correspond to selectivity for a number of image categories such as faces, bodies, and scenes. Among systems found by our method, we identify new areas that are deactivated by face stimuli. In empirical comparisons with perviously proposed exploratory methods, our results appear superior in capturing the structure in the space of visual categories of stimuli. PMID:21884803

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Cracking-assisted fabrication of nanoscale patterns for micro/nanotechnological applications

NASA Astrophysics Data System (ADS)

Kim, Minseok; Kim, Dong-Joo; Ha, Dogyeong; Kim, Taesung

2016-05-01

Cracks are frequently observed in daily life, but they are rarely welcome and are considered as a material failure mode. Interestingly, cracks cause critical problems in various micro/nanofabrication processes such as colloidal assembly, thin film deposition, and even standard photolithography because they are hard to avoid or control. However, increasing attention has been given recently to control and use cracks as a facile, low-cost strategy for producing highly ordered nanopatterns. Specifically, cracking is the breakage of molecular bonds and occurs simultaneously over a large area, enabling fabrication of nanoscale patterns at both high resolution and high throughput, which are difficult to obtain simultaneously using conventional nanofabrication techniques. In this review, we discuss various cracking-assisted nanofabrication techniques, referred to as crack lithography, and summarize the fabrication principles, procedures, and characteristics of the crack patterns such as their position, direction, and dimensions. First, we categorize crack lithography techniques into three technical development levels according to the directional freedom of the crack patterns: randomly oriented, unidirectional, or multidirectional. Then, we describe a wide range of novel practical devices fabricated by crack lithography, including bioassay platforms, nanofluidic devices, nanowire sensors, and even biomimetic mechanosensors.

Evaluation of MPEG-7-Based Audio Descriptors for Animal Voice Recognition over Wireless Acoustic Sensor Networks.

PubMed

Luque, Joaquín; Larios, Diego F; Personal, Enrique; Barbancho, Julio; León, Carlos

2016-05-18

Environmental audio monitoring is a huge area of interest for biologists all over the world. This is why some audio monitoring system have been proposed in the literature, which can be classified into two different approaches: acquirement and compression of all audio patterns in order to send them as raw data to a main server; or specific recognition systems based on audio patterns. The first approach presents the drawback of a high amount of information to be stored in a main server. Moreover, this information requires a considerable amount of effort to be analyzed. The second approach has the drawback of its lack of scalability when new patterns need to be detected. To overcome these limitations, this paper proposes an environmental Wireless Acoustic Sensor Network architecture focused on use of generic descriptors based on an MPEG-7 standard. These descriptors demonstrate it to be suitable to be used in the recognition of different patterns, allowing a high scalability. The proposed parameters have been tested to recognize different behaviors of two anuran species that live in Spanish natural parks; the Epidalea calamita and the Alytes obstetricans toads, demonstrating to have a high classification performance.

Evaluation of MPEG-7-Based Audio Descriptors for Animal Voice Recognition over Wireless Acoustic Sensor Networks

PubMed Central

Luque, Joaquín; Larios, Diego F.; Personal, Enrique; Barbancho, Julio; León, Carlos

2016-01-01

Environmental audio monitoring is a huge area of interest for biologists all over the world. This is why some audio monitoring system have been proposed in the literature, which can be classified into two different approaches: acquirement and compression of all audio patterns in order to send them as raw data to a main server; or specific recognition systems based on audio patterns. The first approach presents the drawback of a high amount of information to be stored in a main server. Moreover, this information requires a considerable amount of effort to be analyzed. The second approach has the drawback of its lack of scalability when new patterns need to be detected. To overcome these limitations, this paper proposes an environmental Wireless Acoustic Sensor Network architecture focused on use of generic descriptors based on an MPEG-7 standard. These descriptors demonstrate it to be suitable to be used in the recognition of different patterns, allowing a high scalability. The proposed parameters have been tested to recognize different behaviors of two anuran species that live in Spanish natural parks; the Epidalea calamita and the Alytes obstetricans toads, demonstrating to have a high classification performance. PMID:27213375

Multivariate pattern analysis of fMRI data reveals deficits in distributed representations in schizophrenia

PubMed Central

Yoon, Jong H.; Tamir, Diana; Minzenberg, Michael J.; Ragland, J. Daniel; Ursu, Stefan; Carter, Cameron S.

2009-01-01

Background Multivariate pattern analysis is an alternative method of analyzing fMRI data, which is capable of decoding distributed neural representations. We applied this method to test the hypothesis of the impairment in distributed representations in schizophrenia. We also compared the results of this method with traditional GLM-based univariate analysis. Methods 19 schizophrenia and 15 control subjects viewed two runs of stimuli--exemplars of faces, scenes, objects, and scrambled images. To verify engagement with stimuli, subjects completed a 1-back matching task. A multi-voxel pattern classifier was trained to identify category-specific activity patterns on one run of fMRI data. Classification testing was conducted on the remaining run. Correlation of voxel-wise activity across runs evaluated variance over time in activity patterns. Results Patients performed the task less accurately. This group difference was reflected in the pattern analysis results with diminished classification accuracy in patients compared to controls, 59% and 72% respectively. In contrast, there was no group difference in GLM-based univariate measures. In both groups, classification accuracy was significantly correlated with behavioral measures. Both groups showed highly significant correlation between inter-run correlations and classification accuracy. Conclusions Distributed representations of visual objects are impaired in schizophrenia. This impairment is correlated with diminished task performance, suggesting that decreased integrity of cortical activity patterns is reflected in impaired behavior. Comparisons with univariate results suggest greater sensitivity of pattern analysis in detecting group differences in neural activity and reduced likelihood of non-specific factors driving these results. PMID:18822407

Effects of perceived school well-being and negative emotionality on students' attentional bias for academic stressors.

PubMed

Scrimin, Sara; Moscardino, Ughetta; Altoè, Gianmarco; Mason, Lucia

2016-06-01

Previous research indicates that children can display different attention allocation patterns in response to threat. However, data are lacking on the possible existence of an attentional bias in response to academic stressors, and whether variables related to school well-being (SWB) and students' individual characteristics may influence such attentional patterns. We aimed to investigate whether students show an attentional bias for school-related stressors. We sought to identify groups of students who differ in their perceived SWB, and to test whether they display different attention allocation patterns. We also examined whether negative emotionality moderates the expected association between students' SWB and attentional bias. Eighth-grade students completed a dot-probe detection task to register attentional patterns towards or away from an academic threatening word. SWB in terms of school anxiety, school-based stress, and perceived class climate was also assessed via self-reports. In addition, participants reported on their negative emotionality. The results indicated that students showed an attentional bias towards words describing academic stressors. Cluster analyses allowed the identification of two groups of students with high versus low SWB. Regression analysis indicated that those with low SWB were more likely to show a greater bias and that negative emotionality moderated this relationship. Specifically, within the context of low SWB, students with high negative emotionality were more prone to biased attention towards school-related stressors compared with students with low negative emotionality. The present data indicate a perceptual bias for the detection of academic threats. Within the school practice, teachers should promote SWB and devote specific attention to students with high negative emotionality to reduce a biased allocation of attention in response to school-related stressors. © 2016 The British Psychological Society.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

PubMed

Glinsky, Gennadi V

2016-09-19

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Low cost tooling material and process for graphite and Kevlar composites

NASA Technical Reports Server (NTRS)

Childs, William I.

1987-01-01

An Extruded Sheet Tooling Compound (ESTC) was developed for use in quickly building low cost molds for fabricating composites. The ESTC is a very highly mineral-filled resin system formed into a 6 mm thick sheet. The sheet is laid on the pattern, vacuum (bag) is applied to remove air from the pattern surface, and the assembly is heat cured. The formed ESTC is then backed and/or framed and ready for use. The cured ESTC exhibits low coefficient of thermal expansion and maintains strength at temperatures of 180 to 200 C. Tools were made and used successfully for: Compression molding of high strength epoxy sheet molding compound, stamping of aluminum, resin transfer molding of polyester, and liquid resin molding of polyester. Several variations of ESTC can be made for specific requirements. Higher thermal conductivity can be achieved by using an aluminum particle filler. Room temperature gel is possible to allow use of foam patterns.

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

PubMed Central

Pandey, Shivendra; Gultepe, Evin; Gracias, David H.

2013-01-01

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two dimensional (2D) structures. These technologies are mature, offer high precision and many of them can be implemented in a high-throughput manner. We leverage the advantages of planar lithography and combine them with self-folding methods1-20 wherein physical forces derived from surface tension or residual stress, are used to curve or fold planar structures into three dimensional (3D) structures. In doing so, we make it possible to mass produce precisely patterned static and reconfigurable particles that are challenging to synthesize. In this paper, we detail visualized experimental protocols to create patterned particles, notably, (a) permanently bonded, hollow, polyhedra that self-assemble and self-seal due to the minimization of surface energy of liquefied hinges21-23 and (b) grippers that self-fold due to residual stress powered hinges24,25. The specific protocol described can be used to create particles with overall sizes ranging from the micrometer to the centimeter length scales. Further, arbitrary patterns can be defined on the surfaces of the particles of importance in colloidal science, electronics, optics and medicine. More generally, the concept of self-assembling mechanically rigid particles with self-sealing hinges is applicable, with some process modifications, to the creation of particles at even smaller, 100 nm length scales22, 26 and with a range of materials including metals21, semiconductors9 and polymers27. With respect to residual stress powered actuation of reconfigurable grasping devices, our specific protocol utilizes chromium hinges of relevance to devices with sizes ranging from 100 μm to 2.5 mm. However, more generally, the concept of such tether-free residual stress powered actuation can be used with alternate high-stress materials such as heteroepitaxially deposited semiconductor films5,7 to possibly create even smaller nanoscale grasping devices. PMID:23407436

Analysis of communication in the standard versus automated aircraft

NASA Technical Reports Server (NTRS)

Veinott, Elizabeth S.; Irwin, Cheryl M.

1993-01-01

Past research has shown crew communication patterns to be associated with overall crew performance, recent flight experience together, low-and high-error crew performance and personality variables. However, differences in communication patterns as a function of aircraft type and level of aircraft automation have not been fully addressed. Crew communications from ten MD-88 and twelve DC-9 crews were obtained during a full-mission simulation. In addition to large differences in overall amount of communication during the normal and abnormal phases of flight (DC-9 crews generating less speech than MD-88 crews), differences in specific speech categories were also found. Log-linear analyses also generated speaker-response patterns related to each aircraft type, although in future analyses these patterns will need to account for variations due to crew performance.

"Machismo," self-esteem, education and high maximum drinking among anglo, black and Mexican-American male drinkers.

PubMed

Neff, J A; Prihoda, T J; Hoppe, S K

1991-09-01

This study seeks to clarify the relevance of machismo to patterns of high maximum drinking among male drinkers. Specifically, the study describes the psychometric properties of a newly developed 7-item machismo measure, compares levels of machismo and self-esteem for a sample of Anglo, black and Mexican-American males, and examines both main and interaction effects of machismo, self-esteem and education as predictors of alcohol use in these racial/ethnic subgroups. Logistic regression analyses document interaction between race/ethnicity, machismo, self-esteem and education, which calls into question the presumed importance of machismo as a cultural element causing heavy drinking patterns among Mexican-American males.

A novel pit pattern identifies the precursor of colorectal cancer derived from sessile serrated adenoma.

PubMed

Kimura, Tomoaki; Yamamoto, Eiichiro; Yamano, Hiro-O; Suzuki, Hiromu; Kamimae, Seiko; Nojima, Masanori; Sawada, Takeshi; Ashida, Masami; Yoshikawa, Kenjiro; Takagi, Ryo; Kato, Ryusuke; Harada, Taku; Suzuki, Ryo; Maruyama, Reo; Kai, Masahiro; Imai, Kohzoh; Shinomura, Yasuhisa; Sugai, Tamotsu; Toyota, Minoru

2012-03-01

Sessile serrated adenomas (SSAs) are known to be precursors of sporadic colorectal cancers (CRCs) with microsatellite instability (MSI), and to be tightly associated with BRAF mutation and the CpG island methylator phenotype (CIMP). Consequently, colonoscopic identification of SSAs has important implications for preventing CRCs, but accurate endoscopic diagnosis is often difficult. Our aim was to clarify which endoscopic findings are specific to SSAs. The morphological, histological and molecular features of 261 specimens from 226 colorectal tumors were analyzed. Surface microstructures were analyzed using magnifying endoscopy. Mutation in BRAF and KRAS was examined by pyrosequencing. Methylation of p16, IGFBP7, MLH1 and MINT1, -2, -12 and -31 was analyzed using bisulfite pyrosequencing. Through retrospective analysis of a training set (n=145), we identified a novel surface microstructure, the Type II open-shape pit pattern (Type II-O), which was specific to SSAs with BRAF mutation and CIMP. Subsequent prospective analysis of an independent validation set (n=116) confirmed that the Type II-O pattern is highly predictive of SSAs (sensitivity, 65.5%; specificity, 97.3%). BRAF mutation and CIMP occurred with significant frequency in Type II-O-positive serrated lesions. Progression of SSAs to more advanced lesions was associated with further accumulation of aberrant DNA methylation and additional morphological changes, including the Type III, IV and V pit patterns. Our results suggest the Type II-O pit pattern is a useful hallmark of the premalignant stage of CRCs with MSI and CIMP, which could serve to improve the efficacy of colonoscopic surveillance.

Beverage-specific patterns of 5+ alcoholic drink consumption by young adults in the U.S.

PubMed

Stern, Stephanie A; Terry-McElrath, Yvonne M; Patrick, Megan E

2017-02-01

Young adult binge drinking prevalence has been widely researched. However, beverage-specific binge drinking rates for beer, liquor, wine, and wine coolers have not yet been documented for this age group. This study examines consumption of specific beverages (i.e., 5+ drinks in a row in the past two weeks) by young adults aged 19/20. Data from the national Monitoring the Future study were collected one or two years after high school from 2004 to 2014 (n=2004). Logistic regression was used to examine associations between beverage-specific 5+ drinking and gender, race/ethnicity, parent education, college status, and cohort year. Overall 5+ drinking in the past two weeks was reported by 31.4% of young adults. Beverage-specific 5+ drinking was most common with liquor (22.6%) and beer (22.4%), followed by wine (4.5%) and wine coolers (3.0%). Men were more likely than women to engage in 5+ drinking with beer and liquor; women were more likely than men to do so with wine and wine coolers. Beverage-specific patterns differed by college attendance. Compared to four-year college students, two-year college/votech students were less likely to have 5+ drinks of liquor or wine, and more likely to have 5+ wine coolers; those not in college were less likely to have 5+ drinks of liquor and more likely to have 5+ wine coolers. Differences in beverage-specific 5+ drinking by gender and college enrollment suggest that intervention efforts should focus on the beverages that are most commonly consumed at high levels within specific early young adult populations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identity-Specific Reward Representations in Orbitofrontal Cortex Are Modulated by Selective Devaluation

PubMed Central

Howard, James D.

2017-01-01

Goal-directed behavior is sensitive to the current value of expected outcomes. This requires independent representations of specific rewards, which have been linked to orbitofrontal cortex (OFC) function. However, the mechanisms by which the human brain updates specific goals on the fly, and translates those updates into choices, have remained unknown. Here we implemented selective devaluation of appetizing food odors in combination with pattern-based neuroimaging and a decision-making task. We found that in a hungry state, participants chose to smell high-intensity versions of two value-matched food odor rewards. After eating a meal corresponding to one of the two odors, participants switched choices toward the low intensity of the sated odor but continued to choose the high intensity of the nonsated odor. This sensory-specific behavioral effect was mirrored by pattern-based changes in fMRI signal in lateral posterior OFC, where specific reward identity representations were altered after the meal for the sated food odor but retained for the nonsated counterpart. In addition, changes in functional connectivity between the OFC and general value coding in ventromedial prefrontal cortex (vmPFC) predicted individual differences in satiety-related choice behavior. These findings demonstrate how flexible representations of specific rewards in the OFC are updated by devaluation, and how functional connections to vmPFC reflect the current value of outcomes and guide goal-directed behavior. SIGNIFICANCE STATEMENT The orbitofrontal cortex (OFC) is critical for goal-directed behavior. A recent proposal is that OFC fulfills this function by representing a variety of state and task variables (“cognitive maps”), including a conjunction of expected reward identity and value. Here we tested how identity-specific representations of food odor reward are updated by satiety. We found that fMRI pattern-based signatures of reward identity in lateral posterior OFC were modulated after selective devaluation, and that connectivity between this region and general value coding ventromedial prefrontal cortex (vmPFC) predicted choice behavior. These results provide evidence for a mechanism by which devaluation modulates a cognitive map of expected reward in OFC and thereby alters general value signals in vmPFC to guide goal-directed behavior. PMID:28159906

Recognition of distinctive patterns of gallium-67 distribution in sarcoidosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sulavik, S.B.; Spencer, R.P.; Weed, D.A.

1990-12-01

Assessment of gallium-67 ({sup 67}Ga) uptake in the salivary and lacrimal glands and intrathoracic lymph nodes was made in 605 consecutive patients including 65 with sarcoidosis. A distinctive intrathoracic lymph node {sup 67}Ga uptake pattern, resembling the Greek letter lambda, was observed only in sarcoidosis (72%). Symmetrical lacrimal gland and parotid gland {sup 67}Ga uptake (panda appearance) was noted in 79% of sarcoidosis patients. A simultaneous lambda and panda pattern (62%) or a panda appearance with radiographic bilateral, symmetrical, hilar lymphadenopathy (6%) was present only in sarcoidosis patients. The presence of either of these patterns was particularly prevalent in roentgenmore » Stages I (80%) or II (74%). We conclude that simultaneous (a) lambda and panda images, or (b) a panda image with bilateral symmetrical hilar lymphadenopathy on chest X-ray represent distinctive patterns which are highly specific for sarcoidosis, and may obviate the need for invasive diagnostic procedures.« less

Carbohydrates and diet patterns in nonalcoholic fatty liver disease in children and adolescents.

PubMed

Sekkarie, Ahlia; Welsh, Jean A; Vos, Miriam B

2018-05-16

The primary treatment for nonalcoholic fatty liver disease (NAFLD) in children is lifestyle change, including a healthier diet. However, there are no agreed upon expert recommendations for a specific diet in the prevention or treatment of NAFLD. In this study, we review studies published between 2015 and 2017 contributing to further understanding of the role of diet in the development and progression of NAFLD, particularly those addressing sugars and dietary patterns. Multiple recent studies have expanded on earlier evidence that suggests that high intake of sugars plays a causal role in the development of NAFLD, including several recent experimental studies in adults and children that support a unique effect of fructose consumption on liver fat accumulation. Evidence also points to protective effects of dietary patterns that include but are not limited to minimizing sugar intake, Dietary Approaches to Stop Hypertension (DASH), high protein and the Mediterranean diet. The effect of diet may act through its impact on the microbiome, and may be modified by presence or absence of genetic polymorphisms (nutrigenomics) and several new studies demonstrate this. Diet appears to be a powerful tool in the prevention and treatment of NAFLD. It is imperative that researchers and clinicians continue to hone in on the mechanistic pathways and specific diets to reverse the growing morbidity and mortality of NAFLD.

High-resolution melting analysis for prenatal diagnosis of beta-thalassemia in northern Thailand.

PubMed

Charoenkwan, Pimlak; Sirichotiyakul, Supatra; Phusua, Arunee; Suanta, Sudjai; Fanhchaksai, Kanda; Sae-Tung, Rattika; Sanguansermsri, Torpong

2017-12-01

High-resolution melting (HRM) analysis is a rapid mutation analysis which assesses the pattern of reduction of fluorescence signal after subjecting the amplified PCR product with saturated fluorescence dye to an increasing temperature. We used HRM analysis for prenatal diagnosis of beta-thalassemia disease in northern Thailand. Five PCR-HRM protocols were used to detect point mutations in five different segments of the beta-globin gene, and one protocol to detect the 3.4 kb beta-globin deletion. We sought to characterize the mutations in carriers and to enable prenatal diagnosis in 126 couples at risk of having a fetus with beta-thalassemia disease. The protocols identified 18 common mutations causing beta-thalassemia, including the rare codon 132 (A-T) mutation. Each mutation showed a specific HRM pattern and all results were in concordance with those from direct DNA sequencing or gap-PCR methods. In cases of beta-thalassemia disease resulting from homozygosity for a mutation or compound heterozygosity for two mutations on the same amplified segment, the HRM patterns were different to those of a single mutation and were specific for each combination. HRM analysis is a simple and useful method for mutation identification in beta-thalassemia carriers and prenatal diagnosis of beta-thalassemia in northern Thailand.

Foxi2 Is an Animally Localized Maternal mRNA in Xenopus, and an Activator of the Zygotic Ectoderm Activator Foxi1e

PubMed Central

Cha, Sang-Wook; McAdams, Meredith; Kormish, Jay; Wylie, Christopher; Kofron, Matthew

2012-01-01

Foxi1e is a zygotic transcription factor that is essential for the expression of early ectodermal genes. It is expressed in a highly specific pattern, only in the deep cell layers of the animal hemisphere, and in a mosaic pattern in which expressing cells are interspersed with non-expressing cells. Previous work has shown that several signals in the blastula control this expression pattern, including nodals, the TGFβ family member Vg1, and Notch. However, these are all inhibitory, which raises the question of what activates Foxi1e. In this work, we show that a related Forkhead family protein, Foxi2, is a maternal activator of Foxi1e. Foxi2 mRNA is maternally encoded, and highly enriched in animal hemisphere cells of the blastula. ChIP assays show that it acts directly on upstream regulatory elements of Foxi1e. Its effect is specific, since animal cells depleted of Foxi2 are able to respond normally to mesoderm inducing signals from vegetal cells. Foxi2 thus acts as a link between the oocyte and the early pathway to ectoderm, in a similar fashion to the vegetally localized VegT acts to initiate endoderm and mesoderm formation. PMID:22848601

Biopsy in idiopathic pulmonary fibrosis: back to the future.

PubMed

Rossi, Giulio; Spagnolo, Paolo

2017-09-01

Idiopathic Pulmonary Fibrosis (IPF) is a relentlessly progressive, fibrosing interstitial pneumonia characterized by a radiologic and/or histologic pattern of usual interstitial pneumonia (UIP). The availability of two effective anti-fibrotic drugs in IPF has encouraged the identification and treatment of patients in early stages in order to maximize clinical benefit. The ability of high-resolution computed tomography (HRCT) to identify a 'definite' UIP pattern is suboptimal, particularly in the absence of honeycombing. Therefore, radiologic criteria for UIP are currently being redefined. Histology represents the major source of information to define a UIP pattern. Novel and less invasive approaches (particularly cryobiopsy) to sample interstitial lung diseases have demonstrated high sensitivity and specificity. In parallel, researchers are focusing on molecular mechanisms underlying IPF with the aim to identify more specific druggable targets. Lung tissue is therefore essential for diagnostic, pathogenetic and therapeutic purposes. Areas covered: We identified and critically reviewed the most relevant recent literature related to the limitations of current radiologic criteria, new lung sampling procedures, and molecular pathways in support of the need of lung tissue to better understand IPF. Expert commentary: The development of truly effective treatments for IPF requires the identification of key pathogenetic molecules and pathways. To this end, the availability of lung tissue is vital.

Prosody and Alignment: A Sequential Perspective

ERIC Educational Resources Information Center

Reed, Beatrice Szczepek

2010-01-01

In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes…

Etching-free patterning method for electrical characterization of atomically thin MoSe2 films grown by chemical vapor deposition.

PubMed

Utama, M Iqbal Bakti; Lu, Xin; Zhan, Da; Ha, Son Tung; Yuan, Yanwen; Shen, Zexiang; Xiong, Qihua

2014-11-07

Patterning two-dimensional materials into specific spatial arrangements and geometries is essential for both fundamental studies of materials and practical applications in electronics. However, the currently available patterning methods generally require etching steps that rely on complicated and expensive procedures. We report here a facile patterning method for atomically thin MoSe2 films using stripping with an SU-8 negative resist layer exposed to electron beam lithography. Additional steps of chemical and physical etching were not necessary in this SU-8 patterning method. The SU-8 patterning was used to define a ribbon channel from a field effect transistor of MoSe2 film, which was grown by chemical vapor deposition. The narrowing of the conduction channel area with SU-8 patterning was crucial in suppressing the leakage current within the device, thereby allowing a more accurate interpretation of the electrical characterization results from the sample. An electrical transport study, enabled by the SU-8 patterning, showed a variable range hopping behavior at high temperatures.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses.

PubMed

Giotto, Nina; Gerard, Jean-François; Ziv, Alon; Bouskila, Amos; Bar-David, Shirli

2015-01-01

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore's space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species' space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species' space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses

PubMed Central

Giotto, Nina; Gerard, Jean-François; Ziv, Alon; Bouskila, Amos; Bar-David, Shirli

2015-01-01

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore’s space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species’ space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species’ space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes. PMID:26630393

Eye-specific retinogeniculate segregation proceeds normally following disruption of patterned spontaneous retinal activity.

PubMed

Speer, Colenso M; Sun, Chao; Liets, Lauren C; Stafford, Ben K; Chapman, Barbara; Cheng, Hwai-Jong

2014-11-07

Spontaneous retinal activity (SRA) is important during eye-specific segregation within the dorsal lateral geniculate nucleus (dLGN), but the feature(s) of activity critical for retinogeniculate refinement are controversial. Pharmacologically or genetically manipulating cholinergic signaling during SRA perturbs correlated retinal ganglion cell (RGC) spiking and disrupts eye-specific retinofugal refinement in vivo, consistent with an instructive role for SRA during visual system development. Paradoxically, ablating the starburst amacrine cells (SACs) that generate cholinergic spontaneous activity disrupts correlated RGC firing without impacting retinal activity levels or eye-specific segregation in the dLGN. Such experiments suggest that patterned SRA during retinal waves is not critical for eye-specific refinement and instead, normal activity levels are permissive for retinogeniculate development. Here we revisit the effects of ablating the cholinergic network during eye-specific segregation and show that SAC ablation disrupts, but does not eliminate, retinal waves with no concomitant impact on normal eye-specific segregation in the dLGN. We induced SAC ablation in postnatal ferret pups beginning at birth by intraocular injection of a novel immunotoxin selective for the ferret vesicular acetylcholine transporter (Ferret VAChT-Sap). Through dual-patch whole-cell and multi-electrode array recording we found that SAC ablation altered SRA patterns and led to significantly smaller retinal waves compared with controls. Despite these defects, eye-specific segregation was normal. Further, interocular competition for target territory in the dLGN proceeded in cases where SAC ablation was asymmetric in the two eyes. Our data demonstrate normal eye-specific retinogeniculate development despite significant abnormalities in patterned SRA. Comparing our current results with earlier studies suggests that defects in retinal wave size, absolute levels of SRA, correlations between RGC pairs, RGC burst frequency, high frequency RGC firing during bursts, and the number of spikes per RGC burst are each uncorrelated with abnormalities in eye-specific segregation in the dLGN. An increase in the fraction of asynchronous spikes occurring outside of bursts and waves correlates with eye-specific segregation defects in studies reported to date. These findings highlight the relative importance of different features of SRA while providing additional constraints for computational models of Hebbian plasticity mechanisms in the developing visual system.

Using a pattern-centered approach to assess sexual risk-taking in study abroad students.

PubMed

Marcantonio, Tiffany; Angelone, D J; Sledjeski, Eve

2016-01-01

The purpose of this study was to examine the impact of several potential factors related to sexually risky behaviors in study abroad students. The authors utilized a pattern-centered analysis to identify specific groups that can be targeted for intervention. The sample consisted of 173 students who studied abroad in a variety of international locations for an average of 4 months. Participants completed questionnaires informed by the Triandis Theory of Interpersonal Behavior that have been predictive of risky sex in traditional traveling environments. The analyses revealed 3 different pathways for risky sexual behavior: Environmental involvement, historical condom use, and intentions to engage in risky sex. These findings can be used for identification of specific high-risk groups of students who can be targeted for predeparture prevention programs.

Development of a Stereovision-Based Technique to Measure the Spread Patterns of Granular Fertilizer Spreaders

PubMed Central

Cool, Simon R.; Pieters, Jan G.; Seatovic, Dejan; Mertens, Koen C.; Nuyttens, David; Van De Gucht, Tim C.; Vangeyte, Jürgen

2017-01-01

Centrifugal fertilizer spreaders are by far the most commonly used granular fertilizer spreader type in Europe. Their spread pattern however is error-prone, potentially leading to an undesired distribution of particles in the field and losses out of the field, which is often caused by poor calibration of the spreader for the specific fertilizer used. Due to the large environmental impact of fertilizer use, it is important to optimize the spreading process and minimize these errors. Spreader calibrations can be performed by using collection trays to determine the (field) spread pattern, but this is very time-consuming and expensive for the farmer and hence not common practice. Therefore, we developed an innovative multi-camera system to predict the spread pattern in a fast and accurate way, independent of the spreader configuration. Using high-speed stereovision, ejection parameters of particles leaving the spreader vanes were determined relative to a coordinate system associated with the spreader. The landing positions and subsequent spread patterns were determined using a ballistic model incorporating the effect of tractor motion and wind. Experiments were conducted with a commercial spreader and showed a high repeatability. The results were transformed to one spatial dimension to enable comparison with transverse spread patterns determined in the field and showed similar results. PMID:28617339

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

PubMed Central

Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

2013-01-01

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

Color vision abnormalities in type II diabetes: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study II report no 2

PubMed Central

Gella, Laxmi; Raman, Rajiv; Kulothungan, Vaitheeswaran; Pal, Swakshyar Saumya; Ganesan, Suganeswari; Srinivasan, Sangeetha; Sharma, Tarun

2017-01-01

Purpose: The purpose of this study is to assess color vision abnormalities in a cohort of subjects with type II diabetes and elucidate associated risk factors. Methods: Subjects were recruited from follow-up cohort of Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study I. Six hundred and seventy-three eyes of 343 subjects were included from this population-based study. All subjects underwent detailed ophthalmic evaluation, including the Farnsworth-Munsell 100 hue test. Results: The prevalence of impaired color vision (ICV) was 43% (CI: 39.2–46.7). Risk factors for ICV were higher heart rate (odds ratio [OR]: 1.043, [1.023–1.064]) and a higher intraocular pressure (IOP) (OR: 1.086, [1.012–1.165]). Subjects with clinically significant macular edema (CSME) had three times higher chance of having ICV. C1, C2, and C3 are the commonly found Early Treatment Diabetic Retinopathy Study (ETDRS) patterns. The moment of inertia method showed that the angle did not reveal any specific pattern of color vision defect. Although the major and minor radii were high in those with ICV, we did not observe polarity. Confusion index was high in subjects with ICV, indicating a severe color vision defect. Conclusions: The prevalence of ICV was 43% among subjects with type II diabetes. The most commonly observed patterns were increasing severities of the blue–yellow defect on ETDRS patterns, but no specific pattern was observed at the moment of inertia analysis. The presence of CSME, a higher heart rate, and IOP was significant risk factors for ICV. This functional impairment in color vision could significantly contribute to morbidity among subjects with diabetes. PMID:29044066

Color vision abnormalities in type II diabetes: Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study II report no 2.

PubMed

Gella, Laxmi; Raman, Rajiv; Kulothungan, Vaitheeswaran; Pal, Swakshyar Saumya; Ganesan, Suganeswari; Srinivasan, Sangeetha; Sharma, Tarun

2017-10-01

The purpose of this study is to assess color vision abnormalities in a cohort of subjects with type II diabetes and elucidate associated risk factors. Subjects were recruited from follow-up cohort of Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetics Study I. Six hundred and seventy-three eyes of 343 subjects were included from this population-based study. All subjects underwent detailed ophthalmic evaluation, including the Farnsworth-Munsell 100 hue test. The prevalence of impaired color vision (ICV) was 43% (CI: 39.2-46.7). Risk factors for ICV were higher heart rate (odds ratio [OR]: 1.043, [1.023-1.064]) and a higher intraocular pressure (IOP) (OR: 1.086, [1.012-1.165]). Subjects with clinically significant macular edema (CSME) had three times higher chance of having ICV. C1, C2, and C3 are the commonly found Early Treatment Diabetic Retinopathy Study (ETDRS) patterns. The moment of inertia method showed that the angle did not reveal any specific pattern of color vision defect. Although the major and minor radii were high in those with ICV, we did not observe polarity. Confusion index was high in subjects with ICV, indicating a severe color vision defect. The prevalence of ICV was 43% among subjects with type II diabetes. The most commonly observed patterns were increasing severities of the blue-yellow defect on ETDRS patterns, but no specific pattern was observed at the moment of inertia analysis. The presence of CSME, a higher heart rate, and IOP was significant risk factors for ICV. This functional impairment in color vision could significantly contribute to morbidity among subjects with diabetes.

Rhythmic activities of hypothalamic magnocellular neurons: autocontrol mechanisms.

PubMed

Richard, P; Moos, F; Dayanithi, G; Gouzènes, L; Sabatier, N

1997-12-01

Electrophysiological recordings in lactating rats show that oxytocin (OT) and vasopressin (AVP) neurons exhibit specific patterns of activities in relation to peripheral stimuli: periodic bursting firing for OT neurons during suckling, phasic firing for AVP neurons during hyperosmolarity (systemic injection of hypertonic saline). These activities are autocontrolled by OT and AVP released somato-dentritically within the hypothalamic magnocellular nuclei. In vivo, OT enhances the amplitude and frequency of bursts, an effect accompanied with an increase in basal firing rate. However, the characteristics of firing change as facilitation proceeds: the spike patterns become very irregular with clusters of spikes spaced by long silences; the firing rate is highly variable and clearly oscillates before facilitated bursts. This unstable behaviour dramatically decreases during intense tonic activation which temporarily interrupts bursting, and could therefore be a prerequisite for bursting. In vivo, the effects of AVP depend on the initial firing pattern of AVP neurons: AVP excites weakly active neurons (increasing duration of active periods and decreasing silences), inhibits highly active neurons, and does not affect neurons with intermediate phasic activity. AVP brings the entire population of AVP neurons to discharge with a medium phasic activity characterised by periods of firing and silence lasting 20-40 s, a pattern shown to optimise the release of AVP from the neurohypophysis. Each of the peptides (OT or AVP) induces an increase in intracellular Ca2+ concentration, specifically in the neurons containing either OT or AVP respectively. OT evokes the release of Ca2+ from IP3-sensitive intracellular stores. AVP induces an influx of Ca2+ through voltage-dependent Ca2+ channels of T-, L- and N-types. We postulate that the facilitatory autocontrol of OT and AVP neurons could be mediated by Ca2+ known to play a key role in the control of the patterns of phasic neurons.

Vertical visual features have a strong influence on cuttlefish camouflage.

PubMed

Ulmer, K M; Buresch, K C; Kossodo, M M; Mäthger, L M; Siemann, L A; Hanlon, R T

2013-04-01

Cuttlefish and other cephalopods use visual cues from their surroundings to adaptively change their body pattern for camouflage. Numerous previous experiments have demonstrated the influence of two-dimensional (2D) substrates (e.g., sand and gravel habitats) on camouflage, yet many marine habitats have varied three-dimensional (3D) structures among which cuttlefish camouflage from predators, including benthic predators that view cuttlefish horizontally against such 3D backgrounds. We conducted laboratory experiments, using Sepia officinalis, to test the relative influence of horizontal versus vertical visual cues on cuttlefish camouflage: 2D patterns on benthic substrates were tested versus 2D wall patterns and 3D objects with patterns. Specifically, we investigated the influence of (i) quantity and (ii) placement of high-contrast elements on a 3D object or a 2D wall, as well as (iii) the diameter and (iv) number of 3D objects with high-contrast elements on cuttlefish body pattern expression. Additionally, we tested the influence of high-contrast visual stimuli covering the entire 2D benthic substrate versus the entire 2D wall. In all experiments, visual cues presented in the vertical plane evoked the strongest body pattern response in cuttlefish. These experiments support field observations that, in some marine habitats, cuttlefish will respond to vertically oriented background features even when the preponderance of visual information in their field of view seems to be from the 2D surrounding substrate. Such choices highlight the selective decision-making that occurs in cephalopods with their adaptive camouflage capability.

Patterning of Functional Antibodies and Other Proteins by Photolithography of Silane Monolayers

NASA Astrophysics Data System (ADS)

Mooney, J. F.; Hunt, A. J.; McIntosh, J. R.; Liberko, C. A.; Walba, D. M.; Rogers, C. T.

1996-10-01

We have demonstrated the assembly of two-dimensional patterns of functional antibodies on a surface. In particular, we have selectively adsorbed micrometer-scale regions of biotinylated immunoglobulin that exhibit specific antigen binding after adsorption. The advantage of this technique is its potential adaptability to adsorbing arbitrary proteins in tightly packed monolayers while retaining functionality. The procedure begins with the formation of a self-assembled monolayer of n-octadecyltrimethoxysilane (OTMS) on a silicon dioxide surface. This monolayer can then be selectively removed by UV photolithography. Under appropriate solution conditions, the OTMS regions will adsorb a monolayer of bovine serum albumin (BSA), while the silicon dioxide regions where the OTMS has been removed by UV light will adsorb less than 2% of a monolayer, thus creating high contrast patterned adsorption of BSA. The attachment of the molecule biotin to the BSA allows the pattern to be replicated in a layer of streptavidin, which bonds to the biotinylated BSA and in turn will bond an additional layer of an arbitrary biotinylated protein. In our test case, functionality of the biotinylated goat antibodies raised against mouse immunoglobulin was demonstrated by the specific binding of fluorescently labeled mouse IgG.

Spectrum of MRI brain lesion patterns in neuromyelitis optica spectrum disorder: a pictorial review.

PubMed

Wang, Kevin Yuqi; Chetta, Justin; Bains, Pavit; Balzer, Anthony; Lincoln, John; Uribe, Tomas; Lincoln, Christie M

2018-06-01

Neuromyelitis optica is a neurotropic autoimmune inflammatory disease of the central nervous system traditionally thought to exclusively involve the optic nerves and spinal cord. With the discovery of the disease-specific aquaporin-4 antibody and the increasing recognition of clinical and characteristic imaging patterns of brain involvement in what is now termed neuromyelitis optica spectrum disorder (NMOSD), MRI now plays a greater role in diagnosis of NMOSD based on the 2015 consensus criteria and in distinguishing it from other inflammatory disorders, particularly multiple sclerosis (MS). Several brain lesion patterns are highly suggestive of NMOSD, whereas others may serve as red flags. Specifically, long corticospinal lesions, hemispheric cerebral white matter lesions and periependymal lesions in the diencephalon, dorsal brainstem and white matter adjacent to lateral ventricles are typical of NMOSD. In contrast, juxtacortical, cortical, or lesions perpendicularly oriented to the surface of the lateral ventricle suggests MS as the diagnosis. Ultimately, a strong recognition of the spectrum of MRI brain findings in NMOSD is essential for accurate diagnosis, and particularly in differentiating from MS. This pictorial review highlights the spectrum of characteristic brain lesion patterns that may be seen in NMOSD and further delineates findings that may help distinguish it from MS.

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.

PubMed

Kim, Taehyung; Tyndel, Marc S; Huang, Haiming; Sidhu, Sachdev S; Bader, Gary D; Gfeller, David; Kim, Philip M

2012-03-01

Peptide recognition domains and transcription factors play crucial roles in cellular signaling. They bind linear stretches of amino acids or nucleotides, respectively, with high specificity. Experimental techniques that assess the binding specificity of these domains, such as microarrays or phage display, can retrieve thousands of distinct ligands, providing detailed insight into binding specificity. In particular, the advent of next-generation sequencing has recently increased the throughput of such methods by several orders of magnitude. These advances have helped reveal the presence of distinct binding specificity classes that co-exist within a set of ligands interacting with the same target. Here, we introduce a software system called MUSI that can rapidly analyze very large data sets of binding sequences to determine the relevant binding specificity patterns. Our pipeline provides two major advances. First, it can detect previously unrecognized multiple specificity patterns in any data set. Second, it offers integrated processing of very large data sets from next-generation sequencing machines. The results are visualized as multiple sequence logos describing the different binding preferences of the protein under investigation. We demonstrate the performance of MUSI by analyzing recent phage display data for human SH3 domains as well as microarray data for mouse transcription factors.

Female-Specific Intergenerational Transmission Patterns of the Human Corticolimbic Circuitry

PubMed Central

Yamagata, Bun; Murayama, Kou; Black, Jessica M.; Hancock, Roeland; Mimura, Masaru; Yang, Tony T.; Reiss, Allan L.

2016-01-01

Parents have large genetic and environmental influences on offspring's cognition, behavior, and brain. These intergenerational effects are observed in mood disorders, with particularly robust association in depression between mothers and daughters. No studies have thus far examined the neural bases of these intergenerational effects in humans. Corticolimbic circuitry is known to be highly relevant in a wide range of processes, including mood regulation and depression. These findings suggest that corticolimbic circuitry may also show matrilineal transmission patterns. Therefore, we examined human parent–offspring association in this neurocircuitry and investigated the degree of association in gray matter volume between parent and offspring. We used voxelwise correlation analysis in a total of 35 healthy families, consisting of parents and their biological offspring. We found positive associations of regional gray matter volume in the corticolimbic circuit, including the amygdala, hippocampus, anterior cingulate cortex, and ventromedial prefrontal cortex between biological mothers and daughters. This association was significantly greater than mother–son, father–daughter, and father–son associations. The current study suggests that the corticolimbic circuitry, which has been implicated in mood regulation, shows a matrilineal-specific transmission patterns. Our preliminary findings are consistent with what has been found behaviorally in depression and may have clinical implications for disorders known to have dysfunction in mood regulation such as depression. Studies such as ours will likely bridge animal work examining gene expression in the brains and clinical symptom-based observations and provide promising ways to investigate intergenerational transmission patterns in the human brain. SIGNIFICANCE STATEMENT Parents have large genetic and environmental influences on the offspring, known as intergenerational effects. Specifically, depression has been shown to exhibit strong matrilineal transmission patterns. Although intergenerational transmission patterns in the human brain are virtually unknown, this would suggest that the corticolimbic circuitry relevant to a wide range of processes including mood regulation may also show matrilineal transmission patterns. Therefore, we examined the degree of association in corticolimbic gray matter volume (GMV) between parent and offspring in 35 healthy families. We found that positive correlations in maternal corticolimbic GMV with daughters were significantly greater than other parent–offspring dyads. Our findings provide new insight into the potential neuroanatomical basis of circuit-based female-specific intergenerational transmission patterns in depression. PMID:26818513

Entangled singularity patterns of photons in Ince-Gauss modes

NASA Astrophysics Data System (ADS)

Krenn, Mario; Fickler, Robert; Huber, Marcus; Lapkiewicz, Radek; Plick, William; Ramelow, Sven; Zeilinger, Anton

2013-01-01

Photons with complex spatial mode structures open up possibilities for new fundamental high-dimensional quantum experiments and for novel quantum information tasks. Here we show entanglement of photons with complex vortex and singularity patterns called Ince-Gauss modes. In these modes, the position and number of singularities vary depending on the mode parameters. We verify two-dimensional and three-dimensional entanglement of Ince-Gauss modes. By measuring one photon and thereby defining its singularity pattern, we nonlocally steer the singularity structure of its entangled partner, while the initial singularity structure of the photons is undefined. In addition we measure an Ince-Gauss specific quantum-correlation function with possible use in future quantum communication protocols.

Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde.

PubMed

Gómez-Gómez, Lourdes; Pacios, Luis F; Diaz-Perales, Araceli; Garrido-Arandia, María; Argandoña, Javier; Rubio-Moraga, Ángela; Ahrazem, Oussama

2018-05-09

In saffron, the cleavage of zeaxanthin by means of CCD2 generates crocetin dialdehyde, which is then converted by an unknown aldehyde dehydrogenase to crocetin. A proteome from saffron stigma was released recently and, based on the expression pattern and correlation analyses, five aldehyde dehydrogenases (ALDHs) were suggested as possible candidates to generate crocetin from crocetin dialdehydes. We selected four of the suggested ALDHs and analyzed their expression in different tissues, determined their activity over crocetin dialdehyde, and performed structure modeling and docking calculation to find their specificity. All the ALDHs were able to convert crocetin dialdehyde to crocetin, but two of them were stigma tissue-specific. Structure modeling and docking analyses revealed that, in all cases, there was a high coverage of residues in the models. All of them showed a very close conformation, indicated by the low root-mean-square deviation (RMSD) values of backbone atoms, which indicate a high similarity among them. However, low affinity between the enzymes and the crocetin dialdehyde were observed. Phylogenetic analysis and binding affinities calculations, including some ALDHs from Gardenia jasmonoides , Crocus sieberi , and Buddleja species that accumulate crocetin and Bixa orellana synthetizing the apocarotenoid bixin selected on their expression pattern matching with the accumulation of either crocins or bixin, pointed out that family 2 C4 members might be involved in the conversion of crocetin dialdehyde to crocetin with high specificity.

Hippocampal maturity promotes memory distinctiveness in childhood and adolescence

PubMed Central

Keresztes, Attila; Bender, Andrew R.; Bodammer, Nils C.; Shing, Yee Lee

2017-01-01

Adaptive learning systems need to meet two complementary and partially conflicting goals: detecting regularities in the world versus remembering specific events. The hippocampus (HC) keeps a fine balance between computations that extract commonalities of incoming information (i.e., pattern completion) and computations that enable encoding of highly similar events into unique representations (i.e., pattern separation). Histological evidence from young rhesus monkeys suggests that HC development is characterized by the differential development of intrahippocampal subfields and associated networks. However, due to challenges in the in vivo investigation of such developmental organization, the ontogenetic timing of HC subfield maturation remains controversial. Delineating its course is important, as it directly influences the fine balance between pattern separation and pattern completion operations and, thus, developmental changes in learning and memory. Here, we relate in vivo, high-resolution structural magnetic resonance imaging data of HC subfields to behavioral memory performance in children aged 6–14 y and in young adults. We identify a multivariate profile of age-related differences in intrahippocampal structures and show that HC maturity as captured by this pattern is associated with age differences in the differential encoding of unique memory representations. PMID:28784801

Determination of polychlorinated biphenyl levels in the serum of residents and in the homogenates of seafood from the New Bedford, Massachusetts, area: a comparison of exposure sources through pattern recognition techniques.

PubMed

Burse, V W; Groce, D F; Caudill, S P; Korver, M P; Phillips, D L; McClure, P C; Lapeza, C R; Head, S L; Miller, D T; Buckley, D J

1994-04-29

We measured the residues of polychlorinated biphenyls (PCBs) in the serum of 23 residents of the New Bedford, Massachusetts, area and from two homogenates each of bluefish and lobsters from the same area. We used congener-specific and total Aroclor quantitative approaches, both of which involved gas chromatography with electron capture detection. Using gas chromatography mass spectrometry (electron ionization mode), we confirmed the presence of PCBs in the combined serum samples and in the aliquots of bluefish and lobsters. In measuring the PCB levels in serum, we found good agreement between the two electron capture detector approaches (r > or = 0.97) when the serum of specific congeners was compared to total Aroclor. We used univariate and multivariate quality control approaches to monitor these analyses. Analytical results for bluefish showed a better agreement between the two techniques than did those for lobsters; however, the small number of samples precluded any statistical comparison. We also measured levels of chlorinated pesticides in the serum samples of two groups of New Bedford residents, those with low PCB levels (< 15 ng/ml) and those with high PCB levels (> or = 15 ng/ml). We found that residents with high PCB levels also tended to have higher levels of hexachlorobenzene (HCB) and 1,1-dichloro-2,2-di-(p-chlorophenyl) ethylene (p,p'-DDE). The higher concentration of all three analytes appears to be influenced by employment in the capacitor industry, by seafood consumption, or both. Using Jaccard measures of similarity and principal component analysis we compared the gas chromatographic patterns of PCBs found in the serum of New Bedford area residents with high serum PCBs with the patterns found in homogenates of lobsters (inclusive of all edible portions except the roe), in homogenates of bluefish fillets taken from local waters, and in serum from goats fed selected technical Aroclors (e.g. Aroclors 1016, 1242, 1254, or 1260). The patterns found in human serum samples were similar to the patterns found in lobster homogenates. Both of these patterns closely resembled patterns found in the serum samples of the goat fed aroclor 1254, as demonstrated by both pattern recognition techniques. In addition, the chromatographic patterns of human serum and of lobsters and bluefish homogenates all indicated the presence of PCBs more characteristic of Aroclors 1016 or 1242.

Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies.

PubMed

Verdu, Paul; Becker, Noémie S A; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

2013-04-01

Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter-gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history.

Sociocultural Behavior, Sex-Biased Admixture, and Effective Population Sizes in Central African Pygmies and Non-Pygmies

PubMed Central

Verdu, Paul; Becker, Noémie S.A.; Froment, Alain; Georges, Myriam; Grugni, Viola; Quintana-Murci, Lluis; Hombert, Jean-Marie; Van der Veen, Lolke; Le Bomin, Sylvie; Bahuchet, Serge; Heyer, Evelyne; Austerlitz, Frédéric

2013-01-01

Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter–gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history. PMID:23300254

Analysis of sex-specific injury patterns and risk factors in young high-level athletes.

PubMed

Frisch, A; Seil, R; Urhausen, A; Croisier, J L; Lair, M L; Theisen, D

2009-12-01

This study analyzed sex-specific injury patterns and risk factors in young athletes (n=256) from 12 sport disciplines practicing at the national or the international level in the Grand-Duchy of Luxembourg. Injury occurrence as a result of sport practice was analyzed retrospectively over the year 2006 using a standardized self-administered questionnaire. Overall incidence was not different between girls and boys (1.20 and 1.21 injuries/1000 athlete-hours, respectively), but in the context of team sport competition girls tended to be at a greater risk (rate ratio 2.05, P=0.053). Girls had a higher proportion of injuries in the ankle/foot region compared with boys (34.8% vs 16.8%). No sex-related differences were found regarding injury severity. Multivariate logistic regression (controlling for age and practice volume) revealed that girls' team sports were associated with a greater injury risk compared with individual sports [odds ratio (OR) of 4.76], while in boys this was observed for racket sports (OR=3.31). Furthermore, physical or emotional stress tended to be a specific risk factor in girls. There was a tendency for injury outside sports to be coupled to a higher injury risk in girls and boys. Consideration of sex-specific injury patterns and risk factors could be of importance for effective injury prevention.

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

PubMed

Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

2016-01-01

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the future.

Dietary patterns and their sociodemographic and behavioural correlates in French middle-aged adults from the SU.VI.MAX cohort.

PubMed

Kesse-Guyot, E; Bertrais, S; Péneau, S; Estaquio, C; Dauchet, L; Vergnaud, A-C; Czernichow, S; Galan, P; Hercberg, S; Bellisle, F

2009-04-01

Few studies have investigated dietary patterns among French adults. We aimed to identify dietary patterns and their relation with nutrient intakes, sociodemographic, lifestyle and other health indicators in a large population of middle-aged subjects living in France. Dietary patterns were identified using factor analysis in 5194 women and men aged 45-60 years enrolled in the SU.VI.MAX (Supplémentation en Vitamines et Minéraux Antioxydants) study. Dietary data were based on repeated 24-h dietary records (at least six records during 2 years). Four patterns were identified: (1) 'alcohol and meat products'; (2) 'prudent diet'; (3) 'convenience foods'; and (4) 'starch, sauces, and vegetables'. The first pattern was positively associated with low education, smoking and overweight in both genders, as well as with abdominal obesity in women and treated hyperlipidaemia and/or hypertension in men. The second pattern was positively correlated with high education and being older than 55 years and negatively correlated with current smoking. This pattern was also associated with overweight and low waist circumference in women and with hyperlipidaemia treatment in men. The third pattern was inversely related to age and positively related to higher education in both genders. In men, higher scores were related to living alone and an urban residence. The fourth pattern was associated with high education and an urban residence in men only. Our study identified four dietary patterns in this population of French middle-aged adults. Associations with sociodemographic, behavioural and health-related factors were found to differ according to dietary patterns. Sex-specific relationships were also found.

Dietary patterns and cardiovascular risk markers in the UK Low Income Diet and Nutrition Survey.

PubMed

Hamer, M; Mishra, G D

2010-09-01

Dietary patterns have been associated with various disease risk markers. There is presently little representative data about the dietary patterns of adults on low income. The objective was therefore to identify dietary patterns and how they relate to cardiovascular (CVD) risk markers in this specific population. Exploratory factor analysis was performed to examine dietary patterns in participants from the UK Low Income Diet and Nutrition Survey (n=2931, aged 49.4+/-20.2 years, 65% female). Dietary intake was assessed from three 24h dietary recalls and blood was drawn for the assessment of CVD risk markers (C-reactive protein [CRP], total and high density lipoprotein [HDL] cholesterol, triglycerides, homocysteine). Results of the factor analysis revealed four interpretable principle components accounting for approximately 16.5% of the total variance, with similar patterns across gender. A 'fast food' diet pattern explained the greatest proportion of the variance (5.5%), followed by 'health aware' (4.1%), 'traditional' (3.6%), and 'sweet' (3.3%) factors. Participants consuming more items from the fast food pattern were younger, more likely to be smokers and employed, but not partnered. The 'health aware' diet pattern was inversely associated with concentrations of CRP and homocysteine, and positively with HDL-cholesterol. A fast food dietary pattern, high in saturated fat, explained the greatest proportion of the variance in a representative sample of adults on low income from the UK. There was, however, considerable heterogeneity in dietary intake among this socially deprived group and healthy eating was associated with lower CVD risk markers. Copyright 2009 Elsevier B.V. All rights reserved.

A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis

PubMed Central

Platre, Matthieu Pierre; Barberon, Marie; Caillieux, Erwann; Colot, Vincent

2016-01-01

Summary Multicellular organisms are composed of many cell types that acquire their specific fate through a precisely controlled pattern of gene expression in time and space dictated in part by cell type-specific promoter activity. Understanding the contribution of highly specialized cell types in the development of a whole organism requires the ability to isolate or analyze different cell types separately. We have characterized and validated a large collection of root cell type-specific promoters and have generated cell type-specific marker lines. These benchmarked promoters can be readily used to evaluate cell type-specific complementation of mutant phenotypes, or to knockdown gene expression using targeted expression of artificial miRNA. We also generated vectors and characterized transgenic lines for cell type-specific induction of gene expression and cell type-specific isolation of nuclei for RNA and chromatin profiling. Vectors and seeds from transgenic Arabidopsis plants will be freely available, and will promote rapid progress in cell type-specific functional genomics. We demonstrate the power of this promoter set for analysis of complex biological processes by investigating the contribution of root cell types in the IRT1-dependent root iron uptake. Our findings revealed the complex spatial expression pattern of IRT1 in both root epidermis and phloem companion cells and the requirement for IRT1 to be expressed in both cell types for proper iron homeostasis. PMID:26662936

Computational Analysis of Intra-Ventricular Flow Pattern Under Partial and Full Support of BJUT-II VAD.

PubMed

Zhang, Qi; Gao, Bin; Chang, Yu

2017-02-27

BACKGROUND Partial support, as a novel support mode, has been widely applied in clinical practice and widely studied. However, the precise mechanism of partial support of LVAD in the intra-ventricular flow pattern is unclear. MATERIAL AND METHODS In this study, a patient-specific left ventricular geometric model was reconstructed based on CT data. The intra-ventricular flow pattern under 3 simulated conditions - "heart failure", "partial support", and "full support" - were simulated by using fluid-structure interaction (FSI). The blood flow pattern, wall shear stress (WSS), time-average wall shear stress (TAWSS), oscillatory shear index (OSI), and relative residence time (RRT) were calculated to evaluate the hemodynamic effects. RESULTS The results demonstrate that the intra-ventricular flow pattern is significantly changed by the support level of BJUT-II VAD. The intra-ventricular vortex was enhanced under partial support and was eliminated under full support, and the high OSI and RRT regions changed from the septum wall to the cardiac apex. CONCLUSIONS In brief, the support level of the BJUT-II VAD has significant effects on the intra-ventricular flow pattern. The partial support mode of BJUT-II VAD can enhance the intra-ventricular vortex, while the distribution of high OSI and RRT moved from the septum wall to the cardiac apex. Hence, the partial support mode of BJUT-II VAD can provide more benefit for intra-ventricular flow pattern.

Long-term consistency in spatial patterns of primate seed dispersal.

PubMed

Heymann, Eckhard W; Culot, Laurence; Knogge, Christoph; Noriega Piña, Tony Enrique; Tirado Herrera, Emérita R; Klapproth, Matthias; Zinner, Dietmar

2017-03-01

Seed dispersal is a key ecological process in tropical forests, with effects on various levels ranging from plant reproductive success to the carbon storage potential of tropical rainforests. On a local and landscape scale, spatial patterns of seed dispersal create the template for the recruitment process and thus influence the population dynamics of plant species. The strength of this influence will depend on the long-term consistency of spatial patterns of seed dispersal. We examined the long-term consistency of spatial patterns of seed dispersal with spatially explicit data on seed dispersal by two neotropical primate species, Leontocebus nigrifrons and Saguinus mystax (Callitrichidae), collected during four independent studies between 1994 and 2013. Using distributions of dispersal probability over distances independent of plant species, cumulative dispersal distances, and kernel density estimates, we show that spatial patterns of seed dispersal are highly consistent over time. For a specific plant species, the legume Parkia panurensis , the convergence of cumulative distributions at a distance of 300 m, and the high probability of dispersal within 100 m from source trees coincide with the dimension of the spatial-genetic structure on the embryo/juvenile (300 m) and adult stage (100 m), respectively, of this plant species. Our results are the first demonstration of long-term consistency of spatial patterns of seed dispersal created by tropical frugivores. Such consistency may translate into idiosyncratic patterns of regeneration.

Exploring the interaction of physical exercise load and pattern recall performance in female handball players.

PubMed

Schapschröer, M; Baker, J; Schorer, J

2016-06-01

Studies examining experts' superiority within domain-specific structured pattern recall tasks have typically had athletes perform them at rest, which is far different from how they are executed in their sport. The aim of this study was to investigate whether performing these tasks under different physical exercise intensities influenced pattern recall results of experts, advanced and novices. In two experiments, 68 participants (experiment 1: n = 33; experiment 2: n = 35) were tested using a handball-specific pattern recall task both at rest and during physical exercise. Physical exercises of 60 % heart rate reserve (constant workload: experiment 1) and of 86.5-90 % HRmax (handball-specific interval load: experiment 2) were induced. Results of both experiments revealed significant group differences with experts recalling patterns more accurately than novices but no significant within-subject differences for the two conditions and no interaction between both factors. Our findings replicate prior research concerning perceptual-cognitive expertise in structured specific pattern recall tasks. However, the lack of intergroup differences between the two conditions or interactions was surprising, suggesting sport-specific pattern recall skill is robust to changes in exercise stimuli. Future work is needed to further examine the impact of "physiological specificity" on perceptual-cognitive expertise.

Network Analysis Reveals Distinct Clinical Syndromes Underlying Acute Mountain Sickness

PubMed Central

Hall, David P.; MacCormick, Ian J. C.; Phythian-Adams, Alex T.; Rzechorzek, Nina M.; Hope-Jones, David; Cosens, Sorrel; Jackson, Stewart; Bates, Matthew G. D.; Collier, David J.; Hume, David A.; Freeman, Thomas; Thompson, A. A. Roger; Baillie, John Kenneth

2014-01-01

Acute mountain sickness (AMS) is a common problem among visitors at high altitude, and may progress to life-threatening pulmonary and cerebral oedema in a minority of cases. International consensus defines AMS as a constellation of subjective, non-specific symptoms. Specifically, headache, sleep disturbance, fatigue and dizziness are given equal diagnostic weighting. Different pathophysiological mechanisms are now thought to underlie headache and sleep disturbance during acute exposure to high altitude. Hence, these symptoms may not belong together as a single syndrome. Using a novel visual analogue scale (VAS), we sought to undertake a systematic exploration of the symptomatology of AMS using an unbiased, data-driven approach originally designed for analysis of gene expression. Symptom scores were collected from 292 subjects during 1110 subject-days at altitudes between 3650 m and 5200 m on Apex expeditions to Bolivia and Kilimanjaro. Three distinct patterns of symptoms were consistently identified. Although fatigue is a ubiquitous finding, sleep disturbance and headache are each commonly reported without the other. The commonest pattern of symptoms was sleep disturbance and fatigue, with little or no headache. In subjects reporting severe headache, 40% did not report sleep disturbance. Sleep disturbance correlates poorly with other symptoms of AMS (Mean Spearman correlation 0.25). These results challenge the accepted paradigm that AMS is a single disease process and describe at least two distinct syndromes following acute ascent to high altitude. This approach to analysing symptom patterns has potential utility in other clinical syndromes. PMID:24465370

Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea

PubMed Central

Bajaj, Deepak; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66–85%) and broader natural allelic diversity (6–64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools. PMID:26208313

Transfer molding processes for nanoscale patterning of poly-L-lactic acid (PLLA) films

NASA Astrophysics Data System (ADS)

Dhakal, Rabin; Peer, Akshit; Biswas, Rana; Kim, Jaeyoun

2016-03-01

Nanoscale patterned structures composed of biomaterials exhibit great potential for the fabrication of functional biostructures. In this paper, we report cost-effective, rapid, and highly reproducible soft lithographic transfer-molding techniques for creating periodic micro- and nano-scale textures on poly (L-lactic acid) (PLLA) surface. These artificial textures can increase the overall surface area and change the release dynamics of the therapeutic agents coated on it. Specifically, we use the double replication technique in which the master pattern is first transferred to the PDMS mold and the pattern on PDMS is then transferred to the PLLA films through drop-casting as well as nano-imprinting. The ensuing comparison studies reveal that the drop-cast PLLA allows pattern transfer at higher levels of fidelity, enabling the realization of nano-hole and nano-cone arrays with pitch down to ~700 nm. The nano-patterned PLLA film was then coated with rapamycin to make it drug-eluting.

Topographic heterogeneity and temperature amplitude explain species richness patterns of birds in the Qinghai-Tibetan Plateau.

PubMed

Zhang, Chunlan; Quan, Qing; Wu, Yongjie; Chen, Youhua; He, Peng; Qu, Yanhua; Lei, Fumin

2017-04-01

Large-scale patterns of species richness have gained much attention in recent years; however, the factors that drive high species richness are still controversial in local regions, especially in highly diversified montane regions. The Qinghai-Tibetan Plateau (QTP) and the surrounding mountains are biodiversity hot spots due to a high number of endemic montane species. Here, we explored the factors underlying this high level of diversity by studying the relationship between species richness and environmental variables. The richness patterns of 758 resident bird species were summarized at the scale of 1°×1° grid cell at different taxonomic levels (order, family, genus, and species) and in different taxonomic groups (Passeriformes, Galliformes, Falconiformes, and Columbiformes). These richness patterns were subsequently analyzed against habitat heterogeneity (topographical heterogeneity and land cover), temperature amplitude (annual temperature, annual precipitation, precipitation seasonality, and temperature seasonality) and a vegetation index (net primary productivity). Our results showed that the highest richness was found in the southeastern part of the QTP, the eastern Himalayas. The lowest richness was observed in the central plateau of the QTP. Topographical heterogeneity and temperature amplitude are the primary factors that explain overall patterns of species richness in the QTP, although the specific effect of each environmental variable varies between the different taxonomic groups depending on their own evolutionary histories and ecological requirements. High species richness in the southeastern QTP is mostly due to highly diversified habitat types and temperature zones along elevation gradients, whereas the low species richness in the central plateau of the QTP may be due to environmental and energetic constraints, as the central plateau is harsh environment.

ROKU: a novel method for identification of tissue-specific genes.

PubMed

Kadota, Koji; Ye, Jiazhen; Nakai, Yuji; Terada, Tohru; Shimizu, Kentaro

2006-06-12

One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes. We describe a method, ROKU, which selects tissue-specific patterns from gene expression data for many tissues and thousands of genes. ROKU ranks genes according to their overall tissue specificity using Shannon entropy and detects tissues specific to each gene if any exist using an outlier detection method. We evaluated the capacity for the detection of various specific expression patterns using synthetic and real data. We observed that ROKU was superior to a conventional entropy-based method in its ability to rank genes according to overall tissue specificity and to detect genes whose expression pattern are specific only to objective tissues. ROKU is useful for the detection of various tissue-specific expression patterns. The framework is also directly applicable to the selection of diagnostic markers for molecular classification of multiple classes.

NEURONAL ACTION ON THE DEVELOPING BLOOD VESSEL PATTERN

PubMed Central

James, Jennifer M.; Mukouyama, Yoh-suke

2011-01-01

The nervous system relies on a highly specialized network of blood vessels for development and neuronal survival. Recent evidence suggests that both the central and peripheral nervous systems (CNS and PNS) employ multiple mechanisms to shape the vascular tree to meet its specific metabolic demands, such as promoting nerve-artery alignment in the PNS or the development the blood brain barrier in the CNS. In this article we discuss how the nervous system directly influences blood vessel patterning resulting in neuro-vascular congruence that is maintained throughout development and in the adult. PMID:21978864

Improved sensitivity high-definition interline CCD using the KODAK TRUESENSE color filter pattern

NASA Astrophysics Data System (ADS)

DiBella, James; Andreghetti, Marco; Enge, Amy; Chen, William; Stanka, Timothy; Kaser, Robert

2010-01-01

The KODAK TRUESENSE Color Filter Pattern has technology that for the first time is applied to a commercially available interline CCD. This 2/3" true-HD sensor will be described along with its performance attributes, including sensitivity improvement as compared to the Bayer CFA version of the same sensor. In addition, an overview of the system developed for demonstration and evaluation will be provided. Examples of the benefits of the new technology in specific applications including surveillance and intelligent traffic systems will be discussed.

Time course of brain activation elicited by basic emotions.

PubMed

Hot, Pascal; Sequeira, Henrique

2013-11-13

Whereas facial emotion recognition protocols have shown that each discrete emotion has a specific time course of brain activation, there is no electrophysiological evidence to support these findings for emotional induction by complex pictures. Our objective was to specify the differences between the time courses of brain activation elicited by feelings of happiness and, with unpleasant pictures, by feelings of disgust and sadness. We compared event-related potentials (ERPs) elicited by the watching of high-arousing pictures from the International Affective Picture System, selected to induce specific emotions. In addition to a classical arousal effect on late positive components, we found specific ERP patterns for each emotion in early temporal windows (<200 ms). Disgust was the first emotion to be associated with different brain processing after 140 ms, whereas happiness and sadness differed in ERPs elicited at the frontal and central sites after 160 ms. Our findings highlight the limits of the classical averaging of ERPs elicited by different emotions inside the same valence and suggest that each emotion could elicit a specific temporal pattern of brain activation, similar to those observed with emotional face recognition.

Modeling seasonal detection patterns for burrowing owl surveys

Treesearch

Quresh S. Latif; Kathleen D. Fleming; Cameron Barrows; John T. Rotenberry

2012-01-01

To guide monitoring of burrowing owls (Athene cunicularia) in the Coachella Valley, California, USA, we analyzed survey-method-specific seasonal variation in detectability. Point-based call-broadcast surveys yielded high early season detectability that then declined through time, whereas detectability on driving surveys increased through the season. Point surveys...

Canada in the 21st Century - Triumph or Tragedy? The Front Line.

ERIC Educational Resources Information Center

Kilgour, David

1996-01-01

Argues that new patterns of trade and production combined with an emphasis on a knowledge-based economy/society make it imperative that Canada upgrade its educational system. Specifically notes that several growing and dominant industries (microelectronics, biotechnology, telecommunications) require a high-tech skilled labor force. (MJP)

Nutrition Goals for Older Adults: A Review.

ERIC Educational Resources Information Center

Horwath, Caroline C.

1991-01-01

Discusses specific goals of nutrition education for older adults and high-risk groups within the elderly population through review of three crucial areas: current knowledge of eating patterns, nutrient intake, and supplement use of older adults; existing information on multiple influences on eating habits of older adults; and potential benefits…

Multiple Drug-Use Patterns Among a Group of High School Students: Regular Users vs. Nonusers of Specific Drug Types

ERIC Educational Resources Information Center

Seffrin, John R.; Seehafer, Roger W.

1976-01-01

Although no cause-effect relationship can be shown, regular drug use seems to predispose one to further drug experimentation and use, while non-use of a particular drug seems to predispose one to non-use of other drugs. (Author/MB)

Report of the Anthropology Curriculum Study Project-Research Program.

ERIC Educational Resources Information Center

Parsons, T. W.; And Others

The study evaluated an Anthropology Curriculum Study Project course, "Patterns in Human History," used with high school students in a one year field test situation. Ethnographic and cognitive components of the curriculum were examined. The specific objective of the research was to examine the behavioral effects on students, teachers, and…

Integrating space and time: A case for phenological context in grazing studies and management

USDA-ARS?s Scientific Manuscript database

In water-limited landscapes, patterns in primary production are highly variable across space and time. Livestock grazing is a common agricultural practice worldwide and a concern is localized overuse of specific pasture resources that can exacerbate grass losses and soil erosion. On a research ranch...

Population-Specific Patterns of Linkage Disequilibrium and SNP Variation in Spring and Winter Polyploid Wheat

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and po...

New aspects of firing pattern autocontrol in oxytocin and vasopressin neurones.

PubMed

Moos, F; Gouzènes, L; Brown, D; Dayanithi, G; Sabatier, N; Boissin, L; Rabié, A; Richard, P

1998-01-01

In the rat, oxytocin (OT) and vasopressin (AVP) neurones exhibit specific electrical activities which are controlled by OT and AVP released from soma and dendrites within the magnocellular hypothalamic nuclei. OT enhances amplitude and frequency of suckling-induced bursts, and changes basal firing characteristics: spike patterning becomes very irregular (spike clusters separated by long silences), firing rate is highly variable, oscillating before facilitated bursts. This unstable behaviour which markedly decreases during hyperosmotic stimulation (interrupting bursting) could be a prerequisite for bursting. The effects of AVP depend on the initial phasic pattern of AVP neurones: AVP excites weakly active neurones (increasing burst duration, decreasing silences) and inhibits highly active neurones; neurones with intermediate phasic activity are unaffected. Thus, AVP ensures all AVP neurones discharge with moderate phasic activity (bursts and silences lasting 20-40 s), known to optimise systemic AVP release. V1a-type receptors are involved in AVP actions. In conclusion, OT and AVP control their respective neurones in a complex manner to favour the patterns of activity which are the best suited for an efficient systemic hormone release.

Heterogeneity in perinatal depression: how far have we come? A systematic review.

PubMed

Santos, Hudson; Tan, Xianming; Salomon, Rebecca

2017-02-01

Despite perinatal depression (PND) being a common mental disorder affecting pregnant women and new mothers, limited attention has been paid to the heterogeneous nature of this disorder. We examined heterogeneity in PND symptom profiles and symptom trajectories. Literature searches revealed 247 studies, 23 of which were included in the final review. The most common statistical approaches used to explore symptom and trajectory heterogeneity were latent class model and growth mixture model. All but one study examined PND symptom trajectories and provided collective evidence of at least three heterogeneous patterns: low, medium, or chronic-high symptom levels. Social and psychological risk factors were the most common group of predictors related to a higher burden (high sum of score) of depressive symptoms. These studies were consistent in reporting poorer health outcomes for children of mothers assigned to high burden symptom trajectories. Only one study explored heterogeneity in symptom profile and was the only one to describe the specific constellations of depressive symptoms related to the PND heterogeneous patterns identified. Therefore, there is limited evidence on the specific symptoms and symptom configurations that make up PND heterogeneity. We suggest directions for future research to further clarify the PND heterogeneity and its related mechanisms.

Continuous High Frequency Activity: A peculiar SEEG pattern related to specific brain regions

PubMed Central

Melani, Federico; Zelmann, Rina; Mari, Francesco; Gotman, Jean

2015-01-01

Objective While visually marking the high frequency oscillations in the stereo-EEG of epileptic patients, we observed a continuous/semicontinuous activity in the ripple band (80–250 Hz), which we defined continuous High Frequency Activity (HFA). We aim to analyze in all brain regions the occurrence and significance of this particular pattern. Methods Twenty patients implanted in mesial temporal and neocortical areas were studied. One minute of slow-wave sleep was reviewed. The background was classified as continuous/semicontinuous, irregular, or sporadic based on the duration of the fast oscillations. Each channel was classified as inside/outside the seizure onset zone (SOZ) or a lesion. Results The continuous/semicontinuous HFA occurred in 54 of the 790 channels analyzed, with a clearly higher prevalence in hippocampus and occipital lobe. No correlation was found with the SOZ or lesions. In the occipital lobe the continuous/semicontinuous HFA was present independently of whether eyes were open or closed. Conclusions We describe what appears to be a new physiological High Frequency Activity, independent of epileptogenicity, present almost exclusively in the hippocampus and occipital cortex but independent of the alpha rhythm. Significance The continuous HFA may be an intrinsic characteristic of specific brain regions, reflecting a particular type of physiological neuronal activity. PMID:23768436

Insight on invasions and resilience derived from spatiotemporal discontinuities of biomass at local and regional scales

USGS Publications Warehouse

Angeler, David G.; Allen, Criag R.; Johnson, Richard K.

2012-01-01

Understanding the social and ecological consequences of species invasions is complicated by nonlinearities in processes, and differences in process and structure as scale is changed. Here we use discontinuity analyses to investigate nonlinear patterns in the distribution of biomass of an invasive nuisance species that could indicate scale-specific organization. We analyze biomass patterns in the flagellate Gonyostomum semen (Raphidophyta) in 75 boreal lakes during an 11-year period (1997-2007). With simulations using a unimodal null model and cluster analysis, we identified regional groupings of lakes based on their biomass patterns. We evaluated the variability of membership of individual lakes in regional biomass groups. Temporal trends in local and regional discontinuity patterns were analyzed using regressions and correlations with environmental variables that characterize nutrient conditions, acidity status, temperature variability, and water clarity. Regionally, there was a significant increase in the number of biomass groups over time, indicative of an increased number of scales at which algal biomass organizes across lakes. This increased complexity correlated with the invasion history of G. semen and broad-scale environmental change (recovery from acidification). Locally, no consistent patterns of lake membership to regional biomass groups were observed, and correlations with environmental variables were lake specific. The increased complexity of regional biomass patterns suggests that processes that act within or between scales reinforce the presence of G. semen and its potential to develop high-biomass blooms in boreal lakes. Emergent regional patterns combined with locally stochastic dynamics suggest a bleak future for managing G. semen, and more generally why invasive species can be ecologically successful.

Four not six: Revealing culturally common facial expressions of emotion.

PubMed

Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

2016-06-01

As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Parallel computing in experimental mechanics and optical measurement: A review (II)

NASA Astrophysics Data System (ADS)

Wang, Tianyi; Kemao, Qian

2018-05-01

With advantages such as non-destructiveness, high sensitivity and high accuracy, optical techniques have successfully integrated into various important physical quantities in experimental mechanics (EM) and optical measurement (OM). However, in pursuit of higher image resolutions for higher accuracy, the computation burden of optical techniques has become much heavier. Therefore, in recent years, heterogeneous platforms composing of hardware such as CPUs and GPUs, have been widely employed to accelerate these techniques due to their cost-effectiveness, short development cycle, easy portability, and high scalability. In this paper, we analyze various works by first illustrating their different architectures, followed by introducing their various parallel patterns for high speed computation. Next, we review the effects of CPU and GPU parallel computing specifically in EM & OM applications in a broad scope, which include digital image/volume correlation, fringe pattern analysis, tomography, hyperspectral imaging, computer-generated holograms, and integral imaging. In our survey, we have found that high parallelism can always be exploited in such applications for the development of high-performance systems.

Retinoic acid and Wnt/beta-catenin have complementary roles in anterior/posterior patterning embryos of the basal chordate amphioxus.

PubMed

Onai, Takayuki; Lin, Hsiu-Chin; Schubert, Michael; Koop, Demian; Osborne, Peter W; Alvarez, Susana; Alvarez, Rosana; Holland, Nicholas D; Holland, Linda Z

2009-08-15

A role for Wnt/beta-catenin signaling in axial patterning has been demonstrated in animals as basal as cnidarians, while roles in axial patterning for retinoic acid (RA) probably evolved in the deuterostomes and may be chordate-specific. In vertebrates, these two pathways interact both directly and indirectly. To investigate the evolutionary origins of interactions between these two pathways, we manipulated Wnt/beta-catenin and RA signaling in the basal chordate amphioxus during the gastrula stage, which is the RA-sensitive period for anterior/posterior (A/P) patterning. The results show that Wnt/beta-catenin and RA signaling have distinctly different roles in patterning the A/P axis of the amphioxus gastrula. Wnt/beta-catenin specifies the identity of the ends of the embryo (high Wnt = posterior; low Wnt = anterior) but not intervening positions. Thus, upregulation of Wnt/beta-catenin signaling induces ectopic expression of posterior markers at the anterior tip of the embryo. In contrast, RA specifies position along the A/P axis, but not the identity of the ends of the embryo-increased RA signaling strongly affects the domains of Hox expression along the A/P axis but has little or no effect on the expression of either anterior or posterior markers. Although the two pathways may both influence such things as specification of neuronal identity, interactions between them in A/P patterning appear to be minimal.

Patterns of anterior and posterior muscle chain interactions during high performance long-hang elements in gymnastics.

PubMed

von Laßberg, Christoph; Rapp, Walter; Krug, Jürgen

2014-06-01

In a prior study with high level gymnasts we could demonstrate that the neuromuscular activation pattern during the "whip-like" leg acceleration phases (LAP) in accelerating movement sequences on high bar, primarily runs in a consecutive succession from the bar (punctum fixum) to the legs (punctum mobile). The current study presents how the neuromuscular activation is represented during movement sequences that immediately follow the LAP by the antagonist muscle chain to generate an effective transfer of momentum for performing specific elements, based on the energy generated by the preceding LAP. Thirteen high level gymnasts were assessed by surface electromyography during high performance elements on high bar and parallel bars. The results show that the neuromuscular succession runs primarily from punctum mobile towards punctum fixum for generating the transfer of momentum. Additionally, further principles of neuromuscular interactions between the anterior and posterior muscle chain during such movement sequences are presented. The findings complement the understanding of neuromuscular activation patterns during rotational movements around fixed axes and will help to form the basis of more direct and better teaching methods regarding earlier optimization and facilitation of the motor learning process concerning fundamental movement requirements. Copyright © 2014 Elsevier Ltd. All rights reserved.

Resist heating effect on e-beam mask writing at 75 kV and 60 A/cm2

NASA Astrophysics Data System (ADS)

Benes, Zdenek; Deverich, Christina; Huang, Chester; Lawliss, Mark

2003-12-01

Resist heating has been known to be one of the main contributors to local CD variation in mask patterning using variable shape e-beam tools. Increasingly complex mask patterns require increased number of shapes which drives the need for higher electron beam current densities to maintain reasonable write times. As beam current density is increased, CD error resulting from resist heating may become a dominating contributor to local CD variations. In this experimental study, the IBM EL4+ mask writer with high voltage and high current density has been used to quantitatively investigate the effect of resist heating on the local CD uniformity. ZEP 7000 and several chemically amplified resists have been evaluated under various exposure conditions (single-pass, multi-pass, variable spot size) and pattern densities. Patterns were designed specifically to allow easy measurement of local CD variations with write strategies designed to maximize the effect of resist heating. Local CD variations as high as 15 nm in 18.75 × 18.75 μm sub-field size have been observed for ZEP 7000 in a single-pass writing with full 1000 nm spots at 50% pattern density. This number can be reduced by increasing the number of passes or by decreasing the maximum spot size. The local CD variation has been reduced to as low as 2 nm for ZEP 7000 for the same pattern under modified exposure conditions. The effectiveness of various writing strategies is discussed as well as their possible deficiencies. Minimal or no resist heating effects have been observed for the chemically amplified resists studied. The results suggest that the resist heating effect can be well controlled by careful selection of the resist/process system and/or writing strategy and that resist heating does not have to pose a problem for high throughput e-beam mask making that requires high voltage and high current densities.

Mediterranean dietary pattern adherence: associations with prediabetes, metabolic syndrome, and related microinflammation.

PubMed

Viscogliosi, Giovanni; Cipriani, Elisa; Liguori, Maria Livia; Marigliano, Benedetta; Saliola, Mirella; Ettorre, Evaristo; Andreozzi, Paola

2013-06-01

The adherence to the Mediterranean Diet (Med Diet) seems to reduce the incidence of metabolic syndrome. The present study aimed to explore whether the adherence to the overall Med Diet pattern and to specific Med Diet items is associated with the presence of metabolic syndrome, impaired fasting glucose (IFG), insulin resistance (IR), and microinflammation in subjects free of diabetes and cardiovascular diseases. Each patient underwent clinical assessment. Adherence to the Med Diet was measured by a previously validated 14-item questionnaire. Metabolic syndrome was defined by the National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) criteria; IR was defined by homeostasis model assessment of insulin resistance (HOMA-IR); inflammation was assessed through a high-sensitivity C-reactive protein (hsCRP) assay. A total of 120 subjects (64.2% women, mean age 59.8±10.2 years) were enrolled at this study. Subjects with lower Med Diet pattern adherence exhibited higher occurrence of metabolic syndrome and all its components and higher HOMA-IR and hsCRP values (P for all <0.0001). Subjects with metabolic syndrome were less likely to consume olive oil (P=0.002) and vegetables (P=0.023). By multivariable analyses, the overall Med Diet score was found to be strongly and inversely associated with the presence of metabolic syndrome [B=-0.066; 95% confidence interval (CI) -0.105 to -0.028; P=0.001], IFG (B=-0.076; 95% CI -0.114 to -0.038; p<0.0001), high HOMA-IR (B=-0.071; 95% CI -0.108 to -0.034; P<0.0001) and high hsCRP (B=-0.082; 95% CI -0.125 to -0.045; P<0.0001). None of specific Med Diet items independently predicted metabolic syndrome, IFG, and high HOMA-IR. Instead, the consumption of white meat over red meat (B=-0.324; 95% CI -0.467 to -0.178; P<0.0001) was found to be inversely associated with increased hsCRP. The inverse associations between adherence to Med Diet and the prevalence of metabolic syndrome and prediabetes may be due more to the effects of the entire dietary pattern rather than to individual food components. Metabolic syndrome-related microinflammation may further be linked to specific Med Diet components.

Optimizing of MALDI-ToF-based low-molecular-weight serum proteome pattern analysis in detection of breast cancer patients; the effect of albumin removal on classification performance.

PubMed

Pietrowska, M; Marczak, L; Polanska, J; Nowicka, E; Behrent, K; Tarnawski, R; Stobiecki, M; Polanski, A; Widlak, P

2010-01-01

Mass spectrometry-based analysis of the serum proteome allows identifying multi-peptide patterns/signatures specific for blood of cancer patients, thus having high potential value for cancer diagnostics. However, because of problems with optimization and standardization of experimental and computational design, none of identified proteome patterns/signatures was approved for diagnostics in clinical practice as yet. Here we compared two methods of serum sample preparation for mass spectrometry-based proteome pattern analysis aimed to identify biomarkers that could be used in early detection of breast cancer patients. Blood samples were collected in a group of 92 patients diagnosed at early (I and II) stages of the disease before the start of therapy, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and analyzed using MALDI-ToF spectrometry, either directly or after membrane filtration (50 kDa cut-off) to remove albumin and other large serum proteins. Mass spectra of the low-molecular-weight fraction (2-10 kDa) of the serum proteome were resolved using the Gaussian mixture decomposition, and identified spectral components were used to build classifiers that differentiated samples from breast cancer patients and healthy persons. Mass spectra of complete serum and membrane-filtered albumin-depleted samples have apparently different structure and peaks specific for both types of samples could be identified. The optimal classifier built for the complete serum specimens consisted of 8 spectral components, and had 81% specificity and 72% sensitivity, while that built for the membrane-filtered samples consisted of 4 components, and had 80% specificity and 81% sensitivity. We concluded that pre-processing of samples to remove albumin might be recommended before MALDI-ToF mass spectrometric analysis of the low-molecular-weight components of human serum Keywords: albumin removal; breast cancer; clinical proteomics; mass spectrometry; pattern analysis; serum proteome.

Understanding adolescents' sleep patterns and school performance: a critical appraisal.

PubMed

Wolfson, Amy R; Carskadon, Mary A

2003-12-01

The present paper reviews and critiques studies assessing the relation between sleep patterns, sleep quality, and school performance of adolescents attending middle school, high school, and/or college. The majority of studies relied on self-report, yet the researchers approached the question with different designs and measures. Specifically, studies looked at (1) sleep/wake patterns and usual grades, (2) school start time and phase preference in relation to sleep habits and quality and academic performance, and (3) sleep patterns and classroom performance (e.g., examination grades). The findings strongly indicate that self-reported shortened total sleep time, erratic sleep/wake schedules, late bed and rise times, and poor sleep quality are negatively associated with academic performance for adolescents from middle school through the college years. Limitations of the current published studies are also discussed in detail in this review.

Process-morphology scaling relations quantify self-organization in capillary densified nanofiber arrays.

PubMed

Kaiser, Ashley L; Stein, Itai Y; Cui, Kehang; Wardle, Brian L

2018-02-07

Capillary-mediated densification is an inexpensive and versatile approach to tune the application-specific properties and packing morphology of bulk nanofiber (NF) arrays, such as aligned carbon nanotubes. While NF length governs elasto-capillary self-assembly, the geometry of cellular patterns formed by capillary densified NFs cannot be precisely predicted by existing theories. This originates from the recently quantified orders of magnitude lower than expected NF array effective axial elastic modulus (E), and here we show via parametric experimentation and modeling that E determines the width, area, and wall thickness of the resulting cellular pattern. Both experiments and models show that further tuning of the cellular pattern is possible by altering the NF-substrate adhesion strength, which could enable the broad use of this facile approach to predictably pattern NF arrays for high value applications.

Multiple bunch HOM evaluation for ERL cavities

DOE PAGES

Xu, Chen; Ben-Zvi, I.; Blaskiewicz, Michael M.; ...

2017-06-15

In this paper we investigate the effect of the bunch pattern in a linac on the Higher Order Mode (HOM) power generation. The future ERL-based electron–ion collider eRHIC at BNL is used as an illustrative example. This ERL has multiple high current Superconducting Radiofrequency (SRF) 5-cell cavities. The HOM power generated when a single bunch traverses the cavity is estimated by the corresponding loss factor. Multiple re-circulations through the Energy Recovery Linac (ERL) create a specific bunch pattern. In this case the loss factor can be different than the single bunch loss factor. HOM power can vary dramatically when themore » ERL bunch pattern changes. The HOM power generation can be surveyed in the time and frequency domains. We estimate the average HOM power in a 5-cell cavity with different ERL bunch patterns.« less

Multiple bunch HOM evaluation for ERL cavities

NASA Astrophysics Data System (ADS)

Xu, Chen; Ben-Zvi, I.; Blaskiewicz, Michael M.; Hao, Yue; Ptitsyn, Vadim

2017-09-01

In this work we investigate the effect of the bunch pattern in a linac on the Higher Order Mode (HOM) power generation. The future ERL-based electron-ion collider eRHIC at BNL is used as an illustrative example. This ERL has multiple high current Superconducting Radiofrequency (SRF) 5-cell cavities. The HOM power generated when a single bunch traverses the cavity is estimated by the corresponding loss factor. Multiple re-circulations through the Energy Recovery Linac (ERL) create a specific bunch pattern. In this case the loss factor can be different than the single bunch loss factor. HOM power can vary dramatically when the ERL bunch pattern changes. The HOM power generation can be surveyed in the time and frequency domains. We estimate the average HOM power in a 5-cell cavity with different ERL bunch patterns.

SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer.

PubMed

Petricoin, Emanuel F; Liotta, Lance A

2004-02-01

Proteomics is more than just generating lists of proteins that increase or decrease in expression as a cause or consequence of pathology. The goal should be to characterize the information flow through the intercellular protein circuitry that communicates with the extracellular microenvironment and then ultimately to the serum/plasma macroenvironment. The nature of this information can be a cause, or a consequence, of disease and toxicity-based processes. Serum proteomic pattern diagnostics is a new type of proteomic platform in which patterns of proteomic signatures from high dimensional mass spectrometry data are used as a diagnostic classifier. This approach has recently shown tremendous promise in the detection of early-stage cancers. The biomarkers found by SELDI-TOF-based pattern recognition analysis are mostly low molecular weight fragments produced at the specific tumor microenvironment.

Multiple bunch HOM evaluation for ERL cavities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Chen; Ben-Zvi, I.; Blaskiewicz, Michael M.

In this paper we investigate the effect of the bunch pattern in a linac on the Higher Order Mode (HOM) power generation. The future ERL-based electron–ion collider eRHIC at BNL is used as an illustrative example. This ERL has multiple high current Superconducting Radiofrequency (SRF) 5-cell cavities. The HOM power generated when a single bunch traverses the cavity is estimated by the corresponding loss factor. Multiple re-circulations through the Energy Recovery Linac (ERL) create a specific bunch pattern. In this case the loss factor can be different than the single bunch loss factor. HOM power can vary dramatically when themore » ERL bunch pattern changes. The HOM power generation can be surveyed in the time and frequency domains. We estimate the average HOM power in a 5-cell cavity with different ERL bunch patterns.« less

Rapid perceptual adaptation to high gravitoinertial force levels Evidence for context-specific adaptation

NASA Technical Reports Server (NTRS)

Lackner, J. R.; Graybiel, A.

1982-01-01

Subjects exposed to periodic variations in gravitoinertial force (2-G peak) in parabolic flight maneuvers quickly come to perceive the peak force level as having decreased in intensity. By the end of a 40-parabola flight, the decrease in apparent force is approximately 40%. On successive flight days, the apparent intensity of the force loads seems to decrease as well, indicating a cumulative adaptive effect. None of the subjects reported feeling abnormally 'light' for more than a minute or two after return to 1-G background force levels. The pattern of findings suggests a context-specific adaptation to high-force levels.

Microbial metabolites are associated with a high adherence to a Mediterranean dietary pattern using a 1H-NMR-based untargeted metabolomics approach.

PubMed

Almanza-Aguilera, Enrique; Urpi-Sarda, Mireia; Llorach, Rafael; Vázquez-Fresno, Rosa; Garcia-Aloy, Mar; Carmona, Francesc; Sanchez, Alex; Madrid-Gambin, Francisco; Estruch, Ramon; Corella, Dolores; Andres-Lacueva, Cristina

2017-10-01

The study of biomarkers of dietary patterns including the Mediterranean diet (MedDiet) is scarce and could improve the assessment of these patterns. Moreover, it could provide a better understanding of health benefits of dietary patterns in nutritional epidemiology. We aimed to determine a robust and accurate biomarker associated with a high adherence to a MedDiet pattern that included dietary assessment and its biological effect. In this cross-sectional study, we included 56 and 63 individuals with high (H-MDA) and low (L-MDA) MedDiet adherence categories, respectively, all from the Prevención con Dieta Mediterránea trial. A 1 H-NMR-based untargeted metabolomics approach was applied to urine samples. Multivariate statistical analyses were conducted to determine the metabolite differences between groups. A stepwise logistic regression and receiver operating characteristic curves were used to build and evaluate the prediction model for H-MDA. Thirty-four metabolites were identified as discriminant between H-MDA and L-MDA. The fingerprint associated with H-MDA included higher excretion of proline betaine and phenylacetylglutamine, among others, and decreased amounts of metabolites related to glucose metabolism. Three microbial metabolites - phenylacetylglutamine, p-cresol and 4-hydroxyphenylacetate - were included in the prediction model of H-MDA (95% specificity, 95% sensitivity and 97% area under the curve). The model composed of microbial metabolites was the biomarker that defined high adherence to a Mediterranean dietary pattern. The overall metabolite profiling identified reflects the metabolic modulation produced by H-MDA. The proposed biomarker may be a better tool for assessing and aiding nutritional epidemiology in future associations between H-MDA and the prevention or amelioration of chronic diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Soybean kinome: functional classification and gene expression patterns

PubMed Central

Liu, Jinyi; Chen, Nana; Grant, Joshua N.; Cheng, Zong-Ming (Max); Stewart, C. Neal; Hewezi, Tarek

2015-01-01

The protein kinase (PK) gene family is one of the largest and most highly conserved gene families in plants and plays a role in nearly all biological functions. While a large number of genes have been predicted to encode PKs in soybean, a comprehensive functional classification and global analysis of expression patterns of this large gene family is lacking. In this study, we identified the entire soybean PK repertoire or kinome, which comprised 2166 putative PK genes, representing 4.67% of all soybean protein-coding genes. The soybean kinome was classified into 19 groups, 81 families, and 122 subfamilies. The receptor-like kinase (RLK) group was remarkably large, containing 1418 genes. Collinearity analysis indicated that whole-genome segmental duplication events may have played a key role in the expansion of the soybean kinome, whereas tandem duplications might have contributed to the expansion of specific subfamilies. Gene structure, subcellular localization prediction, and gene expression patterns indicated extensive functional divergence of PK subfamilies. Global gene expression analysis of soybean PK subfamilies revealed tissue- and stress-specific expression patterns, implying regulatory functions over a wide range of developmental and physiological processes. In addition, tissue and stress co-expression network analysis uncovered specific subfamilies with narrow or wide interconnected relationships, indicative of their association with particular or broad signalling pathways, respectively. Taken together, our analyses provide a foundation for further functional studies to reveal the biological and molecular functions of PKs in soybean. PMID:25614662

Australia's regional innovation systems: inter-industry interaction in innovative activities in three Australian territories

PubMed Central

Schütz, Marlies H.

2017-01-01

ABSTRACT Regional specifics reveal in differences in economic activity and structure, the institutional, socio-economic and cultural environment and not least in the capability of regions to create new knowledge and to generate innovations. Focusing on the regional level, this paper for three Australian territories (New South Wales, Victoria and Queensland) explores patterns of innovative activities in their private business sectors. Furthermore, these patterns are compared to specifics of each region's economic structure. We make use of input–output-based innovation flow networks, which are directed and weighted instead of binary. The value added of the proposed analysis is that we are able to trace a variety of different aspects related to the structure of innovative activities for each territory. It gets evident that mostly innovative activities in each territory are not strong in ‘niche’ branches but in fields of intense economic activity, signalising the high path-dependency of innovative activities in a specific geographical environment. PMID:29097849

Australia's regional innovation systems: inter-industry interaction in innovative activities in three Australian territories.

PubMed

Schütz, Marlies H

2017-07-03

Regional specifics reveal in differences in economic activity and structure, the institutional, socio-economic and cultural environment and not least in the capability of regions to create new knowledge and to generate innovations. Focusing on the regional level, this paper for three Australian territories (New South Wales, Victoria and Queensland) explores patterns of innovative activities in their private business sectors. Furthermore, these patterns are compared to specifics of each region's economic structure. We make use of input-output-based innovation flow networks, which are directed and weighted instead of binary. The value added of the proposed analysis is that we are able to trace a variety of different aspects related to the structure of innovative activities for each territory. It gets evident that mostly innovative activities in each territory are not strong in 'niche' branches but in fields of intense economic activity, signalising the high path-dependency of innovative activities in a specific geographical environment.

Mapping behavioural evolution onto brain evolution: the strategic roles of conserved organization in individuals and species.

PubMed

Finlay, Barbara L; Hinz, Flora; Darlington, Richard B

2011-07-27

The pattern of individual variation in brain component structure in pigs, minks and laboratory mice is very similar to variation across species in the same components, at a reduced scale. This conserved pattern of allometric scaling resembles robotic architectures designed to be robust to changes in computing power and task demands, and may reflect the mechanism by which both growing and evolving brains defend basic sensory, motor and homeostatic functions at multiple scales. Conserved scaling rules also have implications for species-specific sensory and social communication systems, motor competencies and cognitive abilities. The role of relative changes in neuron number in the central nervous system in producing species-specific behaviour is thus highly constrained, while changes in the sensory and motor periphery, and in motivational and attentional systems increase in probability as the principal loci producing important changes in functional neuroanatomy between species. By their nature, these loci require renewed attention to development and life history in the initial organization and production of species-specific behavioural abilities.

Vegetable-based dietary pattern and liver cancer risk: results from the Shanghai women's and men's health studies.

PubMed

Zhang, Wei; Xiang, Yong-Bing; Li, Hong-Lan; Yang, Gong; Cai, Hui; Ji, Bu-Tian; Gao, Yu-Tang; Zheng, Wei; Shu, Xiao-Ou

2013-10-01

Although dietary patterns, specific foods, and their constituents have been linked to cancer risk, the role of dietary patterns and specific food groups in liver cancer risk has not been investigated. In the Shanghai Women's Health Study (SWHS) and Shanghai Men's Health Study (SMHS), two cohort studies of 132 837 Chinese women and men, we evaluated the relationship between dietary patterns, food groups, and liver cancer risk. Through in-person interviews, dietary information intake over the preceding year was collected by using a validated food-frequency questionnaire. Cox regression model was used to estimate hazard ratios and 95% confidence intervals with adjustment for potential confounders. During an average follow-up of 10.9 (SWHS) or 5.5 (SMHS) years, 267 incident liver cancer cases were identified after the first 2 years of study enrolment. Three dietary patterns were derived by factor analysis. A vegetable-based dietary pattern was inversely associated with liver cancer; hazard ratios (95% confidence intervals) for the lowest to highest quartiles were: 1.00; 0.98 (0.71-1.35); 0.93 (0.67-1.29); and 0.58 (0.40-0.84); P(trend) = 0.01. The association was stronger among participants with a history of chronic liver disease. Further analyses showed high intakes of celery, mushrooms, allium vegetables, composite vegetables (including asparagus lettuce and garland chrysanthemum), legumes and legume products were associated with reduced liver cancer risk (all P(trend) < 0.05). Fruit- and meat-based dietary patterns were not associated with liver cancer risk. Our study suggests that a vegetable-based dietary pattern is associated with reduced liver cancer risk. © 2013 Japanese Cancer Association.

Differential expression of members of the annexin multigene family in Arabidopsis

NASA Technical Reports Server (NTRS)

Clark, G. B.; Sessions, A.; Eastburn, D. J.; Roux, S. J.

2001-01-01

Although in most plant species no more than two annexin genes have been reported to date, seven annexin homologs have been identified in Arabidopsis, Annexin Arabidopsis 1-7 (AnnAt1--AnnAt7). This establishes that annexins can be a diverse, multigene protein family in a single plant species. Here we compare and analyze these seven annexin gene sequences and present the in situ RNA localization patterns of two of these genes, AnnAt1 and AnnAt2, during different stages of Arabidopsis development. Sequence analysis of AnnAt1--AnnAt7 reveals that they contain the characteristic four structural repeats including the more highly conserved 17-amino acid endonexin fold region found in vertebrate annexins. Alignment comparisons show that there are differences within the repeat regions that may have functional importance. To assess the relative level of expression in various tissues, reverse transcription-PCR was carried out using gene-specific primers for each of the Arabidopsis annexin genes. In addition, northern blot analysis using gene-specific probes indicates differences in AnnAt1 and AnnAt2 expression levels in different tissues. AnnAt1 is expressed in all tissues examined and is most abundant in stems, whereas AnnAt2 is expressed mainly in root tissue and to a lesser extent in stems and flowers. In situ RNA localization demonstrates that these two annexin genes display developmentally regulated tissue-specific and cell-specific expression patterns. These patterns are both distinct and overlapping. The developmental expression patterns for both annexins provide further support for the hypothesis that annexins are involved in the Golgi-mediated secretion of polysaccharides.

Polymeric Mold For Providing A Microscale Part

DOEpatents

Boehme, Dale R.; Bankert, Michelle A.; Christenson, Todd R.

2005-01-11

The invention is a developer system for developing a PMMA photoresist having exposed patterns comprising features having both very small sizes, and very high aspect ratios. The developer system of the present invention comprises a developer tank, an intermediate rinse tank and a final rinse tank, each tank having a source of high frequency sonic agitation, temperature control, and continuous filtration. It has been found that by moving a patterned wafer, through a specific sequence of developer/rinse solutions, where an intermediate rinse solution completes development of those portions of the exposed resist left undeveloped after the development solution, by agitating the solutions with a source of high frequency sonic vibration, and by adjusting and closely controlling the temperatures and continuously filtering and recirculating these solutions, it is possible to maintain the kinetic dissolution of the exposed PMMA polymer as the rate limiting step.

Spatial Patterns in Water Temperature in Pacific Northwest Rivers: Diversity at Multiple Scales and Potential Influence of Climate Change

NASA Astrophysics Data System (ADS)

Torgersen, C. E.; Fullerton, A.; Lawler, J. J.; Ebersole, J. L.; Leibowitz, S. G.; Steel, E. A.; Beechie, T. J.; Faux, R.

2016-12-01

Understanding spatial patterns in water temperature will be essential for evaluating vulnerability of aquatic biota to future climate and for identifying and protecting diverse thermal habitats. We used high-resolution remotely sensed water temperature data for over 16,000 km of 2nd to 7th-order rivers throughout the Pacific Northwest and California to evaluate spatial patterns of summertime water temperature at multiple spatial scales. We found a diverse and geographically distributed suite of whole-river patterns. About half of rivers warmed asymptotically in a downstream direction, whereas the rest exhibited complex and unique spatial patterns. Patterns were associated with both broad-scale hydroclimatic variables as well as characteristics unique to each basin. Within-river thermal heterogeneity patterns were highly river-specific; across rivers, median size and spacing of cool patches <15 °C were around 250 m. Patches of this size are large enough for juvenile salmon rearing and for resting during migration, and the distance between patches is well within the movement capabilities of both juvenile and adult salmon. We found considerable thermal heterogeneity at fine spatial scales that may be important to fish that would be missed if data were analyzed at coarser scales. We estimated future thermal heterogeneity and concluded that climate change will cause warmer temperatures overall, but that thermal heterogeneity patterns may remain similar in the future for many rivers. We demonstrated considerable spatial complexity in both current and future water temperature, and resolved spatial patterns that could not have been perceived without spatially continuous data.

Use of Order Sets in Inpatient Computerized Provider Order Entry Systems: A Comparative Analysis of Usage Patterns at Seven Sites

PubMed Central

Wright, Adam; Feblowitz, Joshua C.; Pang, Justine E.; Carpenter, James D.; Krall, Michael A.; Middleton, Blackford; Sittig, Dean F.

2012-01-01

Background Many computerized provider order entry (CPOE) systems include the ability to create electronic order sets: collections of clinically-related orders grouped by purpose. Order sets promise to make CPOE systems more efficient, improve care quality and increase adherence to evidence-based guidelines. However, the development and implementation of order sets can be expensive and time-consuming and limited literature exists about their utilization. Methods Based on analysis of order set usage logs from a diverse purposive sample of seven sites with commercially- and internally-developed inpatient CPOE systems, we developed an original order set classification system. Order sets were categorized across seven non-mutually exclusive axes: admission/discharge/transfer (ADT), perioperative, condition-specific, task-specific, service-specific, convenience, and personal. In addition, 731 unique subtypes were identified within five axes: four in ADT (S=4), three in perioperative, 144 in condition-specific, 513 in task-specific, and 67 in service-specific. Results Order sets (n=1,914) were used a total of 676,142 times at the participating sites during a one-year period. ADT and perioperative order sets accounted for 27.6% and 24.2% of usage respectively. Peripartum/labor, chest pain/Acute Coronary Syndrome/Myocardial Infarction and diabetes order sets accounted for 51.6% of condition-specific usage. Insulin, angiography/angioplasty and arthroplasty order sets accounted for 19.4% of task-specific usage. Emergency/trauma, Obstetrics/Gynecology/Labor Delivery and anesthesia accounted for 32.4% of service-specific usage. Overall, the top 20% of order sets accounted for 90.1% of all usage. Additional salient patterns are identified and described. Conclusion We observed recurrent patterns in order set usage across multiple sites as well as meaningful variations between sites. Vendors and institutional developers should identify high-value order set types through concrete data analysis in order to optimize the resources devoted to development and implementation. PMID:22819199

Maintaining embryonic stem cell pluripotency with Wnt signaling.

PubMed

Sokol, Sergei Y

2011-10-01

Wnt signaling pathways control lineage specification in vertebrate embryos and regulate pluripotency in embryonic stem (ES) cells, but how the balance between progenitor self-renewal and differentiation is achieved during axis specification and tissue patterning remains highly controversial. The context- and stage-specific effects of the different Wnt pathways produce complex and sometimes opposite outcomes that help to generate embryonic cell diversity. Although the results of recent studies of the Wnt/β-catenin pathway in ES cells appear to be surprising and controversial, they converge on the same conserved mechanism that leads to the inactivation of TCF3-mediated repression.

Electrochemical sensing of bisphenol using a multilayer graphene nanobelt modified photolithography patterned platinum electrode

NASA Astrophysics Data System (ADS)

Karthick Kannan, Padmanathan; Hu, Chunxiao; Morgan, Hywel; Moshkalev, Stanislav A.; Sekhar Rout, Chandra

2016-09-01

An electrochemical sensor has been developed for the detection of Bisphenol-A (BPA) using photolithographically patterned platinum electrodes modified with multilayer graphene nanobelts (GNB). Compared to bare electrodes, the GNB modified electrode exhibited enhanced BPA oxidation current, due to the high effective surface area and high adsorption capacity of the GNB. The sensor showed a linear response over the concentration range from 0.5 μM-9 μM with a very low limit of detection = 37.33 nM. In addition, the sensor showed very good stability and reproducibility with good specificity, demonstrating that GNB is potentially a new material for the development of a practical BPA electrochemical sensor with application in both industrial and plastic industries.

Motor vehicle-bicycle crashes in Beijing: irregular maneuvers, crash patterns, and injury severity.

PubMed

Yan, Xinping; Ma, Ming; Huang, Helai; Abdel-Aty, Mohamed; Wu, Chaozhong

2011-09-01

This research presents a comprehensive analysis of motor vehicle-bicycle crashes using 4 years of reported crash data (2004-2007) in Beijing. The interrelationship of irregular maneuvers, crash patterns and bicyclist injury severity are investigated by controlling for a variety of risk factors related to bicyclist demographics, roadway geometric design, road environment, etc. Results show that different irregular maneuvers are correlated with a number of risk factors at different roadway locations such as the bicyclist age and gender, weather and traffic condition. Furthermore, angle collisions are the leading pattern of motor vehicle-bicycle crashes, and different irregular maneuvers may lead to some specific crash patterns such as head-on or rear-end crashes. Orthokinetic scrape is more likely to result in running over bicyclists, which may lead to more severe injury. Moreover, bicyclist injury severity level could be elevated by specific crash patterns and risk factors including head-on and angle collisions, occurrence of running over bicyclists, night without streetlight, roads without median/division, higher speed limit, heavy vehicle involvement and older bicyclists. This study suggests installation of median, division between roadway and bikeway, and improvement of illumination on road segments. Reduced speed limit is also recommended at roadway locations with high bicycle traffic volume. Furthermore, it may be necessary to develop safety campaigns aimed at male, teenage and older bicyclists. Copyright © 2011 Elsevier Ltd. All rights reserved.

Identifying and Prioritizing Greater Sage-Grouse Nesting and Brood-Rearing Habitat for Conservation in Human-Modified Landscapes

PubMed Central

Dzialak, Matthew R.; Olson, Chad V.; Harju, Seth M.; Webb, Stephen L.; Mudd, James P.; Winstead, Jeffrey B.; Hayden-Wing, L.D.

2011-01-01

Background Balancing animal conservation and human use of the landscape is an ongoing scientific and practical challenge throughout the world. We investigated reproductive success in female greater sage-grouse (Centrocercus urophasianus) relative to seasonal patterns of resource selection, with the larger goal of developing a spatially-explicit framework for managing human activity and sage-grouse conservation at the landscape level. Methodology/Principal Findings We integrated field-observation, Global Positioning Systems telemetry, and statistical modeling to quantify the spatial pattern of occurrence and risk during nesting and brood-rearing. We linked occurrence and risk models to provide spatially-explicit indices of habitat-performance relationships. As part of the analysis, we offer novel biological information on resource selection during egg-laying, incubation, and night. The spatial pattern of occurrence during all reproductive phases was driven largely by selection or avoidance of terrain features and vegetation, with little variation explained by anthropogenic features. Specifically, sage-grouse consistently avoided rough terrain, selected for moderate shrub cover at the patch level (within 90 m2), and selected for mesic habitat in mid and late brood-rearing phases. In contrast, risk of nest and brood failure was structured by proximity to anthropogenic features including natural gas wells and human-created mesic areas, as well as vegetation features such as shrub cover. Conclusions/Significance Risk in this and perhaps other human-modified landscapes is a top-down (i.e., human-mediated) process that would most effectively be minimized by developing a better understanding of specific mechanisms (e.g., predator subsidization) driving observed patterns, and using habitat-performance indices such as those developed herein for spatially-explicit guidance of conservation intervention. Working under the hypothesis that industrial activity structures risk by enhancing predator abundance or effectiveness, we offer specific recommendations for maintaining high-performance habitat and reducing low-performance habitat, particularly relative to the nesting phase, by managing key high-risk anthropogenic features such as industrial infrastructure and water developments. PMID:22022587

Associations of alcoholic beverage preference with cardiometabolic and lifestyle factors: the NQplus study

PubMed Central

Sluik, Diewertje; Brouwer-Brolsma, Elske M; de Vries, Jeanne H M; Geelen, Anouk; Feskens, Edith J M

2016-01-01

Objectives The preference for a specific alcoholic beverage may be related to an individual's overall lifestyle and health. The objective was to investigate associations between alcoholic beverage preference and several cardiometabolic and lifestyle factors, including adiposity, cholesterol, glycated haemoglobin (HbA1c), liver enzymes and dietary patterns. Design Cross-sectional study. Setting The Dutch Longitudinal Nutrition Questionnaires plus (NQplus) Study. Participants 1653 men and women aged 20–77 years. Methods Diet, including alcohol, was assessed by Food Frequency Questionnaire. Based on the average number of reported glasses of alcoholic beverage, a person was classified as having a preference for beer, wine, spirit/no specific preference, or as a non-consumer. Mixed linear models were used to calculate crude and adjusted means of cardiometabolic and lifestyle factors across alcoholic beverage preference categories. Primary outcome measures Anthropometric measures, blood pressure, lipids, HbA1c, albumin, creatinine, uric acid, liver enzymes and dietary patterns. Results In the study population, 43% had a wine preference, 13% a beer preference, 29% had a spirit or no specific preference, and 15% did not consume alcohol. Men who preferred wine had lowest measures of adiposity; the preference for alcoholic beverages was not associated with adiposity measures in women. Wine consumers had higher high density lipoprotein-cholesterol, lower HbA1c and were more likely to follow the ‘Salad’ pattern. Beer consumers had highest levels of triglycerides and liver enzymes, and had higher scores for the ‘Meat’ and ‘Bread’ pattern. Conclusions Few differences in dietary patterns across alcoholic beverage preference categories were observed. Those differences in cardiometabolic parameters that were observed according to alcoholic beverage preference, suggested that wine consumers have a better health status than beer consumers. PMID:27311903

Adherence to the Western, Prudent and Mediterranean dietary patterns and breast cancer risk: MCC-Spain study.

PubMed

Castelló, Adela; Boldo, Elena; Pérez-Gómez, Beatriz; Lope, Virginia; Altzibar, Jone M; Martín, Vicente; Castaño-Vinyals, Gemma; Guevara, Marcela; Dierssen-Sotos, Trinidad; Tardón, Adonina; Moreno, Víctor; Puig-Vives, Montserrat; Llorens-Ivorra, Cristóbal; Alguacil, Juan; Gómez-Acebo, Inés; Castilla, Jesús; Gràcia-Lavedán, Esther; Dávila-Batista, Verónica; Kogevinas, Manolis; Aragonés, Nuria; Amiano, Pilar; Pollán, Marina

2017-09-01

To externally validate the previously identified effect on breast cancer risk of the Western, Prudent and Mediterranean dietary patterns. MCC-Spain is a multicase-control study that collected epidemiological information on 1181 incident cases of female breast cancer and 1682 healthy controls from 10 Spanish provinces. Three dietary patterns derived in another Spanish case-control study were analysed in the MCC-Spain study. These patterns were termed Western (high intakes of fatty and sugary products and red and processed meat), Prudent (high intakes of low-fat dairy products, vegetables, fruits, whole grains and juices) and Mediterranean (high intake of fish, vegetables, legumes, boiled potatoes, fruits, olives, and vegetable oil, and a low intake of juices). Their association with breast cancer was assessed using logistic regression models with random province-specific intercepts considering an interaction with menopausal status. Risk according to tumour subtypes - based on oestrogen (ER), progesterone (PR) and human epidermal growth factor 2 (HER2) receptors (ER+/PR+ & HER2-; HER2+; ER-/PR- & HER2-) - was evaluated with multinomial regression models. Breast cancer and histological subtype. Our results confirm most of the associations found in the previous case-control study. A high adherence to the Western dietary pattern seems to increase breast cancer risk in both premenopausal women (OR 4 th vs.1 st quartile (95% CI):1.68 (1.02;2.79); OR 1SD-increase (95% CI):1.19 (1.02;1.40)) and postmenopausal women (OR 4 th vs.1 st quartile (95% CI):1.48(1.07;2.05); OR 1SD-increase (95% CI): 1.14 (1.01;1.29)). While high adherence to the Prudent pattern did not show any effect on breast cancer, the Mediterranean dietary pattern seemed to be protective, but only among postmenopausal women (OR 4 th vs.1 st quartile (95% CI): 0.72 (95% CI 0.53;0.98); p-int=0.075). There were no significant differences by tumour subtype. Dietary recommendations based on a departure from the Western dietary pattern in favour of the Mediterranean diet could reduce breast cancer risk in the general population. Copyright © 2017 Elsevier B.V. All rights reserved.

Metal loading levels influence on REE distribution on humic acid: Experimental and Modelling approach

NASA Astrophysics Data System (ADS)

Marsac, R.; Davranche, M.; Gruau, G.; Dia, A.

2009-04-01

In natural organic-rich waters, rare earth elements (REE) speciation is mainly controlled by organic colloids such as humic acid (HA). Different series of REE-HA complexation experiments performed at several metal loading (REE/C) displayed two pattern shapes (i) at high metal loading, a middle-REE (MREE) downward concavity, and (ii) at low metal loading, a regular increase from La to Lu (e.g. Sonke and Salters, 2006; Pourret et al., 2007). Both REE patterns might be related to REE binding with different surface sites on HA. To understand REE-HA binding, REE-HA complexation experiments at various metals loading were carried out using ultrafiltration combined with ICP-MS measurements, for the 14 REE simultaneously. The patterns of the apparent coefficients of REE partition between HA and the inorganic solution (log Kd) evolved regularly according to the metal loading. The REE patterns presented a MREE downward concavity at low loading and a regular increase from La to Lu at high loading. The dataset was modelled with Model VI by adjusting two specific parameters, log KMA, the apparent complexation constant of HA low affinity sites and DLK2, the parameter increasing high affinity sites binding strength. Experiments and modelling provided evidence that HA high affinity sites controlled the REE binding with HA at low metal loading. The REE-HA complex could be as multidentate complexes with carboxylic or phenolic sites or potentially with sites constituted of N, P or S as donor atoms. Moreover, these high affinity sites could be different for light and heavy REE, because heavy REE have higher affinity for these sites, in low density, and could saturate them. These new Model VI parameter sets allowed the prediction of the REE-HA pattern shape evolution on a large range of pH and metal loading. According to the metal loading, the evolution of the calculated REE patterns was similar to the various REE pattern observed in natural acidic organic-rich waters (pH<7 and DOC>10 mg L-1). As a consequence, the metal loading could be the key parameter controlling the REE pattern in organic-rich waters.

Associations of specific phobia and its subtypes with physical diseases: an adult community study.

PubMed

Witthauer, Cornelia; Ajdacic-Gross, Vladeta; Meyer, Andrea Hans; Vollenweider, Peter; Waeber, Gerard; Preisig, Martin; Lieb, Roselind

2016-05-21

Specific phobia is the most prevalent anxiety disorder in the community and is associated with substantial impairment. Comorbidity with physical diseases is assumed and has important implications for etiology, treatment, or prevention of the comorbid conditions. However, due to methodological issues data are limited and subtypes of specific phobia have not been investigated yet. We examined the association of specific phobia and its subtypes with physical diseases in a representative community sample with physician-diagnosed physical diseases and diagnostic criteria of specific phobia. Data of the German Mental Health Survey from 4181 subjects aged 18-65 years were used. Specific phobia was diagnosed using M-CIDI/DIA-X interview; physical diseases were assessed through a self-report questionnaire and a medical interview. Logistic regression analyses adjusted for sex were calculated. Specific phobia was associated with cardiac diseases, gastrointestinal diseases, respiratory diseases, arthritic conditions, migraine, and thyroid diseases (odds ratios between 1.49 and 2.53). Among the subtypes, different patterns of associations with physical diseases were established. The findings were partially replicated in the Swiss PsyCoLaus Study. Our analyses show that subjects with specific phobia have an increased probability for specific physical diseases. From these analyses etiological mechanisms of specific phobia and physical disease can be deduced. As subtypes differed in their patterns of associations with physical diseases, different etiological mechanisms may play a role. The findings are highly relevant for public health in terms of prevention and therapy of the comorbid conditions.

Chemometrics Methods for Specificity, Authenticity and Traceability Analysis of Olive Oils: Principles, Classifications and Applications

PubMed Central

Messai, Habib; Farman, Muhammad; Sarraj-Laabidi, Abir; Hammami-Semmar, Asma; Semmar, Nabil

2016-01-01

Background. Olive oils (OOs) show high chemical variability due to several factors of genetic, environmental and anthropic types. Genetic and environmental factors are responsible for natural compositions and polymorphic diversification resulting in different varietal patterns and phenotypes. Anthropic factors, however, are at the origin of different blends’ preparation leading to normative, labelled or adulterated commercial products. Control of complex OO samples requires their (i) characterization by specific markers; (ii) authentication by fingerprint patterns; and (iii) monitoring by traceability analysis. Methods. These quality control and management aims require the use of several multivariate statistical tools: specificity highlighting requires ordination methods; authentication checking calls for classification and pattern recognition methods; traceability analysis implies the use of network-based approaches able to separate or extract mixed information and memorized signals from complex matrices. Results. This chapter presents a review of different chemometrics methods applied for the control of OO variability from metabolic and physical-chemical measured characteristics. The different chemometrics methods are illustrated by different study cases on monovarietal and blended OO originated from different countries. Conclusion. Chemometrics tools offer multiple ways for quantitative evaluations and qualitative control of complex chemical variability of OO in relation to several intrinsic and extrinsic factors. PMID:28231172

EUV mask pilot line at Intel Corporation

NASA Astrophysics Data System (ADS)

Stivers, Alan R.; Yan, Pei-Yang; Zhang, Guojing; Liang, Ted; Shu, Emily Y.; Tejnil, Edita; Lieberman, Barry; Nagpal, Rajesh; Hsia, Kangmin; Penn, Michael; Lo, Fu-Chang

2004-12-01

The introduction of extreme ultraviolet (EUV) lithography into high volume manufacturing requires the development of a new mask technology. In support of this, Intel Corporation has established a pilot line devoted to encountering and eliminating barriers to manufacturability of EUV masks. It concentrates on EUV-specific process modules and makes use of the captive standard photomask fabrication capability of Intel Corporation. The goal of the pilot line is to accelerate EUV mask development to intersect the 32nm technology node. This requires EUV mask technology to be comparable to standard photomask technology by the beginning of the silicon wafer process development phase for that technology node. The pilot line embodies Intel's strategy to lead EUV mask development in the areas of the mask patterning process, mask fabrication tools, the starting material (blanks) and the understanding of process interdependencies. The patterning process includes all steps from blank defect inspection through final pattern inspection and repair. We have specified and ordered the EUV-specific tools and most will be installed in 2004. We have worked with International Sematech and others to provide for the next generation of EUV-specific mask tools. Our process of record is run repeatedly to ensure its robustness. This primes the supply chain and collects information needed for blank improvement.

On Using the Weimer Statistical Model for Real-Time Ionospheric Specifications and Forecasts

NASA Astrophysics Data System (ADS)

Bekerat, H. A.; Schunk, R. W.; Scherliess, L.

2002-12-01

The Weimer statistical model (Weimer, 2001) for the high-latitude convection pattern was tested with regard to its ability to produce real-time convection patterns. This work is being conducted under the polar section of GAIM (Global Assimilation of Ionospheric Measurements). The method adopted involves the comparison of the cross-track ion drift velocities measured by DMSP satellites with those calculated from the Weimer model. Starting with a Weimer pattern obtained using real-time IMF and solar wind data at the time of a DMSP satellite pass in the high-latitude ionosphere, the cross-track ion drift velocities along the DMSP track were calculated from the Weimer convection model and compared to those measured by the DMSP satellite. Then, in order to improve the agreement between the measurement and the model, two of the input parameters to the model, the IMF clock-angle and the solar wind speed, were varied to get the pattern that gives the best agreement with the DMSP satellite measurements. Four months of data (March, July, September, and December 1998) were used to test the Weimer model. The result shows that the agreement between the measurement and the Weimer model is improved by using this procedure. The Weimer model is good in a statistical sense, it was able to produce the large-scale structure in most cases. However, it is not good enough to be used for real-time ionospheric specifications and forecasts because it failed to produce a lot of the mesoscale structure measured along most DMSP satellite passes. Reference Weimer, D. R., J. Geophys. Res., 106, 407,2001

Design of a backlighting structure for very large-area luminaries

NASA Astrophysics Data System (ADS)

Carraro, L.; Mäyrä, A.; Simonetta, M.; Benetti, G.; Tramonte, A.; Benedetti, M.; Randone, E. M.; Ylisaukko-Oja, A.; Keränen, K.; Facchinetti, T.; Giuliani, G.

2017-02-01

A novel approach for RGB semiconductor LED-based backlighting system is developed to satisfy the requirements of the Project LUMENTILE funded by the European Commission, whose scope is to develop a luminous electronic tile that is foreseen to be manufactured in millions of square meters each year. This unconventionally large-area surface of uniform, high-brightness illumination requires a specific optical design to keep a low production cost, while maintaining high optical extraction efficiency and a reduced thickness of the structure, as imposed by architectural design constraints. The proposed solution is based on a light-guiding layer to be illuminated by LEDs in edge configuration, or in a planar arrangement. The light guiding slab is finished with a reflective top interface and a diffusive or reflective bottom interface/layer. Patterning is used for both the top interface (punctual removal of reflection and generation of a light scattering centers) and for the bottom layer (using dark/bright printed pattern). Computer-based optimization algorithms based on ray-tracing are used to find optimal solutions in terms of uniformity of illumination of the top surface and overall light extraction efficiency. Through a closed-loop optimization process, that assesses the illumination uniformity of the top surface, the algorithm generates the desired optimized top and bottom patterns, depending on the number of LED sources used, their geometry, and the thickness of the guiding layer. Specific low-cost technologies to realize the patterning are discussed, with the goal of keeping the production cost of these very large-area luminaries below the value of 100$/sqm.

Knee Joint Loading during Gait in Healthy Controls and Individuals with Knee Osteoarthritis

PubMed Central

Kumar, Deepak; Manal, Kurt T.; Rudolph, Katherine S.

2013-01-01

Objective People with knee osteoarthritis (OA) are thought to walk with high loads at the knee which are yet to be quantfied using modeling techniques that account for subject specific EMG patterns, kinematics and kinetics. The objective was to estimate medial and lateral loading for people with knee OA and controls using an approach that is sensitive to subject specific muscle activation patterns. Methods 16 OA and 12 control (C) subjects walked while kinematic, kinetic and EMG data were collected. Muscle forces were calculated using an EMG-Driven model and loading was calculated by balancing the external moments with internal muscle and contact forces Results OA subjects walked slower and had greater laxity, static and dynamic varus alignment, less flexion and greater knee adduction moment (KAM). Loading (normalized to body weight) was no different between the groups but OA subjects had greater absolute medial load than controls and maintained a greater %total load on the medial compartment. These patterns were associated with body mass, sagittal and frontal plane moments, static alignment and close to signficance for dynamic alignment. Lateral compartment unloading during mid-late stance was observed in 50% of OA subjects. Conclusions Loading for control subjects was similar to data from instrumented prostheses. Knee OA subjects had high medial contact loads in early stance and half of the OA cohort demonstared lateral compartment lift-off. Results suggest that interventions aimed at reducing body weight and dynamic malalignment might be effective in reducing medial compartment loading and establishing normal medio-lateral load sharing patterns. PMID:23182814

Wavelength specific excitation of gold nanoparticle thin-films

NASA Astrophysics Data System (ADS)

Lucas, Thomas M.; James, Kurtis T.; Beharic, Jasmin; Moiseeva, Evgeniya V.; Keynton, Robert S.; O'Toole, Martin G.; Harnett, Cindy K.

2014-01-01

Advances in microelectromechanical systems (MEMS) continue to empower researchers with the ability to sense and actuate at the micro scale. Thermally driven MEMS components are often used for their rapid response and ability to apply relatively high forces. However, thermally driven MEMS often have high power consumption and require physical wiring to the device. This work demonstrates a basis for designing light-powered MEMS with a wavelength specific response. This is accomplished by patterning surface regions with a thin film containing gold nanoparticles that are tuned to have an absorption peak at a particular wavelength. The heating behavior of these patterned surfaces is selected by the wavelength of laser directed at the sample. This method also eliminates the need for wires to power a device. The results demonstrate that gold nanoparticle films are effective wavelength-selective absorbers. This "hybrid" of infrared absorbent gold nanoparticles and MEMS fabrication technology has potential applications in light-actuated switches and other mechanical structures that must bend at specific regions. Deposition methods and surface chemistry will be integrated with three-dimensional MEMS structures in the next phase of this work. The long-term goal of this project is a system of light-powered microactuators for exploring cellular responses to mechanical stimuli, increasing our fundamental understanding of tissue response to everyday mechanical stresses at the molecular level.

High adherence to the Western, Prudent, and Mediterranean dietary patterns and risk of gastric adenocarcinoma: MCC-Spain study.

PubMed

Castelló, Adela; Fernández de Larrea, Nerea; Martín, Vicente; Dávila-Batista, Verónica; Boldo, Elena; Guevara, Marcela; Moreno, Víctor; Castaño-Vinyals, Gemma; Gómez-Acebo, Inés; Fernández-Tardón, Guillermo; Peiró, Rosana; Olmedo-Requena, Rocío; Capelo, Rocio; Navarro, Carmen; Pacho-Valbuena, Silvino; Pérez-Gómez, Beatriz; Kogevinas, Manolis; Pollán, Marina; Aragonés, Nuria

2018-05-01

The influence of dietary habits on the development of gastric adenocarcinoma is not clear. The objective of the present study was to explore the association of three previously identified dietary patterns with gastric adenocarcinoma by sex, age, cancer site, and morphology. MCC-Spain is a multicase-control study that included 295 incident cases of gastric adenocarcinoma and 3040 controls. The association of the Western, Prudent, and Mediterranean dietary patterns-derived in another Spanish case-control study-with gastric adenocarcinoma was assessed using multivariable logistic regression models with random province-specific intercepts and considering a possible interaction with sex and age. Risk according to tumor site (cardia, non-cardia) and morphology (intestinal/diffuse) was evaluated using multinomial regression models. A high adherence to the Western pattern increased gastric adenocarcinoma risk [odds ratio fourth_vs._first_quartile (95% confidence interval), 2.09 (1.31; 3.33)] even at low levels [odds ratio second_vs._first_quartile (95% confidence interval), 1.63 (1.05; 2.52)]. High adherence to the Mediterranean dietary pattern could prevent gastric adenocarcinoma [odds ratio fourth_vs._first_quartile (95% confidence interval), 0.53 (0.34; 0.82)]. Although no significant heterogeneity of effects was observed, the harmful effect of the Western pattern was stronger among older participants and for non-cardia adenocarcinomas, whereas the protective effect of the Mediterranean pattern was only observed among younger participants and for non-cardia tumors. Decreasing the consumption of fatty and sugary products and of red and processed meat in favor of an increase in the intake of fruits, vegetables, legumes, olive oil, nuts, and fish might prevent gastric adenocarcinoma.

Dynamic Segmentation Of Behavior Patterns Based On Quantity Value Movement Using Fuzzy Subtractive Clustering Method

NASA Astrophysics Data System (ADS)

Sangadji, Iriansyah; Arvio, Yozika; Indrianto

2018-03-01

to understand by analyzing the pattern of changes in value movements that can dynamically vary over a given period with relative accuracy, an equipment is required based on the utilization of technical working principles or specific analytical method. This will affect the level of validity of the output that will occur from this system. Subtractive clustering is based on the density (potential) size of data points in a space (variable). The basic concept of subtractive clustering is to determine the regions in a variable that has high potential for the surrounding points. In this paper result is segmentation of behavior pattern based on quantity value movement. It shows the number of clusters is formed and that has many members.

Single-shot thermal ghost imaging using wavelength-division multiplexing

NASA Astrophysics Data System (ADS)

Deng, Chao; Suo, Jinli; Wang, Yuwang; Zhang, Zhili; Dai, Qionghai

2018-01-01

Ghost imaging (GI) is an emerging technique that reconstructs the target scene from its correlated measurements with a sequence of patterns. Restricted by the multi-shot principle, GI usually requires long acquisition time and is limited in observation of dynamic scenes. To handle this problem, this paper proposes a single-shot thermal ghost imaging scheme via a wavelength-division multiplexing technique. Specifically, we generate thousands of correlated patterns simultaneously by modulating a broadband light source with a wavelength dependent diffuser. These patterns carry the scene's spatial information and then the correlated photons are coupled into a spectrometer for the final reconstruction. This technique increases the speed of ghost imaging and promotes the applications in dynamic ghost imaging with high scalability and compatibility.

ROKU: a novel method for identification of tissue-specific genes

PubMed Central

Kadota, Koji; Ye, Jiazhen; Nakai, Yuji; Terada, Tohru; Shimizu, Kentaro

2006-01-01

Background One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes. Results We describe a method, ROKU, which selects tissue-specific patterns from gene expression data for many tissues and thousands of genes. ROKU ranks genes according to their overall tissue specificity using Shannon entropy and detects tissues specific to each gene if any exist using an outlier detection method. We evaluated the capacity for the detection of various specific expression patterns using synthetic and real data. We observed that ROKU was superior to a conventional entropy-based method in its ability to rank genes according to overall tissue specificity and to detect genes whose expression pattern are specific only to objective tissues. Conclusion ROKU is useful for the detection of various tissue-specific expression patterns. The framework is also directly applicable to the selection of diagnostic markers for molecular classification of multiple classes. PMID:16764735

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing1[C][W][OA

PubMed Central

Loraine, Ann E.; McCormick, Sheila; Estrada, April; Patel, Ketan; Qin, Peng

2013-01-01

Pollen grains of Arabidopsis (Arabidopsis thaliana) contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve our understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein-coding genes expressed in pollen, including 289 assayed only by nonspecific probe sets. Additional exons and previously unannotated 5′ and 3′ untranslated regions for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 were confirmed by polymerase chain reaction. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of ongoing annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser. PMID:23590974

Risk stratification in cervical cancer screening by complete screening history: Applying bioinformatics to a general screening population.

PubMed

Baltzer, Nicholas; Sundström, Karin; Nygård, Jan F; Dillner, Joakim; Komorowski, Jan

2017-07-01

Women screened for cervical cancer in Sweden are currently treated under a one-size-fits-all programme, which has been successful in reducing the incidence of cervical cancer but does not use all of the participants' available medical information. This study aimed to use women's complete cervical screening histories to identify diagnostic patterns that may indicate an increased risk of developing cervical cancer. A nationwide case-control study was performed where cervical cancer screening data from 125,476 women with a maximum follow-up of 10 years were evaluated for patterns of SNOMED diagnoses. The cancer development risk was estimated for a number of different screening history patterns and expressed as Odds Ratios (OR), with a history of 4 benign cervical tests as reference, using logistic regression. The overall performance of the model was moderate (64% accuracy, 71% area under curve) with 61-62% of the study population showing no specific patterns associated with risk. However, predictions for high-risk groups as defined by screening history patterns were highly discriminatory with ORs ranging from 8 to 36. The model for computing risk performed consistently across different screening history lengths, and several patterns predicted cancer outcomes. The results show the presence of risk-increasing and risk-decreasing factors in the screening history. Thus it is feasible to identify subgroups based on their complete screening histories. Several high-risk subgroups identified might benefit from an increased screening density. Some low-risk subgroups identified could likely have a moderately reduced screening density without additional risk. © 2017 UICC.

New entrants' practice patterns in Medicare home health care after the prospective payment system revision in 2008.

PubMed

Kim, Hyunjee; Jung, Jeah Kyoungrae

2015-09-01

Medicare home health care spending increased under the prospective payment system (PPS) that was introduced specifically to control the rising spending. To explain this unexpected spending rise, we focused on new home health agencies that entered the market under the PPS. The high profit margins under the PPS attracted many new agencies to the market partially due to home health care's unique feature of low entry costs. We examined whether new entrants were more likely to adopt the practice patterns leading to higher profit margins than incumbent agencies that had been operating in the market before the PPS. Using 2008 to 2010 Medicare Home Health Claims and Provider of Services File, we estimated regressions of agencies' practice patterns controlling for agency and patient characteristics. We found that new entrants were more likely than incumbents to adopt practice patterns leading to high profit margins. They were more likely to target the 14th and 20th therapy visit where marginal revenue is relatively greater than that of other number of visits. Under the payment system that compensates extra therapy visits but not for other types of visits, entrants were also more likely to provide therapy visits, but less likely to provide medical social service visits. Given the high entry rates of agencies under the PPS, distinct practice patterns among entrants explain the drastic home health spending increase under the PPS. Heterogeneity in agencies' practice patterns also suggests an opportunity to improve efficiency in the Medicare home health care market. Copyright © 2015 Elsevier Inc. All rights reserved.

High power laser energy distribution patterns, apparatus and methods for creating wells

DOEpatents

Faircloth, Brian O.; Zediker, Mark S.; Rinzler, Charles C.; Koblick, Yeshaya; Moxley, Joel F.

2016-03-15

There is provided a system, apparatus and methods for providing a laser beam to borehole surface in a predetermined and energy deposition profile. The predetermined energy deposition profiles may be uniform or tailored to specific downhole applications. Optic assemblies for obtaining these predetermined energy deposition profiles are further provided.

The Relationship between Quality of Attachment and Behavior Problems in Preschool in a High-Risk Sample.

ERIC Educational Resources Information Center

Erickson, Martha Farrell; And Others

1985-01-01

Tests hypothesis that young children who were anxiously attached would be more likely than securely attached children to have behavior problems in preschool. Examines particular patterns of anxious attachment in relation to specific problem behaviors. Studies child, parental, interactional, and environmental factors that account for behavior…

Office Disciplinary Referral Patterns of American Indian Students from Elementary School through High School

ERIC Educational Resources Information Center

Whitford, Denise K.; Levine-Donnerstein, Deborah

2014-01-01

Office disciplinary referrals (ODR) and classroom exclusions among students from minority backgrounds have been a persistent concern for decades. The purpose of this dissertation was to assess disciplinary characteristics of American Indian students in special education. More specifically, the purpose was to determine (a) the rate at which…

Arithmetic Abilities in Children with Developmental Dyslexia: Performance on French ZAREKI-R Test

ERIC Educational Resources Information Center

De Clercq-Quaegebeur, Maryse; Casalis, Séverine; Vilette, Bruno; Lemaitre, Marie-Pierre; Vallée, Louis

2018-01-01

A high comorbidity between reading and arithmetic disabilities has already been reported. The present study aims at identifying more precisely patterns of arithmetic performance in children with developmental dyslexia, defined with severe and specific criteria. By means of a standardized test of achievement in mathematics ("Calculation and…

Use of artificial landscapes to isolate controls on burn probability

Treesearch

Marc-Andre Parisien; Carol Miller; Alan A. Ager; Mark A. Finney

2010-01-01

Techniques for modeling burn probability (BP) combine the stochastic components of fire regimes (ignitions and weather) with sophisticated fire growth algorithms to produce high-resolution spatial estimates of the relative likelihood of burning. Despite the numerous investigations of fire patterns from either observed or simulated sources, the specific influence of...

"Having Our Say": High Achieving African American Male College Graduates Speak about Parental Involvement and Parenting Style

ERIC Educational Resources Information Center

Odom, Lynn Cheryl Lanier

2013-01-01

This study examined the patterns of parental involvement and parenting styles of a particular sample of academically successful African American males who attended and graduated from historically Black colleges or universities. More specifically, investigated was the presence of any relationships between parental involvement, parenting styles,…

Mortality and survival patterns of childhood lymphomas: geographic and age-specific patterns in Southern-Eastern European and SEER/US registration data.

PubMed

Karalexi, Maria A; Georgakis, Marios K; Dessypris, Nick; Ryzhov, Anton; Zborovskaya, Anna; Dimitrova, Nadya; Zivkovic, Snezana; Eser, Sultan; Antunes, Luis; Sekerija, Mario; Zagar, Tina; Bastos, Joana; Demetriou, Anna; Agius, Domenic; Florea, Margareta; Coza, Daniela; Bouka, Evdoxia; Dana, Helen; Hatzipantelis, Emmanuel; Kourti, Maria; Moschovi, Maria; Polychronopoulou, Sophia; Stiakaki, Eftichia; Pourtsidis, Apostolos; Petridou, Eleni Th

2017-12-01

Childhood (0-14 years) lymphomas, nowadays, present a highly curable malignancy compared with other types of cancer. We used readily available cancer registration data to assess mortality and survival disparities among children residing in Southern-Eastern European (SEE) countries and those in the United States. Average age-standardized mortality rates and time trends of Hodgkin (HL) and non-Hodgkin (NHL; including Burkitt [BL]) lymphomas in 14 SEE cancer registries (1990-2014) and the Surveillance, Epidemiology, and End Results Program (SEER, United States; 1990-2012) were calculated. Survival patterns in a total of 8918 cases distinguishing also BL were assessed through Kaplan-Meier curves and multivariate Cox regression models. Variable, rather decreasing, mortality trends were noted among SEE. Rates were overall higher than that in SEER (1.02/10 6 ), which presented a sizeable (-4.8%, P = .0001) annual change. Additionally, remarkable survival improvements were manifested in SEER (10 years: 96%, 86%, and 90% for HL, NHL, and BL, respectively), whereas diverse, still lower, rates were noted in SEE. Non-HL was associated with a poorer outcome and an amphi-directional age-specific pattern; specifically, prognosis was inferior in children younger than 5 years than in those who are 10 to 14 years old from SEE (hazard ratio 1.58, 95% confidence interval 1.28-1.96) and superior in children who are 5 to 9 years old from SEER/United States (hazard ratio 0.63, 95% confidence interval 0.46-0.88) than in those who are 10 to 14 years old. In conclusion, higher SEE lymphoma mortality rates than those in SEER, but overall decreasing trends, were found. Despite significant survival gains among developed countries, there are still substantial geographic, disease subtype-specific, and age-specific outcome disparities pointing to persisting gaps in the implementation of new treatment modalities and indicating further research needs. Copyright © 2016 John Wiley & Sons, Ltd.

IsoMark - a comprehensive assessment of the potential of isotopes in hard parts of freshwater fish to determine origin and migratory patterns using LA-(MC)-ICP-MS

NASA Astrophysics Data System (ADS)

Zitek, Andreas; Irrgeher, Johanna; Sturm, Monika; Brunner, Marion; Dillinger, Benno; Prohaska, Thomas

2010-05-01

The ‘IsoMark' project focuses for the first time on the comprehensive investigation of microchemical information (elemental fingerprint of Ca, Sr, Na, Ba, Mg; isotopic fingerprint of Sr, Ca, and additionally of C and O) in different hard parts of several typical European freshwater fish species like brown trout (Salmo trutta f.f., L.), European grayling (Thymallus thymallus, L.) or nase (Chondrostoma nasus, L.) and the barbel (Barbus barbus, L.). Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is used as major technique for the direct in situ analysis of trace elements and isotopes, whereby the employment of a multiple collector - inductively coupled plasma - mass spectrometer (MC-ICP-MS) enables high precise isotope ratio analysis of such sample matrices due to its simultaneous detection capabilities. Microchemical patterns in hard parts of farmed and wild fish are analysed resulting in natural site specific elemental and isotopic signatures. Within a pilot study the potential to discriminate between wild and hatchery trout by chronological microchemical patterns of different otolith regions in relation to site specific water chemistry was documented. 100% accuracy of classification of fish to life stage specific habitats and therefore to their origin was achieved by the elemental ratios 88Sr/43Ca, 23Na/43Ca and the isotope ratio of 87Sr/86Sr. Clear differences in otolith chemistry were found, when fish experienced different geological units or specific environmental situations (e.g. groundwater) in hatcheries during a certain period of their life. These results proved the concept that natural microchemical patterns in hard parts linked to specific life stages of fish represent a valuable tool for a wide variety of ecological questions, e.g. discriminating wild and hatchery fish without the necessity of inducing any other artificial mark, or studying natural migration phenomena on small spatial scales in freshwater systems within geologically diverse river catchments.

The evolution within us

PubMed Central

Cobey, Sarah; Wilson, Patrick; Matsen, Frederick A.

2015-01-01

The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics. PMID:26194749

Posterior Wnts Have Distinct Roles in Specification and Patterning of the Planarian Posterior Region

PubMed Central

Sureda-Gómez, Miquel; Pascual-Carreras, Eudald; Adell, Teresa

2015-01-01

The wnt signaling pathway is an intercellular communication mechanism essential in cell-fate specification, tissue patterning and regional-identity specification. A βcatenin-dependent signal specifies the AP (Anteroposterior) axis of planarians, both during regeneration of new tissues and during normal homeostasis. Accordingly, four wnts (posterior wnts) are expressed in a nested manner in central and posterior regions of planarians. We have analyzed the specific role of each posterior wnt and the possible cooperation between them in specifying and patterning planarian central and posterior regions. We show that each posterior wnt exerts a distinct role during re-specification and maintenance of the central and posterior planarian regions, and that the integration of the different wnt signals (βcatenin dependent and independent) underlies the patterning of the AP axis from the central region to the tip of the tail. Based on these findings and data from the literature, we propose a model for patterning the planarian AP axis. PMID:26556349

Posterior Wnts Have Distinct Roles in Specification and Patterning of the Planarian Posterior Region.

PubMed

Sureda-Gómez, Miquel; Pascual-Carreras, Eudald; Adell, Teresa

2015-11-05

The wnt signaling pathway is an intercellular communication mechanism essential in cell-fate specification, tissue patterning and regional-identity specification. A βcatenin-dependent signal specifies the AP (Anteroposterior) axis of planarians, both during regeneration of new tissues and during normal homeostasis. Accordingly, four wnts (posterior wnts) are expressed in a nested manner in central and posterior regions of planarians. We have analyzed the specific role of each posterior wnt and the possible cooperation between them in specifying and patterning planarian central and posterior regions. We show that each posterior wnt exerts a distinct role during re-specification and maintenance of the central and posterior planarian regions, and that the integration of the different wnt signals (βcatenin dependent and independent) underlies the patterning of the AP axis from the central region to the tip of the tail. Based on these findings and data from the literature, we propose a model for patterning the planarian AP axis.

[Patterns of dysfunctional parenting styles and psychological disturbances in offspring].

PubMed

Kumnig, Martin; Höfer, Stefan; Huber, Alexandra; Messner, Carmen; Renn, Daniela; Mestel, Robert; Klingelhöfer, Jürgen; Kopp, Martin; Doering, Stephan; Schüßler, Gerhard; Rumpold, Gerhard

2013-01-01

Dysfunctional parenting styles represent a risk factor for the development of psychological disturbances. The present study investigated the differential validity of the German language Fragebogen zur Erfassung dysfunktionaler Erziehungsstile (FDEB; Measurement of Parental Styles, MOPS) and determined whether different forms of psychological disorders are associated with specific patterns of parenting styles. 145 inpatients, 108 outpatients and a control group of 633 representative individuals from the general population were investigated by adapting the FDEB. A comparison of dysfunctional parenting styles showed different distress levels within the diagnostic groups: Patients suffering from depression reported high levels of maternal indifference and over protectiveness together with an abusive rearing behavior on the part of both parents. Patients with anxiety disorders reported having overprotective mothers. Bulimic patients as well as those with personality disorders significantly exhibited stress in almost all areas. However, anorexic patients did not differ significantly from the control group, which appeared to be the least affected of all. The FDEB showed a satisfactory differential validity. There was evidence that specific patterns of dysfunctional parenting styles were associated with different diagnostic groups.

apterous A specifies dorsal wing patterns and sexual traits in butterflies

PubMed Central

2018-01-01

Butterflies have evolved different colour patterns on their dorsal and ventral wing surfaces to serve different signalling functions, yet the developmental mechanisms controlling surface-specific patterning are still unknown. Here, we mutate both copies of the transcription factor apterous in Bicyclus anynana butterflies using CRISPR/Cas9 and show that apterous A, expressed dorsally, functions both as a repressor and modifier of ventral wing colour patterns, as well as a promoter of dorsal sexual ornaments in males. We propose that the surface-specific diversification of wing patterns in butterflies proceeded via the co-option of apterous A or its downstream effectors into various gene regulatory networks involved in the differentiation of discrete wing traits. Further, interactions between apterous and sex-specific factors such as doublesex may have contributed to the origin of sexually dimorphic surface-specific patterns. Finally, we discuss the evolution of eyespot number diversity in the family Nymphalidae within the context of developmental constraints due to apterous regulation. PMID:29467265

Country-specific dietary patterns and associations with socioeconomic status in European children: the IDEFICS study.

PubMed

Fernández-Alvira, J M; Bammann, K; Pala, V; Krogh, V; Barba, G; Eiben, G; Hebestreit, A; Veidebaum, T; Reisch, L; Tornaritis, M; Kovacs, E; Huybrechts, I; Moreno, L A

2014-07-01

Children from lower socioeconomic status (SES) may be at higher risk of unhealthy eating. We described country-specific dietary patterns among children aged 2-9 years from eight European countries participating in the IDEFICS study and assessed the association of dietary patterns with an additive SES indicator. Children aged 2-9 years from eight European countries were recruited in 2007-2008. Principal component analysis was applied to identify dietary country-specific patterns. Linear regression analyses were applied to assess their association with SES. Two to four dietary patterns were identified in the participating regions. The existence of a 'processed' pattern was found in the eight regions. Also, a 'healthy' pattern was identified in seven of the eight regions. In addition, region-specific patterns were identified, reflecting the existing gastronomic and cultural differences in Europe. The 'processed' pattern was significantly inversely associated with the SES additive indicator in all countries except Sweden, whereas the 'healthy' pattern was positively associated with SES in the Belgian, Estonian, German and Hungarian regions, but was not significant in the Italian, Spanish and Swedish regions. A 'processed' pattern and a 'healthy' pattern were found in most of the participating countries in the IDEFICS study, with comparable food item profiles. The results showed a strong inverse association of SES with the 'processed' pattern, suggesting that children of parents with lower SES may be at higher risk of unhealthy eating. Therefore, special focus should be given to parents and their children from lower SES levels when developing healthy eating promotion strategies.

A multitracer approach to assess the spatial contamination pattern of hake (Merluccius merluccius) in the French Mediterranean.

PubMed

Cresson, Pierre; Bouchoucha, Marc; Morat, Fabien; Miralles, Francoise; Chavanon, Fabienne; Loizeau, Veronique; Cossa, Daniel

2015-11-01

Chemical contamination levels and stable isotope ratios provide integrated information about contaminant exposure, trophic position and also biological and environmental influences on marine organisms. By combining these approaches with otolith shape analyses, the aim of the present study was to document the spatial variability of Hg and PCB contamination of the European hake (Merluccius merluccius) in the French Mediterranean, hypothesizing that local contaminant sources, environmental conditions and biological specificities lead to site-specific contamination patterns. High Hg concentrations discriminated Corsica (average: 1.36 ± 0.80 μg g(-1) dm) from the Gulf of Lions (average values<0.5 μg g(-1) dm), where Rhône River input caused high PCB burdens. CB 153 average concentrations ranged between 4.00 ± 0.64 and 18.39 ± 12.38 ng g(-1) dm in the Gulf of Lions, whatever the sex of the individuals, whereas the highest values in Corsica were 6.75 ± 4.22 ng g(-1) dm. Otolith shape discriminated juveniles and adults, due to their different habitats. The use of combined ecotracers was revealed as a powerful tool to discriminate between fish populations at large and small spatial scale, and to enable understanding of the environmental and biological influences on contamination patterns. Copyright © 2015 Elsevier B.V. All rights reserved.

Background and stimulus-induced patterns of high metabolic activity in the visual cortex (area 17) of the squirrel and macaque monkey

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humphrey, A.L.; Hendrickson, A.E.

1983-02-01

The authors have used 2-deoxy-D-(/sup 14/C)glucose (2-DG) autoradiography and cytochrome oxidase histochemistry to examine background and stimulus-induced patterns of metabolic activity in monkey striate cortex. In squirrel monkeys (Saimiri sciureus) that binocularly or monocularly viewed diffuse white light or binocularly viewed bars of many orientations and spatial frequencies, 2-DG consumption was not uniform across the cortex but consisted of regularly spaced radial zones of high uptake. The cytochrome oxidase stain in these animals also revealed patches of high metabolism which coincided with the 2-DG patches. Squirrel monkeys binocularly viewing vertical stripes showed parallel bands of increased 2-DG uptake in themore » cortex, while the cytochrome label in these animals remained patchy. In macaque (Macaca nemestrina) monkeys, binocular stimulation with many orientations and spatial frequencies produced radial zones of high 2-DG uptake. When viewed tangentially, these zones formed a dots-in-rows pattern with a spacing of 350 X 500 microns; cytochrome oxidase staining produced an identical pattern. Macaca differed from Saimiri in that monocular stimulation labeled alternate rows. These results indicate that there are radial zones of high background metabolism across squirrel and macaque monkey striate cortex. In Saimiri these zones do not appear to be related to an eye dominance system, while in Macaca they do. The presence of these zones of high metabolism may complicate the interpretation of 2-DG autoradiographs that result from specific visual stimuli.« less

Insights into Mechanistic Models for Evaporation of Organic Liquids in the Environment Obtained by Position-Specific Carbon Isotope Analysis.

PubMed

Julien, Maxime; Nun, Pierrick; Robins, Richard J; Remaud, Gérald S; Parinet, Julien; Höhener, Patrick

2015-11-03

Position-specific isotope effects (PSIEs) have been measured by isotope ratio monitoring (13)C nuclear magnetic resonance spectrometry during the evaporation of 10 liquids of different polarities under 4 evaporation modes (passive evaporation, air-vented evaporation, low pressure evaporation, distillation). The observed effects are used to assess the validity of the Craig-Gordon isotope model for organic liquids. For seven liquids the overall isotope effect (IE) includes a vapor-liquid contribution that is strongly position-specific in polar compounds but less so in apolar compounds and a diffusive IE that is not position-specific, except in the alcohols, ethanol and propan-1-ol. The diffusive IE is diminished under forced evaporation. The position-specific isotope pattern created by liquid-vapor IEs is manifest in five liquids, which have an air-side limitation for volatilization. For the alcohols, undefined processes in the liquid phase create additional PSIEs. Three other liquids with limitations on the liquid side have a lower, highly position-specific, bulk diffusive IE. It is concluded that evaporation of organic pollutants creates unique position-specific isotope patterns that may be used to assess the progress of remediation or natural attenuation of pollution and that the Craig-Gordon isotope model is valid for the volatilization of nonpolar organic liquids with air-side limitation of the volatilization rate.

Clustering of health-related behaviors, health outcomes and demographics in Dutch adolescents: a cross-sectional study.

PubMed

Busch, Vincent; Van Stel, Henk F; Schrijvers, Augustinus J P; de Leeuw, Johannes R J

2013-12-04

Recent studies show several health-related behaviors to cluster in adolescents. This has important implications for public health. Interrelated behaviors have been shown to be most effectively targeted by multimodal interventions addressing wider-ranging improvements in lifestyle instead of via separate interventions targeting individual behaviors. However, few previous studies have taken into account a broad, multi-disciplinary range of health-related behaviors and connected these behavioral patterns to health-related outcomes. This paper presents an analysis of the clustering of a broad range of health-related behaviors with relevant demographic factors and several health-related outcomes in adolescents. Self-report questionnaire data were collected from a sample of 2,690 Dutch high school adolescents. Behavioral patterns were deducted via Principal Components Analysis. Subsequently a Two-Step Cluster Analysis was used to identify groups of adolescents with similar behavioral patterns and health-related outcomes. Four distinct behavioral patterns describe the analyzed individual behaviors: 1- risk-prone behavior, 2- bully behavior, 3- problematic screen time use, and 4- sedentary behavior. Subsequent cluster analysis identified four clusters of adolescents. Multi-problem behavior was associated with problematic physical and psychosocial health outcomes, as opposed to those exerting relatively few unhealthy behaviors. These associations were relatively independent of demographics such as ethnicity, gender and socio-economic status. The results show that health-related behaviors tend to cluster, indicating that specific behavioral patterns underlie individual health behaviors. In addition, specific patterns of health-related behaviors were associated with specific health outcomes and demographic factors. In general, unhealthy behavior on account of multiple health-related behaviors was associated with both poor psychosocial and physical health. These findings have significant meaning for future public health programs, which should be more tailored with use of such knowledge on behavioral clustering via e.g. Transfer Learning.

Clustering of health-related behaviors, health outcomes and demographics in Dutch adolescents: a cross-sectional study

PubMed Central

2013-01-01

Background Recent studies show several health-related behaviors to cluster in adolescents. This has important implications for public health. Interrelated behaviors have been shown to be most effectively targeted by multimodal interventions addressing wider-ranging improvements in lifestyle instead of via separate interventions targeting individual behaviors. However, few previous studies have taken into account a broad, multi-disciplinary range of health-related behaviors and connected these behavioral patterns to health-related outcomes. This paper presents an analysis of the clustering of a broad range of health-related behaviors with relevant demographic factors and several health-related outcomes in adolescents. Methods Self-report questionnaire data were collected from a sample of 2,690 Dutch high school adolescents. Behavioral patterns were deducted via Principal Components Analysis. Subsequently a Two-Step Cluster Analysis was used to identify groups of adolescents with similar behavioral patterns and health-related outcomes. Results Four distinct behavioral patterns describe the analyzed individual behaviors: 1- risk-prone behavior, 2- bully behavior, 3- problematic screen time use, and 4- sedentary behavior. Subsequent cluster analysis identified four clusters of adolescents. Multi-problem behavior was associated with problematic physical and psychosocial health outcomes, as opposed to those exerting relatively few unhealthy behaviors. These associations were relatively independent of demographics such as ethnicity, gender and socio-economic status. Conclusions The results show that health-related behaviors tend to cluster, indicating that specific behavioral patterns underlie individual health behaviors. In addition, specific patterns of health-related behaviors were associated with specific health outcomes and demographic factors. In general, unhealthy behavior on account of multiple health-related behaviors was associated with both poor psychosocial and physical health. These findings have significant meaning for future public health programs, which should be more tailored with use of such knowledge on behavioral clustering via e.g. Transfer Learning. PMID:24305509

Divergent phenological response to hydroclimate variability in forested mountain watersheds.

PubMed

Hwang, Taehee; Band, Lawrence E; Miniat, Chelcy F; Song, Conghe; Bolstad, Paul V; Vose, James M; Love, Jason P

2014-08-01

Mountain watersheds are primary sources of freshwater, carbon sequestration, and other ecosystem services. There is significant interest in the effects of climate change and variability on these processes over short to long time scales. Much of the impact of hydroclimate variability in forest ecosystems is manifested in vegetation dynamics in space and time. In steep terrain, leaf phenology responds to topoclimate in complex ways, and can produce specific and measurable shifts in landscape forest patterns. The onset of spring is usually delayed at a specific rate with increasing elevation (often called Hopkins' Law; Hopkins, 1918), reflecting the dominant controls of temperature on greenup timing. Contrary with greenup, leaf senescence shows inconsistent trends along elevation gradients. Here, we present mechanisms and an explanation for this variability and its significance for ecosystem patterns and services in response to climate. We use moderate-resolution imaging spectro-radiometer (MODIS) Normalized Difference Vegetation Index (NDVI) data to derive landscape-induced phenological patterns over topoclimate gradients in a humid temperate broadleaf forest in southern Appalachians. These phenological patterns are validated with different sets of field observations. Our data demonstrate that divergent behavior of leaf senescence with elevation is closely related to late growing season hydroclimate variability in temperature and water balance patterns. Specifically, a drier late growing season is associated with earlier leaf senescence at low elevation than at middle elevation. The effect of drought stress on vegetation senescence timing also leads to tighter coupling between growing season length and ecosystem water use estimated from observed precipitation and runoff generation. This study indicates increased late growing season drought may be leading to divergent ecosystem response between high and low elevation forests. Landscape-induced phenological patterns are easily observed over wide areas and may be used as a unique diagnostic for sources of ecosystem vulnerability and sensitivity to hydroclimate change. © 2014 John Wiley & Sons Ltd.

Alternative mechanisms alter the emergent properties of self-organization in mussel beds

PubMed Central

Liu, Quan-Xing; Weerman, Ellen J.; Herman, Peter M. J.; Olff, Han; van de Koppel, Johan

2012-01-01

Theoretical models predict that spatial self-organization can have important, unexpected implications by affecting the functioning of ecosystems in terms of resilience and productivity. Whether and how these emergent effects depend on specific formulations of the underlying mechanisms are questions that are often ignored. Here, we compare two alternative models of regular spatial pattern formation in mussel beds that have different mechanistic descriptions of the facilitative interactions between mussels. The first mechanism involves a reduced mussel loss rate at high density owing to mutual protection between the mussels, which is the basis of prior studies on the pattern formation in mussels. The second mechanism assumes, based on novel experimental evidence, that mussels feed more efficiently on top of mussel-generated hummocks. Model simulations point out that the second mechanism produces very similar types of spatial patterns in mussel beds. Yet the mechanisms predict a strikingly contrasting effect of these spatial patterns on ecosystem functioning, in terms of productivity and resilience. In the first model, where high mussel densities reduce mussel loss rates, patterns are predicted to strongly increase productivity and decrease the recovery time of the bed following a disturbance. When pattern formation is generated by increased feeding efficiency on hummocks, only minor emergent effects of pattern formation on ecosystem functioning are predicted. Our results provide a warning against predictions of the implications and emergent properties of spatial self-organization, when the mechanisms that underlie self-organization are incompletely understood and not based on the experimental study. PMID:22418256

Biogeographic distribution patterns and their correlates in the diverse frog fauna of the Atlantic Forest hotspot.

PubMed

Vasconcelos, Tiago S; Prado, Vitor H M; da Silva, Fernando R; Haddad, Célio F B

2014-01-01

Anurans are a highly diverse group in the Atlantic Forest hotspot (AF), yet distribution patterns and species richness gradients are not randomly distributed throughout the biome. Thus, we explore how anuran species are distributed in this complex and biodiverse hotspot, and hypothesize that this group can be distinguished by different cohesive regions. We used range maps of 497 species to obtain a presence/absence data grid, resolved to 50×50 km grain size, which was submitted to k-means clustering with v-fold cross-validation to determine the biogeographic regions. We also explored the extent to which current environmental variables, topography, and floristic structure of the AF are expected to identify the cluster patterns recognized by the k-means clustering. The biogeographic patterns found for amphibians are broadly congruent with ecoregions identified in the AF, but their edges, and sometimes the whole extent of some clusters, present much less resolved pattern compared to previous classification. We also identified that climate, topography, and vegetation structure of the AF explained a high percentage of variance of the cluster patterns identified, but the magnitude of the regression coefficients shifted regarding their importance in explaining the variance for each cluster. Specifically, we propose that the anuran fauna of the AF can be split into four biogeographic regions: a) less diverse and widely-ranged species that predominantly occur in the inland semideciduous forests; b) northern small-ranged species that presumably evolved within the Pleistocene forest refugia; c) highly diverse and small-ranged species from the southeastern Brazilian mountain chain and its adjacent semideciduous forest; and d) southern species from the Araucaria forest. Finally, the high congruence among the cluster patterns and previous eco-regions identified for the AF suggests that preserving the underlying habitat structure helps to preserve the historical and ecological signals that underlie the geographic distribution of AF anurans.

Discovering biclusters in gene expression data based on high-dimensional linear geometries

PubMed Central

Gan, Xiangchao; Liew, Alan Wee-Chung; Yan, Hong

2008-01-01

Background In DNA microarray experiments, discovering groups of genes that share similar transcriptional characteristics is instrumental in functional annotation, tissue classification and motif identification. However, in many situations a subset of genes only exhibits consistent pattern over a subset of conditions. Conventional clustering algorithms that deal with the entire row or column in an expression matrix would therefore fail to detect these useful patterns in the data. Recently, biclustering has been proposed to detect a subset of genes exhibiting consistent pattern over a subset of conditions. However, most existing biclustering algorithms are based on searching for sub-matrices within a data matrix by optimizing certain heuristically defined merit functions. Moreover, most of these algorithms can only detect a restricted set of bicluster patterns. Results In this paper, we present a novel geometric perspective for the biclustering problem. The biclustering process is interpreted as the detection of linear geometries in a high dimensional data space. Such a new perspective views biclusters with different patterns as hyperplanes in a high dimensional space, and allows us to handle different types of linear patterns simultaneously by matching a specific set of linear geometries. This geometric viewpoint also inspires us to propose a generic bicluster pattern, i.e. the linear coherent model that unifies the seemingly incompatible additive and multiplicative bicluster models. As a particular realization of our framework, we have implemented a Hough transform-based hyperplane detection algorithm. The experimental results on human lymphoma gene expression dataset show that our algorithm can find biologically significant subsets of genes. Conclusion We have proposed a novel geometric interpretation of the biclustering problem. We have shown that many common types of bicluster are just different spatial arrangements of hyperplanes in a high dimensional data space. An implementation of the geometric framework using the Fast Hough transform for hyperplane detection can be used to discover biologically significant subsets of genes under subsets of conditions for microarray data analysis. PMID:18433477

Evaluation of an enzyme immunoassay system for measuring herpes simplex virus (HSV) type 1-specific and HSV type 2-specific IgG antibodies.

PubMed

Prince, H E; Ernst, C E; Hogrefe, W R

2000-01-01

MRL Diagnostics has developed a dual enzyme immunoassay (EIA) system that employs the recombinant Herpes Simplex Virus (HSV) type-specific glycoproteins G1 (HSV1) and G2 (HSV2) to detect HSV type-specific IgG antibodies. This system was evaluated using 155 consecutive sera previously tested in a conventional dual EIA system (Zeus) that employs multiple HSV1 and HSV2 proteins to detect type-common as well as type-specific antibodies. Sera were also analyzed by Western blot to determine the true HSV type-specific IgG reactivity pattern. Of 110 sera giving concordant reactivity patterns in the MRL and Zeus EIA systems, 108 (98%) also displayed concordant Western blot patterns; two sera gave false positive HSV2 reactivity in both EIA systems. Of 45 sera giving discordant MRL and Zeus EIA reactivity patterns, 41 (91%) displayed a Western blot reactivity pattern that matched the MRL reactivity pattern. Both the HSV1 IgG component and the HSV2 IgG component of the MRL EIA system were 100% sensitive and > 95% specific. In contrast, the Zeus HSV1 IgG EIA was 98% sensitive and 79% specific, and the Zeus HSV2 IgG EIA was 85% sensitive and 79% specific. An analysis of the distribution of index values in the MRL EIA system showed that low-positive values (1.0-3.0) were rare, but, when detected, often represented false positive results; only 11 MRL low-positive results were observed, but all 6 MRL false positive results were found within this low-positive subgroup. These findings show that the MRL dual EIA system effectively detects HSV type-specific IgG antibodies. Copyright 2000 Wiley-Liss, Inc.

Student Conceptions of Ionic Bonding: Patterns of thinking across three European contexts

NASA Astrophysics Data System (ADS)

Taber, Keith S.; Tsaparlis, Georgios; Nakiboğlu, Canan

2012-12-01

Previous research has reported that students commonly develop alternative conceptions in the core topic of chemical bonding. Research in England has reported that students there commonly demonstrate an alternative 'molecular' conceptual framework for thinking about ionic bonding: in terms of the formation of molecule-like ions pairs through electron transfer, which are internally bonded, but not bonded to other ions. The present study reports the use of translated versions of a diagnostic instrument to elicit the conceptions of bonding in NaCl (commonly used as the teaching example of an ionic compound) from two samples of students setting out on university courses in Greece and Turkey. The study reports that students in these two contexts displayed high levels of support for statements based upon the alternative conceptual framework identified in the English context. Students commonly develop similar alternative conceptions of ionic bonding in these three different educational contexts. The study also found some quite large differences in the specific response patterns across these three contexts, some of which could reflect specific features of the different curriculum contexts. The study reinforces the cross-national nature of the challenge of effectively teaching the abstract models of chemistry at the submicroscopic level. It also provides intriguing suggestions that a close study of the interactions between specific curriculum contexts and specific patterns in students' thinking offers much potential for identifying particular aspects of subject pedagogy that either support or impede the learning of accepted scientific models.

Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning.

PubMed

Ursache, Robertas; Miyashima, Shunsuke; Chen, Qingguo; Vatén, Anne; Nakajima, Keiji; Carlsbecker, Annelie; Zhao, Yunde; Helariutta, Ykä; Dettmer, Jan

2014-03-01

The development and growth of higher plants is highly dependent on the conduction of water and minerals throughout the plant by xylem vessels. In Arabidopsis roots the xylem is organized as an axis of cell files with two distinct cell fates: the central metaxylem and the peripheral protoxylem. During vascular development, high and low expression levels of the class III HD-ZIP transcription factors promote metaxylem and protoxylem identities, respectively. Protoxylem specification is determined by both mobile, ground tissue-emanating miRNA165/6 species, which downregulate, and auxin concentrated by polar transport, which promotes HD-ZIP III expression. However, the factors promoting high HD-ZIP III expression for metaxylem identity have remained elusive. We show here that auxin biosynthesis promotes HD-ZIP III expression and metaxylem specification. Several auxin biosynthesis genes are expressed in the outer layers surrounding the vascular tissue in Arabidopsis root and downregulation of HD-ZIP III expression accompanied by specific defects in metaxylem development is seen in auxin biosynthesis mutants, such as trp2-12, wei8 tar2 or a quintuple yucca mutant, and in plants treated with L-kynurenine, a pharmacological inhibitor of auxin biosynthesis. Some of the patterning defects can be suppressed by synthetically elevated HD-ZIP III expression. Taken together, our results indicate that polar auxin transport, which was earlier shown to be required for protoxylem formation, is not sufficient to establish a proper xylem axis but that root-based auxin biosynthesis is additionally required.

Motivational patterns as an instrument for predicting success in promising young football players.

PubMed

Zuber, Claudia; Zibung, Marc; Conzelmann, Achim

2015-01-01

Psychological characteristics are crucial to identifying talents, which is why these are being incorporated in today's multidimensional talent models. In addition to multidimensionality, talent studies are increasingly drawing on holistic theories of development, leading to the use of person-oriented approaches. The present study adopts such an approach by looking at the influence that motivational characteristics have on the development of performance, in a person-oriented way. For this purpose, it looks at how the constructs achievement motive, achievement goal orientation and self-determination interact with one another, what patterns they form and how these patterns are linked to subsequent sports success. Ninety-seven top young football players were questioned twice. Another year later, it was enquired which of these players had been selected for the U15 national team. At both measuring points, four patterns were identified, which displayed a high degree of structural and individual stability. As expected, the highly intrinsically achievement-oriented players were significantly more likely to move up into the U15 national team. The results point to the importance of favourable patterns of motivational variables in the form of specific types, for medium-term performance development among promising football talents, and thus provide valuable clues for the selection and promotion of those.

Pattern of morphological variation and diversity of Cocos nucifera (Arecaceae) in Mexico.

PubMed

Zizumbo-Villarreal, D; Piñero, D

1998-06-01

The pattern of morphological variation of Cocos nucifera in Mexico was statistically and numerically evaluated. Forty-one populations were analyzed, using 17 morphological fruit characters. Principal components and cluster analyses indicated four main groups of coconut populations that showed high similarity with four different genotypes recently imported into Mexico from areas that could be the origin of Mexican coconut populations. These four genotypes were evaluated with regard to the lethal yellowing disease in Jamaica and showed a differential susceptibility. Therefore it is possible to speculate upon a difference in susceptibility of the Mexican genotypes. The analysis of correlation between morphological and geographical distances showed a high positive correlation that supports: (1) historical evidence that indicates early introductions of coconut from different regions of the world, (2) that on both coasts of Mexico two different patterns of dispersal were involved: continuous and in jumps. Collectively these results suggest that the impact of the lethal yellowing disease on coconut populations will vary depending on the specific area and the origin of its coconuts.

Scaling Patterns of Natural Urban Places as a Rule for Enhancing Their Urban Functionality Using Trajectory Data

NASA Astrophysics Data System (ADS)

Jia, T.; Yu, X.

2018-04-01

With the availability of massive trajectory data, it is highly valuable to reveal their activity information for many domains such as understanding the functionality of urban regions. This article utilizes the scaling patterns of human activities to enhance functional distribution of natural urban places. Specifically, we proposed a temporal city clustering algorithm to aggregate the stopping locations into natural urban places, which are reported to follow remarkable power law distributions of sizes and obey a universal law of economy of scale on human interactions with urban infrastructure. Besides, we proposed a novel Bayesian inference model with damping factor to estimate the most likely POI type associated with a stopping location. Our results suggest that hot natural urban places could be effectively identified from their scaling patterns and their functionality can be very well enhanced. For instance, natural urban places containing airport or railway station can be highly stressed by accumulating the massive types of human activities.

Patterns of Healthcare Spending in the Last Year of Life

PubMed Central

Davis, Matthew A.; Nallamothu, Brahmajee K.; Banerjee, Mousumi; Bynum, Julie P.W.

2016-01-01

The underlying assumption that healthcare spending skyrockets at the end-of-life may suggest that policymakers should target the last few months of life to control costs. However, spending patterns leading up to death have not been fully examined. We applied a new methodology to administrative claims data for older Medicare beneficiaries who died in 2012 to characterize trajectories of healthcare spending in the last year of life. After adjustment, we identified four unique spending trajectories among decedents: 48.7 percent had High Persistent spending, 29.0 percent had Moderate Persistent spending, 10.2 percent had Progressive spending, and only 12.1 percent had Late Rise spending. High spending throughout the full year before death (approximately half of all decedents) was associated with having multiple chronic conditions but not any specific diseases. These findings suggest that spending at the end-of-life is a marker of general spending patterns often set in motion long before death. PMID:27307350

Smartphone gaming and frequent use pattern associated with smartphone addiction

PubMed Central

Liu, Chun-Hao; Lin, Sheng-Hsuan; Pan, Yuan-Chien; Lin, Yu-Hsuan

2016-01-01

Abstract The aim of this study was to investigate the risk factors of smartphone addiction in high school students. A total of 880 adolescents were recruited from a vocational high school in Taiwan in January 2014 to complete a set of questionnaires, including the 10-item Smartphone Addiction Inventory, Chen Internet Addiction Scale, and a survey of content and patterns of personal smartphone use. Of those recruited, 689 students (646 male) aged 14 to 21 and who owned a smartphone completed the questionnaire. Multiple linear regression models were used to determine the variables associated with smartphone addiction. Smartphone gaming and frequent smartphone use were associated with smartphone addiction. Furthermore, both the smartphone gaming-predominant and gaming with multiple-applications groups showed a similar association with smartphone addiction. Gender, duration of owning a smartphone, and substance use were not associated with smartphone addiction. Our findings suggest that smartphone use patterns should be part of specific measures to prevent and intervene in cases of excessive smartphone use. PMID:27428191

Smartphone gaming and frequent use pattern associated with smartphone addiction.

PubMed

Liu, Chun-Hao; Lin, Sheng-Hsuan; Pan, Yuan-Chien; Lin, Yu-Hsuan

2016-07-01

The aim of this study was to investigate the risk factors of smartphone addiction in high school students.A total of 880 adolescents were recruited from a vocational high school in Taiwan in January 2014 to complete a set of questionnaires, including the 10-item Smartphone Addiction Inventory, Chen Internet Addiction Scale, and a survey of content and patterns of personal smartphone use. Of those recruited, 689 students (646 male) aged 14 to 21 and who owned a smartphone completed the questionnaire. Multiple linear regression models were used to determine the variables associated with smartphone addiction.Smartphone gaming and frequent smartphone use were associated with smartphone addiction. Furthermore, both the smartphone gaming-predominant and gaming with multiple-applications groups showed a similar association with smartphone addiction. Gender, duration of owning a smartphone, and substance use were not associated with smartphone addiction.Our findings suggest that smartphone use patterns should be part of specific measures to prevent and intervene in cases of excessive smartphone use.

Direct growth of single-crystalline III–V semiconductors on amorphous substrates

DOE PAGES

Chen, Kevin; Kapadia, Rehan; Harker, Audrey; ...

2016-01-27

The III–V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III–V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III–V’s on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III–V’s of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. Themore » patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO 2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. In conclusion, the work presents an important advance towards universal integration of III–V’s on application-specific substrates by direct growth.« less

Direct growth of single-crystalline III–V semiconductors on amorphous substrates

PubMed Central

Chen, Kevin; Kapadia, Rehan; Harker, Audrey; Desai, Sujay; Seuk Kang, Jeong; Chuang, Steven; Tosun, Mahmut; Sutter-Fella, Carolin M.; Tsang, Michael; Zeng, Yuping; Kiriya, Daisuke; Hazra, Jubin; Madhvapathy, Surabhi Rao; Hettick, Mark; Chen, Yu-Ze; Mastandrea, James; Amani, Matin; Cabrini, Stefano; Chueh, Yu-Lun; Ager III, Joel W.; Chrzan, Daryl C.; Javey, Ali

2016-01-01

The III–V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III–V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III–V's on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III–V's of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. The patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. The work presents an important advance towards universal integration of III–V's on application-specific substrates by direct growth. PMID:26813257

Environmental Adaptation Contributes to Gene Polymorphism across the Arabidopsis thaliana Genome

PubMed Central

Lee, Cheng-Ruei

2012-01-01

The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the "environmental relevance" of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study. PMID:22798389

Do Media Use and Physical Activity Compete in Adolescents? Results of the MoMo Study

PubMed Central

Spengler, Sarah; Mess, Filip; Woll, Alexander

2015-01-01

Purpose The displacement hypothesis predicts that physical activity and media use compete in adolescents; however, findings are inconsistent. A more differentiated approach at determining the co-occurrence of physical activity and media use behaviors within subjects may be warranted. The aim of this study was to determine the co-occurrence of physical activity and media use by identifying clusters of adolescents with specific behavior patterns including physical activity in various settings (school, sports club, leisure time) and different types of media use (watching TV, playing console games, using PC / Internet). Methods Cross-sectional data of 2,083 adolescents (11–17 years) from all over Germany were collected between 2009 and 2012 in the Motorik-Modul Study. Physical activity and media use were self-reported. Cluster analyses (Ward’s method and K-means analysis) were used to identify behavior patterns of boys and girls separately. Results Eight clusters were identified for boys and seven for girls. The clusters demonstrated that a high proportion of boys (33%) as well as girls (42%) show low engagement in both physical activity and media use, irrespective of setting or type of media. Other adolescents are engaged in both behaviors, but either physical activity (35% of boys, 27% of girls) or media use (31% of boys and girls) predominates. These adolescents belong to different clusters, whereat in most clusters either one specific setting of physical activity or a specific combination of different types of media predominates. Conclusion The results of this study support to some extent the hypothesis that media use and physical activity compete: Very high media use occurred with low physical activity behavior, but very high activity levels co-occurred with considerable amounts of time using any media. There was no evidence that type of used media was related to physical activity levels, neither setting of physical activity was related to amount of media use in any pattern. PMID:26629688

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

PubMed

Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J; Becker, Peter B; Marr, Carsten

2016-01-27

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that models assuming purely unspecific or lysine site-specific acetylation rates were insufficient to explain the experimentally determined motif abundances. Rather, these abundances were best described by an ensemble of models with acetylation rates that were specific to motifs. The model ensemble converged upon four acetylation pathways; we validated three of these using independent data from a systematic enzyme depletion study. Our findings suggest that histone acetylation patterns originate through specific pathways involving motif-specific acetylation activity. Copyright © 2016 Elsevier Inc. All rights reserved.

Automatic hammering of nano-patterns on special polymer film by using a vibrating AFM tip

PubMed Central

2012-01-01

Complicated nano-patterns with linewidth less than 18 nm can be automatically hammered by using atomic force microscopy (AFM) tip in tapping mode with high speed. In this study, the special sample was thin poly(styrene-ethylene/butylenes-styrene) (SEBS) block copolymer film with hexagonal spherical microstructures. An ordinary silicon tip was used as a nano-hammer, and the entire hammering process is controlled by a computer program. Experimental results demonstrate that such structure-tailored thin films enable AFM tip hammering to be performed on their surfaces. Both imprinted and embossed nano-patterns can be generated by using a vibrating tip with a larger tapping load and by using a predefined program to control the route of tip movement as it passes over the sample’s surface. Specific details for the fabrication of structure-tailored SEBS film and the theory for auto-hammering patterns were presented in detail. PMID:22889045

Pairwise Classifier Ensemble with Adaptive Sub-Classifiers for fMRI Pattern Analysis.

PubMed

Kim, Eunwoo; Park, HyunWook

2017-02-01

The multi-voxel pattern analysis technique is applied to fMRI data for classification of high-level brain functions using pattern information distributed over multiple voxels. In this paper, we propose a classifier ensemble for multiclass classification in fMRI analysis, exploiting the fact that specific neighboring voxels can contain spatial pattern information. The proposed method converts the multiclass classification to a pairwise classifier ensemble, and each pairwise classifier consists of multiple sub-classifiers using an adaptive feature set for each class-pair. Simulated and real fMRI data were used to verify the proposed method. Intra- and inter-subject analyses were performed to compare the proposed method with several well-known classifiers, including single and ensemble classifiers. The comparison results showed that the proposed method can be generally applied to multiclass classification in both simulations and real fMRI analyses.

Femtosecond laser patterning, synthesis, defect formation, and structural modification of atomic layered materials

DOE PAGES

Yoo, Jae-Hyuck; Kim, Eunpa; Hwang, David J.

2016-12-06

This article summarizes recent research on laser-based processing of twodimensional (2D) atomic layered materials, including graphene and transition metal dichalcogenides (TMDCs). Ultrafast lasers offer unique processing routes that take advantage of distinct interaction mechanisms with 2D materials to enable extremely localized energy deposition. Experiments have shown that ablative direct patterning of graphene by ultrafast lasers can achieve resolutions of tens of nanometers, as well as single-step pattern transfer. Ultrafast lasers also induce non-thermal excitation mechanisms that are useful for the thinning of TMDCs to tune the 2D material bandgap. Laser-assisted site-specific doping was recently demonstrated where ultrafast laser radiation undermore » ambient air environment could be used for the direct writing of high-quality graphene patterns on insulating substrates. This article concludes with an outlook towards developing further advanced laser processing with scalability, in situ monitoring strategies and potential applications.« less

Quantifying positional and temporal movement patterns in professional rugby union using global positioning system.

PubMed

Jones, Marc R; West, Daniel J; Crewther, Blair T; Cook, Christian J; Kilduff, Liam P

2015-01-01

This study assessed the positional and temporal movement patterns of professional rugby union players during competition using global positioning system (GPS) units. GPS data were collected from 33 professional rugby players from 13 matches throughout the 2012-2013 season sampling at 10 Hz. Players wore GPS units from which information on distances, velocities, accelerations, exertion index, player load, contacts, sprinting and repeated high-intensity efforts (RHIE) were derived. Data files from players who played over 60 min (n = 112) were separated into five positional groups (tight and loose forwards; half, inside and outside backs) for match analysis. A further comparison of temporal changes in movement patterns was also performed using data files from those who played full games (n = 71). Significant positional differences were found for movement characteristics during performance (P < 0.05). Results demonstrate that inside and outside backs have greatest high-speed running demands; however, RHIE and contact demands are greatest in loose forwards during match play. Temporal analysis of all players displayed significant differences in player load, cruising and striding between halves, with measures of low- and high-intensity movement and acceleration/deceleration significantly declining throughout each half. Our data demonstrate significant positional differences for a number of key movement variables which provide a greater understanding of positional requirements of performance. This in turn may be used to develop progressive position-specific drills that elicit specific adaptations and provide objective measures of preparedness. Knowledge of performance changes may be used when developing drills and should be considered when monitoring and evaluating performance.

Transcription factors define the neuroanatomical organization of the medullary reticular formation

PubMed Central

Gray, Paul A.

2013-01-01

The medullary reticular formation contains large populations of inadequately described, excitatory interneurons that have been implicated in multiple homeostatic behaviors including breathing, viserosensory processing, vascular tone, and pain. Many hindbrain nuclei show a highly stereotyped pattern of localization across vertebrates suggesting a strong underlying genetic organization. Whether this is true for neurons within the reticular regions of hindbrain is unknown. Hindbrain neurons are derived from distinct developmental progenitor domains each of which expresses distinct patterns of transcription factors (TFs). These neuronal populations have distinct characteristics such as transmitter identity, migration, and connectivity suggesting developmentally expressed TFs might identify unique subpopulations of neurons within the reticular formation. A fate-mapping strategy using perinatal expression of reporter genes within Atoh1, Dbx1, Lmx1b, and Ptf1a transgenic mice coupled with immunohistochemistry (IHC) and in situ hybridization (ISH) were used to address the developmental organization of a large subset of reticular formation glutamatergic neurons. All hindbrain lineages have relatively large populations that extend the entire length of the hindbrain. Importantly, the location of neurons within each lineage was highly constrained. Lmx1b- and Dbx1- derived populations were both present in partially overlapping stripes within the reticular formation extending from dorsal to ventral brain. Within each lineage, distinct patterns of gene expression and organization were localized to specific hindbrain regions. Rostro-caudally sub-populations differ sequentially corresponding to proposed pseudo-rhombomereic boundaries. Dorsal-ventrally, sub-populations correspond to specific migratory positions. Together these data suggests the reticular formation is organized by a highly stereotyped developmental logic. PMID:23717265

Transcription factors define the neuroanatomical organization of the medullary reticular formation.

PubMed

Gray, Paul A

2013-01-01

The medullary reticular formation contains large populations of inadequately described, excitatory interneurons that have been implicated in multiple homeostatic behaviors including breathing, viserosensory processing, vascular tone, and pain. Many hindbrain nuclei show a highly stereotyped pattern of localization across vertebrates suggesting a strong underlying genetic organization. Whether this is true for neurons within the reticular regions of hindbrain is unknown. Hindbrain neurons are derived from distinct developmental progenitor domains each of which expresses distinct patterns of transcription factors (TFs). These neuronal populations have distinct characteristics such as transmitter identity, migration, and connectivity suggesting developmentally expressed TFs might identify unique subpopulations of neurons within the reticular formation. A fate-mapping strategy using perinatal expression of reporter genes within Atoh1, Dbx1, Lmx1b, and Ptf1a transgenic mice coupled with immunohistochemistry (IHC) and in situ hybridization (ISH) were used to address the developmental organization of a large subset of reticular formation glutamatergic neurons. All hindbrain lineages have relatively large populations that extend the entire length of the hindbrain. Importantly, the location of neurons within each lineage was highly constrained. Lmx1b- and Dbx1- derived populations were both present in partially overlapping stripes within the reticular formation extending from dorsal to ventral brain. Within each lineage, distinct patterns of gene expression and organization were localized to specific hindbrain regions. Rostro-caudally sub-populations differ sequentially corresponding to proposed pseudo-rhombomereic boundaries. Dorsal-ventrally, sub-populations correspond to specific migratory positions. Together these data suggests the reticular formation is organized by a highly stereotyped developmental logic.

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma.

PubMed

Hammel, Jörg U; Herzen, Julia; Beckmann, Felix; Nickel, Michael

2009-09-08

Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. We investigated the budding process in Tethya wilhelma (Demospongiae) by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-muCT) image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM).

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma

PubMed Central

Hammel, Jörg U; Herzen, Julia; Beckmann, Felix; Nickel, Michael

2009-01-01

Background Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. Results We investigated the budding process in Tethya wilhelma (Demospongiae) by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-μCT) image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. Conclusion Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM). PMID:19737392

Identity-Specific Reward Representations in Orbitofrontal Cortex Are Modulated by Selective Devaluation.

PubMed

Howard, James D; Kahnt, Thorsten

2017-03-08

Goal-directed behavior is sensitive to the current value of expected outcomes. This requires independent representations of specific rewards, which have been linked to orbitofrontal cortex (OFC) function. However, the mechanisms by which the human brain updates specific goals on the fly, and translates those updates into choices, have remained unknown. Here we implemented selective devaluation of appetizing food odors in combination with pattern-based neuroimaging and a decision-making task. We found that in a hungry state, participants chose to smell high-intensity versions of two value-matched food odor rewards. After eating a meal corresponding to one of the two odors, participants switched choices toward the low intensity of the sated odor but continued to choose the high intensity of the nonsated odor. This sensory-specific behavioral effect was mirrored by pattern-based changes in fMRI signal in lateral posterior OFC, where specific reward identity representations were altered after the meal for the sated food odor but retained for the nonsated counterpart. In addition, changes in functional connectivity between the OFC and general value coding in ventromedial prefrontal cortex (vmPFC) predicted individual differences in satiety-related choice behavior. These findings demonstrate how flexible representations of specific rewards in the OFC are updated by devaluation, and how functional connections to vmPFC reflect the current value of outcomes and guide goal-directed behavior. SIGNIFICANCE STATEMENT The orbitofrontal cortex (OFC) is critical for goal-directed behavior. A recent proposal is that OFC fulfills this function by representing a variety of state and task variables ("cognitive maps"), including a conjunction of expected reward identity and value. Here we tested how identity-specific representations of food odor reward are updated by satiety. We found that fMRI pattern-based signatures of reward identity in lateral posterior OFC were modulated after selective devaluation, and that connectivity between this region and general value coding ventromedial prefrontal cortex (vmPFC) predicted choice behavior. These results provide evidence for a mechanism by which devaluation modulates a cognitive map of expected reward in OFC and thereby alters general value signals in vmPFC to guide goal-directed behavior. Copyright © 2017 the authors 0270-6474/17/372627-12$15.00/0.

Self-organization in a diversity induced thermodynamics.

PubMed

Scirè, Alessandro; Annovazzi-Lodi, Valerio

2017-01-01

In this work we show how global self-organized patterns can come out of a disordered ensemble of point oscillators, as a result of a deterministic, and not of a random, cooperative process. The resulting system dynamics has many characteristics of classical thermodynamics. To this end, a modified Kuramoto model is introduced, by including Euclidean degrees of freedom and particle polarity. The standard deviation of the frequency distribution is the disorder parameter, diversity, acting as temperature, which is both a source of motion and of disorder. For zero and low diversity, robust static phase-synchronized patterns (crystals) appear, and the problem reverts to a generic dissipative many-body problem. From small to moderate diversity crystals display vibrations followed by structure disintegration in a competition of smaller dynamic patterns, internally synchronized, each of which is capable to manage its internal diversity. In this process a huge variety of self-organized dynamic shapes is formed. Such patterns can be seen again as (more complex) oscillators, where the same description can be applied in turn, renormalizing the problem to a bigger scale, opening the possibility of pattern evolution. The interaction functions are kept local because our idea is to build a system able to produce global patterns when its constituents only interact at the bond scale. By further increasing the oscillator diversity, the dynamics becomes erratic, dynamic patterns show short lifetime, and finally disappear for high diversity. Results are neither qualitatively dependent on the specific choice of the interaction functions nor on the shape of the probability function assumed for the frequencies. The system shows a phase transition and a critical behaviour for a specific value of diversity.

Clinical reasoning in the context of active decision support during medication prescribing.

PubMed

Horsky, Jan; Aarts, Jos; Verheul, Leonie; Seger, Diane L; van der Sijs, Heleen; Bates, David W

2017-01-01

Describe and analyze reasoning patterns of clinicians responding to drug-drug interaction alerts in order to understand the role of patient-specific information in the decision-making process about the risks and benefits of medication therapy. Insights could be used to inform the design of decision-support interventions. Thirty-two clinicians working with five EHRs in two countries completed sets of six medication orders each and responded to high- and low-severity drug-drug interaction alerts while verbalizing their thoughts in a standard think-aloud protocol. Tasks were recorded and analyzed to describe reasoning patterns about patient-risk assessment and strategies to avoid or mitigate it. We observed a total of 171 prescribing decisions. Clinicians actively sought to reduce risk when responding to high-severity alerts, mostly by monitoring patients and making dose adjustments (52 alerts, 40%). In contrast, they routinely left prescriptions unchanged after low-severity alerts when they felt confident that patients would tolerate the drug combination and that treatment benefits outweighed the risks (30 alerts, 71%). Clinicians used similar reasoning patterns regardless of the EHR used and differences in alert design. Clinicians conceptualized risk as a complex set of interdependent tradeoffs specific to individual patients and had a tendency not to follow advice they considered of low clinical value. Omission of patient-specific data, which was not shown in alerts or included in trigger logic, may have contributed to the constancy of reasoning and to similarities in risk-control strategies we observed despite significant differences in interface design and system function. Declining an alert suggestion was preceded by sometimes brief but often complex reasoning, prioritizing different aspects of care quality and safety, especially when the perceived risk was higher. Clinicians believed that the risk indicated in drug-drug interaction alerts needs to be interpreted as one factor in the broader context of care, specific to a patient. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Assessing Weather-Yield Relationships in Rice at Local Scale Using Data Mining Approaches

PubMed Central

Delerce, Sylvain; Dorado, Hugo; Grillon, Alexandre; Rebolledo, Maria Camila; Prager, Steven D.; Patiño, Victor Hugo; Garcés Varón, Gabriel; Jiménez, Daniel

2016-01-01

Seasonal and inter-annual climate variability have become important issues for farmers, and climate change has been shown to increase them. Simultaneously farmers and agricultural organizations are increasingly collecting observational data about in situ crop performance. Agriculture thus needs new tools to cope with changing environmental conditions and to take advantage of these data. Data mining techniques make it possible to extract embedded knowledge associated with farmer experiences from these large observational datasets in order to identify best practices for adapting to climate variability. We introduce new approaches through a case study on irrigated and rainfed rice in Colombia. Preexisting observational datasets of commercial harvest records were combined with in situ daily weather series. Using Conditional Inference Forest and clustering techniques, we assessed the relationships between climatic factors and crop yield variability at the local scale for specific cultivars and growth stages. The analysis showed clear relationships in the various location-cultivar combinations, with climatic factors explaining 6 to 46% of spatiotemporal variability in yield, and with crop responses to weather being non-linear and cultivar-specific. Climatic factors affected cultivars differently during each stage of development. For instance, one cultivar was affected by high nighttime temperatures in the reproductive stage but responded positively to accumulated solar radiation during the ripening stage. Another was affected by high nighttime temperatures during both the vegetative and reproductive stages. Clustering of the weather patterns corresponding to individual cropping events revealed different groups of weather patterns for irrigated and rainfed systems with contrasting yield levels. Best-suited cultivars were identified for some weather patterns, making weather-site-specific recommendations possible. This study illustrates the potential of data mining for adding value to existing observational data in agriculture by allowing embedded knowledge to be quickly leveraged. It generates site-specific information on cultivar response to climatic factors and supports on-farm management decisions for adaptation to climate variability. PMID:27560980

Assessing Weather-Yield Relationships in Rice at Local Scale Using Data Mining Approaches.

PubMed

Delerce, Sylvain; Dorado, Hugo; Grillon, Alexandre; Rebolledo, Maria Camila; Prager, Steven D; Patiño, Victor Hugo; Garcés Varón, Gabriel; Jiménez, Daniel

2016-01-01

Seasonal and inter-annual climate variability have become important issues for farmers, and climate change has been shown to increase them. Simultaneously farmers and agricultural organizations are increasingly collecting observational data about in situ crop performance. Agriculture thus needs new tools to cope with changing environmental conditions and to take advantage of these data. Data mining techniques make it possible to extract embedded knowledge associated with farmer experiences from these large observational datasets in order to identify best practices for adapting to climate variability. We introduce new approaches through a case study on irrigated and rainfed rice in Colombia. Preexisting observational datasets of commercial harvest records were combined with in situ daily weather series. Using Conditional Inference Forest and clustering techniques, we assessed the relationships between climatic factors and crop yield variability at the local scale for specific cultivars and growth stages. The analysis showed clear relationships in the various location-cultivar combinations, with climatic factors explaining 6 to 46% of spatiotemporal variability in yield, and with crop responses to weather being non-linear and cultivar-specific. Climatic factors affected cultivars differently during each stage of development. For instance, one cultivar was affected by high nighttime temperatures in the reproductive stage but responded positively to accumulated solar radiation during the ripening stage. Another was affected by high nighttime temperatures during both the vegetative and reproductive stages. Clustering of the weather patterns corresponding to individual cropping events revealed different groups of weather patterns for irrigated and rainfed systems with contrasting yield levels. Best-suited cultivars were identified for some weather patterns, making weather-site-specific recommendations possible. This study illustrates the potential of data mining for adding value to existing observational data in agriculture by allowing embedded knowledge to be quickly leveraged. It generates site-specific information on cultivar response to climatic factors and supports on-farm management decisions for adaptation to climate variability.

Communication variations and aircrew performance

NASA Technical Reports Server (NTRS)

Kanki, Barbara G.; Folk, Valerie G.; Irwin, Cheryl M.

1991-01-01

The relationship between communication variations and aircrew performance (high-error vs low-error performances) was investigated by analyzing the coded verbal transcripts derived from the videotape records of 18 two-person air transport crews who participated in a high-fidelity, full-mission flight simulation. The flight scenario included a task which involved abnormal operations and required the coordinated efforts of all crew members. It was found that the best-performing crews were characterized by nearly identical patterns of communication, whereas the midrange and poorer performing crews showed a great deal of heterogeneity in their speech patterns. Although some specific speech sequences can be interpreted as being more or less facilitative to the crew-coordination process, predictability appears to be the key ingredient for enhancing crew performance. Crews communicating in highly standard (hence predictable) ways were better able to coordinate their task, whereas crews characterized by multiple, nonstandard communication profiles were less effective in their performance.

Preferential degradation of cognitive networks differentiates Alzheimer's disease from ageing.

PubMed

Chhatwal, Jasmeer P; Schultz, Aaron P; Johnson, Keith A; Hedden, Trey; Jaimes, Sehily; Benzinger, Tammie L S; Jack, Clifford; Ances, Beau M; Ringman, John M; Marcus, Daniel S; Ghetti, Bernardino; Farlow, Martin R; Danek, Adrian; Levin, Johannes; Yakushev, Igor; Laske, Christoph; Koeppe, Robert A; Galasko, Douglas R; Xiong, Chengjie; Masters, Colin L; Schofield, Peter R; Kinnunen, Kirsi M; Salloway, Stephen; Martins, Ralph N; McDade, Eric; Cairns, Nigel J; Buckles, Virginia D; Morris, John C; Bateman, Randall; Sperling, Reisa A

2018-05-01

Converging evidence from structural, metabolic and functional connectivity MRI suggests that neurodegenerative diseases, such as Alzheimer's disease, target specific neural networks. However, age-related network changes commonly co-occur with neuropathological cascades, limiting efforts to disentangle disease-specific alterations in network function from those associated with normal ageing. Here we elucidate the differential effects of ageing and Alzheimer's disease pathology through simultaneous analyses of two functional connectivity MRI datasets: (i) young participants harbouring highly-penetrant mutations leading to autosomal-dominant Alzheimer's disease from the Dominantly Inherited Alzheimer's Network (DIAN), an Alzheimer's disease cohort in which age-related comorbidities are minimal and likelihood of progression along an Alzheimer's disease trajectory is extremely high; and (ii) young and elderly participants from the Harvard Aging Brain Study, a cohort in which imaging biomarkers of amyloid burden and neurodegeneration can be used to disambiguate ageing alone from preclinical Alzheimer's disease. Consonant with prior reports, we observed the preferential degradation of cognitive (especially the default and dorsal attention networks) over motor and sensory networks in early autosomal-dominant Alzheimer's disease, and found that this distinctive degradation pattern was magnified in more advanced stages of disease. Importantly, a nascent form of the pattern observed across the autosomal-dominant Alzheimer's disease spectrum was also detectable in clinically normal elderly with clear biomarker evidence of Alzheimer's disease pathology (preclinical Alzheimer's disease). At the more granular level of individual connections between node pairs, we observed that connections within cognitive networks were preferentially targeted in Alzheimer's disease (with between network connections relatively spared), and that connections between positively coupled nodes (correlations) were preferentially degraded as compared to connections between negatively coupled nodes (anti-correlations). In contrast, ageing in the absence of Alzheimer's disease biomarkers was characterized by a far less network-specific degradation across cognitive and sensory networks, of between- and within-network connections, and of connections between positively and negatively coupled nodes. We go on to demonstrate that formalizing the differential patterns of network degradation in ageing and Alzheimer's disease may have the practical benefit of yielding connectivity measurements that highlight early Alzheimer's disease-related connectivity changes over those due to age-related processes. Together, the contrasting patterns of connectivity in Alzheimer's disease and ageing add to prior work arguing against Alzheimer's disease as a form of accelerated ageing, and suggest multi-network composite functional connectivity MRI metrics may be useful in the detection of early Alzheimer's disease-specific alterations co-occurring with age-related connectivity changes. More broadly, our findings are consistent with a specific pattern of network degradation associated with the spreading of Alzheimer's disease pathology within targeted neural networks.

Prostate-specific Membrane Antigen PET: Clinical Utility in Prostate Cancer, Normal Patterns, Pearls, and Pitfalls.

PubMed

Hofman, Michael S; Hicks, Rodney J; Maurer, Tobias; Eiber, Matthias

2018-01-01

Prostate-specific membrane antigen (PSMA) is a transmembrane glycoprotein that is overexpressed in prostate cancer. Radiolabeled small molecules that bind with high affinity to its active extracellular center have emerged as a potential new diagnostic standard of reference for prostate cancer, resulting in images with extraordinary tumor-to-background contrast. Currently, gallium 68 ( 68 Ga)-PSMA-11 (or HBED-PSMA) is the most widely used radiotracer for PSMA positron emission tomography (PET)/computed tomography (CT) or PSMA PET/magnetic resonance (MR) imaging. Evolving evidence demonstrates superior sensitivity and specificity of PSMA PET compared to conventional imaging, with frequent identification of subcentimeter prostate cancer lesions. PSMA PET is effective for imaging disease in the prostate, lymph nodes, soft tissue, and bone in a "one-stop-shop" examination. There is emerging evidence for its clinical value in staging of high-risk primary prostate cancer and localization of disease in biochemical recurrence. The high sensitivity provided by PSMA PET, with frequent identification of small-volume disease, is redefining patterns of disease spread compared with those seen at conventional imaging. In metastatic castration-resistant prostate cancer, PSMA PET is frequently used for theranostic selection (eg, lutetium 177-PSMA radionuclide therapy), but its potential use for therapy monitoring is still under debate. However, evidence on its proper use to improve patient-related outcomes, particularly in the setting of early biochemical recurrence and targeted treatment of oligometastatic disease, is still missing. Despite the term prostate specific, PSMA functions as a folate hydrolase and is expressed in a range of normal tissues and in other benign and malignant processes. Knowledge of its physiologic distribution and other causes of uptake is essential to minimize false-positive imaging findings. © RSNA, 2018.

Contrasting PCB bioaccumulation patterns among Lake Huron lake trout reflect basin-specific ecology.

PubMed

Paterson, Gordon; Ryder, Mark; Drouillard, Ken G; Haffner, G Douglas

2016-01-01

This study collected multiple age classes of lake trout from Lake Huron's Main Basin, Georgian Bay, and North Channel regions to compare and contrast top predator polychlorinated biphenyl (PCB) bioaccumulation patterns in separate compartments of the same ecosystem. Sum PCB concentrations were highest for Main Basin (260 ± 24.9 ng g(-1) wet wt) fish, followed by Georgian Bay (74.6 ± 16.2 ng g(-1) ) and North Channel (42.0 ± 3.3 ng g(-1)) fish. Discriminant functions analysis of lake trout PCB profiles and stable carbon (δ(13)C) and nitrogen (δ(15)N) isotope values clearly distinguished fish by location, indicating high degrees of basin fidelity throughout their lifetimes in addition to highly contrasting PCB bioaccumulation profiles. These unique profiles were not attributable to significant differences in lake trout lipid contents (p = 0.856) or trophic position (δ(15)N; p = 0.334), with rainbow smelt representing the primary prey across the basins. Furthermore, significant differences were observed among the basins for the relationships between PCB biomagnification factors and hydrophobicity. An empirical model for predicting PCB biomagnification in Lake Huron lake trout indicated that basin-specific population growth rates and prey abundances were significant for explaining these contrasting patterns of PCB bioaccumulation. The results of the present study are fundamental for understanding the role of ecology in legacy persistent organic pollutant (POP) bioaccumulation. Specifically, ecosystem characteristics such as prey abundances, foraging ecology, and ultimately consumer growth can regulate the variability of legacy POP bioaccumulation as observed within and among a wide range of freshwater ecosystems. © 2015 SETAC.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

Development of Farming Diversification with Implementation Plant Patterns as a Strategy of Economic Strengthening

NASA Astrophysics Data System (ADS)

Anwar, S.; Setyohadi, D. P. S.; Utami, M. M. D.; Damanhuri; Hariono, B.

2018-01-01

Bojonegoro, Tulungagung, and Ponorogo districts are an agrarian area and become one of the leading food crops producers in East Java Province. Diversification of farming in this region is done by applying season-based cropping pattern, which is cultivating various commodities in rotation. Farmers need diversification programs wetland cannot provide an optimal contribution to the income of farmers caused because farmers are not able to cultivate high value-added commodities due to limited capital. This research is to identify the characteristics of farming and to analyse the farming system to know the pattern of planting suggestion and prospect. The research used descriptive method, profit farming analysis, and SWOT. The results showed that each region has a specific planting pattern with rice as the main commodity grown in the rainy season followed by crops and horticultural crops and a suggested planting pattern that needs to be implemented by farmers to increase their income. The prospect of diversification of farming development through the implementation of the proposed planting pattern is very suitable with the character of the region and the market demand.

Reliability in endoscopic diagnosis of portal hypertensive gastropathy

PubMed Central

de Macedo, George Fred Soares; Ferreira, Fabio Gonçalves; Ribeiro, Maurício Alves; Szutan, Luiz Arnaldo; Assef, Mauricio Saab; Rossini, Lucio Giovanni Battista

2013-01-01

AIM: To analyze reliability among endoscopists in diagnosing portal hypertensive gastropathy (PHG) and to determine which criteria from the most utilized classifications are the most suitable. METHODS: From January to July 2009, in an academic quaternary referral center at Santa Casa of São Paulo Endoscopy Service, Brazil, we performed this single-center prospective study. In this period, we included 100 patients, including 50 sequential patients who had portal hypertension of various etiologies; who were previously diagnosed based on clinical, laboratory and imaging exams; and who presented with esophageal varices. In addition, our study included 50 sequential patients who had dyspeptic symptoms and were referred for upper digestive endoscopy without portal hypertension. All subjects underwent upper digestive endoscopy, and the images of the exam were digitally recorded. Five endoscopists with more than 15 years of experience answered an electronic questionnaire, which included endoscopic criteria from the 3 most commonly used Portal Hypertensive Gastropathy classifications (McCormack, NIEC and Baveno) and the presence of elevated or flat antral erosive gastritis. All five endoscopists were blinded to the patients’ clinical information, and all images of varices were deliberately excluded for the analysis. RESULTS: The three most common etiologies of portal hypertension were schistosomiasis (36%), alcoholic cirrhosis (20%) and viral cirrhosis (14%). Of the 50 patients with portal hypertension, 84% were Child A, 12% were Child B, 4% were Child C, 64% exhibited previous variceal bleeding and 66% were previously endoscopic treated. The endoscopic parameters, presence or absence of mosaic-like pattern, red point lesions and cherry-red spots were associated with high inter-observer reliability and high specificity for diagnosing Portal Hypertensive Gastropathy. Sensitivity, specificity and reliability for the diagnosis of PHG (%) were as follows: mosaic-like pattern (100; 92.21; High); fine pink speckling (56; 76.62; Unsatisfactory); superficial reddening (69.57; 66.23; Unsatisfactory); red-point lesions (47.83; 90.91; High); cherry-red spots (39.13; 96.10; High); isolated red marks (43.48; 88.31; High); and confluent red marks (21.74; 100; Unsatisfactory). Antral elevated erosive gastritis exhibited high reliability and high specificity with respect to the presence of portal hypertension (92%) and the diagnosis of portal hypertensive gastropathy (88.31%). CONCLUSION: The most suitable endoscopic criteria for the diagnosis of PHG were mosaic-like pattern, red-point lesions and cherry-red spots with no subdivisions, which were associated with a high rate of inter-observer reliability. PMID:23858376

Chronic Malaria Revealed by a New Fluorescence Pattern on the Antinuclear Autoantibodies Test

PubMed Central

Hommel, Benjamin; Charuel, Jean-Luc; Jaureguiberry, Stéphane; Arnaud, Laurent; Courtin, Regis; Kassab, Petra; Prendki, Virginie; Paris, Luc; Ghillani-Dalbin, Pascale; Thellier, Marc; Caumes, Eric; Amoura, Zahir; Mazier, Dominique; Musset, Lucile; Buffet, Pierre; Miyara, Makoto

2014-01-01

Background Several clinical forms of malaria such as chronic carriage, gestational malaria or hyper-reactive malarial splenomegaly may follow a cryptic evolution with afebrile chronic fatigue sometimes accompanied by anemia and/or splenomegaly. Conventional parasitological tests are often negative or not performed, and severe complications may occur. Extensive explorations of these conditions often include the search for antinuclear autoantibodies (ANA). Methods We analysed fluorescence patterns in the ANA test in patients with either chronic cryptic or acute symptomatic malaria, then conducted a one-year prospective study at a single hospital on all available sera drawn for ANA detections. We then identified autoantibodies differentially expressed in malaria patients and in controls using human protein microarray. Results We uncovered and defined a new, malaria-related, nucleo-cytoplasmic ANA pattern displaying the specific association of a nuclear speckled pattern with diffuse cytoplasmic perinuclearly-enhanced fluorescence. In the one-year prospective analysis, 79% of sera displaying this new nucleo-cytoplasmic fluorescence were from patients with malaria. This specific pattern, not seen in other parasitic diseases, allowed a timely reorientation of the diagnosis toward malaria. To assess if the autoantibody immune response was due to autoreactivity or molecular mimicry we isolated 42 autoantigens, targets of malarial autoantibodies. BLAST analysis indicated that 23 of recognized autoantigens were homologous to plasmodial proteins suggesting autoimmune responses directly driven by the plasmodial infection. Conclusion In patients with malaria in whom parasitological tests have not been performed recognition of this new, malaria-related fluorescence pattern on the ANA test is highly suggestive of the diagnosis and triggers immediate, easy confirmation and adapted therapy. PMID:24551116

Attention Modulates Visual-Tactile Interaction in Spatial Pattern Matching

PubMed Central

Göschl, Florian; Engel, Andreas K.; Friese, Uwe

2014-01-01

Factors influencing crossmodal interactions are manifold and operate in a stimulus-driven, bottom-up fashion, as well as via top-down control. Here, we evaluate the interplay of stimulus congruence and attention in a visual-tactile task. To this end, we used a matching paradigm requiring the identification of spatial patterns that were concurrently presented visually on a computer screen and haptically to the fingertips by means of a Braille stimulator. Stimulation in our paradigm was always bimodal with only the allocation of attention being manipulated between conditions. In separate blocks of the experiment, participants were instructed to (a) focus on a single modality to detect a specific target pattern, (b) pay attention to both modalities to detect a specific target pattern, or (c) to explicitly evaluate if the patterns in both modalities were congruent or not. For visual as well as tactile targets, congruent stimulus pairs led to quicker and more accurate detection compared to incongruent stimulation. This congruence facilitation effect was more prominent under divided attention. Incongruent stimulation led to behavioral decrements under divided attention as compared to selectively attending a single sensory channel. Additionally, when participants were asked to evaluate congruence explicitly, congruent stimulation was associated with better performance than incongruent stimulation. Our results extend previous findings from audiovisual studies, showing that stimulus congruence also resulted in behavioral improvements in visuotactile pattern matching. The interplay of stimulus processing and attentional control seems to be organized in a highly flexible fashion, with the integration of signals depending on both bottom-up and top-down factors, rather than occurring in an ‘all-or-nothing’ manner. PMID:25203102

More than one way to see it: Individual heuristics in avian visual computation

PubMed Central

Ravignani, Andrea; Westphal-Fitch, Gesche; Aust, Ulrike; Schlumpp, Martin M.; Fitch, W. Tecumseh

2015-01-01

Comparative pattern learning experiments investigate how different species find regularities in sensory input, providing insights into cognitive processing in humans and other animals. Past research has focused either on one species’ ability to process pattern classes or different species’ performance in recognizing the same pattern, with little attention to individual and species-specific heuristics and decision strategies. We trained and tested two bird species, pigeons (Columba livia) and kea (Nestor notabilis, a parrot species), on visual patterns using touch-screen technology. Patterns were composed of several abstract elements and had varying degrees of structural complexity. We developed a model selection paradigm, based on regular expressions, that allowed us to reconstruct the specific decision strategies and cognitive heuristics adopted by a given individual in our task. Individual birds showed considerable differences in the number, type and heterogeneity of heuristic strategies adopted. Birds’ choices also exhibited consistent species-level differences. Kea adopted effective heuristic strategies, based on matching learned bigrams to stimulus edges. Individual pigeons, in contrast, adopted an idiosyncratic mix of strategies that included local transition probabilities and global string similarity. Although performance was above chance and quite high for kea, no individual of either species provided clear evidence of learning exactly the rule used to generate the training stimuli. Our results show that similar behavioral outcomes can be achieved using dramatically different strategies and highlight the dangers of combining multiple individuals in a group analysis. These findings, and our general approach, have implications for the design of future pattern learning experiments, and the interpretation of comparative cognition research more generally. PMID:26113444

Nutrition and healthy ageing: the key ingredients.

PubMed

Kiefte-de Jong, Jessica C; Mathers, John C; Franco, Oscar H

2014-05-01

Healthy longevity is a tangible possibility for many individuals and populations, with nutritional and other lifestyle factors playing a key role in modulating the likelihood of healthy ageing. Nevertheless, studies of effects of nutrients or single foods on ageing often show inconsistent results and ignore the overall framework of dietary habits. Therefore, the use of dietary patterns (e.g. a Mediterranean dietary pattern) and the specific dietary recommendations (e.g. dietary approaches to stop hypertension, Polymeal and the American Healthy Eating Index) are becoming more widespread in promoting lifelong health. A posteriori defined dietary patterns are described frequently in relation to age-related diseases but their generalisability is often a challenge since these are developed specifically for the population under study. Conversely, the dietary guidelines are often developed based on prevention of disease or nutrient deficiency, but often less attention is paid to how well these dietary guidelines promote health outcomes. In the present paper, we provide an overview of the state of the art of dietary patterns and dietary recommendations in relation to life expectancy and the risk of age-related disorders (with emphasis on cardiometabolic diseases and cognitive outcomes). According to both a posteriori and a priori dietary patterns, some key 'ingredients' can be identified that are associated consistently with longevity and better cardiometabolic and cognitive health. These include high intake of fruit, vegetables, fish, (whole) grains and legumes/pulses and potatoes, whereas dietary patterns rich in red meat and sugar-rich foods have been associated with an increased risk of mortality and cardiometabolic outcomes.

Tissue-Specific, Development-Dependent Phenolic Compounds Accumulation Profile and Gene Expression Pattern in Tea Plant [Camellia sinensis

PubMed Central

Li, Weiwei; Zhao, Lei; Meng, Fei; Wang, Yunsheng; Tan, Huarong; Yang, Hua; Wei, Chaoling; Wan, Xiaochun; Gao, Liping; Xia, Tao

2013-01-01

Phenolic compounds in tea plant [Camellia sinensis (L.)] play a crucial role in dominating tea flavor and possess a number of key pharmacological benefits on human health. The present research aimed to study the profile of tissue-specific, development-dependent accumulation pattern of phenolic compounds in tea plant. A total of 50 phenolic compounds were identified qualitatively using liquid chromatography in tandem mass spectrometry technology. Of which 29 phenolic compounds were quantified based on their fragmentation behaviors. Most of the phenolic compounds were higher in the younger leaves than that in the stem and root, whereas the total amount of proanthocyanidins were unexpectedly higher in the root. The expression patterns of 63 structural and regulator genes involved in the shikimic acid, phenylpropanoid, and flavonoid pathways were analyzed by quantitative real-time polymerase chain reaction and cluster analysis. Based on the similarity of their expression patterns, the genes were classified into two main groups: C1 and C2; and the genes in group C1 had high relative expression level in the root or low in the bud and leaves. The expression patterns of genes in C2-2-1 and C2-2-2-1 groups were probably responsible for the development-dependent accumulation of phenolic compounds in the leaves. Enzymatic analysis suggested that the accumulation of catechins was influenced simultaneously by catabolism and anabolism. Further research is recommended to know the expression patterns of various genes and the reason for the variation in contents of different compounds in different growth stages and also in different organs. PMID:23646127

Lateralization of ERPs to speech and handedness in the early development of Autism Spectrum Disorder.

PubMed

Finch, Kayla H; Seery, Anne M; Talbott, Meagan R; Nelson, Charles A; Tager-Flusberg, Helen

2017-01-01

Language is a highly lateralized function, with typically developing individuals showing left hemispheric specialization. Individuals with autism spectrum disorder (ASD) often show reduced or reversed hemispheric lateralization in response to language. However, it is unclear when this difference emerges and whether or not it can serve as an early ASD biomarker. Additionally, atypical language lateralization is not specific to ASD as it is also seen more frequently in individuals with mixed- and left-handedness. Here, we examined early asymmetry patterns measured through neural responses to speech sounds at 12 months and behavioral observations of handedness at 36 months in children with and without ASD. Three different groups of children participated in the study: low-risk controls (LRC), high risk for ASD (HRA; infants with older sibling with ASD) without ASD, and HRA infants who later receive a diagnosis of ASD (ASD). Event-related potentials (ERPs) to speech sounds were recorded at 12 months. Utilizing a novel observational approach, handedness was measured by hand preference on a variety of behaviors at 36 months. At 12 months, lateralization patterns of ERPs to speech stimuli differed across the groups with the ASD group showing reversed lateralization compared to the LRC group. At 36 months, factor analysis of behavioral observations of hand preferences indicated a one-factor model with medium to high factor loadings. A composite handedness score was derived; no group differences were observed. There was no association between lateralization to speech at 12 months and handedness at 36 months in the LRC and HRA groups. However, children with ASD did show an association such that infants with lateralization patterns more similar to the LRC group at 12 months were stronger right-handers at 36 months. These results highlight early developmental patterns that might be specific to ASD, including a potential early biomarker of reversed lateralization to speech stimuli at 12 months, and a relation between behavioral and neural asymmetries. Future investigations of early asymmetry patterns, especially atypical hemispheric specialization, may be informative in the early identification of ASD.

Seizures and EEG features in 74 patients with genetic-dysmorphic syndromes.

PubMed

Alfei, Enrico; Raviglione, Federico; Franceschetti, Silvana; D'Arrigo, Stefano; Milani, Donatella; Selicorni, Angelo; Riva, Daria; Zuffardi, Orsetta; Pantaleoni, Chiara; Binelli, Simona

2014-12-01

Epilepsy is one of the most common findings in chromosome aberrations. Types of seizures and severity may significantly vary both between different conditions and within the same aberration. Hitherto specific seizures and EEG patterns are identified for only few syndromes. We studied 74 patients with defined genetic-dysmorphic syndromes with and without epilepsy in order to assess clinical and electroencephalographic features, to compare our observation with already described electro-clinical phenotypes, and to identify putative electroencephalographic and/or seizure characteristics useful to address the diagnosis. In our population, 10 patients had chromosomal disorders, 19 microdeletion or microduplication syndromes, and 32 monogenic syndromes. In the remaining 13, syndrome diagnosis was assessed on clinical grounds. Our study confirmed the high incidence of epilepsy in genetic-dysmorphic syndromes. Moreover, febrile seizures and neonatal seizures had a higher incidence compared to general population. In addition, more than one third of epileptic patients had drug-resistant epilepsy. EEG study revealed poor background organization in 42 patients, an excess of diffuse rhythmic activities in beta, alpha or theta frequency bands in 34, and epileptiform patterns in 36. EEG was completely normal only in 20 patients. No specific electro-clinical pattern was identified, except for inv-dup15, Angelman, and Rett syndromes. Nevertheless some specific conditions are described in detail, because of notable differences from what previously reported. Regarding the diagnostic role of EEG, we found that--even without any epileptiform pattern--the generation of excessive rhythmic activities in different frequency bandwidths might support the diagnosis of a genetic syndrome. © 2014 Wiley Periodicals, Inc.

Generating Customized Verifiers for Automatically Generated Code

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2008-01-01

Program verification using Hoare-style techniques requires many logical annotations. We have previously developed a generic annotation inference algorithm that weaves in all annotations required to certify safety properties for automatically generated code. It uses patterns to capture generator- and property-specific code idioms and property-specific meta-program fragments to construct the annotations. The algorithm is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, this is difficult since it involves tedious and error-prone low-level term manipulations. Here, we describe an annotation schema compiler that largely automates this customization task using generative techniques. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all customized analysis functions and glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator, and we demonstrate this by customizing it to certify frame safety of space flight navigation code that was automatically generated from Simulink models by MathWorks' Real-Time Workshop.

Neurophysiology and itch pathways.

PubMed

Schmelz, Martin

2015-01-01

As we all can easily differentiate the sensations of itch and pain, the most straightforward neurophysiologic concept would consist of two specific pathways that independently encode itch and pain. Indeed, a neuronal pathway for histamine-induced itch in the peripheral and central nervous system has been described in animals and humans, and recently several non-histaminergic pathways for itch have been discovered in rodents that support a dichotomous concept differentiated into a pain and an itch pathway, with both pathways being composed of different "flavors." Numerous markers and mediators have been found that are linked to itch processing pathways. Thus, the delineation of neuronal pathways for itch from pain pathways seemingly proves that all sensory aspects of itch are based on an itch-specific neuronal pathway. However, such a concept is incomplete as itch can also be induced by the activation of the pain pathway in particular when the stimulus is applied in a highly localized spatial pattern. These opposite views reflect the old dispute between specificity and pattern theories of itch. Rather than only being of theoretic interest, this conceptual problem has key implication for the strategy to treat chronic itch as key therapeutic targets would be either itch-specific pathways or unspecific nociceptive pathways.

Validity of the Rapid Eating Assessment for Patients for assessing dietary patterns in NCAA athletes.

PubMed

Kurka, Jonathan M; Buman, Matthew P; Ainsworth, Barbara E

2014-01-01

Athletes may be at risk for developing adverse health outcomes due to poor eating behaviors during college. Due to the complex nature of the diet, it is difficult to include or exclude individual food items and specific food groups from the diet. Eating behaviors may better characterize the complex interactions between individual food items and specific food groups. The purpose was to examine the Rapid Eating Assessment for Patients survey (REAP) as a valid tool for analyzing eating behaviors of NCAA Division-I male and female athletes using pattern identification. Also, to investigate the relationships between derived eating behavior patterns and body mass index (BMI) and waist circumference (WC) while stratifying by sex and aesthetic nature of the sport. Two independent samples of male (n = 86; n = 139) and female (n = 64; n = 102) collegiate athletes completed the REAP in June-August 2011 (n = 150) and June-August 2012 (n = 241). Principal component analysis (PCA) determined possible factors using wave-1 athletes. Exploratory (EFA) and confirmatory factor analyses (CFA) determined factors accounting for error and confirmed model fit in wave-2 athletes. Wave-2 athletes' BMI and WC were recorded during a physical exam and sport participation determined classification in aesthetic and non-aesthetic sport. Mean differences in eating behavior pattern score were explored. Regression models examined interactions between pattern scores, participation in aesthetic or non-aesthetic sport, and BMI and waist circumference controlling for age and race. A 5-factor PCA solution accounting for 60.3% of sample variance determined fourteen questions for EFA and CFA. A confirmed solution revealed patterns of Desserts, Healthy food, Meats, High-fat food, and Dairy. Pattern score (mean ± SE) differences were found, as non-aesthetic sport males had a higher (better) Dessert score than aesthetic sport males (2.16 ± 0.07 vs. 1.93 ± 0.11). Female aesthetic athletes had a higher score compared to non-aesthetic female athletes for the Dessert (2.11 ± 0.11 vs. 1.88 ± 0.08), Meat (1.95 ± 0.10 vs. 1.72 ± 0.07), High-fat food (1.70 ± 0.08 vs. 1.46 ± 0.06), and Dairy (1.70 ± 0.11 vs. 1.43 ± 0.07) patterns. REAP is a construct valid tool to assess dietary patterns in college athletes. In light of varying dietary patterns, college athletes should be evaluated for healthful and unhealthful eating behaviors.

Unique processing during a period of high excitation/inhibition balance in adult-born neurons.

PubMed

Marín-Burgin, Antonia; Mongiat, Lucas A; Pardi, M Belén; Schinder, Alejandro F

2012-03-09

The adult dentate gyrus generates new granule cells (GCs) that develop over several weeks and integrate into the preexisting network. Although adult hippocampal neurogenesis has been implicated in learning and memory, the specific role of new GCs remains unclear. We examined whether immature adult-born neurons contribute to information encoding. By combining calcium imaging and electrophysiology in acute slices, we found that weak afferent activity recruits few mature GCs while activating a substantial proportion of the immature neurons. These different activation thresholds are dictated by an enhanced excitation/inhibition balance transiently expressed in immature GCs. Immature GCs exhibit low input specificity that switches with time toward a highly specific responsiveness. Therefore, activity patterns entering the dentate gyrus can undergo differential decoding by a heterogeneous population of GCs originated at different times.

CRISPR/Cas9-loxP-Mediated Gene Editing as a Novel Site-Specific Genetic Manipulation Tool.

PubMed

Yang, Fayu; Liu, Changbao; Chen, Ding; Tu, Mengjun; Xie, Haihua; Sun, Huihui; Ge, Xianglian; Tang, Lianchao; Li, Jin; Zheng, Jiayong; Song, Zongming; Qu, Jia; Gu, Feng

2017-06-16

Cre-loxP, as one of the site-specific genetic manipulation tools, offers a method to study the spatial and temporal regulation of gene expression/inactivation in order to decipher gene function. CRISPR/Cas9-mediated targeted genome engineering technologies are sparking a new revolution in biological research. Whether the traditional site-specific genetic manipulation tool and CRISPR/Cas9 could be combined to create a novel genetic tool for highly specific gene editing is not clear. Here, we successfully generated a CRISPR/Cas9-loxP system to perform gene editing in human cells, providing the proof of principle that these two technologies can be used together for the first time. We also showed that distinct non-homologous end-joining (NHEJ) patterns from CRISPR/Cas9-mediated gene editing of the targeting sequence locates at the level of plasmids (episomal) and chromosomes. Specially, the CRISPR/Cas9-mediated NHEJ pattern in the nuclear genome favors deletions (64%-68% at the human AAVS1 locus versus 4%-28% plasmid DNA). CRISPR/Cas9-loxP, a novel site-specific genetic manipulation tool, offers a platform for the dissection of gene function and molecular insights into DNA-repair pathways. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Neurofilament protein defines regional patterns of cortical organization in the macaque monkey visual system: a quantitative immunohistochemical analysis

NASA Technical Reports Server (NTRS)

Hof, P. R.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

1995-01-01

Visual function in monkeys is subserved at the cortical level by a large number of areas defined by their specific physiological properties and connectivity patterns. For most of these cortical fields, a precise index of their degree of anatomical specialization has not yet been defined, although many regional patterns have been described using Nissl or myelin stains. In the present study, an attempt has been made to elucidate the regional characteristics, and to varying degrees boundaries, of several visual cortical areas in the macaque monkey using an antibody to neurofilament protein (SMI32). This antibody labels a subset of pyramidal neurons with highly specific regional and laminar distribution patterns in the cerebral cortex. Based on the staining patterns and regional quantitative analysis, as many as 28 cortical fields were reliably identified. Each field had a homogeneous distribution of labeled neurons, except area V1, where increases in layer IVB cell and in Meynert cell counts paralleled the increase in the degree of eccentricity in the visual field representation. Within the occipitotemporal pathway, areas V3 and V4 and fields in the inferior temporal cortex were characterized by a distinct population of neurofilament-rich neurons in layers II-IIIa, whereas areas located in the parietal cortex and part of the occipitoparietal pathway had a consistent population of large labeled neurons in layer Va. The mediotemporal areas MT and MST displayed a distinct population of densely labeled neurons in layer VI. Quantitative analysis of the laminar distribution of the labeled neurons demonstrated that the visual cortical areas could be grouped in four hierarchical levels based on the ratio of neuron counts between infragranular and supragranular layers, with the first (areas V1, V2, V3, and V3A) and third (temporal and parietal regions) levels characterized by low ratios and the second (areas MT, MST, and V4) and fourth (frontal regions) levels characterized by high to very high ratios. Such density trends may correspond to differential representation of corticocortically (and corticosubcortically) projecting neurons at several functional steps in the integration of the visual stimuli. In this context, it is possible that neurofilament protein is crucial for the unique capacity of certain subsets of neurons to perform the highly precise mapping functions of the monkey visual system.

Bmp2 and Notch cooperate to pattern the embryonic endocardium.

PubMed

Papoutsi, T; Luna-Zurita, L; Prados, B; Zaffran, S; de la Pompa, J L

2018-05-31

Signaling interactions between myocardium and endocardium pattern embryonic cardiac regions, instructing their development to fulfill specific functions in the mature heart. We show that ectopic Bmp2 expression in the mouse chamber myocardium changes the transcriptional signature of adjacent chamber endocardial cells into valve tissue, and enables them to undergo epithelial-mesenchyme transition. This induction is independent of valve myocardium specification and requires high levels of Notch1 activity. Biochemical experiments suggest that Bmp2-mediated Notch1 induction is achieved through transcriptional activation of the Notch ligand Jag1, and physical interaction of Smad1/5 with the intracellular domain of the Notch1 receptor. Thus, widespread myocardial Bmp2 and endocardial Notch signaling drive presumptive ventricular endocardium to differentiate into valve endocardium. Understanding the molecular basis of valve development is instrumental to designing therapeutic strategies for congenital heart valve defects. © 2018. Published by The Company of Biologists Ltd.

Clinical potential of proteomics in the diagnosis of ovarian cancer.

PubMed

Ardekani, Ali M; Liotta, Lance A; Petricoin, Emanuel F

2002-07-01

The need for specific and sensitive markers of ovarian cancer is critical. Finding a sensitive and specific test for its detection has an important public health impact. Currently, there are no effective screening options available for patients with ovarian cancer. CA-125, the most widely used biomarker for ovarian cancer, does not have a high positive predictive value and it is only effective when used in combination with other diagnostic tests. However, pathologic changes taking place within the ovary may be reflected in biomarker patterns in the serum. Combination of mass spectra generated by new proteomic technologies, such as surface-enhanced laser desorption ionization time-of-flight (SELDI-TOF) and artificial-intelligence-based informatic algorithms, have been used to discover a small set of key protein values and discriminate normal from ovarian cancer patients. Serum proteomic pattern analysis might be applied ultimately in medical screening clinics, as a supplement to the diagnostic work-up and evaluation.

Prosody and alignment: a sequential perspective

NASA Astrophysics Data System (ADS)

Szczepek Reed, Beatrice

2010-12-01

In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.

Detecting Mental States by Machine Learning Techniques: The Berlin Brain-Computer Interface

NASA Astrophysics Data System (ADS)

Blankertz, Benjamin; Tangermann, Michael; Vidaurre, Carmen; Dickhaus, Thorsten; Sannelli, Claudia; Popescu, Florin; Fazli, Siamac; Danóczy, Márton; Curio, Gabriel; Müller, Klaus-Robert

The Berlin Brain-Computer Interface Brain-Computer Interface (BBCI) uses a machine learning approach to extract user-specific patterns from high-dimensional EEG-features optimized for revealing the user's mental state. Classical BCI applications are brain actuated tools for patients such as prostheses (see Section 4.1) or mental text entry systems ([1] and see [2-5] for an overview on BCI). In these applications, the BBCI uses natural motor skills of the users and specifically tailored pattern recognition algorithms for detecting the user's intent. But beyond rehabilitation, there is a wide range of possible applications in which BCI technology is used to monitor other mental states, often even covert ones (see also [6] in the fMRI realm). While this field is still largely unexplored, two examples from our studies are exemplified in Sections 4.3 and 4.4.

Assessing Specific Grapho-Phonemic Skills in Elementary Students

ERIC Educational Resources Information Center

Robbins, Kelly P.; Hosp, John L.; Hosp, Michelle K.; Flynn, Lindsay J.

2010-01-01

This study examines the relation between decoding and spelling performance on tasks that represent identical specific grapho-phonemic patterns. Elementary students (N = 206) were administered a 597 pseudoword decoding inventory representing 12 specific grapho-phonemic patterns and a 104 real-word spelling inventory representing identical…

A parsimonious characterization of change in global age-specific and total fertility rates

PubMed Central

2018-01-01

This study aims to understand trends in global fertility from 1950-2010 though the analysis of age-specific fertility rates. This approach incorporates both the overall level, as when the total fertility rate is modeled, and different patterns of age-specific fertility to examine the relationship between changes in age-specific fertility and fertility decline. Singular value decomposition is used to capture the variation in age-specific fertility curves while reducing the number of dimensions, allowing curves to be described nearly fully with three parameters. Regional patterns and trends over time are evident in parameter values, suggesting this method provides a useful tool for considering fertility decline globally. The second and third parameters were analyzed using model-based clustering to examine patterns of age-specific fertility over time and place; four clusters were obtained. A country’s demographic transition can be traced through time by membership in the different clusters, and regional patterns in the trajectories through time and with fertility decline are identified. PMID:29377899

Recognition of plant parts with problem-specific algorithms

NASA Astrophysics Data System (ADS)

Schwanke, Joerg; Brendel, Thorsten; Jensch, Peter F.; Megnet, Roland

1994-06-01

Automatic micropropagation is necessary to produce cost-effective high amounts of biomass. Juvenile plants are dissected in clean- room environment on particular points on the stem or the leaves. A vision-system detects possible cutting points and controls a specialized robot. This contribution is directed to the pattern- recognition algorithms to detect structural parts of the plant.

All the Stereotypes Confirmed: Differences in How Australian Boys and Girls Use Their Time

ERIC Educational Resources Information Center

Ferrar, Katia E.; Olds, Tim S.; Walters, Julie L.

2012-01-01

Background: To influence adolescent health, a greater understanding of time use and covariates such as gender is required. Purpose: To explore gender-specific time use patterns in Australian adolescents using high-resolution time use data. Method: This study analyzed 24-hour recall time use data collected as part of the 2007 Australian National…

Teaching about the "Economic Crisis" Today. The Example of French "Economic and Social Sciences"

ERIC Educational Resources Information Center

Coléno, Yves-Patrick; Blanchard, Hervé

2017-01-01

Purpose: In France at the high school the subject matter "Sciences Économiques et Sociales" (economic and social sciences) deals with the present economic crisis. We study the ways it is taught about: words, and explanatory patterns. Design/methodology/approach: We use a specific approach, that we call "semantic holism",…

Brain Wiring in the Fourth Dimension.

PubMed

Wernet, Mathias F; Desplan, Claude

2015-07-02

In this issue of Cell, Langen et al. use time-lapse multiphoton microscopy to show how Drosophila photoreceptor growth cones find their targets. Based on the observed dynamics, they develop a simple developmental algorithm recapitulating the highly complex connectivity pattern of these neurons, suggesting a basic framework for establishing wiring specificity. Copyright © 2015 Elsevier Inc. All rights reserved.

Interindividual Differences in Neonatal Imitation and the Development of Action Chains in Rhesus Macaques

ERIC Educational Resources Information Center

Ferrari, Pier Francesco; Paukner, Annika; Ruggiero, Angela; Darcey, Lisa; Unbehagen, Sarah; Suomi, Stephen J.

2009-01-01

The capacity to imitate facial gestures is highly variable in rhesus macaques and this variability may be related to differences in specific neurobehavioral patterns of development. This study evaluated the differential neonatal imitative response of 41 macaques in relation to the development of sensory, motor, and cognitive skills throughout the…

Chatting in L2 Spanish: Interactivity, Self-Efficacy and Interpersonal Relations

ERIC Educational Resources Information Center

Sanchez-Castro, Olga; Mrowa-Hopkins, Colette

2012-01-01

This study seeks to examine variations in patterns of interactivity as they are displayed in the ongoing discourse construction of high and low self-efficacy learners of Spanish in the context of computer-mediated-communication. The paper specifically focuses on the analysis of synchronous text chats of six university students of Spanish at…

"Having Our Say": High Achieving African American Male College Graduates Speak about Parental Involvement and Parenting Style

ERIC Educational Resources Information Center

Odom, Lynn Lanier; McNeese, Rose M.

2014-01-01

The purpose of this study was to examine the patterns of parental involvement and parenting styles of the parents of academically successful African American males who graduated from historically Black colleges or universities (Odom, 2013). More specifically, the study investigated relationships among students' perceptions of their parents'…

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

PubMed Central

Skelly, Daniel A.; Johansson, Marnie; Madeoy, Jennifer; Wakefield, Jon; Akey, Joshua M.

2011-01-01

Variation in gene expression is thought to make a significant contribution to phenotypic diversity among individuals within populations. Although high-throughput cDNA sequencing offers a unique opportunity to delineate the genome-wide architecture of regulatory variation, new statistical methods need to be developed to capitalize on the wealth of information contained in RNA-seq data sets. To this end, we developed a powerful and flexible hierarchical Bayesian model that combines information across loci to allow both global and locus-specific inferences about allele-specific expression (ASE). We applied our methodology to a large RNA-seq data set obtained in a diploid hybrid of two diverse Saccharomyces cerevisiae strains, as well as to RNA-seq data from an individual human genome. Our statistical framework accurately quantifies levels of ASE with specified false-discovery rates, achieving high reproducibility between independent sequencing platforms. We pinpoint loci that show unusual and biologically interesting patterns of ASE, including allele-specific alternative splicing and transcription termination sites. Our methodology provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes. PMID:21873452

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns.

PubMed

De Filippis, Francesca; Pellegrini, Nicoletta; Laghi, Luca; Gobbetti, Marco; Ercolini, Danilo

2016-10-21

Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations. Here, we used oligotyping of 16S rRNA gene sequencing data to exploit the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore and non-omnivore subjects from a previously studied cohort. A great heterogeneity was found in oligotype composition. Nevertheless, different oligotypes within the same genus showed distinctive correlation patterns with dietary components and metabolome. We found that some Prevotella oligotypes are significantly associated with the plant-based diet but some are associated with animal-based nutrients, and the same applies to Bacteroides. Therefore, an indiscriminate association of Bacteroidetes genera with specific dietary patterns may lead to an oversimplified vision that does not take into account sub-genus diversity and the different possible responses to dietary components. We demonstrated that Prevotella and Bacteroides oligotypes show distinctive correlation patterns with dietary components and metabolome. These results substantiate a current oversimplification of diet-dependent microbe-host associations and highlighted that sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits.

Qualitative pattern classification of shear wave elastography for breast masses: how it correlates to quantitative measurements.

PubMed

Yoon, Jung Hyun; Ko, Kyung Hee; Jung, Hae Kyoung; Lee, Jong Tae

2013-12-01

To determine the correlation of qualitative shear wave elastography (SWE) pattern classification to quantitative SWE measurements and whether it is representative of quantitative SWE values with similar performances. From October 2012 to January 2013, 267 breast masses of 236 women (mean age: 45.12 ± 10.54 years, range: 21-88 years) who had undergone ultrasonography (US), SWE, and subsequent biopsy were included. US BI-RADS final assessment and qualitative and quantitative SWE measurements were recorded. Correlation between pattern classification and mean elasticity, maximum elasticity, elasticity ratio and standard deviation were evaluated. Diagnostic performances of grayscale US, SWE parameters, and US combined to SWE values were calculated and compared. Of the 267 breast masses, 208 (77.9%) were benign and 59 (22.1%) were malignant. Pattern classifications significantly correlated with all quantitative SWE measurements, showing highest correlation with maximum elasticity, r = 0.721 (P<0.001). Sensitivity was significantly decreased in US combined to SWE measurements to grayscale US: 69.5-89.8% to 100.0%, while specificity was significantly improved: 62.5-81.7% to 13.9% (P<0.001). Area under the ROC curve (Az) did not show significant differences between grayscale US to US combined to SWE (P>0.05). Pattern classification shows high correlation to maximum stiffness and may be representative of quantitative SWE values. When combined to grayscale US, SWE improves specificity of US. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Effects of Foot Strike and Step Frequency on Achilles Tendon Stress During Running.

PubMed

Lyght, Michael; Nockerts, Matthew; Kernozek, Thomas W; Ragan, Robert

2016-08-01

Achilles tendon (AT) injuries are common in runners. The AT withstands high magnitudes of stress during running which may contribute to injury. Our purpose was to examine the effects of foot strike pattern and step frequency on AT stress and strain during running utilizing muscle forces based on a musculoskeletal model and subject-specific ultrasound-derived AT cross-sectional area. Nineteen female runners performed running trials under 6 conditions, including rearfoot strike and forefoot strike patterns at their preferred cadence, +5%, and -5% preferred cadence. Rearfoot strike patterns had less peak AT stress (P < .001), strain (P < .001), and strain rate (P < .001) compared with the forefoot strike pattern. A reduction in peak AT stress and strain were exhibited with a +5% preferred step frequency relative to the preferred condition using a rearfoot (P < .001) and forefoot (P=.005) strike pattern. Strain rate was not different (P > .05) between step frequencies within each foot strike condition. Our results suggest that a rearfoot pattern may reduce AT stress, strain, and strain rate. Increases in step frequency of 5% above preferred frequency, regardless of foot strike pattern, may also lower peak AT stress and strain.

Plant pattern recognition receptor complexes at the plasma membrane.

PubMed

Monaghan, Jacqueline; Zipfel, Cyril

2012-08-01

A key feature of innate immunity is the ability to recognize and respond to potential pathogens in a highly sensitive and specific manner. In plants, the activation of pattern recognition receptors (PRRs) by pathogen-associated molecular patterns (PAMPs) elicits a defense programme known as PAMP-triggered immunity (PTI). Although only a handful of PAMP-PRR pairs have been defined, all known PRRs are modular transmembrane proteins containing ligand-binding ectodomains. It is becoming clear that PRRs do not act alone but rather function as part of multi-protein complexes at the plasma membrane. Recent studies describing the molecular interactions and protein modifications that occur between PRRs and their regulatory proteins have provided important mechanistic insight into how plants avoid infection and achieve immunity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Navier-Stokes flow field analysis of compressible flow in a high pressure safety relief valve

NASA Technical Reports Server (NTRS)

Vu, Bruce; Wang, Ten-See; Shih, Ming-Hsin; Soni, Bharat

1993-01-01

The objective of this study is to investigate the complex three-dimensional flowfield of an oxygen safety pressure relieve valve during an incident, with a computational fluid dynamic (CFD) analysis. Specifically, the analysis will provide a flow pattern that would lead to the expansion of the eventual erosion pattern of the hardware, so as to combine it with other findings to piece together a most likely scenario for the investigation. The CFD model is a pressure based solver. An adaptive upwind difference scheme is employed for the spatial discretization, and a predictor, multiple corrector method is used for the velocity-pressure coupling. The computational result indicated vortices formation near the opening of the valve which matched the erosion pattern of the damaged hardware.

Spatial frequency filtered images reveal differences between masked and unmasked processing of emotional information.

PubMed

Rohr, Michaela; Wentura, Dirk

2014-10-01

High and low spatial frequency information has been shown to contribute differently to the processing of emotional information. In three priming studies using spatial frequency filtered emotional face primes, emotional face targets, and an emotion categorization task, we investigated this issue further. Differences in the pattern of results between short and masked, and short and long unmasked presentation conditions emerged. Given long and unmasked prime presentation, high and low frequency primes triggered emotion-specific priming effects. Given brief and masked prime presentation in Experiment 2, we found a dissociation: High frequency primes caused a valence priming effect, whereas low frequency primes yielded a differentiation between low and high arousing information within the negative domain. Brief and unmasked prime presentation in Experiment 3 revealed that subliminal processing of primes was responsible for the pattern observed in Experiment 2. The implications of these findings for theories of early emotional information processing are discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Liga developer apparatus system

DOEpatents

Boehme, Dale R.; Bankert, Michelle A.; Christenson, Todd R.

2003-01-01

A system to fabricate precise, high aspect ratio polymeric molds by photolithograpic process is described. The molds for producing micro-scale parts from engineering materials by the LIGA process. The invention is a developer system for developing a PMMA photoresist having exposed patterns comprising features having both very small sizes, and very high aspect ratios. The developer system of the present invention comprises a developer tank, an intermediate rinse tank and a final rinse tank, each tank having a source of high frequency sonic agitation, temperature control, and continuous filtration. It has been found that by moving a patterned wafer, through a specific sequence of developer/rinse solutions, where an intermediate rinse solution completes development of those portions of the exposed resist left undeveloped after the development solution, by agitating the solutions with a source of high frequency sonic vibration, and by adjusting and closely controlling the temperatures and continuously filtering and recirculating these solutions, it is possible to maintain the kinetic dissolution of the exposed PMMA polymer as the rate limiting step.

A High Throughput Protein Microarray Approach to Classify HIV Monoclonal Antibodies and Variant Antigens

PubMed Central

Dotsey, Emmanuel Y.; Gorlani, Andrea; Ingale, Sampat; Achenbach, Chad J.; Forthal, Donald N.; Felgner, Philip L.; Gach, Johannes S.

2015-01-01

In recent years, high throughput discovery of human recombinant monoclonal antibodies (mAbs) has been applied to greatly advance our understanding of the specificity, and functional activity of antibodies against HIV. Thousands of antibodies have been generated and screened in functional neutralization assays, and antibodies associated with cross-strain neutralization and passive protection in primates, have been identified. To facilitate this type of discovery, a high throughput-screening tool is needed to accurately classify mAbs, and their antigen targets. In this study, we analyzed and evaluated a prototype microarray chip comprised of the HIV-1 recombinant proteins gp140, gp120, gp41, and several membrane proximal external region peptides. The protein microarray analysis of 11 HIV-1 envelope-specific mAbs revealed diverse binding affinities and specificities across clades. Half maximal effective concentrations, generated by our chip analysis, correlated significantly (P<0.0001) with concentrations from ELISA binding measurements. Polyclonal immune responses in plasma samples from HIV-1 infected subjects exhibited different binding patterns, and reactivity against printed proteins. Examining the totality of the specificity of the humoral response in this way reveals the exquisite diversity, and specificity of the humoral response to HIV. PMID:25938510

Drug Resistance Patterns of Escherichia coli in Ethiopia: A Meta-Analysis.

PubMed

Tuem, Kald Beshir; Gebre, Abadi Kahsu; Atey, Tesfay Mehari; Bitew, Helen; Yimer, Ebrahim M; Berhe, Derbew Fikadu

2018-01-01

Antimicrobial drug resistance is a global threat for treatment of infectious diseases and costs life and money and threatens health delivery system's effectiveness. The resistance of E. coli to frequently utilized antimicrobial drugs is becoming a major challenge in Ethiopia. However, there is no inclusive countrywide study. Therefore, this study intended to assess the prevalence of E. coli resistance and antimicrobial-specific resistance pattern among E. coli clinical isolates in Ethiopia. Articles were retrieved from PubMed, Embase, and grey literature from 2007 to 2017. The main outcome measures were overall E. coli and drug-specific resistance patterns. A random-effects model was used to determine pooled prevalence with 95% confidence interval (CI), using DerSimonian and Laird method. In addition, subgroup analysis was conducted to improve the outcome. The study bias was assessed by Begg's funnel plot. This study was registered in PROSPERO as follows: PROSPERO 2017: CRD42017070106. Of 164 articles retrieved, 35 articles were included. A total of 19,235 study samples participated in the studies and 2,635 E. coli strains were isolated. Overall, E. coli antibacterial resistance was 45.38% (95% confidence interval (CI): 33.50 to 57.27). The resistance pattern ranges from 62.55% in Addis Ababa to 27.51% in Tigray region. The highest resistance of E. coli reported was to ampicillin (83.81%) and amoxicillin (75.79%), whereas only 13.55% of E. coli isolates showed resistance to nitrofurantoin. E. coli antimicrobial resistance remains high with disparities observed among regions. The bacterium was found to be highly resistant to aminopenicillins. The finding implies the need for effective prevention strategies for the E. coli drug resistance and calls for multifaceted approaches with full involvement of all stakeholders.

Properties of Fructan:Fructan 1-Fructosyltransferases from Chicory and Globe Thistle, Two Asteracean Plants Storing Greatly Different Types of Inulin1

PubMed Central

Vergauwen, Rudy; Van Laere, André; Van den Ende, Wim

2003-01-01

Remarkably, within the Asteraceae, a species-specific fructan pattern can be observed. Some species such as artichoke (Cynara scolymus) and globe thistle (Echinops ritro) store fructans with a considerably higher degree of polymerization than the one observed in chicory (Cichorium intybus) and Jerusalem artichoke (Helianthus tuberosus). Fructan:fructan 1-fructosyltransferase (1-FFT) is the enzyme responsible for chain elongation of inulin-type fructans. 1-FFTs were purified from chicory and globe thistle. A comparison revealed that chicory 1-FFT has a high affinity for sucrose (Suc), fructose (Fru), and 1-kestose as acceptor substrate. This makes redistribution of Fru moieties from large to small fructans very likely during the period of active fructan synthesis in the root when import and concentration of Suc can be expected to be high. In globe thistle, this problem is avoided by the very low affinity of 1-FFT for Suc, Fru, and 1-kestose and the higher affinity for inulin as acceptor substrate. Therefore, the 1-kestose formed by Suc:Suc 1-fructosyltransferase is preferentially used for elongation of inulin molecules, explaining why inulins with a much higher degree of polymerization accumulate in roots of globe thistle. Inulin patterns obtained in vitro from 1-kestose and the purified 1-FFTs from both species closely resemble the in vivo inulin patterns. Therefore, we conclude that the species-specific fructan pattern within the Asteraceae can be explained by the different characteristics of their respective 1-FFTs. Although 1-FFT and bacterial levansucrases clearly differ in their ability to use Suc as a donor substrate, a kinetic analysis suggests that 1-FFT also works via a ping-pong mechanism. PMID:12970504

Chromium-picolinate therapy in diabetes care: molecular and subcellular profiling revealed a necessity for individual outcome prediction, personalised treatment algorithms & new guidelines

PubMed Central

Yeghiazaryan, Kristina; Peeva, Viktoriya; Shenoy, Aparna; Schild, Hans H.; Golubnitschaja, Olga

2013-01-01

Aims Global figures clearly demonstrate inadequacy of current diabetes care: every 10 seconds one patient dies of diabetes-related pathologies. Nephropathy is the leading secondary complication of the disease. Nutritional supplement by chromium-picolinate is assumed to have beneficial therapeutic effects. However, potential toxic effects reported increase concerns about safety of chromium-picolinate. The experimental design aimed at determining, whether the treatment with clinically relevant doses of chromium-picolinate can harm through DNA damage and extensive alterations in central detoxification / cell-cycle regulating pathways in treatment of diabetes. Methods Well-acknowledged animal model of db/db-mice and clinically relevant doses of chromium-picolinate were used. As an index of DNA-damage, measurement of DNA-breaks was performed using “Comet Assay”-analysis. Individual and group-specific expression patterns of SOD-1 and P53 were evaluated to give a clue about central detoxification and cell-cycle regulating pathways under treatment conditions. The study was performed in a double-blind manner. Results Experimental data revealed highly individual reaction under treatment conditions. However, group-specific patterns were monitored: highest amount of damaged DNA - under the longest treatment with high doses, in contrast to groups with low doses of chromium-picolinate. Comet patterns were intermediate between untreated diabetized and control animals. Expression patterns demonstrated a correlation with subcellular imaging and dosage-dependent suppression under chromium-picolinate treatment. Conclusions This article highlights possible risks for individual long-term effects, when chromium-picolinate is used freely as a therapeutic nutritional modality agent without application of advanced diagnostic tools to predict risks and individual outcomes. Targeted measures require a creation of new guidelines for advanced Diabetes care. PMID:21470100

Chromium-picolinate therapy in diabetes care: molecular and subcellular profiling revealed a necessity for individual outcome prediction, personalised treatment algorithms and new guidelines.

PubMed

Yeghiazaryan, Kristina; Peeva, Viktoriya; Shenoy, Aparna; Schild, Hans H; Golubnitschaja, Olga

2011-04-01

Global figures clearly demonstrate inadequacy of current diabetes care: every 10 seconds one patient dies of diabetes-related pathologies. Nephropathy is the leading secondary complication of the disease. Nutritional supplement by chromium-picolinate is assumed to have beneficial therapeutic effects. However, potential toxic effects reported increase concerns about safety of chromium-picolinate. The experimental design aimed at determining, whether the treatment with clinically relevant doses of chromium-picolinate can harm through DNA damage and extensive alterations in central detoxification / cell-cycle regulating pathways in treatment of diabetes. Well-acknowledged animal model of db/db-mice and clinically relevant doses of chromium-picolinate were used. As an index of DNA-damage, measurement of DNA-breaks was performed using "Comet Assay"-analysis. Individual and group-specific expression patterns of SOD-1 and P53 were evaluated to give a clue about central detoxification and cell-cycle regulating pathways under treatment conditions. The study was performed in a double-blind manner. Experimental data revealed highly individual reaction under treatment conditions. However, group-specific patterns were monitored: highest amount of damaged DNA--under the longest treatment with high doses, in contrast to groups with low doses of chromium-picolinate. Comet patterns were intermediate between untreated diabetised and control animals. Expression patterns demonstrated a correlation with subcellular imaging and dosage-dependent suppression under chromium-picolinate treatment. This article highlights possible risks for individual long-term effects, when chromium-picolinate is used freely as a therapeutic nutritional modality agent without application of advanced diagnostic tools to predict risks and individual outcomes. Targeted measures require a creation of new guidelines for advanced Diabetes care.

A combination of plasma phospholipid fatty acids and its association with incidence of type 2 diabetes: The EPIC-InterAct case-cohort study

PubMed Central

Sharp, Stephen J.; Kröger, Janine; Griffin, Julian L.; Sluijs, Ivonne; Agudo, Antonio; Ardanaz, Eva; Balkau, Beverley; Boeing, Heiner; Chajes, Veronique; Dow, Courtney; Fagherazzi, Guy; Feskens, Edith J. M.; Franks, Paul W.; Gavrila, Diana; Gunter, Marc; Kaaks, Rudolf; Key, Timothy J.; Khaw, Kay-Tee; Kühn, Tilman; Melander, Olle; Molina-Portillo, Elena; Nilsson, Peter M.; Olsen, Anja; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Rolandsson, Olov; Sieri, Sabina; Slimani, Nadia; Spijkerman, Annemieke M. W.; Tjønneland, Anne; Langenberg, Claudia; Riboli, Elio

2017-01-01

Background Combinations of multiple fatty acids may influence cardiometabolic risk more than single fatty acids. The association of a combination of fatty acids with incident type 2 diabetes (T2D) has not been evaluated. Methods and findings We measured plasma phospholipid fatty acids by gas chromatography in 27,296 adults, including 12,132 incident cases of T2D, over the follow-up period between baseline (1991–1998) and 31 December 2007 in 8 European countries in EPIC-InterAct, a nested case-cohort study. The first principal component derived by principal component analysis of 27 individual fatty acids (mole percentage) was the main exposure (subsequently called the fatty acid pattern score [FA-pattern score]). The FA-pattern score was partly characterised by high concentrations of linoleic acid, stearic acid, odd-chain fatty acids, and very-long-chain saturated fatty acids and low concentrations of γ-linolenic acid, palmitic acid, and long-chain monounsaturated fatty acids, and it explained 16.1% of the overall variability of the 27 fatty acids. Based on country-specific Prentice-weighted Cox regression and random-effects meta-analysis, the FA-pattern score was associated with lower incident T2D. Comparing the top to the bottom fifth of the score, the hazard ratio of incident T2D was 0.23 (95% CI 0.19–0.29) adjusted for potential confounders and 0.37 (95% CI 0.27–0.50) further adjusted for metabolic risk factors. The association changed little after adjustment for individual fatty acids or fatty acid subclasses. In cross-sectional analyses relating the FA-pattern score to metabolic, genetic, and dietary factors, the FA-pattern score was inversely associated with adiposity, triglycerides, liver enzymes, C-reactive protein, a genetic score representing insulin resistance, and dietary intakes of soft drinks and alcohol and was positively associated with high-density-lipoprotein cholesterol and intakes of polyunsaturated fat, dietary fibre, and coffee (p < 0.05 each). Limitations include potential measurement error in the fatty acids and other model covariates and possible residual confounding. Conclusions A combination of individual fatty acids, characterised by high concentrations of linoleic acid, odd-chain fatty acids, and very long-chain fatty acids, was associated with lower incidence of T2D. The specific fatty acid pattern may be influenced by metabolic, genetic, and dietary factors. PMID:29020051

The measurement capabilities of cross-sectional profile of Nanoimprint template pattern using small angle x-ray scattering

NASA Astrophysics Data System (ADS)

Yamanaka, Eiji; Taniguchi, Rikiya; Itoh, Masamitsu; Omote, Kazuhiko; Ito, Yoshiyasu; Ogata, Kiyoshi; Hayashi, Naoya

2016-05-01

Nanoimprint lithography (NIL) is one of the most potential candidates for the next generation lithography for semiconductor. It will achieve the lithography with high resolution and low cost. High resolution of NIL will be determined by a high definition template. Nanoimprint lithography will faithfully transfer the pattern of NIL template to the wafer. Cross-sectional profile of the template pattern will greatly affect the resist profile on the wafer. Therefore, the management of the cross-sectional profile is essential. Grazing incidence small angle x-ray scattering (GI-SAXS) technique has been proposed as one of the method for measuring cross-sectional profile of periodic nanostructure pattern. Incident x-rays are irradiated to the sample surface with very low glancing angle. It is close to the critical angle of the total reflection of the x-ray. The scattered x-rays from the surface structure are detected on a two-dimensional detector. The observed intensity is discrete in the horizontal (2θ) direction. It is due to the periodicity of the structure, and diffraction is observed only when the diffraction condition is satisfied. In the vertical (β) direction, the diffraction intensity pattern shows interference fringes reflected to height and shape of the structure. Features of the measurement using x-ray are that the optical constant for the materials are well known, and it is possible to calculate a specific diffraction intensity pattern based on a certain model of the cross-sectional profile. The surface structure is estimated by to collate the calculated diffraction intensity pattern that sequentially while changing the model parameters with the measured diffraction intensity pattern. Furthermore, GI-SAXS technique can be measured an object in a non-destructive. It suggests the potential to be an effective tool for product quality assurance. We have developed a cross-sectional profile measurement of quartz template pattern using GI-SAXS technique. In this report, we will report the measurement capabilities of GI-SAXS technique as a cross-sectional profile measurement tool of NIL quartz template pattern.

Epigenetic regulation of somatic angiotensin-converting enzyme by DNA methylation and histone acetylation.

PubMed

Rivière, Guillaume; Lienhard, Daniel; Andrieu, Thomas; Vieau, Didier; Frey, Brigitte M; Frey, Felix J

2011-04-01

Somatic angiotensin-converting enzyme (sACE) is crucial in cardiovascular homeostasis and displays a tissue-specific profile. Epigenetic patterns modulate genes expression and their alterations were implied in pathologies including hypertension. However, the influence of DNA methylation and chromatin condensation state on the expression of sACE is unknown. We examined whether such epigenetic mechanisms could participate in the control of sACE expression in vitro and in vivo. We identified two CpG islands in the human ace-1 gene 3 kb proximal promoter region. Their methylation abolished the luciferase activity of ace-1 promoter/reporter constructs transfected into human liver (HepG2), colon (HT29), microvascular endothelial (HMEC-1) and lung (SUT) cell lines (p < 0.001). Bisulphite sequencing revealed a cell-type specific basal methylation pattern of the ace-1 gene -1,466/+25 region. As assessed by RT-qPCR, inhibition of DNA methylation by 5-aza-2'-deoxycytidine and/or of histone deacetylation by trichostatin A highly stimulated sACE mRNA expression cell-type specifically (p < 0.001 vs. vehicle treated cells). In the rat, in vivo 5-aza-cytidine injections demethylated the ace-1 promoter and increased sACE mRNA expression in the lungs and liver (p = 0.05), but not in the kidney. In conclusion, the expression level of somatic ACE is modulated by CpG-methylation and histone deacetylases inhibition. The basal methylation pattern of the promoter of the ace-1 gene is cell-type specific and correlates to sACE transcription. DNMT inhibition is associated with altered methylation of the ace-1 promoter and a cell-type and tissue-specific increase of sACE mRNA levels. This study indicates a strong influence of epigenetic mechanisms on sACE expression.

Role of phytohormones in insect-specific plant reactions

PubMed Central

Erb, Matthias; Meldau, Stefan; Howe, Gregg A.

2012-01-01

The capacity to perceive and respond is integral to biological immune systems, but to what extent can plants specifically recognize and respond to insects? Recent findings suggest that plants possess surveillance systems that are able to detect general patterns of cellular damage as well as highly specific herbivore-associated cues. The jasmonate (JA) pathway has emerged as the major signaling cassette that integrates information perceived at the plant–insect interface into broad-spectrum defense responses. Specificity can be achieved via JA-independent processes and spatio-temporal changes of JA-modulating hormones, including ethylene, salicylic acid, abscisic acid, auxin, cytokinins, brassinosteroids and gibberellins. The identification of receptors and ligands and an integrative view of hormone-mediated response systems are crucial to understand specificity in plant immunity to herbivores. PMID:22305233

Geomorphological analysis of boulders and polygons on Martian periglacial patterned ground terrains

NASA Astrophysics Data System (ADS)

Orloff, Travis C.

Images from the High Resolution Imaging Science Experiment Camera onboard the Mars Reconnaisance Orbiter show the surface in higher detail than previously capable. I look at a landscape on Mars called permafrost patterned ground which covers ˜10 million square kilometers of the surface at high latitudes (>50°). Using the new high resolution images available we objectively characterize permafrost patterned ground terrains as an alternative to observational surveys which while detailed suffer from subjective bias. I take two dimensional Fourier transforms of individual images of Martian permafrost patterned ground to find the scale most representative of the terrain. This scale acts as a proxy for the size of the polygons themselves. Then I look at the distribution of spectral scales in the northern hemisphere between 50-70° and find correlations to previous studies and with the extent of ground ice in the surface. The high resolution images also show boulders clustering with respect to the underlying pattern. I make the first detailed observations of these clustered boulders and use crater counting to place constraints on the time it takes for boulders to cluster. Finally, I present a potential mechanism for the process that clusters the boulders that takes the specifics of the Martian environment to account. Boulders lying on the surface get trapped in seasonal CO2 frost while ice in the near surface contracts in the winter. The CO2 frost sublimates in spring/summer allowing the boulders to move when the near surface ice expands in summer. Repeated iterations lead to boulders that cluster in the polygon edges. Using a thermal model of the subsurface with Mars conditions and an elastic model of a polygon I show boulders could move as much as ˜0.1mm per year in the present day.

Expression patterns of WRKY genes in di-haploid Populus simonii × P. nigra in response to salinity stress revealed by quantitative real-time PCR and RNA sequencing.

PubMed

Wang, Shengji; Wang, Jiying; Yao, Wenjing; Zhou, Boru; Li, Renhua; Jiang, Tingbo

2014-10-01

Spatio-temporal expression patterns of 13 out of 119 poplar WRKY genes indicated dynamic and tissue-specific roles of WRKY family proteins in salinity stress tolerance. To understand the expression patterns of poplar WRKY genes under salinity stress, 51 of the 119 WRKY genes were selected from di-haploid Populus simonii × P. nigra by quantitative real-time PCR (qRT-PCR). We used qRT-PCR to profile the expression of the top 13 genes under salinity stress across seven time points, and employed RNA-Seq platforms to cross-validate it. Results demonstrated that all the 13 WRKY genes were expressed in root, stem, and leaf tissues, but their expression levels and overall patterns varied notably in these tissues. Regarding overall gene expression in roots, the 13 genes were significantly highly expressed at all six time points after the treatment, reaching the plateau of expression at hour 9. In leaves, the 13 genes were similarly up-regulated from 3 to 12 h in response to NaCl treatment. In stems, however, expression levels of the 13 genes did not show significant changes after the NaCl treatment. Regarding individual gene expression across the time points and the three tissues, the 13 genes can be classified into three clusters: the lowly expressed Cluster 1 containing PthWRKY28, 45 and 105; intermediately expressed Clusters 2 including PthWRKY56, 88 and 116; and highly expressed Cluster 3 consisting of PthWRKY41, 44, 51, 61, 62, 75 and 106. In general, genes in Cluster 2 and 3 displayed a dynamic pattern of "induced amplification-recovering", suggesting that these WRKY genes and corresponding pathways may play a critical role in mediating salt response and tolerance in a dynamic and tissue-specific manner.

CDU improvement technology of etching pattern using photo lithography

NASA Astrophysics Data System (ADS)

Tadokoro, Masahide; Shinozuka, Shinichi; Jyousaka, Megumi; Ogata, Kunie; Morimoto, Tamotsu; Konishi, Yoshitaka

2008-03-01

Semiconductor manufacturing technology has shifted towards finer design rules, and demands for critical dimension uniformity (CDU) of resist patterns have become greater than ever. One of the methods for improving Resist Pattern CDU is to control post-exposure bake (PEB) temperature. When ArF resist is used, there is a certain relationship between critical dimension (CD) and PEB temperature. By utilizing this relationship, Resist Pattern CDU can be improved through control of within-wafer temperature distribution in the PEB process. Resist Pattern CDU improvement contributes to Etching Pattern CDU improvement to a certain degree. To further improve Etching Pattern CDU, etcher-specific CD variation needs to be controlled. In this evaluation, 1. We verified whether etcher-specific CD variation can be controlled and consequently Etching Pattern CDU can be further improved by controlling resist patterns through PEB control. 2. Verifying whether Etching Pattern CDU improvement through has any effect on the reduction in wiring resistance variation. The evaluation procedure is as follows.1. Wafers with base film of Doped Poly-Si (D-Poly) were prepared. 2. Resist patterns were created on them. 3. To determine etcher-specific characteristics, the first etching was performed, and after cleaning off the resist and BARC, CD of etched D-Poly was measured. 4. Using the obtained within-wafer CD distribution of the etching patterns, within-wafer temperature distribution in the PEB process was modified. 5. Resist patterns were created again, followed by the second etching and cleaning, which was followed by CD measurement. We used Optical CD Measurement (OCD) for measurement of resist patterns and etching patterns as OCD is minimally affected by Line Edge Roughness (LER). As a result, 1. We confirmed the effect of Resist Pattern CD control through PEB control on the reduction in etcher-specific CD variation and the improvement in Etching Pattern CDU. 2. The improvement in Etching Pattern CDU has an effect on the reduction in wiring resistance variation. The method for Etching Pattern CDU improvement through PEB control reduces within-wafer variation of MOS transistor's gate length. Therefore, with this method, we can expect to observe uniform within-wafer MOS transistor characteristics.

Distributional patterns in an insect community inhabiting a sandy beach of Uruguay

NASA Astrophysics Data System (ADS)

Mourglia, Virginia; González-Vainer, Patricia; Defeo, Omar

2015-12-01

Most studies of sandy beach macrofauna have been restricted to semiterrestrial species and do not include insects when providing species richness and abundance estimates. Particularly, spatio-temporal patterns of community structure of the entomofauna inhabiting these ecosystems have been scarcely documented. This study assessed spatio-temporal distributional patterns of the night active entomofauna on a beach-dune system of Uruguay, including variations in species richness, abundance and diversity, and their relationship with environmental factors. A deconstructive taxonomic analysis was also performed, considering richness and abundance patterns separately for the most abundant insect Orders (Hymenoptera and Coleoptera) to better understand the factors which drive their patterns. We found clear temporal and across-shore patterns in the insect community inhabiting a land-ocean interface, which matched spatiotemporal variations in the environment. Abundance and species richness were highest in spring and summer, concurrently with high temperatures and low values of sediment moisture and compaction. Multivariate ordinations showed two well-defined species groups, which separated summer, autumn and spring samples from winter ones. Generalized Linear Models allowed us to describe a clear segregation in space of the most important orders of the insect community, with specific preferences for the terrestrial (Hymenoptera) and beach (Coleoptera) fringes. Hymenoptera preferred the dune zone, characterized by high elevation and low sand moisture and compaction levels, whereas Coleoptera preferred gentle slopes and fine and humid sands of the beach. Our results suggest that beach and dune ecosystems operate as two separate components in regard to their physical and biological features. The high values of species richness and abundance of insects reveal that this group has a more significant ecological role than that originally considered so far in sandy beach ecology.

Predicting workload profiles of brain-robot interface and electromygraphic neurofeedback with cortical resting-state networks: personal trait or task-specific challenge?

NASA Astrophysics Data System (ADS)

Fels, Meike; Bauer, Robert; Gharabaghi, Alireza

2015-08-01

Objective. Novel rehabilitation strategies apply robot-assisted exercises and neurofeedback tasks to facilitate intensive motor training. We aimed to disentangle task-specific and subject-related contributions to the perceived workload of these interventions and the related cortical activation patterns. Approach. We assessed the perceived workload with the NASA Task Load Index in twenty-one subjects who were exposed to two different feedback tasks in a cross-over design: (i) brain-robot interface (BRI) with haptic/proprioceptive feedback of sensorimotor oscillations related to motor imagery, and (ii) control of neuromuscular activity with feedback of the electromyography (EMG) of the same hand. We also used electroencephalography to examine the cortical activation patterns beforehand in resting state and during the training session of each task. Main results. The workload profile of BRI feedback differed from EMG feedback and was particularly characterized by the experience of frustration. The frustration level was highly correlated across tasks, suggesting subject-related relevance of this workload component. Those subjects who were specifically challenged by the respective tasks could be detected by an interhemispheric alpha-band network in resting state before the training and by their sensorimotor theta-band activation pattern during the exercise. Significance. Neurophysiological profiles in resting state and during the exercise may provide task-independent workload markers for monitoring and matching participants’ ability and task difficulty of neurofeedback interventions.

Machine Learning-based Individual Assessment of Cortical Atrophy Pattern in Alzheimer's Disease Spectrum: Development of the Classifier and Longitudinal Evaluation.

PubMed

Lee, Jin San; Kim, Changsoo; Shin, Jeong-Hyeon; Cho, Hanna; Shin, Dae-Seock; Kim, Nakyoung; Kim, Hee Jin; Kim, Yeshin; Lockhart, Samuel N; Na, Duk L; Seo, Sang Won; Seong, Joon-Kyung

2018-03-07

To develop a new method for measuring Alzheimer's disease (AD)-specific similarity of cortical atrophy patterns at the individual-level, we employed an individual-level machine learning algorithm. A total of 869 cognitively normal (CN) individuals and 473 patients with probable AD dementia who underwent high-resolution 3T brain MRI were included. We propose a machine learning-based method for measuring the similarity of an individual subject's cortical atrophy pattern with that of a representative AD patient cohort. In addition, we validated this similarity measure in two longitudinal cohorts consisting of 79 patients with amnestic-mild cognitive impairment (aMCI) and 27 patients with probable AD dementia. Surface-based morphometry classifier for discriminating AD from CN showed sensitivity and specificity values of 87.1% and 93.3%, respectively. In the longitudinal validation study, aMCI-converts had higher atrophy similarity at both baseline (p < 0.001) and first year visits (p < 0.001) relative to non-converters. Similarly, AD patients with faster decline had higher atrophy similarity than slower decliners at baseline (p = 0.042), first year (p = 0.028), and third year visits (p = 0.027). The AD-specific atrophy similarity measure is a novel approach for the prediction of dementia risk and for the evaluation of AD trajectories on an individual subject level.

Coordination in Fast Repetitive Violin-Bowing Patterns

PubMed Central

Schoonderwaldt, Erwin; Altenmüller, Eckart

2014-01-01

We present a study of coordination behavior in complex violin-bowing patterns involving simultaneous bow changes (reversal of bowing direction) and string crossings (changing from one string to another). Twenty-two violinists (8 advanced amateurs, 8 students with violin as major subject, and 6 elite professionals) participated in the experiment. We investigated the influence of a variety of performance conditions (specific bowing patterns, dynamic level, tempo, and transposition) and level of expertise on coordination behavior (a.o., relative phase and amplitude) and stability. It was found that the general coordination behavior was highly consistent, characterized by a systematic phase lead of bow inclination over bow velocity of about 15° (i.e., string crossings were consistently timed earlier than bow changes). Within similar conditions, a high individual consistency was found, whereas the inter-individual agreement was considerably less. Furthermore, systematic influences of performance conditions on coordination behavior and stability were found, which could be partly explained in terms of particular performance constraints. Concerning level of expertise, only subtle differences were found, the student and professional groups (higher level of expertise) showing a slightly higher stability than the amateur group (lower level of expertise). The general coordination behavior as observed in the current study showed a high agreement with perceptual preferences reported in an earlier study to similar bowing patterns, implying that complex bowing trajectories for an important part emerge from auditory-motor interaction. PMID:25207542

Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments.

PubMed

Luna, Gian Marco; Corinaldesi, Cinzia; Rastelli, Eugenio; Danovaro, Roberto

2013-10-01

We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Storage and utilization of HLA genomic data--new approaches to HLA typing.

PubMed

Helmberg, W

2000-01-01

Currently available DNA-based HLA typing assays can provide detailed information about sequence motifs of a tested sample. It is still a common practice, however, for information acquired by high-resolution sequence specific oligonucleotide probe (SSOP) typing or sequence specific priming (SSP) to be presented in a low-resolution serological format. Unfortunately, this representation can lead to significant loss of useful data in many cases. An alternative to assigning allele equivalents to suchDNA typing results is simply to store the observed typing pattern and utilize the information with the help of Virtual DNA Analysis (VDA). Interpretation of the stored typing patterns can then be updated based on newly defined alleles, assuming the sequence motifs detected by the typing reagents are known. Rather than updating reagent specificities in individual laboratories, such updates should be performed in a central, publicly available sequence database. By referring to this database, HLA genomic data can then be stored and transferred between laboratories without loss of information. The 13th International Histocompatibility Workshop offers an ideal opportunity to begin building this common database for the entire human MHC.

Beyond Columnar Organization: Cell Type- and Target Layer-Specific Principles of Horizontal Axon Projection Patterns in Rat Vibrissal Cortex

PubMed Central

Narayanan, Rajeevan T.; Egger, Robert; Johnson, Andrew S.; Mansvelder, Huibert D.; Sakmann, Bert; de Kock, Christiaan P.J.; Oberlaender, Marcel

2015-01-01

Vertical thalamocortical afferents give rise to the elementary functional units of sensory cortex, cortical columns. Principles that underlie communication between columns remain however unknown. Here we unravel these by reconstructing in vivo-labeled neurons from all excitatory cell types in the vibrissal part of rat primary somatosensory cortex (vS1). Integrating the morphologies into an exact 3D model of vS1 revealed that the majority of intracortical (IC) axons project far beyond the borders of the principal column. We defined the corresponding innervation volume as the IC-unit. Deconstructing this structural cortical unit into its cell type-specific components, we found asymmetric projections that innervate columns of either the same whisker row or arc, and which subdivide vS1 into 2 orthogonal [supra-]granular and infragranular strata. We show that such organization could be most effective for encoding multi whisker inputs. Communication between columns is thus organized by multiple highly specific horizontal projection patterns, rendering IC-units as the primary structural entities for processing complex sensory stimuli. PMID:25838038

Lineage-specific responses of microbial communities to environmental change.

PubMed

Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

2013-01-01

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

What an anticardiovascular diet should be in 2015.

PubMed

Jacobs, David R; Tapsell, Linda C

2015-08-01

Given scientific and public debate about optimal diet to prevent cardiovascular disease, and interest in diet and other chronic diseases, we propose that following a few simple dietary principles would reduce chronic disease incidence. Nutrition research has been criticized for focusing on individual nutrients and foods, treated like drug therapy. With a few important exceptions, clinical trials of supplemental nutrients have not shown benefit. Although highly specific nutrition information is elusive, diet patterns have provided consistent answers, important for public health. Observational cohort studies have found that some dietary patterns are reported with high reliability over long periods and predict future cardiovascular and other inflammatory-related diseases. Two randomized clinical trials confirmed this finding. There are many common features of Mediterranean and prudent diets, particularly the plant-centered aspect, coupled with variety of foods eaten. A dietary pattern characterized by high fruit, vegetable, legume, whole grain, nut, berry, seed, and fish intakes, and possibly by intakes of dairy, coffee, tea, chocolate, and alcohol (not in excess), but low meat and detrimentally processed foods is associated with reduced incidence of cardiovascular disease and rates of noncardiovascular, noncancer chronic inflammatory-related mortality. A plant-centered diet may be broadly recommended.

Wetting in Color: Designing a colorometric indicator for wettability

NASA Astrophysics Data System (ADS)

Raymond, Kevin; Burgess, Ian B.; Koay, Natalie; Kolle, Mathias; Loncar, Marko; Aizenberg, Joanna

2012-02-01

Colorimetric litmus tests such as pH paper have enjoyed wide commercial success due to their inexpensive production and exceptional ease of use. While such indicators commonly rely on a specific photochemical response to an analyte, we exploit structural color, derived from coherent scattering from wavelength-scale porosity rather than molecular absorption or luminescence, to create a Wetting-in-Color-Kit (WICK). This inexpensive and highly selective colorimetric indicator for organic liquids employs chemically encoded inverse-opal photonic crystals to translate minute differences in liquids' wettability to macroscopically distinct, easy-to-visualize color patterns. The highly symmetric re-entrant inter-pore geometry imparts a highly specific wetting threshold for liquids. We developed surface modification techniques to generate built-in chemistry gradients within the porous network. These let us tailor the wettability threshold to specific liquids across a continuous range. As wetting is a generic fluidic phenomenon, we envision that WICK could be suitable for applications in authentication or identification of unknown liquids across a broad range of industries.

Investigating Patterns of Errors for Specific Comprehension and Fluency Difficulties

ERIC Educational Resources Information Center

Koriakin, Taylor A.; Kaufman, Alan S.

2017-01-01

Although word reading has traditionally been viewed as a foundational skill for development of reading fluency and comprehension, some children demonstrate "specific" reading comprehension problems, in the context of intact word reading. The purpose of this study was to identify specific patterns of errors associated with reading…

Specification Theory, Patterns, and Models in Information Systems Domains: An Exploratory Investigation

ERIC Educational Resources Information Center

Woolridge, Richard William

2010-01-01

Application and project domain specifications are an important aspect of Information Systems (IS) development. Observations of over thirty IS projects suggest dimly perceived structural patterns in specifications that are unaccounted for in research and practice. This investigation utilizes a theory building with case studies methodology to…

Distinct Visual Evoked Potential Morphological Patterns for Apparent Motion Processing in School-Aged Children.

PubMed

Campbell, Julia; Sharma, Anu

2016-01-01

Measures of visual cortical development in children demonstrate high variability and inconsistency throughout the literature. This is partly due to the specificity of the visual system in processing certain features. It may then be advantageous to activate multiple cortical pathways in order to observe maturation of coinciding networks. Visual stimuli eliciting the percept of apparent motion and shape change is designed to simultaneously activate both dorsal and ventral visual streams. However, research has shown that such stimuli also elicit variable visual evoked potential (VEP) morphology in children. The aim of this study was to describe developmental changes in VEPs, including morphological patterns, and underlying visual cortical generators, elicited by apparent motion and shape change in school-aged children. Forty-one typically developing children underwent high-density EEG recordings in response to a continuously morphing, radially modulated, circle-star grating. VEPs were then compared across the age groups of 5-7, 8-10, and 11-15 years according to latency and amplitude. Current density reconstructions (CDR) were performed on VEP data in order to observe activated cortical regions. It was found that two distinct VEP morphological patterns occurred in each age group. However, there were no major developmental differences between the age groups according to each pattern. CDR further demonstrated consistent visual generators across age and pattern. These results describe two novel VEP morphological patterns in typically developing children, but with similar underlying cortical sources. The importance of these morphological patterns is discussed in terms of future studies and the investigation of a relationship to visual cognitive performance.

Longitudinal trajectory patterns of social support: correlates and associated mental health in an Australian national cohort of young women.

PubMed

Holden, Libby; Dobson, Annette J; Ware, Robert S; Hockey, Richard; Lee, Christina

2015-09-01

Although social support is a significant contributor to health and well-being, little is known about patterns of perceived social support over time in young adulthood. It is also unclear which personal characteristics are associated with different patterns, and whether there is an association between social support and mental health over time. We explore these issues in a large national cohort of young women. We used six waves of longitudinal data spanning 16 years, from 10,369 women from the Australian Longitudinal Study on Women's Health, initially aged 18-23. We used group-based trajectory modelling to identify patterns of social support across Surveys 2-6; multinomial logistic regression to identify socio-demographic and health-behaviour predictors at Survey 1 and correlates at Survey 6 for each trajectory group; and generalised linear mixed modelling to estimate mean levels of mental health over the trajectory period for each group, adjusted for confounders. Four distinct trajectory groups of social support were identified: 'High' (58.5 %), 'Decreasing' (20.6 %), 'Low' (9.3 %), and 'Increasing' (11.6 %). Poor health and living outside metropolitan areas at both Surveys 1 and 6 were characteristics of women in all trajectory groups other than the 'High' group, as were early motherhood and being un-partnered at age 34-39. Other characteristics were specific to one or two trajectory groups. Patterns of mental health over time were consistent with patterns of social support. Longitudinal trajectory patterns of social support are associated with mental health, health behaviours, and demographic factors even in early adulthood.