NHash: Randomized N-Gram Hashing for Distributed Generation of Validatable Unique Study Identifiers in Multicenter Research

PubMed Central

Zhang, Guo-Qiang; Tao, Shiqiang; Xing, Guangming; Mozes, Jeno; Zonjy, Bilal; Lhatoo, Samden D

2015-01-01

Background A unique study identifier serves as a key for linking research data about a study subject without revealing protected health information in the identifier. While sufficient for single-site and limited-scale studies, the use of common unique study identifiers has several drawbacks for large multicenter studies, where thousands of research participants may be recruited from multiple sites. An important property of study identifiers is error tolerance (or validatable), in that inadvertent editing mistakes during their transmission and use will most likely result in invalid study identifiers. Objective This paper introduces a novel method called "Randomized N-gram Hashing (NHash)," for generating unique study identifiers in a distributed and validatable fashion, in multicenter research. NHash has a unique set of properties: (1) it is a pseudonym serving the purpose of linking research data about a study participant for research purposes; (2) it can be generated automatically in a completely distributed fashion with virtually no risk for identifier collision; (3) it incorporates a set of cryptographic hash functions based on N-grams, with a combination of additional encryption techniques such as a shift cipher; (d) it is validatable (error tolerant) in the sense that inadvertent edit errors will mostly result in invalid identifiers. Methods NHash consists of 2 phases. First, an intermediate string using randomized N-gram hashing is generated. This string consists of a collection of N-gram hashes f 1, f 2, ..., f k. The input for each function f i has 3 components: a random number r, an integer n, and input data m. The result, f i(r, n, m), is an n-gram of m with a starting position s, which is computed as (r mod |m|), where |m| represents the length of m. The output for Step 1 is the concatenation of the sequence f 1(r 1, n 1, m 1), f 2(r 2, n 2, m 2), ..., f k(r k, n k, m k). In the second phase, the intermediate string generated in Phase 1 is encrypted using techniques such as shift cipher. The result of the encryption, concatenated with the random number r, is the final NHash study identifier. Results We performed experiments using a large synthesized dataset comparing NHash with random strings, and demonstrated neglegible probability for collision. We implemented NHash for the Center for SUDEP Research (CSR), a National Institute for Neurological Disorders and Stroke-funded Center Without Walls for Collaborative Research in the Epilepsies. This multicenter collaboration involves 14 institutions across the United States and Europe, bringing together extensive and diverse expertise to understand sudden unexpected death in epilepsy patients (SUDEP). Conclusions The CSR Data Repository has successfully used NHash to link deidentified multimodal clinical data collected in participating CSR institutions, meeting all desired objectives of NHash. PMID:26554419

Using network screening methods to determine locations with specific safety issues: A design consistency case study.

PubMed

Butsick, Andrew J; Wood, Jonathan S; Jovanis, Paul P

2017-09-01

The Highway Safety Manual provides multiple methods that can be used to identify sites with promise (SWiPs) for safety improvement. However, most of these methods cannot be used to identify sites with specific problems. Furthermore, given that infrastructure funding is often specified for use related to specific problems/programs, a method for identifying SWiPs related to those programs would be very useful. This research establishes a method for Identifying SWiPs with specific issues. This is accomplished using two safety performance functions (SPFs). This method is applied to identifying SWiPs with geometric design consistency issues. Mixed effects negative binomial regression was used to develop two SPFs using 5 years of crash data and over 8754km of two-lane rural roadway. The first SPF contained typical roadway elements while the second contained additional geometric design consistency parameters. After empirical Bayes adjustments, sites with promise (SWiPs) were identified. The disparity between SWiPs identified by the two SPFs was evident; 40 unique sites were identified by each model out of the top 220 segments. By comparing sites across the two models, candidate road segments can be identified where a lack design consistency may be contributing to an increase in expected crashes. Practitioners can use this method to more effectively identify roadway segments suffering from reduced safety performance due to geometric design inconsistency, with detailed engineering studies of identified sites required to confirm the initial assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Realization of a universal patient identifier for electronic medical records through biometric technology.

PubMed

Leonard, D C; Pons, Alexander P; Asfour, Shihab S

2009-07-01

The technology exists for the migration of healthcare data from its archaic paper-based system to an electronic one, and, once in digital form, to be transported anywhere in the world in a matter of seconds. The advent of universally accessible healthcare data has benefited all participants, but one of the outstanding problems that must be addressed is how the creation of a standardized nationwide electronic healthcare record system in the United States would uniquely identify and match a composite of an individual's recorded healthcare information to an identified individual patients out of approximately 300 million people to a 1:1 match. To date, a few solutions to this problem have been proposed that are limited in their effectiveness. We propose the use of biometric technology within our fingerprint, iris, retina scan, and DNA (FIRD) framework, which is a multiphase system whose primary phase is a multilayer consisting of these four types of biometric identifiers: 1) fingerprint; 2) iris; 3) retina scan; and 4) DNA. In addition, it also consists of additional phases of integration, consolidation, and data discrepancy functions to solve the unique association of a patient to their medical data distinctively. This would allow a patient to have real-time access to all of their recorded healthcare information electronically whenever it is necessary, securely with minimal effort, greater effectiveness, and ease.

Developing perspectives on Korean nursing theory: the influences of Taoism.

PubMed

Shin, K R

2001-10-01

Nursing theory provides a systematic explanation and description of nursing phenomena. Western nursing theories have widely influenced Korean nursing. And yet, although nursing theory has universal aspects, the differences in philosophy and culture that are unique to each country need to be considered. This inquiry seeks to investigate the Korean cultural heritage, which integrates Confucianism, Buddhism, and Taoism, and how it provides a unique worldview of human beings, the universe, health, and nursing. Essential principles and therapies consistent with Taoist philosophy are also identified. This framework is proffered as the basis for establishing understanding between Korean nurses and patients.

Theoretical Significance in Q Methodology: A Qualitative Approach to a Mixed Method

ERIC Educational Resources Information Center

Ramlo, Susan

2015-01-01

Q methodology (Q) has offered researchers a unique scientific measure of subjectivity since William Stephenson's first article in 1935. Q's focus on subjectivity includes self-referential meaning and interpretation. Q is most often identified with its technique (Q-sort) and its method (factor analysis to group people); yet, it consists of a…

Organized Sport Trajectories from Childhood to Adolescence and Health Associations.

PubMed

Howie, Erin K; McVeigh, Joanne A; Smith, Anne J; Straker, Leon M

2016-07-01

The purpose of this study was to identify unique organized sport trajectories from early childhood to late adolescence in an Australian pregnancy cohort, the Raine Study. Participation in organized sport was assessed at ages 5, 8, 10, 14, and 17 yr. Physical activity, body composition, and self-rated physical and mental health were assessed at the age of 20 yr. Latent class analysis was used to identify patterns of sport participation. To assess the internal validity of the trajectory classes, differences in health characteristics between trajectories were analyzed using generalized linear models. For girls, three trajectory classes were identified: consistent sport participators (47.5%), sport dropouts (34.3%), and sport nonparticipators (18.1%). For boys, three trajectory classes were identified: consistent sport participators (55.2%), sport dropouts (36.9%), and sport joiners (8.1%). For girls, there were overall differences across trajectory classes in lean body mass (P = 0.003), lean mass index (P = 0.06), and physical health (P = 0.004). For boys, there were differences across classes in physical activity (P = 0.018), percent body fat (P = 0.002), lean body mass (P < 0.001), lean mass index (P < 0.001), physical health (P = 0.06), and depression scores (P = 0.27). This study identified unique, sex-specific trajectories of organized sport participation. The differences in health outcomes between trajectory classes, such as participants with consistent sport participation having more preferable health outcomes at the age of 20 yr, support the internal validity of the trajectories. Strategies are needed to identify and encourage those in the dropout trajectory to maintain their participation and those in the nonparticipator or joiner trajectories to join sport earlier. Specifically, interventions to encourage early sport participation in girls and help nonparticipating boys to join sport during adolescence may help more children receive the benefits of sport participation.

Factor information retrieval system version 2. 0 (fire) (for microcomputers). Software

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

Not Available

FIRE Version 2.0 contains EPA's unique recommended criteria and toxic air emission estimation factors. FIRE consists of: (1) an EPA internal repository system that contains emission factor data identified and collected, and (2) an external distribution system that contains only EPA's recommended factors. The emission factors, compiled from a review of the literature, are identified by pollutant name, CAS number, process and emission source descriptions, SIC code, SCC, and control status. The factors are rated for quality using AP-42 rating criteria.

A Review of Intelligent Driving Style Analysis Systems and Related Artificial Intelligence Algorithms

PubMed Central

Meiring, Gys Albertus Marthinus; Myburgh, Hermanus Carel

2015-01-01

In this paper the various driving style analysis solutions are investigated. An in-depth investigation is performed to identify the relevant machine learning and artificial intelligence algorithms utilised in current driver behaviour and driving style analysis systems. This review therefore serves as a trove of information, and will inform the specialist and the student regarding the current state of the art in driver style analysis systems, the application of these systems and the underlying artificial intelligence algorithms applied to these applications. The aim of the investigation is to evaluate the possibilities for unique driver identification utilizing the approaches identified in other driver behaviour studies. It was found that Fuzzy Logic inference systems, Hidden Markov Models and Support Vector Machines consist of promising capabilities to address unique driver identification algorithms if model complexity can be reduced. PMID:26690164

A Review of Intelligent Driving Style Analysis Systems and Related Artificial Intelligence Algorithms.

PubMed

Meiring, Gys Albertus Marthinus; Myburgh, Hermanus Carel

2015-12-04

In this paper the various driving style analysis solutions are investigated. An in-depth investigation is performed to identify the relevant machine learning and artificial intelligence algorithms utilised in current driver behaviour and driving style analysis systems. This review therefore serves as a trove of information, and will inform the specialist and the student regarding the current state of the art in driver style analysis systems, the application of these systems and the underlying artificial intelligence algorithms applied to these applications. The aim of the investigation is to evaluate the possibilities for unique driver identification utilizing the approaches identified in other driver behaviour studies. It was found that Fuzzy Logic inference systems, Hidden Markov Models and Support Vector Machines consist of promising capabilities to address unique driver identification algorithms if model complexity can be reduced.

A comparison of the performance of seven key bibliographic databases in identifying all relevant systematic reviews of interventions for hypertension.

PubMed

Rathbone, John; Carter, Matt; Hoffmann, Tammy; Glasziou, Paul

2016-02-09

Bibliographic databases are the primary resource for identifying systematic reviews of health care interventions. Reliable retrieval of systematic reviews depends on the scope of indexing used by database providers. Therefore, searching one database may be insufficient, but it is unclear how many need to be searched. We sought to evaluate the performance of seven major bibliographic databases for the identification of systematic reviews for hypertension. We searched seven databases (Cochrane library, Database of Abstracts of Reviews of Effects (DARE), Excerpta Medica Database (EMBASE), Epistemonikos, Medical Literature Analysis and Retrieval System Online (MEDLINE), PubMed Health and Turning Research Into Practice (TRIP)) from 2003 to 2015 for systematic reviews of any intervention for hypertension. Citations retrieved were screened for relevance, coded and checked for screening consistency using a fuzzy text matching query. The performance of each database was assessed by calculating its sensitivity, precision, the number of missed reviews and the number of unique records retrieved. Four hundred systematic reviews were identified for inclusion from 11,381 citations retrieved from seven databases. No single database identified all the retrieved systematic reviews for hypertension. EMBASE identified the most reviews (sensitivity 69 %) but also retrieved the most irrelevant citations with 7.2 % precision (Pr). The sensitivity of the Cochrane library was 60 %, DARE 57 %, MEDLINE 57 %, PubMed Health 53 %, Epistemonikos 49 % and TRIP 33 %. EMBASE contained the highest number of unique records (n = 43). The Cochrane library identified seven unique records and had the highest precision (Pr = 30 %), followed by Epistemonikos (n = 2, Pr = 19 %). No unique records were found in PubMed Health (Pr = 24 %) DARE (Pr = 21 %), TRIP (Pr = 10 %) or MEDLINE (Pr = 10 %). Searching EMBASE and the Cochrane library identified 88 % of all systematic reviews in the reference set, and searching the freely available databases (Cochrane, Epistemonikos, MEDLINE) identified 83 % of all the reviews. The databases were re-analysed after systematic reviews of non-conventional interventions (e.g. yoga, acupuncture) were removed. Similarly, no database identified all the retrieved systematic reviews. EMBASE identified the most relevant systematic reviews (sensitivity 73 %) but also retrieved the most irrelevant citations with Pr = 5 %. The sensitivity of the Cochrane database was 62 %, followed by MEDLINE (60 %), DARE (55 %), PubMed Health (54 %), Epistemonikos (50 %) and TRIP (31 %). The precision of the Cochrane library was the highest (20 %), followed by PubMed Health (Pr = 16 %), DARE (Pr = 13 %), Epistemonikos (Pr = 12 %), MEDLINE (Pr = 6 %), TRIP (Pr = 6 %) and EMBASE (Pr = 5 %). EMBASE contained the most unique records (n = 34). The Cochrane library identified seven unique records. The other databases held no unique records. The coverage of bibliographic databases varies considerably due to differences in their scope and content. Researchers wishing to identify systematic reviews should not rely on one database but search multiple databases.

Mothers Consistently Alter Their Unique Vocal Fingerprints When Communicating with Infants.

PubMed

Piazza, Elise A; Iordan, Marius Cătălin; Lew-Williams, Casey

2017-10-23

The voice is the most direct link we have to others' minds, allowing us to communicate using a rich variety of speech cues [1, 2]. This link is particularly critical early in life as parents draw infants into the structure of their environment using infant-directed speech (IDS), a communicative code with unique pitch and rhythmic characteristics relative to adult-directed speech (ADS) [3, 4]. To begin breaking into language, infants must discern subtle statistical differences about people and voices in order to direct their attention toward the most relevant signals. Here, we uncover a new defining feature of IDS: mothers significantly alter statistical properties of vocal timbre when speaking to their infants. Timbre, the tone color or unique quality of a sound, is a spectral fingerprint that helps us instantly identify and classify sound sources, such as individual people and musical instruments [5-7]. We recorded 24 mothers' naturalistic speech while they interacted with their infants and with adult experimenters in their native language. Half of the participants were English speakers, and half were not. Using a support vector machine classifier, we found that mothers consistently shifted their timbre between ADS and IDS. Importantly, this shift was similar across languages, suggesting that such alterations of timbre may be universal. These findings have theoretical implications for understanding how infants tune in to their local communicative environments. Moreover, our classification algorithm for identifying infant-directed timbre has direct translational implications for speech recognition technology. Copyright © 2017 Elsevier Ltd. All rights reserved.

His Eye Is on the Sparrow: A Counselor of Color's Perception of Facilitating Groups with Predominantly White Members

ERIC Educational Resources Information Center

Marbley, Aretha Faye

2004-01-01

The author uses her personal experience as a co-facilitator of color of groups consisting of predominantly White members to discuss the literature on the group dynamics of multicultural counseling and to identify unique and common issues for diverse counselors facilitating White and culturally different race groups. Included in the discussions of…

A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.

PubMed

Stewart, Paul A; Parapatics, Katja; Welsh, Eric A; Müller, André C; Cao, Haoyun; Fang, Bin; Koomen, John M; Eschrich, Steven A; Bennett, Keiryn L; Haura, Eric B

2015-01-01

We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.

IDGenerator: unique identifier generator for epidemiologic or clinical studies.

PubMed

Olden, Matthias; Holle, Rolf; Heid, Iris M; Stark, Klaus

2016-09-15

Creating study identifiers and assigning them to study participants is an important feature in epidemiologic studies, ensuring the consistency and privacy of the study data. The numbering system for identifiers needs to be random within certain number constraints, to carry extensions coding for organizational information, or to contain multiple layers of numbers per participant to diversify data access. Available software can generate globally-unique identifiers, but identifier-creating tools meeting the special needs of epidemiological studies are lacking. We have thus set out to develop a software program to generate IDs for epidemiological or clinical studies. Our software IDGenerator creates unique identifiers that not only carry a random identifier for a study participant, but also support the creation of structured IDs, where organizational information is coded into the ID directly. This may include study center (for multicenter-studies), study track (for studies with diversified study programs), or study visit (baseline, follow-up, regularly repeated visits). Our software can be used to add a check digit to the ID to minimize data entry errors. It facilitates the generation of IDs in batches and the creation of layered IDs (personal data ID, study data ID, temporary ID, external data ID) to ensure a high standard of data privacy. The software is supported by a user-friendly graphic interface that enables the generation of IDs in both standard text and barcode 128B format. Our software IDGenerator can create identifiers meeting the specific needs for epidemiologic or clinical studies to facilitate study organization and data privacy. IDGenerator is freeware under the GNU General Public License version 3; a Windows port and the source code can be downloaded at the Open Science Framework website: https://osf.io/urs2g/ .

Tool making, hand morphology and fossil hominins.

PubMed

Marzke, Mary W

2013-11-19

Was stone tool making a factor in the evolution of human hand morphology? Is it possible to find evidence in fossil hominin hands for this capability? These questions are being addressed with increasingly sophisticated studies that are testing two hypotheses; (i) that humans have unique patterns of grip and hand movement capabilities compatible with effective stone tool making and use of the tools and, if this is the case, (ii) that there exist unique patterns of morphology in human hands that are consistent with these capabilities. Comparative analyses of human stone tool behaviours and chimpanzee feeding behaviours have revealed a distinctive set of forceful pinch grips by humans that are effective in the control of stones by one hand during manufacture and use of the tools. Comparative dissections, kinematic analyses and biomechanical studies indicate that humans do have a unique pattern of muscle architecture and joint surface form and functions consistent with the derived capabilities. A major remaining challenge is to identify skeletal features that reflect the full morphological pattern, and therefore may serve as clues to fossil hominin manipulative capabilities. Hominin fossils are evaluated for evidence of patterns of derived human grip and stress-accommodation features.

Distinguishing tracheal and esophageal tissues with hyperspectral imaging and fiber-optic sensing

NASA Astrophysics Data System (ADS)

Nawn, Corinne D.; Souhan, Brian E.; Carter, Robert, III; Kneapler, Caitlin; Fell, Nicholas; Ye, Jing Yong

2016-11-01

During emergency medical situations, where the patient has an obstructed airway or necessitates respiratory support, endotracheal intubation (ETI) is the medical technique of placing a tube into the trachea in order to facilitate adequate ventilation of the lungs. Complications during ETI, such as repeated attempts, failed intubation, or accidental intubation of the esophagus, can lead to severe consequences or ultimately death. Consequently, a need exists for a feedback mechanism to aid providers in performing successful ETI. Our study examined the spectral reflectance properties of the tracheal and esophageal tissue to determine whether a unique spectral profile exists for either tissue for the purpose of detection. The study began by using a hyperspectral camera to image excised pig tissue samples exposed to white and UV light in order to capture the spectral reflectance properties with high fidelity. After identifying a unique spectral characteristic of the trachea that significantly differed from esophageal tissue, a follow-up investigation used a fiber optic probe to confirm the detectability and consistency of the different reflectance characteristics in a pig model. Our results characterize the unique and consistent spectral reflectance characteristic of tracheal tissue, thereby providing foundational support for exploiting spectral properties to detect the trachea during medical procedures.

Tool making, hand morphology and fossil hominins

PubMed Central

Marzke, Mary W.

2013-01-01

Was stone tool making a factor in the evolution of human hand morphology? Is it possible to find evidence in fossil hominin hands for this capability? These questions are being addressed with increasingly sophisticated studies that are testing two hypotheses; (i) that humans have unique patterns of grip and hand movement capabilities compatible with effective stone tool making and use of the tools and, if this is the case, (ii) that there exist unique patterns of morphology in human hands that are consistent with these capabilities. Comparative analyses of human stone tool behaviours and chimpanzee feeding behaviours have revealed a distinctive set of forceful pinch grips by humans that are effective in the control of stones by one hand during manufacture and use of the tools. Comparative dissections, kinematic analyses and biomechanical studies indicate that humans do have a unique pattern of muscle architecture and joint surface form and functions consistent with the derived capabilities. A major remaining challenge is to identify skeletal features that reflect the full morphological pattern, and therefore may serve as clues to fossil hominin manipulative capabilities. Hominin fossils are evaluated for evidence of patterns of derived human grip and stress-accommodation features. PMID:24101624

Use of an electronic-nose device for profiling headspace volatile metabolites to rapidly identify phytopathogenic microbes [Abstract].

Treesearch

A. Dan Wilson; D.G. Lester

1997-01-01

A new electronic-nose device (AromaScan A32S), consisting of an organic matrix-coated polymer-type 32-detector array, was tested as a novel tool for the detection, identification, and discrimination of phytopathogenic microbes. The sensor array detects the unique mixture of volatile metabolites released by microbes growing on standardized growth media by measuring...

Data cleaning and management protocols for linked perinatal research data: a good practice example from the Smoking MUMS (Maternal Use of Medications and Safety) Study.

PubMed

Tran, Duong Thuy; Havard, Alys; Jorm, Louisa R

2017-07-11

Data cleaning is an important quality assurance in data linkage research studies. This paper presents the data cleaning and preparation process for a large-scale cross-jurisdictional Australian study (the Smoking MUMS Study) to evaluate the utilisation and safety of smoking cessation pharmacotherapies during pregnancy. Perinatal records for all deliveries (2003-2012) in the States of New South Wales (NSW) and Western Australia were linked to State-based data collections including hospital separation, emergency department and death data (mothers and babies) and congenital defect notifications (babies in NSW) by State-based data linkage units. A national data linkage unit linked pharmaceutical dispensing data for the mothers. All linkages were probabilistic. Twenty two steps assessed the uniqueness of records and consistency of items within and across data sources, resolved discrepancies in the linkages between units, and identified women having records in both States. State-based linkages yielded a cohort of 783,471 mothers and 1,232,440 babies. Likely false positive links relating to 3703 mothers were identified. Corrections of baby's date of birth and age, and parity were made for 43,578 records while 1996 records were flagged as duplicates. Checks for the uniqueness of the matches between State and national linkages detected 3404 ID clusters, suggestive of missed links in the State linkages, and identified 1986 women who had records in both States. Analysis of content data can identify inaccurate links that cannot be detected by data linkage units that have access to personal identifiers only. Perinatal researchers are encouraged to adopt the methods presented to ensure quality and consistency among studies using linked administrative data.

Cancer risks in twins and singletons from twin and non-twin families.

PubMed

Chen, Lingjing; Cnattingius, Sven; Nyman Iliadou, Anastasia; Oberg, Anna Sara

2016-03-01

The unique intrauterine environment has been proposed to put twins at increased risk of certain cancers compared to singletons, still large population comparisons have generally indicated lower risks in twins. To improve the understanding of potential twin influence on cancer we compared twins to their singletons siblings, to target a unique twinning influence. Singletons from twin families were contrasted to singletons from non-twin families to further capture potential twin family influence on risk of cancer. Family relations were identified using the Swedish Multi-Generation Register. Among individuals born between 1932 and 1958, 49,156 twins and N = 35,227 singletons were identified from 18,098 unique twin families. All incident cases of specific cancer types were identified in the National Cancer Register up to the end of 2007. Standardized survival functions were estimated using weighted Cox proportional hazard regression and the corresponding cumulative risks plotted against age. Overall, primary cancers were identified in 9% and 18% of all male and female twins, compared to 11% and 19% of their male and female singleton siblings. When specific cancer sites were compared using standardized cumulative risk plots, no consistent statistically significant differences were noted either between twins and singletons of twin families or between singletons of twin and non-twin families. Despite a different intrauterine experience, twinning does not seem to have any greater negative influence on life-time risks of cancer. The findings also indicate that twin family membership has no substantial influence on cancer risks. © 2015 UICC.

Early adolescents’ unique perspectives of maternal and paternal rejection: Examining their across-dyad generalizability and relations with adjustment one year later

PubMed Central

Jager, Justin; Mahler, Alissa; An, Danming; Putnick, Diane L.; Bornstein, Marc H.; Lansford, Jennifer E.; Dodge, Kenneth A.; Skinner, Ann T.; Deater-Deckard, Kirby

2017-01-01

Parental rejection is linked to deep and enduring adjustment problems during adolescence. This study aims to further clarify this relation by demonstrating what has long been posited by parental acceptance/rejection theory but never validated empirically – namely that adolescents’ unique or subjective experience of parental rejection independently informs their future adjustment. Among a longitudinal, multi-informant sample of 161 families (early adolescents were 47% female and 40% European American) this study utilized a multitrait-multimethod confirmatory factor analysis to isolate for each early adolescent-parent dyad, the adolescent’s distinct view of parental rejection (i.e., the adolescent unique perspective) from the portion of his or her view that overlaps with his or her parent’s view. The findings indicated that adolescents’ unique perspectives of maternal rejection were not differentiated from their unique perspectives of paternal rejection. Also, consistent with parental acceptance-rejection theory, early adolescents’ unique perspectives of parental rejection were associated with worse adjustment (internalizing and externalizing) one year later. This study further demonstrates the utility and validity of the multitrait-multimethod confirmatory factor analysis approach for identifying and examining adolescent unique perspectives. Both conceptually and analytically, this study also integrates research focused on unique perspectives with a distinct but related line of research focused on discrepancies in perspectives. PMID:27262697

Early Adolescents' Unique Perspectives of Maternal and Paternal Rejection: Examining Their Across-Dyad Generalizability and Relations with Adjustment 1 Year Later.

PubMed

Jager, Justin; Mahler, Alissa; An, Danming; Putnick, Diane L; Bornstein, Marc H; Lansford, Jennifer E; Dodge, Kenneth A; Skinner, Ann T; Deater-Deckard, Kirby

2016-10-01

Parental rejection is linked to deep and enduring adjustment problems during adolescence. This study aims to further clarify this relation by demonstrating what has long been posited by parental acceptance/rejection theory but never validated empirically-namely that adolescents' unique or subjective experience of parental rejection independently informs their future adjustment. Among a longitudinal, multi-informant sample of 161 families (early adolescents were 47 % female and 40 % European American) this study utilized a multitrait-multimethod confirmatory factor analysis to isolate for each early adolescent-parent dyad, the adolescent's distinct view of parental rejection (i.e., the adolescent unique perspective) from the portion of his or her view that overlaps with his or her parent's view. The findings indicated that adolescents' unique perspectives of maternal rejection were not differentiated from their unique perspectives of paternal rejection. Also, consistent with parental acceptance-rejection theory, early adolescents' unique perspectives of parental rejection were associated with worse adjustment (internalizing and externalizing) 1 year later. This study further demonstrates the utility and validity of the multitrait-multimethod confirmatory factor analysis approach for identifying and examining adolescent unique perspectives. Both conceptually and analytically, this study also integrates research focused on unique perspectives with a distinct but related line of research focused on discrepancies in perspectives.

The operation, products and promotion of waterpipe businesses in New York City, Abu Dhabi and Dubai.

PubMed

Joudrey, P J; Jasie, K A; Pykalo, L; Singer, S T; Woodin, M B; Sherman, S

2016-07-10

We evaluated the customers, operations, products and advertising of these businesses to explore the unique policy challenges created by the suppliers of waterpipes. We completed a cross-sectional survey consisting of structured site observations and in-person interviews of businesses in New York City, Abu Dhabi and Dubai identified using Google, Yelp, Timeout Dubai and Timeout Abu Dhabi and neighbourhood visits in 2014. Regular customers made up 59% of customers. Franchises or chains were 28% of businesses. Waterpipes made up 39% of sales with 87% of businesses offering food within their menu. Flavoured tobacco made up 94% of sales. Discounts were offered by 47% of businesses and 94% of businesses used advertising, often through social media. The market consists of largely independent businesses, with a large regular customer base, frequently offering diversified services beyond waterpipes. These businesses advertise using both traditional and social media. The economics of waterpipe businesses is very different from the economics of cigarettes, and unique regulatory strategies are needed to control this epidemic.

Automated response matching for organic scintillation detector arrays

NASA Astrophysics Data System (ADS)

Aspinall, M. D.; Joyce, M. J.; Cave, F. D.; Plenteda, R.; Tomanin, A.

2017-07-01

This paper identifies a digitizer technology with unique features that facilitates feedback control for the realization of a software-based technique for automatically calibrating detector responses. Three such auto-calibration techniques have been developed and are described along with an explanation of the main configuration settings and potential pitfalls. Automating this process increases repeatability, simplifies user operation, enables remote and periodic system calibration where consistency across detectors' responses are critical.

Validation of intellectual disability coding through hospital morbidity records using an intellectual disability population-based database in Western Australia.

PubMed

Bourke, Jenny; Wong, Kingsley; Leonard, Helen

2018-01-23

To investigate how well intellectual disability (ID) can be ascertained using hospital morbidity data compared with a population-based data source. All children born in 1983-2010 with a hospital admission in the Western Australian Hospital Morbidity Data System (HMDS) were linked with the Western Australian Intellectual Disability Exploring Answers (IDEA) database. The International Classification of Diseases hospital codes consistent with ID were also identified. The characteristics of those children identified with ID through either or both sources were investigated. Of the 488 905 individuals in the study, 10 218 (2.1%) were identified with ID in either IDEA or HMDS with 1435 (14.0%) individuals identified in both databases, 8305 (81.3%) unique to the IDEA database and 478 (4.7%) unique to the HMDS dataset only. Of those unique to the HMDS dataset, about a quarter (n=124) had died before 1 year of age and most of these (75%) before 1 month. Children with ID who were also coded as such in the HMDS data were more likely to be aged under 1 year, female, non-Aboriginal and have a severe level of ID, compared with those not coded in the HMDS data. The sensitivity of using HMDS to identify ID was 14.7%, whereas the specificity was much higher at 99.9%. Hospital morbidity data are not a reliable source for identifying ID within a population, and epidemiological researchers need to take these findings into account in their study design. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Validation of intellectual disability coding through hospital morbidity records using an intellectual disability population-based database in Western Australia

PubMed Central

Bourke, Jenny; Wong, Kingsley

2018-01-01

Objectives To investigate how well intellectual disability (ID) can be ascertained using hospital morbidity data compared with a population-based data source. Design, setting and participants All children born in 1983–2010 with a hospital admission in the Western Australian Hospital Morbidity Data System (HMDS) were linked with the Western Australian Intellectual Disability Exploring Answers (IDEA) database. The International Classification of Diseases hospital codes consistent with ID were also identified. Main outcome measures The characteristics of those children identified with ID through either or both sources were investigated. Results Of the 488 905 individuals in the study, 10 218 (2.1%) were identified with ID in either IDEA or HMDS with 1435 (14.0%) individuals identified in both databases, 8305 (81.3%) unique to the IDEA database and 478 (4.7%) unique to the HMDS dataset only. Of those unique to the HMDS dataset, about a quarter (n=124) had died before 1 year of age and most of these (75%) before 1 month. Children with ID who were also coded as such in the HMDS data were more likely to be aged under 1 year, female, non-Aboriginal and have a severe level of ID, compared with those not coded in the HMDS data. The sensitivity of using HMDS to identify ID was 14.7%, whereas the specificity was much higher at 99.9%. Conclusion Hospital morbidity data are not a reliable source for identifying ID within a population, and epidemiological researchers need to take these findings into account in their study design. PMID:29362262

Chocolate smells pink and stripy: Exploring olfactory-visual synesthesia

PubMed Central

Russell, Alex; Stevenson, Richard J.; Rich, Anina N.

2015-01-01

Odors are often difficult to identify, and can be perceived either via the nose or mouth (“flavor”; not usually perceived as a “smell”). These features provide a unique opportunity to contrast conceptual and perceptual accounts of synesthesia. We presented six olfactory-visual synesthetes with a range of odorants. They tried to identify each smell, evaluate its attributes and illustrate their elicited visual experience. Judges rated the similarity of each synesthetes’ illustrations over time (test-retest reliability). Synesthetic images were most similar from the same odor named consistently, but even inconsistently named same odors generated more similar images than different odors. This was driven by hedonic similarity. Odors presented as flavors only resulted in similar images when consistently named. Thus, the primary factor in generating a reliable synesthetic image is the name, with some influence of odor hedonics. Hedonics are a basic form of semantic knowledge, making this consistent with a conceptual basis for synaesthetic links. PMID:25895152

Using Java to generate globally unique identifiers for DICOM objects.

PubMed

Kamauu, Aaron W C; Duvall, Scott L; Avrin, David E

2009-03-01

Digital imaging and communication in medicine (DICOM) specifies that all DICOM objects have globally unique identifiers (UIDs). Creating these UIDs can be a difficult task due to the variety of techniques in use and the requirement to ensure global uniqueness. We present a simple technique of combining a root organization identifier, assigned descriptive identifiers, and JAVA generated unique identifiers to construct DICOM compliant UIDs.

A study of parameter identification

NASA Technical Reports Server (NTRS)

Herget, C. J.; Patterson, R. E., III

1978-01-01

A set of definitions for deterministic parameter identification ability were proposed. Deterministic parameter identificability properties are presented based on four system characteristics: direct parameter recoverability, properties of the system transfer function, properties of output distinguishability, and uniqueness properties of a quadratic cost functional. Stochastic parameter identifiability was defined in terms of the existence of an estimation sequence for the unknown parameters which is consistent in probability. Stochastic parameter identifiability properties are presented based on the following characteristics: convergence properties of the maximum likelihood estimate, properties of the joint probability density functions of the observations, and properties of the information matrix.

Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico

PubMed Central

2017-01-01

ABSTRACT HIV circumvents HLA class I-restricted CD8+ T-cell responses through selection of escape mutations that leave characteristic mutational “footprints,” also known as HLA-associated polymorphisms (HAPs), on HIV sequences at the population level. While many HLA footprints are universal across HIV subtypes and human populations, others can be region specific as a result of the unique immunogenetic background of each host population. Using a published probabilistic phylogenetically informed model, we compared HAPs in HIV Gag and Pol (PR-RT) in 1,612 subtype B-infected, antiretroviral treatment-naive individuals from Mexico and 1,641 individuals from Canada/United States. A total of 252 HLA class I allele subtypes were represented, including 140 observed in both cohorts, 67 unique to Mexico, and 45 unique to Canada/United States. At the predefined statistical threshold of a q value of <0.2, 358 HAPs (201 in Gag, 157 in PR-RT) were identified in Mexico, while 905 (534 in Gag and 371 in PR-RT) were identified in Canada/United States. HAPs identified in Mexico included both canonical HLA-associated escape pathways and novel associations, in particular with HLA alleles enriched in Amerindian and mestizo populations. Remarkably, HLA footprints on HIV in Mexico were not only fewer but also, on average, significantly weaker than those in Canada/United States, although some exceptions were noted. Moreover, exploratory analyses suggested that the weaker HLA footprint on HIV in Mexico may be due, at least in part, to weaker and/or less reproducible HLA-mediated immune pressures on HIV in this population. The implications of these differences for natural and vaccine-induced anti-HIV immunity merit further investigation. IMPORTANCE HLA footprints on HIV identify viral regions under intense and consistent pressure by HLA-restricted immune responses and the common mutational pathways that HIV uses to evade them. In particular, HLA footprints can identify novel immunogenic regions and/or epitopes targeted by understudied HLA alleles; moreover, comparative analyses across immunogenetically distinct populations can illuminate the extent to which HIV immunogenic regions and escape pathways are shared versus population-specific pathways, information which can in turn inform the design of universal or geographically tailored HIV vaccines. We compared HLA-associated footprints on HIV in two immunogenetically distinct North American populations, those of Mexico and Canada/United States. We identify both shared and population-specific pathways of HIV adaptation but also make the surprising observation that HLA footprints on HIV in Mexico overall are fewer and weaker than those in Canada/United States, raising the possibility that HLA-restricted antiviral immune responses in Mexico are weaker, and/or escape pathways somewhat less consistent, than those in other populations. PMID:29093100

Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico.

PubMed

Soto-Nava, Maribel; Avila-Ríos, Santiago; Valenzuela-Ponce, Humberto; García-Morales, Claudia; Carlson, Jonathan M; Tapia-Trejo, Daniela; Garrido-Rodriguez, Daniela; Alva-Hernández, Selma N; García-Tellez, Thalía A; Murakami-Ogasawara, Akio; Mallal, Simon A; John, Mina; Brockman, Mark A; Brumme, Chanson J; Brumme, Zabrina L; Reyes-Teran, Gustavo

2018-01-15

HIV circumvents HLA class I-restricted CD8 + T-cell responses through selection of escape mutations that leave characteristic mutational "footprints," also known as HLA-associated polymorphisms (HAPs), on HIV sequences at the population level. While many HLA footprints are universal across HIV subtypes and human populations, others can be region specific as a result of the unique immunogenetic background of each host population. Using a published probabilistic phylogenetically informed model, we compared HAPs in HIV Gag and Pol (PR-RT) in 1,612 subtype B-infected, antiretroviral treatment-naive individuals from Mexico and 1,641 individuals from Canada/United States. A total of 252 HLA class I allele subtypes were represented, including 140 observed in both cohorts, 67 unique to Mexico, and 45 unique to Canada/United States. At the predefined statistical threshold of a q value of <0.2, 358 HAPs (201 in Gag, 157 in PR-RT) were identified in Mexico, while 905 (534 in Gag and 371 in PR-RT) were identified in Canada/United States. HAPs identified in Mexico included both canonical HLA-associated escape pathways and novel associations, in particular with HLA alleles enriched in Amerindian and mestizo populations. Remarkably, HLA footprints on HIV in Mexico were not only fewer but also, on average, significantly weaker than those in Canada/United States, although some exceptions were noted. Moreover, exploratory analyses suggested that the weaker HLA footprint on HIV in Mexico may be due, at least in part, to weaker and/or less reproducible HLA-mediated immune pressures on HIV in this population. The implications of these differences for natural and vaccine-induced anti-HIV immunity merit further investigation. IMPORTANCE HLA footprints on HIV identify viral regions under intense and consistent pressure by HLA-restricted immune responses and the common mutational pathways that HIV uses to evade them. In particular, HLA footprints can identify novel immunogenic regions and/or epitopes targeted by understudied HLA alleles; moreover, comparative analyses across immunogenetically distinct populations can illuminate the extent to which HIV immunogenic regions and escape pathways are shared versus population-specific pathways, information which can in turn inform the design of universal or geographically tailored HIV vaccines. We compared HLA-associated footprints on HIV in two immunogenetically distinct North American populations, those of Mexico and Canada/United States. We identify both shared and population-specific pathways of HIV adaptation but also make the surprising observation that HLA footprints on HIV in Mexico overall are fewer and weaker than those in Canada/United States, raising the possibility that HLA-restricted antiviral immune responses in Mexico are weaker, and/or escape pathways somewhat less consistent, than those in other populations. Copyright © 2018 Soto-Nava et al.

Development of a DNA microarray for species identification of quarantine aphids.

PubMed

Lee, Won Sun; Choi, Hwalran; Kang, Jinseok; Kim, Ji-Hoon; Lee, Si Hyeock; Lee, Seunghwan; Hwang, Seung Yong

2013-12-01

Aphid pests are being brought into Korea as a result of increased crop trading. Aphids exist on growth areas of plants, and thus plant growth is seriously affected by aphid pests. However, aphids are very small and have several sexual morphs and life stages, so it is difficult to identify species on the basis of morphological features. This problem was approached using DNA microarray technology. DNA targets of the cytochrome c oxidase subunit I gene were generated with a fluorescent dye-labelled primer and were hybridised onto a DNA microarray consisting of specific probes. After analysing the signal intensity of the specific probes, the unique patterns from the DNA microarray, consisting of 47 species-specific probes, were obtained to identify 23 aphid species. To confirm the accuracy of the developed DNA microarray, ten individual blind samples were used in blind trials, and the identifications were completely consistent with the sequencing data of all individual blind samples. A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management. © 2013 Society of Chemical Industry.

Genome-wide gene expression effects in B6C3F1 mouse intestinal epithelia following 7 and 90days of exposure to hexavalent chromium in drinking water.

PubMed

Kopec, Anna K; Kim, Suntae; Forgacs, Agnes L; Zacharewski, Timothy R; Proctor, Deborah M; Harris, Mark A; Haws, Laurie C; Thompson, Chad M

2012-02-15

Chronic administration of high doses of hexavalent chromium [Cr(VI)] as sodium dichromate dihydrate (SDD) elicits alimentary cancers in mice. To further elucidate key events underlying tumor formation, a 90-day drinking water study was conducted in B6C3F1 mice. Differential gene expression was examined in duodenal and jejunal epithelial samples following 7 or 90days of exposure to 0, 0.3, 4, 14, 60, 170 or 520mg/L SDD in drinking water. Genome-wide microarray analyses identified 6562 duodenal and 4448 jejunal unique differentially expressed genes at day 8, and 4630 and 4845 unique changes, respectively, in the duodenum and jejunum at day 91. Comparative analysis identified significant overlap in duodenal and jejunal differential gene expression. Automated dose-response modeling identified >80% of the differentially expressed genes exhibited sigmoidal dose-response curves with EC(50) values ranging from 10 to 100mg/L SDD. Only 16 genes satisfying the dose-dependent differential expression criteria had EC(50) values <10mg/L SDD, 3 of which were regulated by Nrf2, suggesting oxidative stress in response to SDD at low concentrations. Analyses of differentially expressed genes identified over-represented functions associated with oxidative stress, cell cycle, lipid metabolism, and immune responses consistent with the reported effects on redox status and histopathology at corresponding SDD drinking water concentrations. Collectively, these data are consistent with a mode of action involving oxidative stress and cytotoxicity as early key events. This suggests that the tumorigenic effects of chronic Cr(VI) oral exposure likely require chronic tissue damage and compensatory epithelial cell proliferation. Copyright © 2011 Elsevier Inc. All rights reserved.

Disease Heritability Inferred from Familial Relationships Reported in Medical Records.

PubMed

Polubriaginof, Fernanda C G; Vanguri, Rami; Quinnies, Kayla; Belbin, Gillian M; Yahi, Alexandre; Salmasian, Hojjat; Lorberbaum, Tal; Nwankwo, Victor; Li, Li; Shervey, Mark M; Glowe, Patricia; Ionita-Laza, Iuliana; Simmerling, Mary; Hripcsak, George; Bakken, Suzanne; Goldstein, David; Kiryluk, Krzysztof; Kenny, Eimear E; Dudley, Joel; Vawdrey, David K; Tatonetti, Nicholas P

2018-05-15

Heritability is essential for understanding the biological causes of disease but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHRs) passively capture a wide range of clinically relevant data and provide a resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified 7.4 million familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with the literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research. These analyses provide a validation of the use of EHRs for genetics and disease research. Copyright © 2018 Elsevier Inc. All rights reserved.

Identification of a key structural element for protein folding within beta-hairpin turns.

PubMed

Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

2003-05-09

Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

Identification of genes associated with survival of salmonellaenterica serovar enteridis in chicken egg albumen

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

Clavijo, Raul I.; Loui, Cindy; Andersen, Gary L.

Salmonella enterica consists of over 2,000 serovars that aremajor causes of morbidity and mortality associated with contaminatedfood. Despite similarities among serovars of Salmonella enterica, manydemonstrate unique host specificities, epidemiological characteristics,and clinical manifestations. One of the unique epidemiologicalcharacteristics of the serovar Enteritidis is that it is the onlybacterium routinely transmitted to humans through intact chicken eggs.Therefore, Salmonella enterica serovar Enteritidis must be able topersist inside chicken eggs to be transmitted to humans, and its survivalin egg is important for its transmission to the human population. Theability of Salmonella enterica serovar Enteritidis to survive in andtransmit through eggs may have contributed tomore » its drastically increasedprevalence in the 1980s and 1990s. In the present study, usingtransposon-mediated mutagenesis, we have identified genes important forthe association of Salmonella enterica serovar Enteritidis with chickeneggs. Our results indicate that genes involved in cell wall structuraland functional integrity, and nucleic acid and amino acid metabolism areimportant for Salmonella enterica serovar Enteritidis to persist in eggalbumen. Two regions unique toSalmonella enterica serovar Enteritidiswere also identified, one of which enhanced the survival of a Salmonellaenterica serovar Typhimurium isolate in egg albumen. The implication ofour results to the serovar specificity of Salmonella enterica is alsoexplored in the present study.« less

Common and unique responses to dopamine agonist therapy and deep brain stimulation in Parkinson's disease: an H(2)(15)O PET study.

PubMed

Bradberry, Trent J; Metman, Leonard Verhagen; Contreras-Vidal, José L; van den Munckhof, Pepijn; Hosey, Lara A; Thompson, Jennifer L W; Schulz, Geralyn M; Lenz, Fredrick; Pahwa, Rajesh; Lyons, Kelly E; Braun, Allen R

2012-10-01

Dopamine agonist therapy and deep brain stimulation (DBS) of the subthalamic nucleus (STN) are antiparkinsonian treatments that act on a different part of the basal ganglia-thalamocortical motor circuitry, yet produce similar symptomatic improvements. The purpose of this study was to identify common and unique brain network features of these standard treatments. We analyzed images produced by H(2)(15)O positron emission tomography (PET) of patients with Parkinson's disease (PD) at rest. Nine patients were scanned before and after injection of apomorphine, and 11 patients were scanned while bilateral stimulators were off and while they were on. Both treatments produced common deactivations of the neocortical sensorimotor areas, including the supplementary motor area, precentral gyrus, and postcentral gyrus, and in subcortical structures, including the putamen and cerebellum. We observed concomitant activations of the superior parietal lobule and the midbrain in the region of the substantia nigra/STN. We also detected unique, treatment-specific changes with possible motor-related consequences in the basal ganglia, thalamus, neocortical sensorimotor cortex, and posterolateral cerebellum. Unique changes in nonmotor regions may reflect treatment-specific effects on verbal fluency and limbic functions. Many of the common effects of these treatments are consistent with the standard pathophysiologic model of PD. However, the common effects in the cerebellum are not readily explained by the model. Consistent deactivation of the cerebellum is interesting in light of recent reports of synaptic pathways directly connecting the cerebellum and basal ganglia, and may warrant further consideration for incorporation into the model. Published by Elsevier Inc.

The influence of and the identification of nonlinearity in flexible structures

NASA Technical Reports Server (NTRS)

Zavodney, Lawrence D.

1988-01-01

Several models were built at NASA Langley and used to demonstrate the following nonlinear behavior: internal resonance in a free response, principal parametric resonance and subcritical instability in a cantilever beam-lumped mass structure, combination resonance in a parametrically excited flexible beam, autoparametric interaction in a two-degree-of-freedom system, instability of the linear solution, saturation of the excited mode, subharmonic bifurcation, and chaotic responses. A video tape documenting these phenomena was made. An attempt to identify a simple structure consisting of two light-weight beams and two lumped masses using the Eigensystem Realization Algorithm showed the inherent difficulty of using a linear based theory to identify a particular nonlinearity. Preliminary results show the technique requires novel interpretation, and hence may not be useful for structural modes that are coupled by a guadratic nonlinearity. A literature survey was also completed on recent work in parametrically excited nonlinear system. In summary, nonlinear systems may possess unique behaviors that require nonlinear identification techniques based on an understanding of how nonlinearity affects the dynamic response of structures. In this was, the unique behaviors of nonlinear systems may be properly identified. Moreover, more accutate quantifiable estimates can be made once the qualitative model has been determined.

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2011 CFR

2011-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2013 CFR

2013-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2014 CFR

2014-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2012 CFR

2012-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

Code of Federal Regulations, 2010 CFR

2010-07-01

... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton; cotton...

Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China.

PubMed

Pagaling, Eulyn; Grant, William D; Cowan, Don A; Jones, Brian E; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun

2012-07-01

We investigated the bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong in the Yunnan Province, China, using direct molecular analyses. The Langpu (LP) laminated mat was found by the side of a boiling pool with temperature of 60-65 °C and a pH of 8.5, while the Tengchong (TC) streamer mat consisted of white streamers in a slightly acidic (pH 6.5) hot pool outflow with a temperature of 72 °C. Four 16S rRNA gene clone libraries were constructed and restriction enzyme analysis of the inserts was used to identify unique sequences and clone frequencies. From almost 200 clones screened, 55 unique sequences were retrieved. Phylogenetic analysis showed that the LP mat consisted of a diverse bacterial population [Cyanobacteria, Chloroflexi, Chlorobia, Nitrospirae, 'Deinococcus-Thermus', Proteobacteria (alpha, beta and delta subdivisions), Firmicutes, Bacteroidetes and Actinobacteria], while the archaeal population was dominated by methanogenic Euryarchaeota and Crenarchaeota. In contrast, the TC streamer mat consisted of a bacterial population dominated by Aquificae, while the archaeal population also contained Korarchaeota as well as Crenarchaeota and methanogenic Euryarchaeota. These mats harboured clone sequences affiliated to unidentified lineages, suggesting that they are a potential source for discovering novel bacteria and archaea.

76 FR 39234 - Federal Acquisition Regulation; Unique Procurement Instrument Identifier

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-05

...-AL70 Federal Acquisition Regulation; Unique Procurement Instrument Identifier AGENCIES: Department of... Acquisition Regulation (FAR) to standardize use of unique Procurement Instrument Identifiers (PIID) throughout... Acquisition Council and the Defense Acquisition Regulations Council (the Councils) reviewed the public...

Resting State Correlates of Subdimensions of Anxious Affect

PubMed Central

Bijsterbosch, Janine; Smith, Stephen; Forster, Sophie; John, Oliver P.; Bishop, Sonia J.

2014-01-01

Resting state fMRI may help identify markers of risk for affective disorder. Given the comorbidity of anxiety and depressive disorders and the heterogeneity of these disorders as defined by DSM, an important challenge is to identify alterations in resting state brain connectivity uniquely associated with distinct profiles of negative affect. The current study aimed to address this by identifying differences in brain connectivity specifically linked to cognitive and physiological profiles of anxiety, controlling for depressed affect. We adopted a two-stage multivariate approach. Hierarchical clustering was used to independently identify dimensions of negative affective style and resting state brain networks. Combining the clustering results, we examined individual differences in resting state connectivity uniquely associated with subdimensions of anxious affect, controlling for depressed affect. Physiological and cognitive subdimensions of anxious affect were identified. Physiological anxiety was associated with widespread alterations in insula connectivity, including decreased connectivity between insula subregions and between the insula and other medial frontal and subcortical networks. This is consistent with the insula facilitating communication between medial frontal and subcortical regions to enable control of physiological affective states. Meanwhile, increased connectivity within a frontoparietal–posterior cingulate cortex–precunous network was specifically associated with cognitive anxiety, potentially reflecting increased spontaneous negative cognition (e.g., worry). These findings suggest that physiological and cognitive anxiety comprise subdimensions of anxiety-related affect and reveal associated alterations in brain connectivity. PMID:24168223

Department of Defense Logistics Roadmap 2008. Volume 1

DTIC Science & Technology

2008-07-01

machine readable identification mark on the Department’s tangible qualifying assets, and establishes the data management protocols needed to...uniquely identify items with a Unique Item Identifier (UII) via machine - readable information (MRI) marking represented by a two-dimensional data...property items with a machine -readable Unique Item Identifier (UII), which is a set of globally unique data elements. The UII is used in functional

What is Next? Linking all Samples of Planet Earth.

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Lehnert, K.; Klump, J. F.; Arko, R. A.; Cox, S. J. D.; Devaraju, A.; Elger, K.; Murphy, F.; Fleischer, D.

2016-12-01

The process of sampling, observing and analyzing physical samples is not unique to the geosciences. Physical sampling (taking specimens) is a fundamental strategy in many natural sciences, typically to support ex-situ observations in laboratories with the goal of characterizing real-world entities or populations. Observations and measurements are made on individual specimens and their derived samples in various ways, with results reported in research publications. Research on an individual sample is often published in numerous articles, based on multiple, potentially unrelated research programs conducted over many years. Even high-volume Earth observation datasets are proxies of real world phenomena and require calibration by measurements made on position located, well described physical samples. Unique, persistent web-compatible identifiers for physical objects and related sampling features are required to ensure their unambiguous citation and connection to related datasets through web identifiers. Identifier systems have been established within specific domains (e.g., bio, geo, hydro) or different sectors (e.g., museums, government agencies, universities), including the International Geo Sample Number (IGSN) in the geosciences, which has been used for rock, fossil, mineral, soil, regolith, fluid, plant and synthetic materials. IGSNs are issued through a governance system that ensures they are globally unique. Each IGSN directs to a digital representation of the physical object via the Handle.net global resolver system, the same system used for resolving DOI. To enable the unique identification of all samples on Planet Earth and of data derived from them, the next step is to ensure IGSNs can either be integrated with comparable identifier systems in other domains/sectors, or introduced into domains that do not have a viable system. A registry of persistent identifier systems for physical samples would allow users to choose which system best suits their needs. Such a registry may also facilitate unifying best practice in these multiple systems to enable consistent referencing of physical samples and of methods used to link digital data to its sources. IGSNs could be extended into other domains, but additional methodologies of sample collection, curation and processing may need to be considered.

Understanding why veterans are reluctant to access help for alcohol problems: Considerations for nurse education.

PubMed

Kiernan, Matthew D; Moran, Sandra; Hill, Mick

2016-12-01

To effectively engage veterans with substance misuse services, nurses need to understand their unique needs and the potential barriers that prevent them from accessing care. Nurses need to have an understanding and awareness of the cultural sensitivities associated with having been a member of the armed forces. The aim of this study was to investigate the perceived barriers to care amongst those planning, commissioning and delivering services for veterans with substance misuse problems, and to identify and explore subject areas which nurse educators should consider for inclusion in nursing and health education programmes. The findings reported in this paper come from one phase of a larger three phase research project and used an applied qualitative research approached based on methods developed for applied social policy research. The study was undertaken in the north-east of England. The study consisted of a purposive sample of planners, commissioners of services, and service providers in the North East of England. Data was collected using a semi-structured interview schedule. Framework analysis was used to analyse the data. Complexity of services and care, complexity of need and a lack of understanding of veterans were identified as factors that made accessing substance misuse care difficult. To help nurses better understand the unique needs of veterans three educational topics were identified for consideration in pre-registration nurse education: understanding military and veteran culture and the nature of modern warfare, the military 'veteran as institutionalised' hypothesis and stigma. Health and social services can struggle to truly understand the unique needs and experiences of the veteran community. We have identified three broad subject areas that should be considered as the theoretical basis for a veteran specific education programme within pre and post-registration nurse education. Copyright © 2016 Elsevier Ltd. All rights reserved.

45 CFR 162.506 - Standard unique health plan identifier.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 45 Public Welfare 1 2014-10-01 2014-10-01 false Standard unique health plan identifier. 162.506 Section 162.506 Public Welfare Department of Health and Human Services ADMINISTRATIVE DATA STANDARDS AND RELATED REQUIREMENTS ADMINISTRATIVE REQUIREMENTS Standard Unique Health Identifier for Health Plans § 162...

45 CFR 162.506 - Standard unique health plan identifier.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 45 Public Welfare 1 2013-10-01 2013-10-01 false Standard unique health plan identifier. 162.506 Section 162.506 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE DATA STANDARDS AND RELATED REQUIREMENTS ADMINISTRATIVE REQUIREMENTS Standard Unique Health Identifier for Health Plans § 162...

Integrated use of surface geophysical methods for site characterization — A case study in North Kingstown, Rhode Island

USGS Publications Warehouse

Johnson, Carole D.; Lane, John W.; Brandon, William C.; Williams, Christine A.P.; White, Eric A.

2010-01-01

A suite of complementary, non‐invasive surface geophysical methods was used to assess their utility for site characterization in a pilot investigation at a former defense site in North Kingstown, Rhode Island. The methods included frequency‐domain electromagnetics (FDEM), ground‐penetrating radar (GPR), electrical resistivity tomography (ERT), and multi‐channel analysis of surface‐wave (MASW) seismic. The results of each method were compared to each other and to drive‐point data from the site. FDEM was used as a reconnaissance method to assess buried utilities and anthropogenic structures; to identify near‐surface changes in water chemistry related to conductive leachate from road‐salt storage; and to investigate a resistive signature possibly caused by groundwater discharge. Shallow anomalies observed in the GPR and ERT data were caused by near‐surface infrastructure and were consistent with anomalies observed in the FDEM data. Several parabolic reflectors were observed in the upper part of the GPR profiles, and a fairly continuous reflector that was interpreted as bedrock could be traced across the lower part of the profiles. MASW seismic data showed a sharp break in shear wave velocity at depth, which was interpreted as the overburden/bedrock interface. The MASW profile indicates the presence of a trough in the bedrock surface in the same location where the ERT data indicate lateral variations in resistivity. Depths to bedrock interpreted from the ERT, MASW, and GPR profiles were similar and consistent with the depths of refusal identified in the direct‐push wells. The interpretations of data collected using the individual methods yielded non‐unique solutions with considerable uncertainty. Integrated interpretation of the electrical, electromagnetic, and seismic geophysical profiles produced a more consistent and unique estimation of depth to bedrock that is consistent with ground‐truth data at the site. This test case shows that using complementary techniques that measure different properties can be more effective for site characterization than a single‐method investigation.

45 CFR 162.406 - Standard unique health identifier for health care providers.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 45 Public Welfare 1 2014-10-01 2014-10-01 false Standard unique health identifier for health care providers. 162.406 Section 162.406 Public Welfare Department of Health and Human Services ADMINISTRATIVE DATA STANDARDS AND RELATED REQUIREMENTS ADMINISTRATIVE REQUIREMENTS Standard Unique Health Identifier...

45 CFR 162.406 - Standard unique health identifier for health care providers.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 45 Public Welfare 1 2013-10-01 2013-10-01 false Standard unique health identifier for health care providers. 162.406 Section 162.406 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE DATA STANDARDS AND RELATED REQUIREMENTS ADMINISTRATIVE REQUIREMENTS Standard Unique Health Identifier...

Low-Resolution Near-infrared Stellar Spectra Observed by the Cosmic Infrared Background Experiment (CIBER)

NASA Astrophysics Data System (ADS)

Kim, Min Gyu; Lee, Hyung Mok; Arai, Toshiaki; Bock, James; Cooray, Asantha; Jeong, Woong-Seob; Kim, Seong Jin; Korngut, Phillip; Lanz, Alicia; Lee, Dae Hee; Lee, Myung Gyoon; Matsumoto, Toshio; Matsuura, Shuji; Nam, Uk Won; Onishi, Yosuke; Shirahata, Mai; Smidt, Joseph; Tsumura, Kohji; Yamamura, Issei; Zemcov, Michael

2017-02-01

We present near-infrared (0.8-1.8 μm) spectra of 105 bright ({m}J < 10) stars observed with the low-resolution spectrometer on the rocket-borne Cosmic Infrared Background Experiment. As our observations are performed above the Earth's atmosphere, our spectra are free from telluric contamination, which makes them a unique resource for near-infrared spectral calibration. Two-Micron All-Sky Survey photometry information is used to identify cross-matched stars after reduction and extraction of the spectra. We identify the spectral types of the observed stars by comparing them with spectral templates from the Infrared Telescope Facility library. All the observed spectra are consistent with late F to M stellar spectral types, and we identify various infrared absorption lines.

Hydrometeorological application of an extratropical cyclone classification scheme in the southern United States

NASA Astrophysics Data System (ADS)

Senkbeil, J. C.; Brommer, D. M.; Comstock, I. J.; Loyd, T.

2012-07-01

Extratropical cyclones (ETCs) in the southern United States are often overlooked when compared with tropical cyclones in the region and ETCs in the northern United States. Although southern ETCs are significant weather events, there is currently not an operational scheme used for identifying and discussing these nameless storms. In this research, we classified 84 ETCs (1970-2009). We manually identified five distinct formation regions and seven unique ETC types using statistical classification. Statistical classification employed the use of principal components analysis and two methods of cluster analysis. Both manual and statistical storm types generally showed positive (negative) relationships with El Niño (La Niña). Manual storm types displayed precipitation swaths consistent with discrete storm tracks which further legitimizes the existence of multiple modes of southern ETCs. Statistical storm types also displayed unique precipitation intensity swaths, but these swaths were less indicative of track location. It is hoped that by classifying southern ETCs into types, that forecasters, hydrologists, and broadcast meteorologists might be able to better anticipate projected amounts of precipitation at their locations.

Disambiguation of patent inventors and assignees using high-resolution geolocation data.

PubMed

Morrison, Greg; Riccaboni, Massimo; Pammolli, Fabio

2017-05-16

Patent data represent a significant source of information on innovation, knowledge production, and the evolution of technology through networks of citations, co-invention and co-assignment. A major obstacle to extracting useful information from this data is the problem of name disambiguation: linking alternate spellings of individuals or institutions to a single identifier to uniquely determine the parties involved in knowledge production and diffusion. In this paper, we describe a new algorithm that uses high-resolution geolocation to disambiguate both inventors and assignees on about 8.5 million patents found in the European Patent Office (EPO), under the Patent Cooperation Treaty (PCT), and in the US Patent and Trademark Office (USPTO). We show this disambiguation is consistent with a number of ground-truth benchmarks of both assignees and inventors, significantly outperforming the use of undisambiguated names to identify unique entities. A significant benefit of this work is the high quality assignee disambiguation with coverage across the world coupled with an inventor disambiguation (that is competitive with other state of the art approaches) in multiple patent offices.

Disambiguation of patent inventors and assignees using high-resolution geolocation data

PubMed Central

Morrison, Greg; Riccaboni, Massimo; Pammolli, Fabio

2017-01-01

Patent data represent a significant source of information on innovation, knowledge production, and the evolution of technology through networks of citations, co-invention and co-assignment. A major obstacle to extracting useful information from this data is the problem of name disambiguation: linking alternate spellings of individuals or institutions to a single identifier to uniquely determine the parties involved in knowledge production and diffusion. In this paper, we describe a new algorithm that uses high-resolution geolocation to disambiguate both inventors and assignees on about 8.5 million patents found in the European Patent Office (EPO), under the Patent Cooperation Treaty (PCT), and in the US Patent and Trademark Office (USPTO). We show this disambiguation is consistent with a number of ground-truth benchmarks of both assignees and inventors, significantly outperforming the use of undisambiguated names to identify unique entities. A significant benefit of this work is the high quality assignee disambiguation with coverage across the world coupled with an inventor disambiguation (that is competitive with other state of the art approaches) in multiple patent offices. PMID:28509897

Caveolin1 Identifies a Specific Subpopulation of Cerebral Cortex Callosal Projection Neurons (CPN) Including Dual Projecting Cortical Callosal/Frontal Projection Neurons (CPN/FPN)

PubMed Central

2018-01-01

Abstract The neocortex is composed of many distinct subtypes of neurons that must form precise subtype-specific connections to enable the cortex to perform complex functions. Callosal projection neurons (CPN) are the broad population of commissural neurons that connect the cerebral hemispheres via the corpus callosum (CC). Currently, how the remarkable diversity of CPN subtypes and connectivity is specified, and how they differentiate to form highly precise and specific circuits, are largely unknown. We identify in mouse that the lipid-bound scaffolding domain protein Caveolin 1 (CAV1) is specifically expressed by a unique subpopulation of Layer V CPN that maintain dual ipsilateral frontal projections to premotor cortex. CAV1 is expressed by over 80% of these dual projecting callosal/frontal projection neurons (CPN/FPN), with expression peaking early postnatally as axonal and dendritic targets are being reached and refined. CAV1 is localized to the soma and dendrites of CPN/FPN, a unique population of neurons that shares information both between hemispheres and with premotor cortex, suggesting function during postmitotic development and refinement of these neurons, rather than in their specification. Consistent with this, we find that Cav1 function is not necessary for the early specification of CPN/FPN, or for projecting to their dual axonal targets. CPN subtype-specific expression of Cav1 identifies and characterizes a first molecular component that distinguishes this functionally unique projection neuron population, a population that expands in primates, and is prototypical of additional dual and higher-order projection neuron subtypes. PMID:29379878

Common functionally important motions of the nucleotide-binding domain of Hsp70.

PubMed

Gołaś, Ewa I; Czaplewski, Cezary; Scheraga, Harold A; Liwo, Adam

2015-02-01

The 70 kDa heat shock proteins (Hsp70) are a family of molecular chaperones involved in protein folding, aggregate prevention, and protein disaggregation. They consist of the substrate-binding domain (SBD) that binds client substrates, and the nucleotide-binding domain (NBD), whose cycles of nucleotide hydrolysis and exchange underpin the activity of the chaperone. To characterize the structure-function relationships that link the binding state of the NBD to its conformational behavior, we analyzed the dynamics of the NBD of the Hsp70 chaperone from Bos taurus (PDB 3C7N:B) by all-atom canonical molecular dynamics simulations. It was found that essential motions within the NBD fall into three major classes: the mutual class, reflecting tendencies common to all binding states, and the ADP- and ATP-unique classes, which reflect conformational trends that are unique to either the ADP- or ATP-bound states, respectively. "Mutual" class motions generally describe "in-plane" and/or "out-of-plane" (scissor-like) rotation of the subdomains within the NBD. This result is consistent with experimental nuclear magnetic resonance data on the NBD. The "unique" class motions target specific regions on the NBD, usually surface loops or sites involved in nucleotide binding and are, therefore, expected to be involved in allostery and signal transmission. For all classes, and especially for those of the "unique" type, regions of enhanced mobility can be identified; these are termed "hot spots," and their locations generally parallel those found by NMR spectroscopy. The presence of magnesium and potassium cations in the nucleotide-binding pocket was also found to influence the dynamics of the NBD significantly. © 2014 Wiley Periodicals, Inc.

Reaction products of hexamethylene diisocyanate vapors with “self” molecules in the airways of rabbits exposed via tracheostomy

PubMed Central

Wisnewski, Adam V.; Kanyo, Jean; Asher, Jennifer; Goodrich, James A.; Barnett, Grace; Patrylak, Lyn; Liu, Jian; Redlich, Carrie A.; Nassar, Ala F.

2018-01-01

Hexamethylenediisocyanate (HDI) is a widely used aliphatic diisocyanate and a well-recognized cause of occupational asthma.“Self” molecules (peptides/proteins) in the lower airways, susceptible to chemical reactivity with HDI, have been hypothesized to play a role in asthma pathogenesis and/or chemical metabolism, but remain poorly characterized.This study employed unique approaches to identify and characterize “self” targets of HDI reactivity in the lower airways. Anesthetized rabbits free breathed through a tracheostomy tube connected to chambers containing either, O2, or O2 plus ~200 ppb HDI vapors. Following 60 minutes of exposure, the airways were lavaged and the fluid was analyzed by LC-MS and LC-MS/MS.The low-molecular weight (<3 kDa) fraction of HDI exposed, but not control rabbit bronchoalveolar lavage (BAL) fluid identified 783.26 and 476.18 m/z [M+H]+ ions with high energy collision-induced dissociation (HCD) fragmentation patterns consistent with bis glutathione (GSH)-HDI and mono(GSH)-HDI. Proteomic analyses of the high molecular weight (>3 kDa) fraction of exposed rabbit BAL fluid identified HDI modification of specific lysines in uteroglobin (aka clara cell protein) and albumin.In summary, this study utilized a unique approach to chemical vapor exposure in rabbits, to identify HDI reaction products with “self” molecules in the lower airways. PMID:28489470

Identifying airborne fungi in Seoul, Korea using metagenomics.

PubMed

Oh, Seung-Yoon; Fong, Jonathan J; Park, Myung Soo; Chang, Limseok; Lim, Young Woon

2014-06-01

Fungal spores are widespread and common in the atmosphere. In this study, we use a metagenomic approach to study the fungal diversity in six total air samples collected from April to May 2012 in Seoul, Korea. This springtime period is important in Korea because of the peak in fungal spore concentration and Asian dust storms, although the year of this study (2012) was unique in that were no major Asian dust events. Clustering sequences for operational taxonomic unit (OTU) identification recovered 1,266 unique OTUs in the combined dataset, with between 223᾿96 OTUs present in individual samples. OTUs from three fungal phyla were identified. For Ascomycota, Davidiella (anamorph: Cladosporium) was the most common genus in all samples, often accounting for more than 50% of all sequences in a sample. Other common Ascomycota genera identified were Alternaria, Didymella, Khuskia, Geosmitha, Penicillium, and Aspergillus. While several Basidiomycota genera were observed, Chytridiomycota OTUs were only present in one sample. Consistency was observed within sampling days, but there was a large shift in species composition from Ascomycota dominant to Basidiomycota dominant in the middle of the sampling period. This marked change may have been caused by meteorological events. A potential set of 40 allergy-inducing genera were identified, accounting for a large proportion of the diversity present (22.5᾿7.2%). Our study identifies high fungal diversity and potentially high levels of fungal allergens in springtime air of Korea, and provides a good baseline for future comparisons with Asian dust storms.

Maintaining High Quality Data and Consistency Across a Diverse Flux Network: The Ameriflux QA/QC Technical Team

NASA Astrophysics Data System (ADS)

Chan, S.; Billesbach, D. P.; Hanson, C. V.; Biraud, S.

2014-12-01

The AmeriFlux quality assurance and quality control (QA/QC) technical team conducts short term (<2 weeks) intercomparisons using a portable eddy covariance system (PECS) to maintain high quality data observations and data consistency across the AmeriFlux network (http://ameriflux.lbl.gov/). Site intercomparisons identify discrepancies between the in situ and portable measurements and calculated fluxes. Findings are jointly discussed by the site staff and the QA/QC team to improve in the situ observations. Despite the relatively short duration of an individual site intercomparison, the accumulated record of all site visits (numbering over 100 since 2002) is a unique dataset. The ability to deploy redundant sensors provides a rare opportunity to identify, quantify, and understand uncertainties in eddy covariance and ancillary measurements. We present a few specific case studies from QA/QC site visits to highlight and share new and relevant findings related to eddy covariance instrumentation and operation.

Post-translationally modified muscle-specific ubiquitin ligases as circulating biomarkers in experimental cancer cachexia

PubMed Central

Mota, Roberto; Rodríguez, Jessica E; Bonetto, Andrea; O’Connell, Thomas M; Asher, Scott A; Parry, Traci L; Lockyer, Pamela; McCudden, Christopher R; Couch, Marion E; Willis, Monte S

2017-01-01

Cancer cachexia is a severe wasting syndrome characterized by the progressive loss of lean body mass and systemic inflammation. Up to 80% of cancer patients experience cachexia, with 20-30% of cancer-related deaths directly linked to cachexia. Despite efforts to identify early cachexia and cancer relapse, clinically useful markers are lacking. Recently, we identified the role of muscle-specific ubiquitin ligases Atrogin-1 (MAFbx, FBXO32) and Muscle Ring Finger-1 in the pathogenesis of cardiac atrophy and hypertrophy. We hypothesized that during cachexia, the Atrogin-1 and MuRF1 ubiquitin ligases are released from muscle and migrate to the circulation where they could be detected and serve as a cachexia biomarker. To test this, we induced cachexia in mice using the C26 adenocarcinoma cells or vehicle (control). Body weight, tumor volume, and food consumption were measured from inoculation until ~day 14 to document cachexia. Western blot analysis of serum identified the presence of Atrogin-1 and MuRF1 with unique post-translational modifications consistent with mono- and poly- ubiquitination of Atrogin-1 and MuRF1 found only in cachectic serum. These findings suggest that both increased Atrogin-1 and the presence of unique post-translational modifications may serve as a surrogate marker specific for cachexia. PMID:28979816

Transcriptomic analysis of Ruditapes philippinarum hemocytes reveals cytoskeleton disruption after in vitro Vibrio tapetis challenge.

PubMed

Brulle, Franck; Jeffroy, Fanny; Madec, Stéphanie; Nicolas, Jean-Louis; Paillard, Christine

2012-10-01

The Manila clam, Ruditapes philippinarum, is an economically-important, commercial shellfish; harvests are diminished in some European waters by a pathogenic bacterium, Vibrio tapetis, that causes Brown Ring disease. To identify molecular characteristics associated with susceptibility or resistance to Brown Ring disease, Suppression Subtractive Hybridization (SSH) analyzes were performed to construct cDNA libraries enriched in up- or down-regulated transcripts from clam immune cells, hemocytes, after a 3-h in vitro challenge with cultured V. tapetis. Nine hundred and ninety eight sequences from the two libraries were sequenced, and an in silico analysis identified 235 unique genes. BLAST and "Gene ontology" classification analyzes revealed that 60.4% of the Expressed Sequence Tags (ESTs) have high similarities with genes involved in various physiological functions, such as immunity, apoptosis and cytoskeleton organization; whereas, 39.6% remain unidentified. From the 235 unique genes, we selected 22 candidates based upon physiological function and redundancy in the libraries. Then, Real-Time PCR analysis identified 3 genes related to cytoskeleton organization showing significant variation in expression attributable to V. tapetis exposure. Disruption in regulation of these genes is consistent with the etiologic agent of Brown Ring disease in Manila clams. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development and Initial Validation of Military Deployment-Related TBI Quality-of-Life Item Banks.

PubMed

Toyinbo, Peter A; Vanderploeg, Rodney D; Donnell, Alison J; Mutolo, Sandra A; Cook, Karon F; Kisala, Pamela A; Tulsky, David S

2016-01-01

To investigate unique factors that affect health-related quality of life (QOL) in individuals with military deployment-related traumatic brain injury (MDR-TBI) and to develop appropriate assessment tools, consistent with the TBI-QOL/PROMIS/Neuro-QOL systems. Three focus groups from each of the 4 Veterans Administration (VA) Polytrauma Rehabilitation Centers, consisting of 20 veterans with mild to severe MDR-TBI, and 36 VA providers were involved in early stage of new item banks development. The item banks were field tested in a sample (N = 485) of veterans enrolled in VA and diagnosed with an MDR-TBI. Focus groups and survey. Developed item banks and short forms for Guilt, Posttraumatic Stress Disorder/Trauma, and Military-Related Loss. Three new item banks representing unique domains of MDR-TBI health outcomes were created: 15 new Posttraumatic Stress Disorder items plus 16 SCI-QOL legacy Trauma items, 37 new Military-Related Loss items plus 18 TBI-QOL legacy Grief/Loss items, and 33 new Guilt items. Exploratory and confirmatory factor analyses plus bifactor analysis of the items supported sufficient unidimensionality of the new item pools. Convergent and discriminant analyses results, as well as known group comparisons, provided initial support for the validity and clinical utility of the new item response theory-calibrated item banks and their short forms. This work provides a unique opportunity to identify issues specific to individuals with MDR-TBI and ensure that they are captured in QOL assessment, thus extending the existing TBI-QOL measurement system.

Aveiro method in reproducing kernel Hilbert spaces under complete dictionary

NASA Astrophysics Data System (ADS)

Mai, Weixiong; Qian, Tao

2017-12-01

Aveiro Method is a sparse representation method in reproducing kernel Hilbert spaces (RKHS) that gives orthogonal projections in linear combinations of reproducing kernels over uniqueness sets. It, however, suffers from determination of uniqueness sets in the underlying RKHS. In fact, in general spaces, uniqueness sets are not easy to be identified, let alone the convergence speed aspect with Aveiro Method. To avoid those difficulties we propose an anew Aveiro Method based on a dictionary and the matching pursuit idea. What we do, in fact, are more: The new Aveiro method will be in relation to the recently proposed, the so called Pre-Orthogonal Greedy Algorithm (P-OGA) involving completion of a given dictionary. The new method is called Aveiro Method Under Complete Dictionary (AMUCD). The complete dictionary consists of all directional derivatives of the underlying reproducing kernels. We show that, under the boundary vanishing condition, bring available for the classical Hardy and Paley-Wiener spaces, the complete dictionary enables an efficient expansion of any given element in the Hilbert space. The proposed method reveals new and advanced aspects in both the Aveiro Method and the greedy algorithm.

The Erevan howardite: Petrology of glassy clasts and mineral chemistry

NASA Technical Reports Server (NTRS)

Nazarov, M. A.; Ariskin, A. A.

1993-01-01

The Erevan howardite is a polymict regolith breccia containing xenoliths of carbonaceous chondrites. In this work, we studied glassy clasts, which could be considered as primary quenched melts, and mineral chemistry of the breccia. The study reveals that the Erevan howardite consists of common rocks of the HED suite. However, unique glassy clasts, which are present in some eucritic melts, were identified. The mineral chemistry and the simulation of crystallization of the melts suggest that the compositions of the melts reflect those of some primary lithologies of EPB.

The semantics of Chemical Markup Language (CML): dictionaries and conventions.

PubMed

Murray-Rust, Peter; Townsend, Joe A; Adams, Sam E; Phadungsukanan, Weerapong; Thomas, Jens

2011-10-14

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs.

The semantics of Chemical Markup Language (CML): dictionaries and conventions

PubMed Central

2011-01-01

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs. PMID:21999509

Quasi-two-dimensional complex plasma containing spherical particles and their binary agglomerates.

PubMed

Chaudhuri, M; Semenov, I; Nosenko, V; Thomas, H M

2016-05-01

A unique type of quasi-two-dimensional complex plasma system was observed which consisted of monodisperse microspheres and their binary agglomerations (dimers). The particles and their dimers levitated in a plasma sheath at slightly different heights and formed two distinct sublayers. The system did not crystallize and may be characterized as a disordered solid. The dimers were identified based on their characteristic appearance in defocused images, i.e., rotating interference fringe patterns. The in-plane and interplane particle separations exhibit nonmonotonic dependence on the discharge pressure.

Chromophobe hepatocellular carcinoma with abrupt anaplasia: a proposal for a new subtype of hepatocellular carcinoma with unique morphological and molecular features

PubMed Central

Wood, Laura D; Heaphy, Christopher M; Daniel, Hubert Darius-J; Naini, Bita V; Lassman, Charles R; Arroyo, May R; Kamel, Ihab R; Cosgrove, David P; Boitnott, John K; Meeker, Alan K; Torbenson, Michael S

2014-01-01

Hepatocellular carcinomas exhibit heterogeneous morphologies by routine light microscopy. Although some morphologies represent insignificant variations in growth patterns, others may represent unrecognized subtypes of hepatocellular carcinoma. Identification of these subtypes could lead to separation of hepatocellular carcinomas into discrete groups with unique underlying genetic changes, prognosis, or therapeutic responses. In order to identify potential subtypes, two pathologists independently screened a cohort of 219 unselected hepatocellular carcinoma resection specimens and divided cases into potential subtypes. One of these promising candidate subtypes was further evaluated using histological and molecular techniques. This subtype was characterized by a unique and consistent set of histological features: smooth chromophobic cytoplasm, abrupt focal nuclear anaplasia (small clusters of tumor cells with marked nuclear anaplasia in a background of tumor cells with bland nuclear cytology), and scattered microscopic pseudocysts—we designate this variant as ‘chromophobe hepatocellular carcinoma with abrupt anaplasia’. Thirteen cases were identified (6% of all hepatocellular carcinomas), including 6 men and 7 women with an average age of 61 years. Six cases occurred in cirrhotic livers. Serum AFP was elevated in 6 out of 10 cases. There were a variety of underlying liver diseases, but cases were enrichment for chronic hepatitis B, P = 0.006. Interestingly, at the molecular level, this variant was strongly associated with the alternative lengthening of telomere (ALT) phenotype by telomere FISH. ALT is a telomerase-independent mechanism of telomere maintenance and is found in approximately 8% of unselected hepatocellular carcinomas. In contrast, 11/12 (92%) of the cases of chromophobe hepatocellular carcinoma with abrupt anaplasia were ALT-positive. In summary, we propose that chromophobe hepatocellular carcinoma with abrupt anaplasia represents a new subtype of hepatocellular carcinoma with unique morphological and molecular features. PMID:23640129

Chromophobe hepatocellular carcinoma with abrupt anaplasia: a proposal for a new subtype of hepatocellular carcinoma with unique morphological and molecular features.

PubMed

Wood, Laura D; Heaphy, Christopher M; Daniel, Hubert Darius-J; Naini, Bita V; Lassman, Charles R; Arroyo, May R; Kamel, Ihab R; Cosgrove, David P; Boitnott, John K; Meeker, Alan K; Torbenson, Michael S

2013-12-01

Hepatocellular carcinomas exhibit heterogeneous morphologies by routine light microscopy. Although some morphologies represent insignificant variations in growth patterns, others may represent unrecognized subtypes of hepatocellular carcinoma. Identification of these subtypes could lead to separation of hepatocellular carcinomas into discrete groups with unique underlying genetic changes, prognosis, or therapeutic responses. In order to identify potential subtypes, two pathologists independently screened a cohort of 219 unselected hepatocellular carcinoma resection specimens and divided cases into potential subtypes. One of these promising candidate subtypes was further evaluated using histological and molecular techniques. This subtype was characterized by a unique and consistent set of histological features: smooth chromophobic cytoplasm, abrupt focal nuclear anaplasia (small clusters of tumor cells with marked nuclear anaplasia in a background of tumor cells with bland nuclear cytology), and scattered microscopic pseudocysts--we designate this variant as 'chromophobe hepatocellular carcinoma with abrupt anaplasia'. Thirteen cases were identified (6% of all hepatocellular carcinomas), including 6 men and 7 women with an average age of 61 years. Six cases occurred in cirrhotic livers. Serum AFP was elevated in 6 out of 10 cases. There were a variety of underlying liver diseases, but cases were enrichment for chronic hepatitis B, P=0.006. Interestingly, at the molecular level, this variant was strongly associated with the alternative lengthening of telomere (ALT) phenotype by telomere FISH. ALT is a telomerase-independent mechanism of telomere maintenance and is found in approximately 8% of unselected hepatocellular carcinomas. In contrast, 11/12 (92%) of the cases of chromophobe hepatocellular carcinoma with abrupt anaplasia were ALT-positive. In summary, we propose that chromophobe hepatocellular carcinoma with abrupt anaplasia represents a new subtype of hepatocellular carcinoma with unique morphological and molecular features.

Faculty perceptions of academic advising: "I don't get no respect".

PubMed

Harrison, Elizabeth

2009-01-01

Best practices in teaching and learning may begin with effective academic advising. Nursing research and scholarship in the area of advising, however, is virtually nonexistent. The purpose of this exploratory study was to determine nurse faculty perceptions of the characteristics and functions of an effective academic adviser. The study was conducted at a comprehensive state university in southeastern Minnesota. Content analysis of 17 completed questionnaires was consistent with extant education and pedagogical research. Authenticity and accountability were unique characteristics of an effective adviser identified by participants in this study. The findings will facilitate faculty development in the area of academic advising and help improve services to students. Further, the results have helped identify areas for continuing scholarship in nursing.

Engineering Weyl Superfluid in Ultracold Fermionic Gases by One-Dimensional Optical Superlattices

NASA Astrophysics Data System (ADS)

Huang, Beibing

2018-01-01

In this paper, we theoretically demonstrate by using one-dimensional superlattices to couple two-dimensional time-reversal-breaking gapped topological superfluid models, an anomalous Weyl superfluid (WS) can be obtained. This new phase features its unique Fermi arc states (FAS) on the surfaces. In the conventional WS, FAS exist only for a part of the line connecting the projections of Weyl points and extending to the border and/or center of surface Brillouin zone. But for the anomalous WS, FAS exist for the whole line. As a proof of principle, we self-consistently at the mean-field level claim the achievement of the anomalous WS in the model with a dichromatic superlattice. In addition, inversion symmetry and band inversion in this model are analyzed to provide the unique features of identifying the anomalous WS experimentally by the momentum-resolved radio-frequency spectroscopy.

Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies

PubMed Central

Huo, Zhiguang; Ding, Ying; Liu, Silvia; Oesterreich, Steffi; Tseng, George

2016-01-01

Disease phenotyping by omics data has become a popular approach that potentially can lead to better personalized treatment. Identifying disease subtypes via unsupervised machine learning is the first step towards this goal. In this paper, we extend a sparse K-means method towards a meta-analytic framework to identify novel disease subtypes when expression profiles of multiple cohorts are available. The lasso regularization and meta-analysis identify a unique set of gene features for subtype characterization. An additional pattern matching reward function guarantees consistent subtype signatures across studies. The method was evaluated by simulations and leukemia and breast cancer data sets. The identified disease subtypes from meta-analysis were characterized with improved accuracy and stability compared to single study analysis. The breast cancer model was applied to an independent METABRIC dataset and generated improved survival difference between subtypes. These results provide a basis for diagnosis and development of targeted treatments for disease subgroups. PMID:27330233

Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies.

PubMed

Huo, Zhiguang; Ding, Ying; Liu, Silvia; Oesterreich, Steffi; Tseng, George

Disease phenotyping by omics data has become a popular approach that potentially can lead to better personalized treatment. Identifying disease subtypes via unsupervised machine learning is the first step towards this goal. In this paper, we extend a sparse K -means method towards a meta-analytic framework to identify novel disease subtypes when expression profiles of multiple cohorts are available. The lasso regularization and meta-analysis identify a unique set of gene features for subtype characterization. An additional pattern matching reward function guarantees consistent subtype signatures across studies. The method was evaluated by simulations and leukemia and breast cancer data sets. The identified disease subtypes from meta-analysis were characterized with improved accuracy and stability compared to single study analysis. The breast cancer model was applied to an independent METABRIC dataset and generated improved survival difference between subtypes. These results provide a basis for diagnosis and development of targeted treatments for disease subgroups.

Development of tools to study personal weight control strategies: OxFAB taxonomy

PubMed Central

Aveyard, Paul; Koshiaris, Constantinos; Jebb, Susan A.

2016-01-01

Objective To describe the development of the Oxford Food and Activity Behaviors (OxFAB) taxonomy and questionnaire to explore the cognitive and behavioral strategies used by individuals during weight management attempts. Methods The taxonomy was constructed through a qualitative analysis of existing resources and a review of existing behavior change taxonomies and theories. The taxonomy was translated into a questionnaire to identify strategies used by individuals. Think‐aloud interviews were conducted to test the face/concept validity of the questionnaire, and test–retest reliability was assessed in a sample of 138 participants. Results The OxFAB taxonomy consists of 117 strategies grouped into 23 domains. Compared to taxonomies used to describe interventions, around half of the domains and strategies identified are unique to the OxFAB taxonomy. The OxFAB questionnaire consists of 117 questions, one for each strategy from the taxonomy. Test–retest resulted in a mean PABAK score of 0.61 (SD 0.15). Questions were revised where appropriate. Conclusions The OxFAB taxonomy and questionnaire provide a conceptual framework to identify the cognitive and behavioral strategies used by individuals during attempts at weight control. PMID:26748902

Development of tools to study personal weight control strategies: OxFAB taxonomy.

PubMed

Hartmann-Boyce, Jamie; Aveyard, Paul; Koshiaris, Constantinos; Jebb, Susan A

2016-02-01

To describe the development of the Oxford Food and Activity Behaviors (OxFAB) taxonomy and questionnaire to explore the cognitive and behavioral strategies used by individuals during weight management attempts. The taxonomy was constructed through a qualitative analysis of existing resources and a review of existing behavior change taxonomies and theories. The taxonomy was translated into a questionnaire to identify strategies used by individuals. Think-aloud interviews were conducted to test the face/concept validity of the questionnaire, and test-retest reliability was assessed in a sample of 138 participants. The OxFAB taxonomy consists of 117 strategies grouped into 23 domains. Compared to taxonomies used to describe interventions, around half of the domains and strategies identified are unique to the OxFAB taxonomy. The OxFAB questionnaire consists of 117 questions, one for each strategy from the taxonomy. Test-retest resulted in a mean PABAK score of 0.61 (SD 0.15). Questions were revised where appropriate. The OxFAB taxonomy and questionnaire provide a conceptual framework to identify the cognitive and behavioral strategies used by individuals during attempts at weight control. © 2016 The Authors. Obesity published by Wiley Periodicals, Inc. on behalf of The Obesity Society (TOS).

A Comparison of Trap Types for Assessing Diversity of Scarabaeoidea on South Carolina Golf Courses.

PubMed

Chong, Juang-Horng; Hinson, Kevin R

2015-10-01

A 2-yr survey was conducted on golf courses in South Carolina to 1) document the species richness and seasonal activity of Scarabaeoidea; 2) assess any species compositional differences among three trap types (ultraviolet light, unbaited flight-intercept, and unbaited pitfall); and 3) identify any dominant taxa in each trap type. A total of 74,326 scarabaeoid beetles were captured, of which 77.4% were Aphodiinae (not identified to species). The remaining specimens belong to 104 species in 47 genera and 6 families. The most abundant species were Cyclocephala lurida Bland, Dyscinetus morator (F.), Euetheola humilis (Burmeister), Hybosorus illigeri Reiche, and Maladera castanea (Arrow). In all trap types, >90% of all specimens and taxa were collected between April and August. Ultraviolet light traps collected ∼94% of total specimens consisting of 83 taxa (of which 51 were unique to this trap type), whereas flight-intercept traps captured ∼2% of all specimens representing 53 taxa (18 of which were unique), and pitfall traps captured ∼4% of all specimens representing 15 taxa (no unique species; all species also captured by ultraviolet light traps). Indicator species analysis identified 2-3 and 10-13 taxa that were most frequently collected by flight-intercept and ultraviolet light traps, respectively. Flight-intercept traps complemented ultraviolet light traps by capturing more species of dung and carrion beetles and diurnal phytophagous scarab beetles. Results suggested that a similar survey for domestic or exotic scarabaeoid beetles in turfgrass systems should be conducted between April and August using ultraviolet light and flight-intercept traps at 13-58 sites. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Educational Objectives of International Medical Electives – a narrative literature review

PubMed Central

Cherniak, William A.; Drain, Paul K.; Brewer, Timothy F.

2014-01-01

Purpose Most medical schools and residency programs offer international medical electives [IMEs], but there is little guidance on educational objectives for these rotations. We reviewed the literature to compile and categorize a comprehensive set of educational objectives for IMEs. Methods We conducted a narrative literature review with specified search criteria using SciVerse Scopus online, which includes Embase and Medline databases. From manuscripts that met inclusion criteria, we extracted data on educational objectives and sorted them into pre-elective, intra-elective, and post-elective categories. Results We identified and reviewed 255 articles, of which 11 (4%) manuscripts described 22 unique educational objectives. Among those, 5 (23%), 15 (68%), and 2 (9%) objectives were categorized in the pre-elective, intra-elective, and post-elective periods, respectively. Among pre-elective objectives, only cultural awareness was listed by more than two articles (3/11, 27%). Among intra-elective objectives, the most commonly defined objectives for students were enhancing clinical skills and understanding different health care systems (9/11, 82%). Learning to manage diseases rarely seen at home and increasing cultural awareness were described by nearly half (5/11, 46%) of all papers. Among post-elective objectives, reflecting on experiences through a written project was most common (9/11, 82%). Conclusions We identified 22 unique educational objectives for IMEs in the published literature, some of which were consistent. These consistencies can be used as a framework upon which institutions can build their own IME curriculums, ultimately helping to ensure that their students have a meaningful learning experience while abroad. PMID:24072105

Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803.

PubMed

Qiao, Jianjun; Wang, Jiangxin; Chen, Lei; Tian, Xiaoxu; Huang, Siqiang; Ren, Xiaoyue; Zhang, Weiwen

2012-11-02

Recent progress in metabolic engineering has led to autotrophic production of ethanol in various cyanobacterial hosts. However, cyanobacteria are known to be sensitive to ethanol, which restricts further efforts to increase ethanol production levels in these renewable host systems. To understand the mechanisms of ethanol tolerance so that engineering more robust cyanobacterial hosts can be possible, in this study, the responses of model cyanobacterial Synechocystis sp. PCC 6803 to ethanol were determined using a quantitative proteomics approach with iTRAQ LC-MS/MS technologies. The resulting high-quality proteomic data set consisted of 24,887 unique peptides corresponding to 1509 identified proteins, a coverage of approximately 42% of the predicted proteins in the Synechocystis genome. Using a cutoff of 1.5-fold change and a p-value less than 0.05, 135 and 293 unique proteins with differential abundance levels were identified between control and ethanol-treated samples at 24 and 48 h, respectively. Functional analysis showed that the Synechocystis cells employed a combination of induced common stress response, modifications of cell membrane and envelope, and induction of multiple transporters and cell mobility-related proteins as protection mechanisms against ethanol toxicity. Interestingly, our proteomic analysis revealed that proteins related to multiple aspects of photosynthesis were up-regulated in the ethanol-treated Synechocystis cells, consistent with increased chlorophyll a concentration in the cells upon ethanol exposure. The study provided the first comprehensive view of the complicated molecular mechanisms against ethanol stress and also provided a list of potential gene targets for further engineering ethanol tolerance in Synechocystis PCC 6803.

Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome.

PubMed

Choong, Wai-Kok; Lih, Tung-Shing Mamie; Chen, Yu-Ju; Sung, Ting-Yi

2017-12-01

To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass-spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues. Therefore, we conducted a thorough comparative analysis on data sets in PeptideAtlas Tiered Human Integrated Search Proteome (THISP, 2017-03 release), including neXtProt (2017-01 release), to systematically investigate the possibility of unique peptides in missing proteins (PE2-4), unique peptides in dubious proteins, and variant peptides affected by isobaric substitutions, causing doubtful identification results. In this study, we considered 11 isobaric substitutions. From our analysis, we found <5% of the unique peptides of missing proteins and >6% of variant peptides became shared with peptides of PE1 proteins after isobaric substitutions.

MRAP and MRAP2 are bidirectional regulators of the melanocortin receptor family

PubMed Central

Chan, Li F.; Webb, Tom R.; Chung, Teng-Teng; Meimaridou, Eirini; Cooray, Sadani N.; Guasti, Leonardo; Chapple, J. Paul; Egertová, Michaela; Elphick, Maurice R.; Cheetham, Michael E.; Metherell, Louise A.; Clark, Adrian J. L.

2009-01-01

The melanocortin receptor (MCR) family consists of 5 G protein-coupled receptors (MC1R–MC5R) with diverse physiologic roles. MC2R is a critical component of the hypothalamic–pituitary–adrenal axis, whereas MC3R and MC4R have an essential role in energy homeostasis. Mutations in MC4R are the single most common cause of monogenic obesity. Investigating the way in which these receptors signal and traffic to the cell membrane is vital in understanding disease processes related to MCR dysfunction. MRAP is an MC2R accessory protein, responsible for adrenal MC2R trafficking and function. Here we identify MRAP2 as a unique homologue of MRAP, expressed in brain and the adrenal gland. We report that MRAP and MRAP2 can interact with all 5 MCRs. This interaction results in MC2R surface expression and signaling. In contrast, MRAP and MRAP2 can reduce MC1R, MC3R, MC4R, and MC5R responsiveness to [Nle4,D-Phe7]alpha-melanocyte-stimulating hormone (NDP-MSH). Collectively, our data identify MRAP and MRAP2 as unique bidirectional regulators of the MCR family. PMID:19329486

Proteomic Characterization of the Major Arthropod Associates of the Carnivorous Pitcher Plant Sarracenia purpurea

PubMed Central

Gotelli, Nicholas J.; Smith, Aidan M.; Ellison, Aaron M.; Ballif, Bryan A.

2012-01-01

The array of biomolecules generated by a functioning ecosystem represents both a potential resource for sustainable harvest and a potential indicator of ecosystem health and function. The cupped leaves of the carnivorous pitcher plant, Sarracenia purpurea, harbor a dynamic food web of aquatic invertebrates in a fully functional miniature ecosystem. The energetic base of this food web consists of insect prey, which is shredded by aquatic invertebrates and decomposed by microbes. Biomolecules and metabolites produced by this food web are actively exchanged with the photosynthesizing plant. In this report, we provide the first proteomic characterization of the sacrophagid fly (Fletcherimyia fletcheri), the pitcher plant mosquito (Wyeomyia smithii), and the pitcher-plant midge (Metriocnemus knabi). These three arthropods act as predators, filter feeders, and shredders at distinct trophic levels within the S. purpurea food web. More than 50 proteins from each species were identified, 10 of which were predominantly or uniquely found in one species. Furthermore, 19 peptides unique to one of the three species were identified using an assembled database of 100 metazoan myosin heavy chain orthologs. These molecular signatures may be useful in species monitoring within heterogeneous ecosystem biomass and may also serve as indicators of ecosystem state. PMID:21538880

Using naturalistic driving data to identify variables associated with infrequent, occasional, and consistent seat belt use.

PubMed

Reagan, Ian J; McClafferty, Julie A; Berlin, Sharon P; Hankey, Jonathan M

2013-01-01

Seat belt use is one of the most effective countermeasures to reduce traffic fatalities and injuries. The success of efforts to increase use is measured by road side observations and self-report questionnaires. These methods have shortcomings, with the former requiring a binary point estimate and the latter being subjective. The 100-car naturalistic driving study presented a unique opportunity to study seat belt use in that seat belt status was known for every trip each driver made during a 12-month period. Drivers were grouped into infrequent, occasional, or consistent seat belt users based on the frequency of belt use. Analyses were then completed to assess if these groups differed on several measures including personality, demographics, self-reported driving style variables as well as measures from the 100-car study instrumentation suite (average trip speed, trips per day). In addition, detailed analyses of the occasional belt user group were completed to identify factors that were predictive of occasional belt users wearing their belts. The analyses indicated that consistent seat belt users took fewer trips per day, and that increased average trip speed was associated with increased belt use among occasional belt users. The results of this project may help focus messaging efforts to convert occasional and inconsistent seat belt users to consistent users. Copyright © 2012 Elsevier Ltd. All rights reserved.

Health and wellbeing boards: public health decision making bodies or political pawns?

PubMed

Greaves, Z; McCafferty, S

2017-02-01

Health and Wellbeing boards in England are uniquely constituted; embedded in the local authorities with membership drawn from a range of stakeholders and partner organizations. This raises the question of how decision making functions of the boards reflects wider public health decision making, if criteria are applied to decision making, and what prioritization processes, if any, are used. Qualitative research methods were employed and five local boards were approached, interview dyads were conducted with the boards Chair and Director of Public Health across four of these (n = 4). Three questions were addressed: how are decisions made? What are the criteria applied to decision making? And how are criteria then prioritized? A thematic approach was used to analyse data identifying codes and extracting key themes. Equity, effectiveness and consistency with strategies of board and partners were most consistently identified by participants as criteria influencing decisions. Prioritization was described as an engaged and collaborative process, but criteria were not explicitly referenced in the decision making of the boards which instead made unstructured prioritization of population sub-groups or interventions agreed by consensus. Criteria identified are broadly consistent with those used in wider public health practice but additionally incorporated criteria which recognizes the political siting of the boards. The study explored the variety in different board's approaches to prioritization and identified a lack of clarity and rigour in the identification and use of criteria in prioritization processes. Decision making may benefit from the explicit inclusion of criteria in the prioritization process. Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Depression is not a consistent syndrome: An investigation of unique symptom patterns in the STAR*D study.

PubMed

Fried, Eiko I; Nesse, Randolph M

2015-02-01

The DSM-5 encompasses a wide range of symptoms for Major Depressive Disorder (MDD). Symptoms are commonly added up to sum-scores, and thresholds differentiate between healthy and depressed individuals. The underlying assumption is that all patients diagnosed with MDD have a similar condition, and that sum-scores accurately reflect the severity of this condition. To test this assumption, we examined the number of DSM-5 depression symptom patterns in the "Sequenced Treatment Alternatives to Relieve Depression" (STAR*D) study. We investigated the number of unique symptom profiles reported by 3703 depressed outpatients at the beginning of the first treatment stage of STAR*D. Overall, we identified 1030 unique symptom profiles. Of these profiles, 864 profiles (83.9%) were endorsed by five or fewer subjects, and 501 profiles (48.6%) were endorsed by only one individual. The most common symptom profile exhibited a frequency of only 1.8%. Controlling for overall depression severity did not reduce the amount of observed heterogeneity. Symptoms were dichotomized to construct symptom profiles. Many subjects enrolled in STAR*D reported medical conditions for which prescribed medications may have affected symptom presentation. The substantial symptom variation among individuals who all qualify for one diagnosis calls into question the status of MDD as a specific consistent syndrome and offers a potential explanation for the difficulty in documenting treatment efficacy. We suggest that the analysis of individual symptoms, their patterns, and their causal associations will provide insights that could not be discovered in studies relying on only sum-scores. Copyright © 2014 Elsevier B.V. All rights reserved.

Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network

PubMed Central

McDavid, Andrew; Weston, Noah; Nelson, Sarah C.; Zheng, Xiuwen; Hart, Eugene; de Andrade, Mariza; Kullo, Iftikhar J.; McCarty, Catherine A.; Doheny, Kimberly F.; Pugh, Elizabeth; Kho, Abel; Hayes, M. Geoffrey; Pretel, Stephanie; Saip, Alexander; Ritchie, Marylyn D.; Crawford, Dana C.; Crane, Paul K.; Newton, Katherine; Li, Rongling; Mirel, Daniel B.; Crenshaw, Andrew; Larson, Eric B.; Carlson, Chris S.; Jarvik, Gail P.

2013-01-01

White blood cell count (WBC) is unique among identified inflammatory predictors of chronic disease in that it is routinely measured in asymptomatic patients in the course of routine patient care. We led a genome-wide association analysis to identify variants associated with WBC levels in 13,923 subjects in the electronic Medical Records and Genomics (eMERGE) Network. We identified two regions of interest that were each unique to subjects of genetically determined ancestry to the African continent (AA) or to the European continent (EA). WBC varies among different ancestry groups. Despite being ancestry specific, these regions were identifiable in the combined analysis. In AA subjects, the region surrounding the Duffy antigen/chemokine receptor gene (DARC) on 1q21 exhibited significant association (p value = 6.71e–55). These results validate the previously reported association between WBC and of the regulatory variant rs2814778 in the promoter region, which causes the Duffy negative phenotype (Fy−/−). A second missense variant (rs12075) is responsible for the two principal antigens, Fya and Fyb of the Duffy blood group system. The two variants, consisting of four alleles, act in concert to produce five antigens and subsequent phenotypes. We were able to identify the marginal and novel interaction effects of these two variants on WBC. In the EA subjects, we identified significantly associated SNPs tagging three separate genes in the 17q21 region: (1) GSDMA, (2) MED24, and (3) PSMD3. Variants in this region have been reported to be associated with WBC, neutrophil count, and inflammatory diseases including asthma and Crohn’s disease. PMID:22037903

Empowering the "Cheerers": Role of Surgical Intensive Care Unit Nurses in Enhancing Family Resilience.

PubMed

Ellis, Lauren; Gergen, Jessica; Wohlgemuth, Leah; Nolan, Marie T; Aslakson, Rebecca

2016-01-01

Supporting family resilience, the ability of families to rebound from stressful events, is a goal of family nursing. Critical care nurses act as liaisons between patients' families and other clinicians and thus are uniquely situated to promote family resilience. To explore how nurses perceive the experiences of long-stay surgical intensive care unit patients and their families in order to gain insights on how nurses could cultivate family resilience. A qualitative study including semistructured interviews (n = 13) and 4 focus groups (n = 17) with nurses in 3 surgical intensive care units in a large teaching hospital. Three themes were identified: expectations, support, and communication. Nurses noted that clinicians' and families' unrealistic expectations regarding the patient's recovery can foster false hope. Nurses recognized families as "cheerers" who provide support by being involved in patient care and observed how extensive family involvement can be beneficial to patients but overwhelming for families. Nurses noted that communication among providers, families, and patients is the cornerstone of creating meaningful relationships. Nurses stated that with many teams involved, discrepancies in information can occur and often confuse and disturb patients' families. Thus, nurses identified ways to enhance family resilience through routine and consistent communication. Nurses note unique stresses faced by families of patients in surgical intensive care units. Using the family resilience model, nurses can identify and enhance key family resilience factors. ©2016 American Association of Critical-Care Nurses.

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.

PubMed

Chase, John H; Bolyen, Evan; Rideout, Jai Ram; Caporaso, J Gregory

2016-01-01

The number of samples in high-throughput comparative "omics" studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use "cual-id" to refer to the software, "CualID" to refer to the short, human-friendly identifiers, and "UUID" to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.

Understanding identifiability as a crucial step in uncertainty assessment

NASA Astrophysics Data System (ADS)

Jakeman, A. J.; Guillaume, J. H. A.; Hill, M. C.; Seo, L.

2016-12-01

The topic of identifiability analysis offers concepts and approaches to identify why unique model parameter values cannot be identified, and can suggest possible responses that either increase uniqueness or help to understand the effect of non-uniqueness on predictions. Identifiability analysis typically involves evaluation of the model equations and the parameter estimation process. Non-identifiability can have a number of undesirable effects. In terms of model parameters these effects include: parameters not being estimated uniquely even with ideal data; wildly different values being returned for different initialisations of a parameter optimisation algorithm; and parameters not being physically meaningful in a model attempting to represent a process. This presentation illustrates some of the drastic consequences of ignoring model identifiability analysis. It argues for a more cogent framework and use of identifiability analysis as a way of understanding model limitations and systematically learning about sources of uncertainty and their importance. The presentation specifically distinguishes between five sources of parameter non-uniqueness (and hence uncertainty) within the modelling process, pragmatically capturing key distinctions within existing identifiability literature. It enumerates many of the various approaches discussed in the literature. Admittedly, improving identifiability is often non-trivial. It requires thorough understanding of the cause of non-identifiability, and the time, knowledge and resources to collect or select new data, modify model structures or objective functions, or improve conditioning. But ignoring these problems is not a viable solution. Even simple approaches such as fixing parameter values or naively using a different model structure may have significant impacts on results which are too often overlooked because identifiability analysis is neglected.

Hyperactive antifreeze proteins from longhorn beetles: some structural insights.

PubMed

Kristiansen, Erlend; Wilkens, Casper; Vincents, Bjarne; Friis, Dennis; Lorentzen, Anders Blomkild; Jenssen, Håvard; Løbner-Olesen, Anders; Ramløv, Hans

2012-11-01

This study reports on structural characteristics of hyperactive antifreeze proteins (AFPs) from two species of longhorn beetles. In Rhagium mordax, eight unique mRNAs coding for five different mature AFPs were identified from cold-hardy individuals. These AFPs are apparently homologues to a previously characterized AFP from the closely related species Rhagium inquisitor, and consist of six identifiable repeats of a putative ice binding motif TxTxTxT spaced irregularly apart by segments varying in length from 13 to 20 residues. Circular dichroism spectra show that the AFPs from both species have a high content of β-sheet and low levels of α-helix and random coil. Theoretical predictions of residue-specific secondary structure locate these β-sheets within the putative ice-binding motifs and the central parts of the segments separating them, consistent with an overall β-helical structure with the ice-binding motifs stacked in a β-sheet on one side of the coil. Molecular dynamics models based on these findings show that these AFPs would be energetically stable in a β-helical conformation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Population structure of Fusarium fujikuroi from California rice and water grass.

PubMed

Carter, L L A; Leslie, J F; Webster, R K

2008-09-01

The recent observance of Fusarium fujikuroi, the causal agent of Bakanae disease of rice, in California provides a unique opportunity to assess the population diversity of an introduced pathogen in a new environment. We collected 172 isolates of this pathogen between 2000 and 2003 from California rice and two from water grass (Echinochloa spp.). Pathogenicity of F. fujikuroi was demonstrated on early water grass (E. oryzoides) and barnyard grass (E. crus-galli) indicating that weed control should be part of Bakanae management programs. Both mating types and six unique amplified fragment length polymorphism haplotypes corresponding to six identified vegetative compatibility groups were detected. The two most frequently isolated haplotypes encompassed 94% of the collected isolates, suggesting that clonal reproduction dominates. Coefficients of similarity between the unique haplotypes ranged from 0.94 to 0.98, and indicate that there is very little genotypic variation in the F. fujikuroi population in California. The near fixation of the MAT-1 idiomorph (observed ratio 170 MAT-1:4 MAT-2), is consistent with a hypothesis of predominant or exclusive asexual reproduction. The low level of introduced genotypic diversity, in conjunction with the asexual reproductive strategy of this population will slow evolutionary processes, including adaptation to the California environment.

Diversity of human copy number variation and multicopy genes.

PubMed

Sudmant, Peter H; Kitzman, Jacob O; Antonacci, Francesca; Alkan, Can; Malig, Maika; Tsalenko, Anya; Sampas, Nick; Bruhn, Laurakay; Shendure, Jay; Eichler, Evan E

2010-10-29

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

Rapid needs assessment among Hurricane Katrina evacuees in metro-Denver.

PubMed

Ghosh, Tista S; Patnaik, Jennifer L; Vogt, Richard L

2007-05-01

During September 2005, 3,600 Gulf Coast evacuees arrived in metropolitan Denver, in the aftermath of Hurricane Katrina. To better meet the medical and non-medical needs of this displaced population, a rapid needs assessment was conducted among 106 evacuee households. The assessment identified a large need for prescription medications, with 60.2% of households requiring prescription medications and 38.8% of these households lacking these medications at the time of the survey. The assessment also identified self-reported symptoms consistent with altitude sickness and the region-specific need for education on the effects of Denver's mile-high altitude. Finally, the assessment identified differential needs based on race; non-Hispanic Black households were more likely than non-Hispanic White households to require employment, housing, and dental services. These findings illustrate the importance of conducting rapid needs assessments in displaced populations, to identify unique regional, cultural, and other unanticipated needs, as well as to recognize the needs of specific sub-populations.

Suspended marine particulate proteins in coastal and oligotrophic waters

NASA Astrophysics Data System (ADS)

Bridoux, Maxime C.; Neibauer, Jaqui; Ingalls, Anitra E.; Nunn, Brook L.; Keil, Richard G.

2015-03-01

Metaproteomic analyses were performed on suspended sediments collected in one coastal environment (Washington margin, Pacific Ocean, n = 5) and two oligotrophic environments (Atlantic Ocean near BATS, n = 5, and Pacific Ocean near HOTS, n = 5). Using a database of 2.3 million marine proteins developed using the NCBI database, 443 unique peptides were detected from which 363 unique proteins were identified. Samples from the euphotic zone contained on average 2-3x more identifiable proteins than deeper waters (150-1500 m) and these proteins were predominately from photosynthetic organisms. Diatom peptides dominate the spectra of the Washington margin while peptides from cyanobacteria, such as Synechococcus sp. dominated the spectra of both oligotrophic sites. Despite differences in the exact proteins identified at each location, there is good agreement for protein function and cellular location. Proteins in surface waters code for a variety of cellular functions including photosynthesis (24% of detected proteins), energy production (10%), membrane production (9%) and genetic coding and reading (9%), and are split 60-40 between membrane proteins and intracellular cytoplasmic proteins. Sargasso Sea surface waters contain a suite of peptides consistent with proteins involved in circadian rhythms that promote both C and N fixation at night. At depth in the Sargasso Sea, both muscle-derived myosin protein and the muscle-hydrolyzing proteases deseasin MCP-01 and metalloprotease Mcp02 from γ-proteobacteria were observed. Deeper waters contain peptides predominately sourced from γ-proteobacteria (37% of detected proteins) and α-proteobacteria (26%), although peptides from membrane and photosynthetic proteins attributable to phytoplankton were still observed (13%). Relative to surface values, detection frequencies for bacterial membrane proteins and extracellular enzymes rose from 9 to 16 and 2 to 4% respectively below the thermocline and the overall balance between membrane proteins and intracellular proteins grows to an approximate 75-25 split. Unlike the phytoplankton membrane proteins, which are detrital in nature, the bacterial protein suite at depth is consistent with living biomass.

Novel entries in a fungal biofilm matrix encyclopedia.

PubMed

Zarnowski, Robert; Westler, William M; Lacmbouh, Ghislain Ade; Marita, Jane M; Bothe, Jameson R; Bernhardt, Jörg; Lounes-Hadj Sahraoui, Anissa; Fontaine, Joël; Sanchez, Hiram; Hatfield, Ronald D; Ntambi, James M; Nett, Jeniel E; Mitchell, Aaron P; Andes, David R

2014-08-05

Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components. Importance: This report is the first to decipher the complex and unique macromolecular composition of the Candida biofilm matrix, demonstrate the clinical relevance of matrix components, and show that multiple matrix components are needed for protection from antifungal drugs. The availability of these biochemical analyses provides a unique resource for further functional investigation of the biofilm matrix, a defining trait of this lifestyle. Copyright © 2014 Zarnowski et al.

Modularity, comparative cognition and human uniqueness.

PubMed

Shettleworth, Sara J

2012-10-05

Darwin's claim 'that the difference in mind between man and the higher animals … is certainly one of degree and not of kind' is at the core of the comparative study of cognition. Recent research provides unprecedented support for Darwin's claim as well as new reasons to question it, stimulating new theories of human cognitive uniqueness. This article compares and evaluates approaches to such theories. Some prominent theories propose sweeping domain-general characterizations of the difference in cognitive capabilities and/or mechanisms between adult humans and other animals. Dual-process theories for some cognitive domains propose that adult human cognition shares simple basic processes with that of other animals while additionally including slower-developing and more explicit uniquely human processes. These theories are consistent with a modular account of cognition and the 'core knowledge' account of children's cognitive development. A complementary proposal is that human infants have unique social and/or cognitive adaptations for uniquely human learning. A view of human cognitive architecture as a mosaic of unique and species-general modular and domain-general processes together with a focus on uniquely human developmental mechanisms is consistent with modern evolutionary-developmental biology and suggests new questions for comparative research.

Modularity, comparative cognition and human uniqueness

PubMed Central

Shettleworth, Sara J.

2012-01-01

Darwin's claim ‘that the difference in mind between man and the higher animals … is certainly one of degree and not of kind’ is at the core of the comparative study of cognition. Recent research provides unprecedented support for Darwin's claim as well as new reasons to question it, stimulating new theories of human cognitive uniqueness. This article compares and evaluates approaches to such theories. Some prominent theories propose sweeping domain-general characterizations of the difference in cognitive capabilities and/or mechanisms between adult humans and other animals. Dual-process theories for some cognitive domains propose that adult human cognition shares simple basic processes with that of other animals while additionally including slower-developing and more explicit uniquely human processes. These theories are consistent with a modular account of cognition and the ‘core knowledge’ account of children's cognitive development. A complementary proposal is that human infants have unique social and/or cognitive adaptations for uniquely human learning. A view of human cognitive architecture as a mosaic of unique and species-general modular and domain-general processes together with a focus on uniquely human developmental mechanisms is consistent with modern evolutionary-developmental biology and suggests new questions for comparative research. PMID:22927578

Genome-wide gene expression effects in B6C3F1 mouse intestinal epithelia following 7 and 90 days of exposure to hexavalent chromium in drinking water

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

Kopec, Anna K.; Kim, Suntae; Forgacs, Agnes L.

2012-02-15

Chronic administration of high doses of hexavalent chromium [Cr(VI)] as sodium dichromate dihydrate (SDD) elicits alimentary cancers in mice. To further elucidate key events underlying tumor formation, a 90-day drinking water study was conducted in B6C3F1 mice. Differential gene expression was examined in duodenal and jejunal epithelial samples following 7 or 90 days of exposure to 0, 0.3, 4, 14, 60, 170 or 520 mg/L SDD in drinking water. Genome-wide microarray analyses identified 6562 duodenal and 4448 jejunal unique differentially expressed genes at day 8, and 4630 and 4845 unique changes, respectively, in the duodenum and jejunum at day 91.more » Comparative analysis identified significant overlap in duodenal and jejunal differential gene expression. Automated dose–response modeling identified > 80% of the differentially expressed genes exhibited sigmoidal dose–response curves with EC{sub 50} values ranging from 10 to 100 mg/L SDD. Only 16 genes satisfying the dose-dependent differential expression criteria had EC{sub 50} values < 10 mg/L SDD, 3 of which were regulated by Nrf2, suggesting oxidative stress in response to SDD at low concentrations. Analyses of differentially expressed genes identified over-represented functions associated with oxidative stress, cell cycle, lipid metabolism, and immune responses consistent with the reported effects on redox status and histopathology at corresponding SDD drinking water concentrations. Collectively, these data are consistent with a mode of action involving oxidative stress and cytotoxicity as early key events. This suggests that the tumorigenic effects of chronic Cr(VI) oral exposure likely require chronic tissue damage and compensatory epithelial cell proliferation. Highlights: ► Mouse small intestine gene expression is highly responsive to hexavalent chromium [Cr(VI)]. ► Cr(VI) elicits more differential gene expression after 7 days of exposure than 90 days of exposure. ► Oral exposure to Cr(VI) leads to oxidative stress, cell cycle, lipid and immune dysregulation. ► Cr(VI) elicits dose-dependent changes in gene expression with an overall median EC{sub 50} of 47 mg/L SDD.« less

What Do We Know about the Chemistry of Strawberry Aroma?

PubMed

Ulrich, Detlef; Kecke, Steffen; Olbricht, Klaus

2018-04-04

The strawberry, with its unique aroma, is one of the most popular fruits worldwide. The demand for specific knowledge of metabolism in strawberries is increasing. This knowledge is applicable for genetic studies, plant breeding, resistance research, nutritional science, and the processing industry. The molecular basis of strawberry aroma has been studied for more than 80 years. Thus far, hundreds of volatile organic compounds (VOC) have been identified. The qualitative composition of the strawberry volatilome remains controversial though considerable progress has been made during the past several decades. Between 1997 and 2016, 25 significant analytical studies were published. Qualitative VOC data were harmonized and digitized. In total, 979 VOC were identified, 590 of which were found since 1997. However, 659 VOC (67%) were only listed once (single entries). Interestingly, none of the identified compounds were consistently reported in all of the studies analyzed. The present need of data exchange between "omic" technologies requires high quality and robust metabolic data. Such data are unavailable for the strawberry volatilome thus far. This review discusses the divergence of published data regarding both the biological material and the analytical methods. The VOC extraction method is an essential step that restricts interlaboratory comparability. Finally, standardization of sample preparation and data documentation are suggested to improve consistency for VOC quantification and measurement.

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics.

PubMed

Chen, Tsute; Siddiqui, Huma; Olsen, Ingar

2017-01-01

Currently, genome sequences of a total of 19 Porphyromonas gingivalis strains are available, including eight completed genomes (strains W83, ATCC 33277, TDC60, HG66, A7436, AJW4, 381, and A7A1-28) and 11 high-coverage draft sequences (JCVI SC001, F0185, F0566, F0568, F0569, F0570, SJD2, W4087, W50, Ando, and MP4-504) that are assembled into fewer than 300 contigs. The objective was to compare these genomes at both nucleotide and protein sequence levels in order to understand their phylogenetic and functional relatedness. Four copies of 16S rRNA gene sequences were identified in each of the eight complete genomes and one in the other 11 unfinished genomes. These 43 16S rRNA sequences represent only 24 unique sequences and the derived phylogenetic tree suggests a possible evolutionary history for these strains. Phylogenomic comparison based on shared proteins and whole genome nucleotide sequences consistently showed two groups with closely related members: one consisted of ATCC 33277, 381, and HG66, another of W83, W50, and A7436. At least 1,037 core/shared proteins were identified in the 19 P. gingivalis genomes based on the most stringent detecting parameters. Comparative functional genomics based on genome-wide comparisons between NCBI and RAST annotations, as well as additional approaches, revealed functions that are unique or missing in individual P. gingivalis strains, or species-specific in all P. gingivalis strains, when compared to a neighboring species P. asaccharolytica . All the comparative results of this study are available online for download at ftp://www.homd.org/publication_data/20160425/.

Quantitative proteomic analysis of amniocytes reveals potentially dysregulated molecular networks in Down syndrome

PubMed Central

2013-01-01

Background Down syndrome (DS), caused by an extra copy of chromosome 21, affects 1 in 750 live births and is characterized by cognitive impairment and a constellation of congenital defects. Currently, little is known about the molecular pathogenesis and no direct genotype-phenotype relationship has yet been confirmed. Since DS amniocytes are expected to have a distinct biological behaviour compared to normal amniocytes, we hypothesize that relative quantification of proteins produced from trisomy and euploid (chromosomally normal) amniocytes will reveal dysregulated molecular pathways. Results Chromosomally normal- and Trisomy 21-amniocytes were quantitatively analyzed by using Stable Isotope Labeling of Amino acids in Cell culture and tandem mass spectrometry. A total of 4919 unique proteins were identified from the supernatant and cell lysate proteome. More specifically, 4548 unique proteins were identified from the lysate, and 91% of these proteins were quantified based on MS/MS spectra ratios of peptides containing isotope-labeled amino acids. A total of 904 proteins showed significant differential expression and were involved in 25 molecular pathways, each containing a minimum of 16 proteins. Sixty of these proteins consistently showed aberrant expression from trisomy 21 affected amniocytes, indicating their potential role in DS pathogenesis. Nine proteins were analyzed with a multiplex selected reaction monitoring assay in an independent set of Trisomy 21-amniocyte samples and two of them (SOD1 and NES) showed a consistent differential expression. Conclusions The most extensive proteome of amniocytes and amniotic fluid has been generated and differentially expressed proteins from amniocytes with Trisomy 21 revealed molecular pathways that seem to be most significantly affected by the presence of an extra copy of chromosome 21. PMID:23394617

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

PubMed Central

Chen, Tsute; Siddiqui, Huma; Olsen, Ingar

2017-01-01

Currently, genome sequences of a total of 19 Porphyromonas gingivalis strains are available, including eight completed genomes (strains W83, ATCC 33277, TDC60, HG66, A7436, AJW4, 381, and A7A1-28) and 11 high-coverage draft sequences (JCVI SC001, F0185, F0566, F0568, F0569, F0570, SJD2, W4087, W50, Ando, and MP4-504) that are assembled into fewer than 300 contigs. The objective was to compare these genomes at both nucleotide and protein sequence levels in order to understand their phylogenetic and functional relatedness. Four copies of 16S rRNA gene sequences were identified in each of the eight complete genomes and one in the other 11 unfinished genomes. These 43 16S rRNA sequences represent only 24 unique sequences and the derived phylogenetic tree suggests a possible evolutionary history for these strains. Phylogenomic comparison based on shared proteins and whole genome nucleotide sequences consistently showed two groups with closely related members: one consisted of ATCC 33277, 381, and HG66, another of W83, W50, and A7436. At least 1,037 core/shared proteins were identified in the 19 P. gingivalis genomes based on the most stringent detecting parameters. Comparative functional genomics based on genome-wide comparisons between NCBI and RAST annotations, as well as additional approaches, revealed functions that are unique or missing in individual P. gingivalis strains, or species-specific in all P. gingivalis strains, when compared to a neighboring species P. asaccharolytica. All the comparative results of this study are available online for download at ftp://www.homd.org/publication_data/20160425/. PMID:28261563

The Human Airway Epithelial Basal Cell Transcriptome

PubMed Central

Wang, Rui; Zwick, Rachel K.; Ferris, Barbara; Witover, Bradley; Salit, Jacqueline; Crystal, Ronald G.

2011-01-01

Background The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population. Methodology/Principal Findings Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the “human airway basal cell signature” as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels. Conclusion/Significance The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium. PMID:21572528

The cryptic Y-autosome translocation in the small Indian mongoose, Herpestes auropunctatus, revealed by molecular cytogenetic approaches.

PubMed

Murata, Chie; Sawaya, Hirohito; Nakata, Katsushi; Yamada, Fumio; Imoto, Issei; Kuroiwa, Asato

2016-09-01

In initial studies of the eutherian small Indian mongoose (Herpestes auropunctatus), the Y chromosome could not be identified in somatic cells. The male chromosome number is uniquely odd, 2n = 35, whereas that of females is 2n = 36. Previous reports indicated that this unique karyotype resulted from a translocation of the ancestral Y chromosome to an autosome. However, it has been difficult to identify the chromosomes that harbor the translocated Y chromosomal segment because it is an extremely small euchromatic region. Using a Southern blot analysis, we detected four conserved Y-linked genes, SRY, EIF2S3Y, KDM5D, and ZFY, in the male genome. We cloned homologues of these genes and determined their sequences, which showed high homology to genes in two carnivore species, cat and dog. To unambiguously identify the Y-bearing autosome, we performed immunostaining of pachytene spermatocytes using antibodies against SYCP3, γH2AX, and the centromere. We observed trivalent chromosomes, and the associations between the distal ends of the chromosomes were consistent with those of Y and X1 chromosomes. The centromere of the Y chromosome was located on the ancestral Y chromosomal segment. We mapped the complementary DNA (cDNA) clones of these genes to the male chromosomes using fluorescence in situ hybridization (FISH), and the linear localization of all genes was confirmed by two-colored FISH. These Y-linked genes were localized to the proximal region of the long arm of a single telomeric chromosome, and we successfully identified the chromosome harboring the ancestral Y chromosomal segment.

Cytomorphology of non-small cell lung carcinoma with anaplastic lymphoma kinase gene rearrangement.

PubMed

Toll, Adam D; Maleki, Zahra

2015-01-01

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase demonstrating activating mutations in several malignancies including a subset (1-5%) of non-small cell lung carcinomas (NSCLC). Prior work examining, the histologic features of these tumors found a spectrum of findings, notably a solid/acinar pattern, as well as a mucinous cribriform pattern. We present the first study to date describing the cytomorphology of NSCLC harboring ALK rearrangements. A retrospective database search was conducted to identify cytologic specimens of NSCLC demonstrating ALK rearrangement. Cytogenetic analysis was performed with fluorescence in situ hybridization. A total of 12 patients were identified, 10 with available material. Cellular morphology and smear background was evaluated in the study group, as well as control cases lacking ALK rearrangement. A total of 25 specimens from 10 patients were obtained. Five patients never smoked, and four patients had a remote smoking history. ALK rearrangements were identified in cells with unique cytologic characteristics. All cases demonstrated moderate to poor differentiation with a predominance of single cells showing anisonucleosis and frequent intracytoplasmic neutrophils. The control cases showed cells with smaller, less pleomorphic nuclei, and smaller nucleoli with more clusters/tissue fragments. Several unique cytomorphologic features were consistently identified in the study population relative to the control population and include a prominence of single, markedly enlarged tumor cells with plasmacytoid features and anisonucleosis, as well as intracytoplasmic neutrophils. Larger studies are warranted to confirm our preliminary findings, as these features may help establish a more cost-effective means to select patients being tested for ALK mutational analysis. © 2014 Wiley Periodicals, Inc.

The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms.

PubMed

Schulze, Waltraud X; Sanggaard, Kristian W; Kreuzer, Ines; Knudsen, Anders D; Bemm, Felix; Thøgersen, Ida B; Bräutigam, Andrea; Thomsen, Line R; Schliesky, Simon; Dyrlund, Thomas F; Escalante-Perez, Maria; Becker, Dirk; Schultz, Jörg; Karring, Henrik; Weber, Andreas; Højrup, Peter; Hedrich, Rainer; Enghild, Jan J

2012-11-01

The Venus flytrap (Dionaea muscipula) is one of the most well-known carnivorous plants because of its unique ability to capture small animals, usually insects or spiders, through a unique snap-trapping mechanism. The animals are subsequently killed and digested so that the plants can assimilate nutrients, as they grow in mineral-deficient soils. We deep sequenced the cDNA from Dionaea traps to obtain transcript libraries, which were used in the mass spectrometry-based identification of the proteins secreted during digestion. The identified proteins consisted of peroxidases, nucleases, phosphatases, phospholipases, a glucanase, chitinases, and proteolytic enzymes, including four cysteine proteases, two aspartic proteases, and a serine carboxypeptidase. The majority of the most abundant proteins were categorized as pathogenesis-related proteins, suggesting that the plant's digestive system evolved from defense-related processes. This in-depth characterization of a highly specialized secreted fluid from a carnivorous plant provides new information about the plant's prey digestion mechanism and the evolutionary processes driving its defense pathways and nutrient acquisition.

Incorporating Cultural Perspectives into Diabetes Self-Management Programs for East Asian Immigrants: A Mixed-Study Review.

PubMed

Park, Chorong; Nam, Soohyun; Whittemore, Robin

2016-04-01

It is important to understand East Asian immigrants (EAIs)' unique perspectives in managing diabetes in order to provide culturally-competent care. However, it is not known whether EAIs' perspectives are addressed in diabetes self-management interventions developed for EAIs. Therefore, a mixed-study review was conducted to identify EAIs' perspective from qualitative research (n = 9 studies) and to evaluate the components of EAI diabetes self-management interventions (n = 7). Themes from the qualitative synthesis demonstrated that EAIs have unique cultural values and traditional health beliefs while struggling with multi-contextual barriers due to immigration. The evaluation of EAI diabetes self-management interventions revealed that there was a lack of consensus on cultural strategies for EAIs' across the interventions. Addressing language barriers was the only factor consistently integrated in the cultural components of intervention by employing bilingual interventionists. EAIs' perspectives and experiences need to be incorporated in the future diabetes self-management interventions to better provide culturally-competent care.

Diversity of Penicillium section Citrina within the fynbos biome of South Africa, including a new species from a Protea repens infructescence.

PubMed

Visagie, Cobus M; Seifert, Keith A; Houbraken, Jos; Samson, Robert A; Jacobs, Karin

2014-01-01

During a survey of the fynbos biome in the Western Cape of South Africa, 61 Penicillium species were isolated and nine belong to Penicillium section Citrina. Based on morphology and multigene phylogenies, section Citrina species were identified as P. cairnsense, P. citrinum, P. pancosmium, P. pasqualense, P. sanguifluum, P. sizovae, P. sumatrense and P. ubiquetum. One of the species displayed unique phenotypic characters and DNA sequences and is described here as P. sucrivorum. Multigene phylogenies consistently resolved the new species in a clade with P. aurantiacobrunneum, P. cairnsense, P. miczynksii, P. neomiczynskii and P. quebecense. However, ITS, β-tubulin and calmodulin gene sequences are unique for P. sucrivorum and growth rates on various media, the ability to grow at 30 C, a positive Ehrlich reaction and the absence of sclerotia on all media examined, distinguish P. sucrivorum from all of its close relatives. © 2014 by The Mycological Society of America.

Mapping Multiplex Hubs in Human Functional Brain Networks

PubMed Central

De Domenico, Manlio; Sasai, Shuntaro; Arenas, Alex

2016-01-01

Typical brain networks consist of many peripheral regions and a few highly central ones, i.e., hubs, playing key functional roles in cerebral inter-regional interactions. Studies have shown that networks, obtained from the analysis of specific frequency components of brain activity, present peculiar architectures with unique profiles of region centrality. However, the identification of hubs in networks built from different frequency bands simultaneously is still a challenging problem, remaining largely unexplored. Here we identify each frequency component with one layer of a multiplex network and face this challenge by exploiting the recent advances in the analysis of multiplex topologies. First, we show that each frequency band carries unique topological information, fundamental to accurately model brain functional networks. We then demonstrate that hubs in the multiplex network, in general different from those ones obtained after discarding or aggregating the measured signals as usual, provide a more accurate map of brain's most important functional regions, allowing to distinguish between healthy and schizophrenic populations better than conventional network approaches. PMID:27471443

Behavioral Assessment of Emotion Discrimination, Emotion Regulation, and Cognitive Control in Childhood, Adolescence, and Adulthood

PubMed Central

Tottenham, Nim; Hare, Todd A.; Casey, B. J.

2011-01-01

Emotion discrimination, emotion regulation, and cognitive control are three related, yet separable processes that emerge over the course of development. The current study tested 100 children, adolescents, and adults on an Emotional Go/Nogo task, illustrating the ability of this paradigm to identify the unique developmental patterns for each of these three processes in the context of both positive (happy) and negative emotions (fear, sad, and anger), across three different age groups. Consistent with previous literature, our findings show that emotion discrimination and regulatory abilities (both cognitive control and emotion regulation) improve steadily for each age group, with each age group showing unique patterns of performance. The findings suggest that emotion regulation is constructed from basic cognition control and emotion discrimination skills. The patterns of behavior from the Emotional Go/Nogo task provide normative benchmark data across a wide range of emotions that can be used for future behavioral and neuroimaging studies that examine the developmental construction of emotion regulatory processes. PMID:21716604

Single-round selection yields a unique retroviral envelope utilizing GPR172A as its host receptor.

PubMed

Mazari, Peter M; Linder-Basso, Daniela; Sarangi, Anindita; Chang, Yehchung; Roth, Monica J

2009-04-07

The recognition by a viral envelope of its cognate host-cell receptor is the initial critical step in defining the viral host-range and tissue specificity. This study combines a single-round of selection of a random envelope library with a parallel cDNA screen for receptor function to identify a distinct retroviral envelope/receptor pair. The 11-aa targeting domain of the modified feline leukemia virus envelope consists of a constrained peptide. Critical to the binding of the constrained peptide envelope to its cellular receptor are a pair of internal cysteines and an essential Trp required for maintenance of titers >10(5) lacZ staining units per milliliter. The receptor used for viral entry is the human GPR172A protein, a G-protein-coupled receptor isolated from osteosarcoma cells. The ability to generate unique envelopes capable of using tissue- or disease-specific receptors marks an advance in the development of efficient gene-therapy vectors.

Description of the control system design for the SSF PMAD DC testbed

NASA Technical Reports Server (NTRS)

Baez, Anastacio N.; Kimnach, Greg L.

1991-01-01

The Power Management and Distribution (PMAD) DC Testbed Control System for Space Station Freedom was developed using a top down approach based on classical control system and conventional terrestrial power utilities design techniques. The design methodology includes the development of a testbed operating concept. This operating concept describes the operation of the testbed under all possible scenarios. A unique set of operating states was identified and a description of each state, along with state transitions, was generated. Each state is represented by a unique set of attributes and constraints, and its description reflects the degree of system security within which the power system is operating. Using the testbed operating states description, a functional design for the control system was developed. This functional design consists of a functional outline, a text description, and a logical flowchart for all the major control system functions. Described here are the control system design techniques, various control system functions, and the status of the design and implementation.

Developing a leadership laboratory for nurse managers based on lived experiences: a participatory action research model for leadership development.

PubMed

Mackoff, Barbara L; Glassman, Kimberly; Budin, Wendy

2013-09-01

The aim of the pilot study was to design an innovative model of leadership development, Leadership Laboratory (LL), grounded in the lived experiences and peer best practices of 43 cross-disciplinary nurse managers. The Institute of Medicine/Robert Wood Johnson Foundation study, The Future of Nursing, reinforces the need to prepare nurses for leadership positions. A 1-year participatory action research study was designed to develop 3 LLs involving nurse managers as participants, co-creators, and evaluators of the unique learning format. Analysis of qualitative and quantitative data revealed consistent and significantly positive results in leadership skill areas in all 3 LLs. Participants identified elements that distinguished LLs from traditional seminars and trainings sessions, including opportunities to gain from peer-to peer consultation, strategies, and support. Participants in the 1-year pilot demonstrated significant learning based on postsession and postproject assessments of the LLs. Data also described the unique attributes of a peer-driven approach to leadership development.

28 CFR 25.7 - Querying records in the system.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) Name; (2) Sex; (3) Race; (4) Complete date of birth; and (5) State of residence. (b) A unique numeric identifier may also be provided to search for additional records based on exact matches by the numeric identifier. Examples of unique numeric identifiers for purposes of this system are: Social Security number...

28 CFR 25.7 - Querying records in the system.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) Name; (2) Sex; (3) Race; (4) Complete date of birth; and (5) State of residence. (b) A unique numeric identifier may also be provided to search for additional records based on exact matches by the numeric identifier. Examples of unique numeric identifiers for purposes of this system are: Social Security number...

28 CFR 25.7 - Querying records in the system.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) Name; (2) Sex; (3) Race; (4) Complete date of birth; and (5) State of residence. (b) A unique numeric identifier may also be provided to search for additional records based on exact matches by the numeric identifier. Examples of unique numeric identifiers for purposes of this system are: Social Security number...

28 CFR 25.7 - Querying records in the system.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) Name; (2) Sex; (3) Race; (4) Complete date of birth; and (5) State of residence. (b) A unique numeric identifier may also be provided to search for additional records based on exact matches by the numeric identifier. Examples of unique numeric identifiers for purposes of this system are: Social Security number...

Clinically Detectable Dental Identifiers Observed in Intra-oral Photographs and Extra-oral Radiographs, Validated for Human Identification Purposes.

PubMed

Angelakopoulos, Nikolaos; Franco, Ademir; Willems, Guy; Fieuws, Steffen; Thevissen, Patrick

2017-07-01

Screening the prevalence and pattern of dental identifiers contributes toward the process of human identification. This research investigated the uniqueness of clinical dental identifiers in photographs and radiographs. Panoramic and lateral cephalometric radiographs and five intra-oral photographs of 1727 subjects were used. In a target set, two observers examined different subjects. In a subset, both observers examined the same subjects (source set). The distance between source and target subjects was quantified for each identifier. The percentage of subjects in the target set being at least as close as the correct subject was assessed. The number of molars (34.6%), missing teeth (42%), and displaced teeth (59.9%) were the most unique identifiers in photographs and panoramic and lateral cephalometric radiographs, respectively. The pattern of rotated teeth (14.9%) was the most unique in photographs, while displaced teeth was in panoramic (37.6%) and lateral cephalometric (54.8%) radiographs. Morphological identifiers were the most unique, highlighting their importance for human identifications. © 2016 American Academy of Forensic Sciences.

Proteomic characterization of the major arthropod associates of the carnivorous pitcher plant Sarracenia purpurea.

PubMed

Gotelli, Nicholas J; Smith, Aidan M; Ellison, Aaron M; Ballif, Bryan A

2011-06-01

The array of biomolecules generated by a functioning ecosystem represents both a potential resource for sustainable harvest and a potential indicator of ecosystem health and function. The cupped leaves of the carnivorous pitcher plant, Sarracenia purpurea, harbor a dynamic food web of aquatic invertebrates in a fully functional miniature ecosystem. The energetic base of this food web consists of insect prey, which is shredded by aquatic invertebrates and decomposed by microbes. Biomolecules and metabolites produced by this food web are actively exchanged with the photosynthesizing plant. In this report, we provide the first proteomic characterization of the sacrophagid fly (Fletcherimyia fletcheri), the pitcher plant mosquito (Wyeomyia smithii), and the pitcher-plant midge (Metriocnemus knabi). These three arthropods act as predators, filter feeders, and shredders at distinct trophic levels within the S. purpurea food web. More than 50 proteins from each species were identified, ten of which were predominantly or uniquely found in one species. Furthermore, 19 peptides unique to one of the three species were identified using an assembled database of 100 metazoan myosin heavy chain orthologs. These molecular signatures may be useful in species monitoring within heterogeneous ecosystem biomass and may also serve as indicators of ecosystem state. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Distribution of circular proteins in plants: large-scale mapping of cyclotides in the Violaceae.

PubMed

Burman, Robert; Yeshak, Mariamawit Y; Larsson, Sonny; Craik, David J; Rosengren, K Johan; Göransson, Ulf

2015-01-01

During the last decade there has been increasing interest in small circular proteins found in plants of the violet family (Violaceae). These so-called cyclotides consist of a circular chain of approximately 30 amino acids, including six cysteines forming three disulfide bonds, arranged in a cyclic cystine knot (CCK) motif. In this study we map the occurrence and distribution of cyclotides throughout the Violaceae. Plant material was obtained from herbarium sheets containing samples up to 200 years of age. Even the oldest specimens contained cyclotides in the preserved leaves, with no degradation products observable, confirming their place as one of the most stable proteins in nature. Over 200 samples covering 17 of the 23-31 genera in Violaceae were analyzed, and cyclotides were positively identified in 150 species. Each species contained a unique set of between one and 25 cyclotides, with many exclusive to individual plant species. We estimate the number of different cyclotides in the Violaceae to be 5000-25,000, and propose that cyclotides are ubiquitous among all Violaceae species. Twelve new cyclotides from six phylogenetically dispersed genera were sequenced. Furthermore, the first glycosylated derivatives of cyclotides were identified and characterized, further increasing the diversity and complexity of this unique protein family.

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

PubMed Central

Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M. T.; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D.; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D.; Henry, Christopher S.

2014-01-01

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today’s annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed. PMID:24927599

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

PubMed

Seaver, Samuel M D; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M T; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D; Henry, Christopher S

2014-07-01

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.

A Unique Sample of Extreme-BCG Clusters at 0.2 < z < 0.5

NASA Astrophysics Data System (ADS)

Garmire, Gordon

2017-09-01

The recently-discovered Phoenix cluster harbors the most extreme BCG in the known universe. Despite the cluster's high mass and X-ray luminosity, it was consistently identified by surveys as an isolated AGN, due to the bright central point source and the compact cool core. Armed with hindsight, we have undertaken an all-sky survey based on archival X-ray, OIR, and radio data to identify other similarly-extreme systems that were likewise missed. A pilot study demonstrated that this strategy works, leading to the discovery of a new, massive cluster at z 0.2 which was missed by previous X-ray surveys due to the presence of a bright central QSO. We propose here to observe 6 new clusters from our complete northern-sky survey, which harbor some of the most extreme central galaxies known.

A comparison of approaches for finding minimum identifying codes on graphs

NASA Astrophysics Data System (ADS)

Horan, Victoria; Adachi, Steve; Bak, Stanley

2016-05-01

In order to formulate mathematical conjectures likely to be true, a number of base cases must be determined. However, many combinatorial problems are NP-hard and the computational complexity makes this research approach difficult using a standard brute force approach on a typical computer. One sample problem explored is that of finding a minimum identifying code. To work around the computational issues, a variety of methods are explored and consist of a parallel computing approach using MATLAB, an adiabatic quantum optimization approach using a D-Wave quantum annealing processor, and lastly using satisfiability modulo theory (SMT) and corresponding SMT solvers. Each of these methods requires the problem to be formulated in a unique manner. In this paper, we address the challenges of computing solutions to this NP-hard problem with respect to each of these methods.

Global reach of direct-to-consumer advertising using social media for illicit online drug sales.

PubMed

Mackey, Tim Ken; Liang, Bryan A

2013-05-29

Illicit or rogue Internet pharmacies are a recognized global public health threat that have been identified as utilizing various forms of online marketing and promotion, including social media. To assess the accessibility of creating illicit no prescription direct-to-consumer advertising (DTCA) online pharmacy social media marketing (eDTCA2.0) and evaluate its potential global reach. We identified the top 4 social media platforms allowing eDTCA2.0. After determining applicable platforms (ie, Facebook, Twitter, Google+, and MySpace), we created a fictitious advertisement advertising no prescription drugs online and posted it to the identified social media platforms. Each advertisement linked to a unique website URL that consisted of a site error page. Employing Web search analytics, we tracked the number of users visiting these sites and their location. We used commercially available Internet tools and services, including website hosting, domain registration, and website analytic services. Illicit online pharmacy social media content for Facebook, Twitter, and MySpace remained accessible despite highly questionable and potentially illegal content. Fictitious advertisements promoting illicit sale of drugs generated aggregate unique user traffic of 2795 visits over a 10-month period. Further, traffic to our websites originated from a number of countries, including high-income and middle-income countries, and emerging markets. Our results indicate there are few barriers to entry for social media-based illicit online drug marketing. Further, illicit eDTCA2.0 has globalized outside US borders to other countries through unregulated Internet marketing.

Molecular Profile of Peripheral Blood Mononuclear Cells from Patients with Rheumatoid Arthritis

PubMed Central

Edwards, Christopher J; Feldman, Jeffrey L; Beech, Jonathan; Shields, Kathleen M; Stover, Jennifer A; Trepicchio, William L; Larsen, Glenn; Foxwell, Brian MJ; Brennan, Fionula M; Feldmann, Marc; Pittman, Debra D

2007-01-01

Rheumatoid arthritis (RA) is a chronic inflammatory arthritis. Currently, diagnosis of RA may take several weeks, and factors used to predict a poor prognosis are not always reliable. Gene expression in RA may consist of a unique signature. Gene expression analysis has been applied to synovial tissue to define molecularly distinct forms of RA; however, expression analysis of tissue taken from a synovial joint is invasive and clinically impractical. Recent studies have demonstrated that unique gene expression changes can be identified in peripheral blood mononuclear cells (PBMCs) from patients with cancer, multiple sclerosis, and lupus. To identify RA disease-related genes, we performed a global gene expression analysis. RNA from PBMCs of 9 RA patients and 13 normal volunteers was analyzed on an oligonucleotide array. Compared with normal PBMCs, 330 transcripts were differentially expressed in RA. The differentially regulated genes belong to diverse functional classes and include genes involved in calcium binding, chaperones, cytokines, transcription, translation, signal transduction, extracellular matrix, integral to plasma membrane, integral to intracellular membrane, mitochondrial, ribosomal, structural, enzymes, and proteases. A k-nearest neighbor analysis identified 29 transcripts that were preferentially expressed in RA. Ten genes with increased expression in RA PBMCs compared with controls mapped to a RA susceptibility locus, 6p21.3. These results suggest that analysis of RA PBMCs at the molecular level may provide a set of candidate genes that could yield an easily accessible gene signature to aid in early diagnosis and treatment. PMID:17515956

Determinants of Propranolol's Selective Effect on Loss Aversion.

PubMed

Sokol-Hessner, Peter; Lackovic, Sandra F; Tobe, Russell H; Camerer, Colin F; Leventhal, Bennett L; Phelps, Elizabeth A

2015-07-01

Research on emotion and decision making has suggested that arousal mediates risky decisions, but several distinct and often confounded processes drive such choices. We used econometric modeling to separate and quantify the unique contributions of loss aversion, risk attitudes, and choice consistency to risky decision making. We administered the beta-blocker propranolol in a double-blind, placebo-controlled within-subjects study, targeting the neurohormonal basis of physiological arousal. Matching our intervention's pharmacological specificity with a quantitative model delineating decision-making components allowed us to identify the causal relationships between arousal and decision making that do and do not exist. Propranolol selectively reduced loss aversion in a baseline- and dose-dependent manner (i.e., as a function of initial loss aversion and body mass index), and did not affect risk attitudes or choice consistency. These findings provide evidence for a specific, modulatory, and causal relationship between precise components of emotion and risky decision making. © The Author(s) 2015.

Entropy production of active particles and for particles in active baths

NASA Astrophysics Data System (ADS)

Pietzonka, Patrick; Seifert, Udo

2018-01-01

Entropy production of an active particle in an external potential is identified through a thermodynamically consistent minimal lattice model that includes the chemical reaction providing the propulsion and ordinary translational noise. In the continuum limit, a unique expression follows, comprising a direct contribution from the active process and an indirect contribution from ordinary diffusive motion. From the corresponding Langevin equation, this physical entropy production cannot be inferred through the conventional, yet here ambiguous, comparison of forward and time-reversed trajectories. Generalizations to several interacting active particles and passive particles in a bath of active ones are presented explicitly, further ones are briefly indicated.

Identification of a novel astrovirus in domestic sheep in Hungary.

PubMed

Reuter, Gábor; Pankovics, Péter; Delwart, Eric; Boros, Ákos

2012-02-01

The family Astroviridae consists of two genera, Avastrovirus and Mamastrovirus, whose members are associated with gastroenteritis in avian and mammalian hosts, respectively. We serendipitously identified a novel ovine astrovirus in a fecal specimen from a domestic sheep (Ovis aries) in Hungary by viral metagenomic analysis. Sequencing of the fragment indicated that it was an ORF1b/ORF2/3'UTR sequence, and it has been submitted to the GenBank database as ovine astrovirus type 2 (OAstV-2/Hungary/2009) with accession number JN592482. The unique sequence characteristics and the phylogenetic position of OAstV-2 suggest that genetically divergent lineages of astroviruses exist in sheep.

Inferential Processing among Adequate and Struggling Adolescent Comprehenders and Relations to Reading Comprehension

PubMed Central

Barth, Amy E.; Barnes, Marcia; Francis, David J.; Vaughn, Sharon; York, Mary

2015-01-01

Separate mixed model analyses of variance (ANOVA) were conducted to examine the effect of textual distance on the accuracy and speed of text consistency judgments among adequate and struggling comprehenders across grades 6–12 (n = 1203). Multiple regressions examined whether accuracy in text consistency judgments uniquely accounted for variance in comprehension. Results suggest that there is considerable growth across the middle and high school years, particularly for adequate comprehenders in those text integration processes that maintain local coherence. Accuracy in text consistency judgments accounted for significant unique variance for passage-level, but not sentence-level comprehension, particularly for adequate comprehenders. PMID:26166946

Decision-making about complementary and alternative medicine by cancer patients: integrative literature review.

PubMed

Weeks, Laura; Balneaves, Lynda G; Paterson, Charlotte; Verhoef, Marja

2014-01-01

Patients with cancer consistently report conflict and anxiety when making decisions about complementary and alternative medicine (CAM) treatment. To design evidence-informed decision-support strategies, a better understanding is needed of how the decision-making process unfolds for these patients during their experience with cancer. We undertook this study to review the research literature regarding CAM-related decision-making by patients with cancer within the context of treatment, survivorship, and palliation. We also aimed to summarize emergent concepts within a preliminary conceptual framework. We conducted an integrative literature review, searching 12 electronic databases for articles published in English that described studies of the process, context, or outcomes of CAM-related decision-making. We summarized descriptive data using frequencies and used a descriptive constant comparative method to analyze statements about original qualitative results, with the goal of identifying distinct concepts pertaining to CAM-related decision-making by patients with cancer and the relationships among these concepts. Of 425 articles initially identified, 35 met our inclusion criteria. Seven unique concepts related to CAM and cancer decision-making emerged: decision-making phases, information-seeking and evaluation, decision-making roles, beliefs, contextual factors, decision-making outcomes, and the relationship between CAM and conventional medical decision-making. CAM decision-making begins with the diagnosis of cancer and encompasses 3 distinct phases (early, mid, and late), each marked by unique aims for CAM treatment and distinct patterns of information-seeking and evaluation. Phase transitions correspond to changes in health status or other milestones within the cancer trajectory. An emergent conceptual framework illustrating relationships among the 7 central concepts is presented. CAM-related decision-making by patients with cancer occurs as a nonlinear, complex, dynamic process. The conceptual framework presented here identifies influential factors within that process, as well as patients' unique needs during different phases. The framework can guide the development and evaluation of theory-based decision-support programs that are responsive to patients' beliefs and preferences.

PubMed Central

Weeks, Laura; Balneaves, Lynda G; Paterson, Charlotte

2014-01-01

Background: Patients with cancer consistently report conflict and anxiety when making decisions about complementary and alternative medicine (CAM) treatment. To design evidence-informed decision-support strategies, a better understanding is needed of how the decision-making process unfolds for these patients during their experience with cancer. We undertook this study to review the research literature regarding CAM-related decisionmaking by patients with cancer within the context of treatment, survivorship, and palliation. We also aimed to summarize emergent concepts within a preliminary conceptual framework. Methods: We conducted an integrative literature review, searching 12 electronic databases for articles published in English that described studies of the process, context, or outcomes of CAM-related decision-making. We summarized descriptive data using frequencies and used a descriptive constant comparative method to analyze statements about original qualitative results, with the goal of identifying distinct concepts pertaining to CAM-related decision-making by patients with cancer and the relationships among these concepts. Results: Of 425 articles initially identified, 35 met our inclusion criteria. Seven unique concepts related to CAM and cancer decision-making emerged: decision-making phases, information-seeking and evaluation, decision-making roles, beliefs, contextual factors, decision-making outcomes, and the relationship between CAM and conventional medical decision-making. CAM decision-making begins with the diagnosis of cancer and encompasses 3 distinct phases (early, mid, and late), each marked by unique aims for CAM treatment and distinct patterns of informationseeking and evaluation. Phase transitions correspond to changes in health status or other milestones within the cancer trajectory. An emergent conceptual framework illustrating relationships among the 7 central concepts is presented. Interpretation: CAM-related decision-making by patients with cancer occurs as a nonlinear, complex, dynamic process. The conceptual framework presented here identifies influential factors within that process, as well as patients' unique needs during different phases. The framework can guide the development and evaluation of theorybased decision-support programs that are responsive to patients' beliefs and preferences. PMID:25009685

Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii

PubMed Central

2014-01-01

Background Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. Results In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. Conclusions Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes. PMID:24628833

16 CFR 1102.12 - Manufacturer comments.

Code of Federal Regulations, 2012 CFR

2012-01-01

... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.12 Manufacturer... Database if such manufacturer comment meets the following requirements: (1) Manufacturer comment relates to... publication in the Database. (2) Unique identifier. A manufacturer comment must state the unique identifier...

16 CFR 1102.12 - Manufacturer comments.

Code of Federal Regulations, 2014 CFR

2014-01-01

... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.12 Manufacturer... Database if such manufacturer comment meets the following requirements: (1) Manufacturer comment relates to... publication in the Database. (2) Unique identifier. A manufacturer comment must state the unique identifier...

Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

PubMed Central

Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

2012-01-01

Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

The REFLECT statement: methods and processes of creating reporting guidelines for randomized controlled trials for livestock and food safety.

PubMed

O'Connor, A M; Sargeant, J M; Gardner, I A; Dickson, J S; Torrence, M E; Dewey, C E; Dohoo, I R; Evans, R B; Gray, J T; Greiner, M; Keefe, G; Lefebvre, S L; Morley, P S; Ramirez, A; Sischo, W; Smith, D R; Snedeker, K; Sofos, J; Ward, M P; Wills, R

2010-01-01

The conduct of randomized controlled trials in livestock with production, health, and food-safety outcomes presents unique challenges that might not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A 2-day consensus meeting was held on November 18-19, 2008 in Chicago, IL, to achieve the objective. Before the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock production specialists, journal editors, assistant editors, and associate editors. Before the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items would need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines for Randomized Control Trials) statement for livestock and food safety and 22-item checklist. Fourteen items were modified from the CONSORT checklist, and an additional subitem was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health, and food-safety outcomes.

Personality disorder risk factors for suicide attempts over 10 years of follow-up.

PubMed

Ansell, Emily B; Wright, Aidan G C; Markowitz, John C; Sanislow, Charles A; Hopwood, Christopher J; Zanarini, Mary C; Yen, Shirley; Pinto, Anthony; McGlashan, Thomas H; Grilo, Carlos M

2015-04-01

Identifying personality disorder (PD) risk factors for suicide attempts is an important consideration for research and clinical care alike. However, most prior research has focused on single PDs or categorical PD diagnoses without considering unique influences of different PDs or of severity (sum) of PD criteria on the risk for suicide-related outcomes. This has usually been done with cross-sectional or retrospective assessment methods. Rarely are dimensional models of PDs examined in longitudinal, naturalistic prospective designs. In addition, it is important to consider divergent risk factors in predicting the risk of ever making a suicide attempt versus the risk of making an increasing number of attempts within the same model. This study examined 431 participants who were followed for 10 years in the Collaborative Longitudinal Personality Disorders Study. Baseline assessments of personality disorder criteria were summed as dimensional counts of personality pathology and examined as predictors of suicide attempts reported at annual interviews throughout the 10-year follow-up period. We used univariate and multivariate zero-inflated Poisson regression models to simultaneously evaluate PD risk factors for ever attempting suicide and for increasing numbers of attempts among attempters. Consistent with prior research, borderline PD was uniquely associated with ever attempting. However, only narcissistic PD was uniquely associated with an increasing number of attempts. These findings highlight the relevance of both borderline and narcissistic personality pathology as unique contributors to suicide-related outcomes. (c) 2015 APA, all rights reserved).

Fiberprint: A subject fingerprint based on sparse code pooling for white matter fiber analysis.

PubMed

Kumar, Kuldeep; Desrosiers, Christian; Siddiqi, Kaleem; Colliot, Olivier; Toews, Matthew

2017-09-01

White matter characterization studies use the information provided by diffusion magnetic resonance imaging (dMRI) to draw cross-population inferences. However, the structure, function, and white matter geometry vary across individuals. Here, we propose a subject fingerprint, called Fiberprint, to quantify the individual uniqueness in white matter geometry using fiber trajectories. We learn a sparse coding representation for fiber trajectories by mapping them to a common space defined by a dictionary. A subject fingerprint is then generated by applying a pooling function for each bundle, thus providing a vector of bundle-wise features describing a particular subject's white matter geometry. These features encode unique properties of fiber trajectories, such as their density along prominent bundles. An analysis of data from 861 Human Connectome Project subjects reveals that a fingerprint based on approximately 3000 fiber trajectories can uniquely identify exemplars from the same individual. We also use fingerprints for twin/sibling identification, our observations consistent with the twin data studies of white matter integrity. Our results demonstrate that the proposed Fiberprint can effectively capture the variability in white matter fiber geometry across individuals, using a compact feature vector (dimension of 50), making this framework particularly attractive for handling large datasets. Copyright © 2017 Elsevier Inc. All rights reserved.

Cost Estimation of Post Production Software Support in Ground Combat Systems

DTIC Science & Technology

2007-09-01

request, year of the request, EINOMEN (a word description of the system), and a PRON (a unique identifier containing the year and weapons system...variance. The fiscal year of request, descriptive name (coded as EINOMEN), unique program identifier ( PRON ), amount funded, and total amount requested...entire data set loses this sophistication. Most of the unique PRONs in the database map to a specific ground combat system, as described in the

Trench Safety–Using a Qualitative Approach to Understand Barriers and Develop Strategies to Improve Trenching Practices

PubMed Central

FLYNN, MICHAEL A.; SAMPSON, JULIE M.

2015-01-01

Despite efforts to ensure workplace safety and health, injuries and fatalities related to trenching and excavation remain alarmingly high in the construction industry. Because properly installed trenching protective systems can potentially reduce the significant number of trenching fatalities, there is clearly a need to identify the barriers to the use of these systems and to develop strategies to ensure these systems are utilized consistently. The current study reports on the results of focus groups with construction workers and safety management personnel to better understand these barriers and to identify solutions. The results suggest several factors, from poor planning to pressures from experienced workers and supervisors, which present barriers to safe trenching practices. Based on the results, it is recommended that safety trainings incorporate unique messages for new workers, experienced workers and management in an effort to motivate each group to work safely as well as provide them with solutions to overcome the identified barriers. PMID:26550006

Microplastic and macroplastic ingestion by a deep diving, oceanic cetacean: the True's beaked whale Mesoplodon mirus.

PubMed

Lusher, Amy L; Hernandez-Milian, Gema; O'Brien, Joanne; Berrow, Simon; O'Connor, Ian; Officer, Rick

2015-04-01

When mammals strand, they present a unique opportunity to obtain insights into their ecology. In May 2013, three True's beaked whales (two adult females and a female calf) stranded on the north and west coasts of Ireland and the contents of their stomachs and intestines were analysed for anthropogenic debris. A method for identifying microplastics ingested by larger marine organisms was developed. Microplastics were identified throughout the digestive tract of the single whale that was examined for the presence of microplastics. The two adult females had macroplastic items in their stomachs. Food remains recovered from the adult whales consisted of mesopelagic fish (Benthosema glaciale, Nansenia spp., Chauliodius sloani) and cephalopods, although trophic transfer has been discussed, it was not possible to ascertain whether prey were the source of microplastics. This is the first study to directly identify microplastics <5 mm in a cetacean species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Employment Trajectories: Exploring Gender Differences and Impacts of Drug Use

PubMed Central

Huang, David Y.C.; Evans, Elizabeth; Hara, Motoaki; Weiss, Robert E.; Hser, Yih-Ing

2010-01-01

This study investigated the impact of drug use on employment over 20 years among men and women, utilizing data on 7,661 participants in the National Longitudinal Survey of Youth. Growth mixture modeling was applied, and five distinct employment trajectory groups were identified for both men and women. The identified patterns were largely similar for men and women except that a U-shape employment trajectory was uniquely identified for women. Early-initiation drug users, users of “hard” drugs, and frequent drug users were more likely to demonstrate consistently low levels of employment, and the negative relationship between drug use and employment was more apparent among men than women. Also, positive associations between employment and marriage became more salient for men over time, as did negative associations between employment and childrearing among women. Processes are dynamic and complex, suggesting that throughout the life course, protective factors that reduce the risk of employment problems emerge and change, as do critical periods for maximizing the impact of drug prevention and intervention efforts. PMID:21765533

Engaging Communities in Identifying Local Strategies for Expanding Integrated Employment During and After High School.

PubMed

Carter, Erik W; Blustein, Carly L; Bumble, Jennifer L; Harvey, Sarah; Henderson, Lynnette M; McMillan, Elise D

2016-09-01

Amidst decades of attention directed toward improving employment outcomes for people with intellectual and developmental disabilities (IDD), few efforts have been made to engage communities in identifying local solutions for expanding integrated employment opportunities. We examined the implementation and outcomes of "community conversation" events held in 6 geographically and economically diverse locales. Each event used an asset-based dialogue approach called the World Café ( Brown & Isaacs, 2005 ) to solicit ideas from a broad cross-section of community members on improving integrated employment that reflect local priorities and possibilities. Six key themes encapsulated the 1,556 strategies generated by the almost 400 attendees. Although considerable consistency was found among the categories of strategies raised across events, the manner in which those individual strategies would be implemented locally reflected the unique accent of each community. Attendees also viewed these events as promising and productive pathways for identifying next steps for their community. We offer recommendations for community-level intervention efforts and suggest directions for future research.

Genomic identification of potential targets unique to Candida albicans for the discovery of antifungal agents.

PubMed

Tripathi, Himanshu; Luqman, Suaib; Meena, Abha; Khan, Feroz

2014-01-01

Despite of modern antifungal therapy, the mortality rates of invasive infection with human fungal pathogen Candida albicans are up to 40%. Studies suggest that drug resistance in the three most common species of human fungal pathogens viz., C. albicans, Aspergillus fumigatus (causing mortality rate up to 90%) and Cryptococcus neoformans (causing mortality rate up to 70%) is due to mutations in the target enzymes or high expression of drug transporter genes. Drug resistance in human fungal pathogens has led to an imperative need for the identification of new targets unique to fungal pathogens. In the present study, we have used a comparative genomics approach to find out potential target proteins unique to C. albicans, an opportunistic fungus responsible for severe infection in immune-compromised human. Interestingly, many target proteins of existing antifungal agents showed orthologs in human cells. To identify unique proteins, we have compared proteome of C. albicans [SC5314] i.e., 14,633 total proteins retrieved from the RefSeq database of NCBI, USA with proteome of human and non-pathogenic yeast Saccharomyces cerevisiae. Results showed that 4,568 proteins were identified unique to C. albicans as compared to those of human and later when these unique proteins were compared with S. cerevisiae proteome, finally 2,161 proteins were identified as unique proteins and after removing repeats total 1,618 unique proteins (42 functionally known, 1,566 hypothetical and 10 unknown) were selected as potential antifungal drug targets unique to C. albicans.

16 CFR § 1102.12 - Manufacturer comments.

Code of Federal Regulations, 2013 CFR

2013-01-01

... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.12 Manufacturer... Database if such manufacturer comment meets the following requirements: (1) Manufacturer comment relates to... publication in the Database. (2) Unique identifier. A manufacturer comment must state the unique identifier...

Proteomic Phenotyping of Novosphingobium nitrogenifigens Reveals a Robust Capacity for Simultaneous Nitrogen Fixation, Polyhydroxyalkanoate Production, and Resistance to Reactive Oxygen Species

PubMed Central

Strabala, Timothy J.; Peng, Lifeng; Rawson, Pisana; Lloyd-Jones, Gareth; Jordan, T. William

2012-01-01

Novosphingobium nitrogenifigens Y88T (Y88) is a free-living, diazotrophic Alphaproteobacterium, capable of producing 80% of its biomass as the biopolymer polyhydroxybutyrate (PHB). We explored the potential utility of this species as a polyhydroxybutyrate production strain, correlating the effects of glucose, nitrogen availability, dissolved oxygen concentration, and extracellular pH with polyhydroxybutyrate production and changes in the Y88 proteomic profile. Using two-dimensional differential in-gel electrophoresis and tandem mass spectrometry, we identified 217 unique proteins from six growth conditions. We observed reproducible, characteristic proteomic signatures for each of the physiological states we examined. We identified proteins that changed in abundance in correlation with either nitrogen fixation, dissolved oxygen concentration, or acidification of the growth medium. The proteins that correlated with nitrogen fixation were identified either as known nitrogen fixation proteins or as novel proteins that we predict play roles in aspects of nitrogen fixation based on their proteomic profiles. In contrast, the proteins involved in central carbon and polyhydroxybutyrate metabolism were constitutively abundant, consistent with the constitutive polyhydroxybutyrate production that we observed in this species. Three proteins with roles in detoxification of reactive oxygen species were identified in this obligate aerobe. The most abundant protein in all experiments was a polyhydroxyalkanoate granule-associated protein, phasin. The full-length isoform of this protein has a long, intrinsically disordered Ala/Pro/Lys-rich N-terminal segment, a feature that appears to be unique to sphingomonad phasins. The data suggest that Y88 has potential as a PHB production strain due to its aerobic tolerance and metabolic orientation toward polyhydroxybutyrate accumulation, even in low-nitrogen growth medium. PMID:22582058

Comprehensive Proteomic Analysis of Human Milk-derived Extracellular Vesicles Unveils a Novel Functional Proteome Distinct from Other Milk Components*

PubMed Central

van Herwijnen, Martijn J.C.; Zonneveld, Marijke I.; Goerdayal, Soenita; Nolte – 't Hoen, Esther N.M.; Garssen, Johan; Stahl, Bernd; Maarten Altelaar, A.F.; Redegeld, Frank A.; Wauben, Marca H.M.

2016-01-01

Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins. Because of the difficulty in separating EV from other milk components, an in-depth analysis of the proteome of human milk-derived EV is lacking. In this study, an extensive LC-MS/MS proteomic analysis was performed of EV that had been purified from breast milk of seven individual donors using a recently established, optimized density-gradient-based EV isolation protocol. A total of 1963 proteins were identified in milk-derived EV, including EV-associated proteins like CD9, Annexin A5, and Flotillin-1, with a remarkable overlap between the different donors. Interestingly, 198 of the identified proteins are not present in the human EV database Vesiclepedia, indicating that milk-derived EV harbor proteins not yet identified in EV of different origin. Similarly, the proteome of milk-derived EV was compared with that of other milk components. For this, data from 38 published milk proteomic studies were combined in order to construct the total milk proteome, which consists of 2698 unique proteins. Remarkably, 633 proteins identified in milk-derived EV have not yet been identified in human milk to date. Interestingly, these novel proteins include proteins involved in regulation of cell growth and controlling inflammatory signaling pathways, suggesting that milk-derived EVs could support the newborn's developing gastrointestinal tract and immune system. Overall, this study provides an expansion of the whole milk proteome and illustrates that milk-derived EV are macromolecular components with a unique functional proteome. PMID:27601599

On the existence, uniqueness, and asymptotic normality of a consistent solution of the likelihood equations for nonidentically distributed observations: Applications to missing data problems

NASA Technical Reports Server (NTRS)

Peters, C. (Principal Investigator)

1980-01-01

A general theorem is given which establishes the existence and uniqueness of a consistent solution of the likelihood equations given a sequence of independent random vectors whose distributions are not identical but have the same parameter set. In addition, it is shown that the consistent solution is a MLE and that it is asymptotically normal and efficient. Two applications are discussed: one in which independent observations of a normal random vector have missing components, and the other in which the parameters in a mixture from an exponential family are estimated using independent homogeneous sample blocks of different sizes.

Modifiable worker risk factors contributing to workplace absence: a stakeholder-centred best-evidence synthesis of systematic reviews.

PubMed

Wagner, Shannon; White, Marc; Schultz, Izabela; Murray, Eleanor; Bradley, Susan M; Hsu, Vernita; McGuire, Lisa; Schulz, Werner

2014-01-01

A challenge facing stakeholders is the identification and translation of relevant high quality research to inform policy and practice. This study engaged academic and community stakeholders in conducting a best evidence-synthesis to identify modifiable risk and protective worker factors across health conditions impacting work-related absence. To identify modifiable worker disability risk and protective factors across common health conditions impacting work-related absence. We searched Medline, Embase, CINHAL, The Cochrane Library, PsycINFO, BusinessSourceComplete, and ABI/Inform from 2000 to 2011. Quantitative, qualitative, or mixed methods systematic reviews of work-focused population were considered for inclusion. Two or more reviewers independently reviewed articles for inclusion and methodological screening. The search strategy, expert input and grey literature identified 2,467 unique records. One hundred and forty-two full text articles underwent comprehensive review. Twenty-four systematic reviews met eligibility criteria. Modifiable worker factors found to have consistent evidence across two or more health conditions included emotional distress, negative enduring psychology/personality factors, negative health and disability perception, decreased physical activity, lack of family support, poor general health, increased functional disability, increased pain, increased fatigue and lack of motivation to return to work. Systematic reviews are limited by availability of high quality studies, lack of consistency of methodological screening and reporting, and variability of outcome measures used.

A qualitative analysis of barriers, challenges, and successes in meeting the needs of Hurricane Katrina evacuee families.

PubMed

Legerski, John-Paul; Vernberg, Eric M; Noland, Brian J

2012-12-01

Hurricane Katrina caused many individuals to evacuate to towns and cities throughout the United States. Psychological First Aid (PFA) is a treatment program designed to help clinicians and other disaster relief workers address the needs of adults, youth, and families immediately following disasters. We conducted focus groups with disaster relief and evacuee service providers in the Kansas City Metro Area as an exploratory study to identify their perceptions of the needs of evacuees. Participants identified a number of mental health needs, as well as displacement-related challenges, including loss of social support, material loss, unemployment, and other stressful life events that were secondary to the hurricane. Many of these needs are consistent with principles presented in the PFA manual. We also found that service providers faced unique challenges when attempting to assist evacuees. We discuss implications of these findings for treatment programs and provide suggestions for addressing barriers to care.

Molecular Basis of Infrared Detection by Snakes

PubMed Central

Gracheva, Elena O.; Ingolia, Nicolas T.; Kelly, Yvonne M.; Cordero-Morales, Julio F.; Hollopeter, Gunther; Chesler, Alexander T.; Sánchez, Elda E.; Perez, John C.; Weissman, Jonathan S.; Julius, David

2010-01-01

Snakes possess a unique sensory system for detecting infrared radiation, enabling them to generate a ‘thermal image’ of predators or prey. Infrared signals are initially received by the pit organ, a highly specialized facial structure that is innervated by nerve fibers of the somatosensory system. How this organ detects and transduces infrared signals into nerve impulses is not known. Here we use an unbiased transcriptional profiling approach to identify TRPA1 channels as infrared receptors on sensory nerve fibers that innervate the pit organ. TRPA1 orthologues from pit bearing snakes (vipers, pythons, and boas) are the most heat sensitive vertebrate ion channels thus far identified, consistent with their role as primary transducers of infrared stimuli. Thus, snakes detect infrared signals through a mechanism involving radiant heating of the pit organ, rather than photochemical transduction. These findings illustrate the broad evolutionary tuning of TRP channels as thermosensors in the vertebrate nervous system. PMID:20228791

Diffractive optics technology and the NASA Geostationary Earth Observatory (GEO)

NASA Technical Reports Server (NTRS)

Morris, G. Michael; Michaels, Robert L.; Faklis, Dean

1992-01-01

Diffractive (or binary) optics offers unique capabilities for the development of large-aperture, high-performance, light-weight optical systems. The Geostationary Earth Observatory (GEO) will consist of a variety of instruments to monitor the environmental conditions of the earth and its atmosphere. The aim of this investigation is to analyze the design of the GEO instrument that is being proposed and to identify the areas in which diffractive (or binary) optics technology can make a significant impact in GEO sensor design. Several potential applications where diffractive optics may indeed serve as a key technology for improving the performance and reducing the weight and cost of the GEO sensors have been identified. Applications include the use of diffractive/refractive hybrid lenses for aft-optic imagers, diffractive telescopes for narrowband imaging, subwavelength structured surfaces for anti-reflection and polarization control, and aberration compensation for reflective imaging systems and grating spectrometers.

Personality Constellations of Adolescents with Histories of Traumatic Parental Separations

PubMed Central

Malone, Johanna C.; Westen, Drew; Levendosky, Alytia A.

2014-01-01

Consistent with attachment theory and a developmental psychopathology framework, a growing body of research suggests that traumatic parental separations may lead to unique pathways of personality adaptation and maladaptation. The present study both examined personality characteristics and identified personality subtypes of adolescents with histories of traumatic separations. Randomly selected psychologists and psychiatrists provided data on 236 adolescents with histories of traumatic separations using a personality pathology instrument designed for use by clinically experienced observers, the Shedler-Westen Assessment Procedure (SWAP-II-A). Using a Q factor analysis, five distinct personality subtypes were identified: internalizing/avoidant, psychopathic, resilient, impulsive dysregulated, and immature dysregulated. Initial support for the validity of the subtypes was established based on Axis I and Axis II pathology, adaptive functioning, developmental history, and family history variables. The personality subtypes demonstrated substantial incremental validity in predicting adaptive functioning, above and beyond demographic variables and histories of other traumatic experiences. PMID:24647212

Individually Identifiable Surface Acoustic Wave Sensors, Tags and Systems

NASA Technical Reports Server (NTRS)

Hines, Jacqueline H. (Inventor); Solie, Leland P. (Inventor); Tucker, Dana Y. G. (Inventor); Hines, Andrew T. (Inventor)

2017-01-01

A surface-launched acoustic wave sensor tag system for remotely sensing and/or providing identification information using sets of surface acoustic wave (SAW) sensor tag devices is characterized by acoustic wave device embodiments that include coding and other diversity techniques to produce groups of sensors that interact minimally, reducing or alleviating code collision problems typical of prior art coded SAW sensors and tags, and specific device embodiments of said coded SAW sensor tags and systems. These sensor/tag devices operate in a system which consists of one or more uniquely identifiable sensor/tag devices and a wireless interrogator. The sensor device incorporates an antenna for receiving incident RF energy and re-radiating the tag identification information and the sensor measured parameter(s). Since there is no power source in or connected to the sensor, it is a passive sensor. The device is wirelessly interrogated by the interrogator.

Bringing Culture Into Parent Training With Latinos

PubMed Central

Calzada, Esther J.

2015-01-01

Traditional frameworks of parenting have failed to capture the distinctive nature of parenting in Latino families. Cultural values likely influence parenting practices. The study of cultural values may allow us to identify aspects of parenting that are unique to Latinos and which complement traditional frameworks of parenting. This paper presents qualitative work on two Latino cultural values, familismo and respeto, and examines ways in which these values may inform the provision of standard parent training programs with Latinos. The first study is an ethnography that explored the value of familismo. The second study consisted of focus groups in which Latina mothers discussed the value of respeto. Findings from these two studies are used to examine the cultural congruence of the characteristics of parent training programs and the Latino values of familismo and respeto. In light of the issues identified, clinical guidelines for working with Latino parents in parent training programs are offered. PMID:25960630

Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.

PubMed

Hur, Junguk; Özgür, Arzucan; He, Yongqun

2017-03-14

Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks. In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E. coli vaccines and genes used in the vaccine development. We also normalized E. coli gene names compiled from the annotations of various E. coli strains using a pan-genome-based annotation strategy. The Interaction Network Ontology (INO) includes a hierarchy of various interaction-related keywords useful for literature mining. Using VO, INO, and normalized E. coli gene names, we applied an ontology-based SciMiner literature mining strategy to mine all PubMed abstracts and retrieve E. coli vaccine-associated E. coli gene interactions. Four centrality metrics (i.e., degree, eigenvector, closeness, and betweenness) were calculated for identifying highly ranked genes and interaction types. Using vaccine-related PubMed abstracts, our study identified 11,350 sentences that contain 88 unique INO interactions types and 1,781 unique E. coli genes. Each sentence contained at least one interaction type and two unique E. coli genes. An E. coli gene interaction network of genes and INO interaction types was created. From this big network, a sub-network consisting of 5 E. coli vaccine genes, including carA, carB, fimH, fepA, and vat, and 62 other E. coli genes, and 25 INO interaction types was identified. While many interaction types represent direct interactions between two indicated genes, our study has also shown that many of these retrieved interaction types are indirect in that the two genes participated in the specified interaction process in a required but indirect process. Our centrality analysis of these gene interaction networks identified top ranked E. coli genes and 6 INO interaction types (e.g., regulation and gene expression). Vaccine-related E. coli gene-gene interaction network was constructed using ontology-based literature mining strategy, which identified important E. coli vaccine genes and their interactions with other genes through specific interaction types.

No difference in variability of unique hue selections and binary hue selections.

PubMed

Bosten, J M; Lawrance-Owen, A J

2014-04-01

If unique hues have special status in phenomenological experience as perceptually pure, it seems reasonable to assume that they are represented more precisely by the visual system than are other colors. Following the method of Malkoc et al. (J. Opt. Soc. Am. A22, 2154 [2005]), we gathered unique and binary hue selections from 50 subjects. For these subjects we repeated the measurements in two separate sessions, allowing us to measure test-retest reliabilities (0.52≤ρ≤0.78; p≪0.01). We quantified the within-individual variability for selections of each hue. Adjusting for the differences in variability intrinsic to different regions of chromaticity space, we compared the within-individual variability for unique hues to that for binary hues. Surprisingly, we found that selections of unique hues did not show consistently lower variability than selections of binary hues. We repeated hue measurements in a single session for an independent sample of 58 subjects, using a different relative scaling of the cardinal axes of MacLeod-Boynton chromaticity space. Again, we found no consistent difference in adjusted within-individual variability for selections of unique and binary hues. Our finding does not depend on the particular scaling chosen for the Y axis of MacLeod-Boynton chromaticity space.

A unique tripartite collision tumor of the esophagus

PubMed Central

Schizas, Dimitrios; Michalinos, Adamantios; Alexandrou, Paraskevi; Moris, Demetrios; Baliou, Evangelia; Tsilimigras, Diamantis; Throupis, Theodore; Liakakos, Theodore

2017-01-01

Abstract Rationale: We report a unique case of a tripartite esophageal collision tumor consisting of three separate histologic types. Patients concerns: Therapeutic dilemmas on the proper treatment of those rare neoplasms remain unanswered considering both proper surgical therapy and adjuvant therapy. Diagnose: In this paper, we report a unique case of a patient with a tripartite esophageal collision tumor consisting of a small cell carcinoma, an adenocarcinoma of medium differentiation and a signet ring cell carcinoma. Diagnosis is difficult as clinical presentation of the patient was undistinguishable from other, commoner tumor types. Interventions: The patient's diagnostic and therapeutic course along with available data on the collisions tumor's biological behavior and treatment are briefly discussed. Outcomes: Esophagectomy is the best treatment options for these patients. Unique nature of this tumor demands aggresive oncologic treatment. Lessons: Collision tumors are rare neoplasms consisting of distinct cell populations developing in juxtaposition to one another without any areas of intermingling. Various cell types can be found. However, collision neoplasms of the esophagus combining adenomatous and neuroendocrine components are exceedingly rare, with only 5 cases described to date in the literature. Given their rarity, limited information is available on their tumorigenesis, biological behavior and clinical course. In general, these tumors are aggressive neoplasms and significantly affect patient treatment and prognosis. PMID:29245236

The Identification and Tracking of Uterine Contractions Using Template Based Cross-Correlation.

PubMed

McDonald, Sarah C; Brooker, Graham; Phipps, Hala; Hyett, Jon

2017-09-01

The purpose of this paper is to outline a novel method of using template based cross-correlation to identify and track uterine contractions during labour. A purpose built six-channel Electromyography (EMG) device was used to collect data from consenting women during labour and birth. A range of templates were constructed for the purpose of identifying and tracking uterine activity when cross-correlated with the EMG signal. Peak finding techniques were applied on the cross-correlated result to simplify and automate the identification and tracking of contractions. The EMG data showed a unique pattern when a woman was contracting with key features of the contraction signal remaining consistent and identifiable across subjects. Contraction profiles across subjects were automatically identified using template based cross-correlation. Synthetic templates from a rectangular function with a duration of between 5 and 10 s performed best at identifying and tracking uterine activity across subjects. The successful application of this technique provides opportunity for both simple and accurate real-time analysis of contraction data while enabling investigations into the application of techniques such as machine learning which could enable automated learning from contraction data as part of real-time monitoring and post analysis.

45 CFR 162.610 - Implementation specifications for covered entities.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 1 2011-10-01 2011-10-01 false Implementation specifications for covered entities... Implementation specifications for covered entities. (a) The standard unique employer identifier of an employer of... Statement, from the employer. (b) A covered entity must use the standard unique employer identifier (EIN) of...

45 CFR 162.610 - Implementation specifications for covered entities.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 1 2010-10-01 2010-10-01 false Implementation specifications for covered entities... Implementation specifications for covered entities. (a) The standard unique employer identifier of an employer of... Statement, from the employer. (b) A covered entity must use the standard unique employer identifier (EIN) of...

77 FR 35921 - Defense Federal Acquisition Regulation Supplement: Item Unique Identifier Update (DFARS Case 2011...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... DEPARTMENT OF DEFENSE Defense Acquisition Regulations System 48 CFR Parts 211, 212, 218, 246, 252 and Appendix F to Chapter 2 RIN 0750-AH64 Defense Federal Acquisition Regulation Supplement: Item Unique Identifier Update (DFARS Case 2011-D055) AGENCY: Defense Acquisition Regulations System...

77 FR 69715 - Federal Acquisition Regulation; Updates to Contract Reporting and Central Contractor Registration

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-20

... Contractor Registration AGENCY: Department of Defense (DoD), General Services Administration (GSA), and... changes the clauses requiring contractor registration in the Central Contractor Registration (CCR... unique identifier for contractors. It is used (1) to uniquely identify a contractor entity, and (2) to...

Island of stability for consistent deformations of Einstein's gravity.

PubMed

Berkhahn, Felix; Dietrich, Dennis D; Hofmann, Stefan; Kühnel, Florian; Moyassari, Parvin

2012-03-30

We construct deformations of general relativity that are consistent and phenomenologically viable, since they respect, in particular, cosmological backgrounds. These deformations have unique symmetries in accordance with their Minkowski cousins (Fierz-Pauli theory for massive gravitons) and incorporate a background curvature induced self-stabilizing mechanism. Self-stabilization is essential in order to guarantee hyperbolic evolution in and unitarity of the covariantized theory, as well as the deformation's uniqueness. We show that the deformation's parameter space contains islands of absolute stability that are persistent through the entire cosmic evolution.

Multi-Disciplinary Management of Athletes with Post-Concussion Syndrome: An Evolving Pathophysiological Approach.

PubMed

Ellis, Michael J; Leddy, John; Willer, Barry

2016-01-01

Historically, patients with sports-related concussion (SRC) have been managed in a uniform fashion consisting mostly of prescribed physical and cognitive rest with the expectation that all symptoms will spontaneously resolve with time. Although this approach will result in successful return to school and sports activities in the majority of athletes, an important proportion will develop persistent concussion symptoms characteristic of post-concussion syndrome (PCS). Recent advances in exercise science, neuroimaging, and clinical research suggest that the clinical manifestations of PCS are mediated by unique pathophysiological processes that can be identified by features of the clinical history and physical examination as well as the use of graded aerobic treadmill testing. Athletes who develop PCS represent a unique population whose care must be individualized and must incorporate a rehabilitative strategy that promotes enhanced recovery of concussion-related symptoms while preventing physical deconditioning. In this review, we present our evolving evidence-based approach to evaluation and management of athletes with PCS that aims to identify the pathophysiological mechanisms mediating persistent concussion symptoms and guides the initiation of individually tailored rehabilitation programs that target these processes. In addition, we outline the important qualified roles that multi-disciplinary healthcare professionals can play in the management of this patient population, and discuss where future research efforts must be focused to further evaluate this evolving pathophysiological approach.

Multi-Disciplinary Management of Athletes with Post-Concussion Syndrome: An Evolving Pathophysiological Approach

PubMed Central

Ellis, Michael J.; Leddy, John; Willer, Barry

2016-01-01

Historically, patients with sports-related concussion (SRC) have been managed in a uniform fashion consisting mostly of prescribed physical and cognitive rest with the expectation that all symptoms will spontaneously resolve with time. Although this approach will result in successful return to school and sports activities in the majority of athletes, an important proportion will develop persistent concussion symptoms characteristic of post-concussion syndrome (PCS). Recent advances in exercise science, neuroimaging, and clinical research suggest that the clinical manifestations of PCS are mediated by unique pathophysiological processes that can be identified by features of the clinical history and physical examination as well as the use of graded aerobic treadmill testing. Athletes who develop PCS represent a unique population whose care must be individualized and must incorporate a rehabilitative strategy that promotes enhanced recovery of concussion-related symptoms while preventing physical deconditioning. In this review, we present our evolving evidence-based approach to evaluation and management of athletes with PCS that aims to identify the pathophysiological mechanisms mediating persistent concussion symptoms and guides the initiation of individually tailored rehabilitation programs that target these processes. In addition, we outline the important qualified roles that multi-disciplinary healthcare professionals can play in the management of this patient population, and discuss where future research efforts must be focused to further evaluate this evolving pathophysiological approach. PMID:27605923

Common and unique representations in pFC for face and place attractiveness.

PubMed

Pegors, Teresa K; Kable, Joseph W; Chatterjee, Anjan; Epstein, Russell A

2015-05-01

Although previous neuroimaging research has identified overlapping correlates of subjective value across different reward types in the ventromedial pFC (vmPFC), it is not clear whether this "common currency" evaluative signal extends to the aesthetic domain. To examine this issue, we scanned human participants with fMRI while they made attractiveness judgments of faces and places-two stimulus categories that are associated with different underlying rewards, have very different visual properties, and are rarely compared with each other. We found overlapping signals for face and place attractiveness in the vmPFC, consistent with the idea that this region codes a signal for value that applies across disparate reward types and across both economic and aesthetic judgments. However, we also identified a subregion of vmPFC within which activity patterns for face and place attractiveness were distinguishable, suggesting that some category-specific attractiveness information is retained in this region. Finally, we observed two separate functional regions in lateral OFC: one region that exhibited a category-unique response to face attractiveness and another region that responded strongly to faces but was insensitive to their value. Our results suggest that vmPFC supports a common mechanism for reward evaluation while also retaining a degree of category-specific information, whereas lateral OFC may be involved in basic reward processing that is specific to only some stimulus categories.

Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes.

PubMed

Carlson, David E; Hedin, Marshal

2017-01-01

Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.

Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response.

PubMed

Jones, Jana; Mirzaei, Mehdi; Ravishankar, Prathiba; Xavier, Dylan; Lim, Do Seon; Shin, Dong Hoon; Bianucci, Raffaella; Haynes, Paul A

2016-10-28

We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Author(s).

Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response

PubMed Central

Jones, Jana; Mirzaei, Mehdi; Ravishankar, Prathiba; Xavier, Dylan; Lim, Do Seon; Shin, Dong Hoon; Bianucci, Raffaella

2016-01-01

We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS–PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography–mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644972

Gene cloning and characterization of a novel esterase from activated sludge metagenome

PubMed Central

2009-01-01

A metagenomic library was prepared using pCC2FOS vector containing about 3.0 Gbp of community DNA from the microbial assemblage of activated sludge. Screening of a part of the un-amplified library resulted in the finding of 1 unique lipolytic clone capable of hydrolyzing tributyrin, in which an esterase gene was identified. This esterase/lipase gene consists of 834 bp and encodes a polypeptide (designated EstAS) of 277 amino acid residuals with a molecular mass of 31 kDa. Sequence analysis indicated that it showed 33% and 31% amino acid identity to esterase/lipase from Gemmata obscuriglobus UQM 2246 (ZP_02733109) and Yarrowia lipolytica CLIB122 (XP_504639), respectively; and several conserved regions were identified, including the putative active site, HSMGG, a catalytic triad (Ser92, His125 and Asp216) and a LHYFRG conserved motif. The EstAS was overexpressed, purified and shown to hydrolyse p-nitrophenyl (NP) esters of fatty acids with short chain lengths (≤ C8). This EstAS had optimal temperature and pH at 35°C and 9.0, respectively, by hydrolysis of p-NP hexanoate. It also exhibited the same level of stability over wide temperature and pH ranges and in the presence of metal ions or detergents. The high level of stability of esterase EstAS with its unique substrate specificities make itself highly useful for biotechnological applications. PMID:20028524

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

PubMed Central

Xue, Liang; Wang, Wen-Horng; Iliuk, Anton; Hu, Lianghai; Galan, Jacob A.; Yu, Shuai; Hans, Michael; Geahlen, Robert L.; Tao, W. Andy

2012-01-01

Our understanding of the molecular control of many disease pathologies requires the identification of direct substrates targeted by specific protein kinases. Here we describe an integrated proteomic strategy, termed kinase assay linked with phosphoproteomics, which combines a sensitive kinase reaction with endogenous kinase-dependent phosphoproteomics to identify direct substrates of protein kinases. The unique in vitro kinase reaction is carried out in a highly efficient manner using a pool of peptides derived directly from cellular kinase substrates and then dephosphorylated as substrate candidates. The resulting newly phosphorylated peptides are then isolated and identified by mass spectrometry. A further comparison of these in vitro phosphorylated peptides with phosphopeptides derived from endogenous proteins isolated from cells in which the kinase is either active or inhibited reveals new candidate protein substrates. The kinase assay linked with phosphoproteomics strategy was applied to identify unique substrates of spleen tyrosine kinase (Syk), a protein-tyrosine kinase with duel properties of an oncogene and a tumor suppressor in distinctive cell types. We identified 64 and 23 direct substrates of Syk specific to B cells and breast cancer cells, respectively. Both known and unique substrates, including multiple centrosomal substrates for Syk, were identified, supporting a unique mechanism that Syk negatively affects cell division through its centrosomal kinase activity. PMID:22451900

Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations

PubMed Central

Swings, Toon; Weytjens, Bram; Schalck, Thomas; Bonte, Camille; Verstraeten, Natalie; Michiels, Jan

2017-01-01

Abstract Efficient production of ethanol for use as a renewable fuel requires organisms with a high level of ethanol tolerance. However, this trait is complex and increased tolerance therefore requires mutations in multiple genes and pathways. Here, we use experimental evolution for a system-level analysis of adaptation of Escherichia coli to high ethanol stress. As adaptation to extreme stress often results in complex mutational data sets consisting of both causal and noncausal passenger mutations, identifying the true adaptive mutations in these settings is not trivial. Therefore, we developed a novel method named IAMBEE (Identification of Adaptive Mutations in Bacterial Evolution Experiments). IAMBEE exploits the temporal profile of the acquisition of mutations during evolution in combination with the functional implications of each mutation at the protein level. These data are mapped to a genome-wide interaction network to search for adaptive mutations at the level of pathways. The 16 evolved populations in our data set together harbored 2,286 mutated genes with 4,470 unique mutations. Analysis by IAMBEE significantly reduced this number and resulted in identification of 90 mutated genes and 345 unique mutations that are most likely to be adaptive. Moreover, IAMBEE not only enabled the identification of previously known pathways involved in ethanol tolerance, but also identified novel systems such as the AcrAB-TolC efflux pump and fatty acids biosynthesis and even allowed to gain insight into the temporal profile of adaptation to ethanol stress. Furthermore, this method offers a solid framework for identifying the molecular underpinnings of other complex traits as well. PMID:28961727

Global Reach of Direct-to-Consumer Advertising Using Social Media for Illicit Online Drug Sales

PubMed Central

Liang, Bryan A

2013-01-01

Background Illicit or rogue Internet pharmacies are a recognized global public health threat that have been identified as utilizing various forms of online marketing and promotion, including social media. Objective To assess the accessibility of creating illicit no prescription direct-to-consumer advertising (DTCA) online pharmacy social media marketing (eDTCA2.0) and evaluate its potential global reach. Methods We identified the top 4 social media platforms allowing eDTCA2.0. After determining applicable platforms (ie, Facebook, Twitter, Google+, and MySpace), we created a fictitious advertisement advertising no prescription drugs online and posted it to the identified social media platforms. Each advertisement linked to a unique website URL that consisted of a site error page. Employing Web search analytics, we tracked the number of users visiting these sites and their location. We used commercially available Internet tools and services, including website hosting, domain registration, and website analytic services. Results Illicit online pharmacy social media content for Facebook, Twitter, and MySpace remained accessible despite highly questionable and potentially illegal content. Fictitious advertisements promoting illicit sale of drugs generated aggregate unique user traffic of 2795 visits over a 10-month period. Further, traffic to our websites originated from a number of countries, including high-income and middle-income countries, and emerging markets. Conclusions Our results indicate there are few barriers to entry for social media–based illicit online drug marketing. Further, illicit eDTCA2.0 has globalized outside US borders to other countries through unregulated Internet marketing. PMID:23718965

Uniform resolution of compact identifiers for biomedical data

PubMed Central

Wimalaratne, Sarala M.; Juty, Nick; Kunze, John; Janée, Greg; McMurry, Julie A.; Beard, Niall; Jimenez, Rafael; Grethe, Jeffrey S.; Hermjakob, Henning; Martone, Maryann E.; Clark, Tim

2018-01-01

Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such “compact identifiers” have been widely used in biomedical informatics to support global resource identification with local identifier assignment. We report here on our project to provide robust support for machine-resolvable, persistent compact identifiers in biomedical data citation, by harmonizing the Identifiers.org and N2T.net (Name-To-Thing) meta-resolvers and extending their capabilities. Identifiers.org services hosted at the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), and N2T.net services hosted at the California Digital Library (CDL), can now resolve any given identifier from over 600 source databases to its original source on the Web, using a common registry of prefix-based redirection rules. We believe these services will be of significant help to publishers and others implementing persistent, machine-resolvable citation of research data. PMID:29737976

TRL-6 for JWST wavefront sensing and control

NASA Astrophysics Data System (ADS)

Feinberg, Lee D.; Dean, Bruce H.; Aronstein, David L.; Bowers, Charles W.; Hayden, William; Lyon, Richard G.; Shiri, Ron; Smith, J. Scott; Acton, D. Scott; Carey, Larkin; Contos, Adam; Sabatke, Erin; Schwenker, John; Shields, Duncan; Towell, Tim; Shi, Fang; Meza, Luis

2007-09-01

NASA's Technology Readiness Level (TRL)-6 is documented for the James Webb Space Telescope (JWST) Wavefront Sensing and Control (WFSC) subsystem. The WFSC subsystem is needed to align the Optical Telescope Element (OTE) after all deployments have occurred, and achieves that requirement through a robust commissioning sequence consisting of unique commissioning algorithms, all of which are part of the WFSC algorithm suite. This paper identifies the technology need, algorithm heritage, describes the finished TRL-6 design platform, and summarizes the TRL-6 test results and compliance. Additionally, the performance requirements needed to satisfy JWST science goals as well as the criterion that relate to the TRL-6 Testbed Telescope (TBT) performance requirements are discussed.

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

PubMed Central

Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.

2016-01-01

PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. PMID:26958584

TRL-6 for JWST Wavefront Sensing and Control

NASA Technical Reports Server (NTRS)

Feinberg, Lee; Dean, Bruce; Smith, Scott; Aronstein, David; Shiri, Ron; Lyon, Rick; Hayden, Bill; Bowers, Chuck; Acton, D. Scott; Shields, Duncan;

Discovery and Biological Evaluation of a Series of Pyrrolo[2,3-b]pyrazines as Novel FGFR Inhibitors.

PubMed

Zhang, Yan; Liu, Hongchun; Zhang, Zhen; Wang, Ruifeng; Liu, Tongchao; Wang, Chaoyun; Ma, Yuchi; Ai, Jing; Zhao, Dongmei; Shen, Jingkang; Xiong, Bing

2017-04-05

Abnormality of fibroblast growth factor receptor (FGFR)-mediated signaling pathways were frequently found in various human malignancies, making FGFRs hot targets for cancer treatment. To address the consistent need for a new chemotype of FGFR inhibitors, here, we started with a hit structure identified from our internal hepatocyte growth factor receptor (also called c-Met) inhibitor project, and conducted a chemical optimization. After exploring three parts of the hit compound, we finally discovered a new series of pyrrolo[2,3- b ]pyrazine FGFR inhibitors, which contain a novel scaffold and unique molecular shape. We believe that our findings can help others to further develop selective FGFR inhibitors.

Beyond an Elevator Speech: Define Your Story to Find Success - 13581

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

Drouhard, Rachael

Diversify or die has been a familiar industry chant, growing louder over the past five years. As companies seek opportunities in new markets, succinctly communicating who they are and what they do to people they've never met becomes common practice. Large and small, most companies lack a clear, concise story and communication tools to articulate what makes them unique amongst the competition. As a result business is lost with prospects and needs of current customers may never be identified. These, along with a common set of core challenges can be overcome by definition, standardization, on-going education and consistent / accuratemore » communication at the brand level. (author)« less

The role of forensic anthropology in mass disaster resolution.

PubMed

Hinkes, M J

1989-07-01

On Dec.12, 1985, a military charter DC-8 crashed shortly after takeoff at Gander, Nfld., Canada. All 256 aboard were killed, making this the deadliest U.S. military aircraft accident in history. The investigation team (consisting of forensic pathologists, odontologists, radiologists, anthropologists, graves registration personnel, and systems engineers) succeeded in identifying the remains of all 248 manifested passengers and 8 crewmembers. The unique contribution of anthropology necessitates that a forensic anthropologist be included in all phases of casualty resolution from recovery and initial processing to final evaluation, rather than being summoned as a last resort. This approach would yield immediate information on "unknowns" and would eliminate subsequent duplication of effort.

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

PubMed Central

Gupta, Radhey S.; Lo, Brian; Son, Jeen

2018-01-01

The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the “Tuberculosis-Simiae,” “Terrae,” “Triviale,” “Fortuitum-Vaccae,” and “Abscessus-Chelonae” clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the “Abscessus-Chelonae” clade forms the deepest branching lineage and does not form a monophyletic grouping with the “Fortuitum-Vaccae” clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the “Tuberculosis-Simiae” clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the “Fortuitum-Vaccae,” “Terrae,” “Triviale,” and “Abscessus-Chelonae” clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups. PMID:29497402

The Protein Composition of the Digestive Fluid from the Venus Flytrap Sheds Light on Prey Digestion Mechanisms*

PubMed Central

Schulze, Waltraud X.; Sanggaard, Kristian W.; Kreuzer, Ines; Knudsen, Anders D.; Bemm, Felix; Thøgersen, Ida B.; Bräutigam, Andrea; Thomsen, Line R.; Schliesky, Simon; Dyrlund, Thomas F.; Escalante-Perez, Maria; Becker, Dirk; Schultz, Jörg; Karring, Henrik; Weber, Andreas; Højrup, Peter; Hedrich, Rainer; Enghild, Jan J.

2012-01-01

The Venus flytrap (Dionaea muscipula) is one of the most well-known carnivorous plants because of its unique ability to capture small animals, usually insects or spiders, through a unique snap-trapping mechanism. The animals are subsequently killed and digested so that the plants can assimilate nutrients, as they grow in mineral-deficient soils. We deep sequenced the cDNA from Dionaea traps to obtain transcript libraries, which were used in the mass spectrometry-based identification of the proteins secreted during digestion. The identified proteins consisted of peroxidases, nucleases, phosphatases, phospholipases, a glucanase, chitinases, and proteolytic enzymes, including four cysteine proteases, two aspartic proteases, and a serine carboxypeptidase. The majority of the most abundant proteins were categorized as pathogenesis-related proteins, suggesting that the plant's digestive system evolved from defense-related processes. This in-depth characterization of a highly specialized secreted fluid from a carnivorous plant provides new information about the plant's prey digestion mechanism and the evolutionary processes driving its defense pathways and nutrient acquisition. PMID:22891002

The role of saliva in tick feeding.

PubMed

Francischetti, Ivo M B; Sa-Nunes, Anderson; Mans, Ben J; Santos, Isabel M; Ribeiro, Jose M C

2009-01-01

When attempting to feed on their hosts, ticks face the problem of host hemostasis (the vertebrate mechanisms that prevent blood loss), inflammation (that can produce itching or pain and thus initiate defensive behavior on their hosts) and adaptive immunity (by way of both cellular and humoral responses). Against these barriers, ticks evolved a complex and sophisticated pharmacological armamentarium, consisting of bioactive lipids and proteins, to assist blood feeding. Recent progress in transcriptome research has uncovered that hard ticks have hundreds of different proteins expressed in their salivary glands, the majority of which have no known function, and include many novel protein families (e.g., their primary structure is unique to ticks). This review will address the vertebrate mechanisms of these barriers as a guide to identify the possible targets of these large numbers of known salivary proteins with unknown function. We additionally provide a supplemental Table that catalogues over 3,500 putative salivary proteins from various tick species, which might assist the scientific community in the process of functional identification of these unique proteins. This supplemental file is accessble fromhttp://exon.niaid.nih.gov/transcriptome/tick_review/Sup-Table-1.xls.gz.

Invented Spelling, Word Stress, and Syllable Awareness in Relation to Reading Difficulties in Children.

PubMed

Mehta, Sheena; Ding, Yi; Ness, Molly; Chen, Eric C

2018-06-01

The study assessed the clinical utility of an invented spelling tool and determined whether invented spelling with linguistic manipulation at segmental and supra-segmental levels can be used to better identify reading difficulties. We conducted linguistic manipulation by using real and nonreal words, incorporating word stress, alternating the order of consonants and vowels, and alternating the number of syllables. We recruited 60 third-grade students, of which half were typical readers and half were poor readers. The invented spelling task consistently differentiated those with reading difficulties from typical readers. It explained unique variance in conventional spelling, but not in word reading. Word stress explained unique variance in both word reading and conventional spelling, highlighting the importance of addressing phonological awareness at the supra-segmental level. Poor readers had poorer performance when spelling both real and nonreal words and demonstrated substantial difficulty in detecting word stress. Poor readers struggled with spelling words with double consonants at the beginning and ending of words, and performed worse on spelling two- and three-syllable words than typical readers. Practical implications for early identification and instruction are discussed.

A Joint Time-Frequency and Matrix Decomposition Feature Extraction Methodology for Pathological Voice Classification

NASA Astrophysics Data System (ADS)

Ghoraani, Behnaz; Krishnan, Sridhar

2009-12-01

The number of people affected by speech problems is increasing as the modern world places increasing demands on the human voice via mobile telephones, voice recognition software, and interpersonal verbal communications. In this paper, we propose a novel methodology for automatic pattern classification of pathological voices. The main contribution of this paper is extraction of meaningful and unique features using Adaptive time-frequency distribution (TFD) and nonnegative matrix factorization (NMF). We construct Adaptive TFD as an effective signal analysis domain to dynamically track the nonstationarity in the speech and utilize NMF as a matrix decomposition (MD) technique to quantify the constructed TFD. The proposed method extracts meaningful and unique features from the joint TFD of the speech, and automatically identifies and measures the abnormality of the signal. Depending on the abnormality measure of each signal, we classify the signal into normal or pathological. The proposed method is applied on the Massachusetts Eye and Ear Infirmary (MEEI) voice disorders database which consists of 161 pathological and 51 normal speakers, and an overall classification accuracy of 98.6% was achieved.

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.

Application of Ionic Liquids to Energy Storage and Conversion Materials and Devices.

PubMed

Watanabe, Masayoshi; Thomas, Morgan L; Zhang, Shiguo; Ueno, Kazuhide; Yasuda, Tomohiro; Dokko, Kaoru

2017-05-24

Ionic liquids (ILs) are liquids consisting entirely of ions and can be further defined as molten salts having melting points lower than 100 °C. One of the most important research areas for IL utilization is undoubtedly their energy application, especially for energy storage and conversion materials and devices, because there is a continuously increasing demand for clean and sustainable energy. In this article, various application of ILs are reviewed by focusing on their use as electrolyte materials for Li/Na ion batteries, Li-sulfur batteries, Li-oxygen batteries, and nonhumidified fuel cells and as carbon precursors for electrode catalysts of fuel cells and electrode materials for batteries and supercapacitors. Due to their characteristic properties such as nonvolatility, high thermal stability, and high ionic conductivity, ILs appear to meet the rigorous demands/criteria of these various applications. However, for further development, specific applications for which these characteristic properties become unique (i.e., not easily achieved by other materials) must be explored. Thus, through strong demands for research and consideration of ILs unique properties, we will be able to identify indispensable applications for ILs.

Contextuality in canonical systems of random variables

NASA Astrophysics Data System (ADS)

Dzhafarov, Ehtibar N.; Cervantes, Víctor H.; Kujala, Janne V.

2017-10-01

Random variables representing measurements, broadly understood to include any responses to any inputs, form a system in which each of them is uniquely identified by its content (that which it measures) and its context (the conditions under which it is recorded). Two random variables are jointly distributed if and only if they share a context. In a canonical representation of a system, all random variables are binary, and every content-sharing pair of random variables has a unique maximal coupling (the joint distribution imposed on them so that they coincide with maximal possible probability). The system is contextual if these maximal couplings are incompatible with the joint distributions of the context-sharing random variables. We propose to represent any system of measurements in a canonical form and to consider the system contextual if and only if its canonical representation is contextual. As an illustration, we establish a criterion for contextuality of the canonical system consisting of all dichotomizations of a single pair of content-sharing categorical random variables. This article is part of the themed issue `Second quantum revolution: foundational questions'.

The REFLECT statement: methods and processes of creating reporting guidelines for randomized controlled trials for livestock and food safety.

PubMed

O'Connor, A M; Sargeant, J M; Gardner, I A; Dickson, J S; Torrence, M E; Dewey, C E; Dohoo, I R; Evans, R B; Gray, J T; Greiner, M; Keefe, G; Lefebvre, S L; Morley, P S; Ramirez, A; Sischo, W; Smith, D R; Snedeker, K; Sofos, J; Ward, M P; Wills, R

2010-01-01

The conduct of randomized controlled trials in livestock with production, health, and food-safety outcomes presents unique challenges that may not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A two-day consensus meeting was held on November 18-19, 2008 in Chicago, IL, United States of America, to achieve the objective. Prior to the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock-production specialists, journal editors, assistant editors, and associate editors. Prior to the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items may need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines For Randomized Control Trials) statement for livestock and food safety (LFS) and 22-item checklist. Fourteen items were modified from the CONSORT checklist, and an additional sub-item was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health, and food-safety outcomes.

The REFLECT statement: methods and processes of creating reporting guidelines for randomized controlled trials for livestock and food safety by modifying the CONSORT statement.

PubMed

O'Connor, A M; Sargeant, J M; Gardner, I A; Dickson, J S; Torrence, M E; Dewey, C E; Dohoo, I R; Evans, R B; Gray, J T; Greiner, M; Keefe, G; Lefebvre, S L; Morley, P S; Ramirez, A; Sischo, W; Smith, D R; Snedeker, K; Sofos, J; Ward, M P; Wills, R

2010-03-01

The conduct of randomized controlled trials in livestock with production, health and food-safety outcomes presents unique challenges that may not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A 2-day consensus meeting was held on 18-19 November 2008 in Chicago, IL, USA, to achieve the objective. Prior to the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock-production specialists, journal editors, assistant editors and associate editors. Prior to the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items may need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines for Randomized Control Trials) statement for livestock and food safety and 22-item checklist. Fourteen items were modified from the CONSORT checklist and an additional sub-item was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health and food-safety outcomes.

The REFLECT statement: methods and processes of creating reporting guidelines for randomized controlled trials for livestock and food safety.

PubMed

O'Connor, A M; Sargeant, J M; Gardner, I A; Dickson, J S; Torrence, M E; Dewey, C E; Dohoo, I R; Evans, R B; Gray, J T; Greiner, M; Keefe, G; Lefebvre, S L; Morley, P S; Ramirez, A; Sischo, W; Smith, D R; Snedeker, K; Sofos, J N; Ward, M P; Wills, R

2010-01-01

The conduct of randomized controlled trials in livestock with production, health, and food-safety outcomes presents unique challenges that may not be adequately reported in trial reports. The objective of this project was to modify the CONSORT (Consolidated Standards of Reporting Trials) statement to reflect the unique aspects of reporting these livestock trials. A two-day consensus meeting was held on November 18-19, 2008 in Chicago, Ill, United States of America, to achieve the objective. Prior to the meeting, a Web-based survey was conducted to identify issues for discussion. The 24 attendees were biostatisticians, epidemiologists, food-safety researchers, livestock production specialists, journal editors, assistant editors, and associate editors. Prior to the meeting, the attendees completed a Web-based survey indicating which CONSORT statement items may need to be modified to address unique issues for livestock trials. The consensus meeting resulted in the production of the REFLECT (Reporting Guidelines for Randomized Control Trials) statement for livestock and food safety (LFS) and 22-item checklist. Fourteen items were modified from the CONSORT checklist, and an additional sub-item was proposed to address challenge trials. The REFLECT statement proposes new terminology, more consistent with common usage in livestock production, to describe study subjects. Evidence was not always available to support modification to or inclusion of an item. The use of the REFLECT statement, which addresses issues unique to livestock trials, should improve the quality of reporting and design for trials reporting production, health, and food-safety outcomes.

45 CFR 162.406 - Standard unique health identifier for health care providers.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 1 2011-10-01 2011-10-01 false Standard unique health identifier for health care providers. 162.406 Section 162.406 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE... no intelligence about the health care provider in the number. (b) Required and permitted uses for the...

45 CFR 162.406 - Standard unique health identifier for health care providers.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 1 2010-10-01 2010-10-01 false Standard unique health identifier for health care providers. 162.406 Section 162.406 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE... no intelligence about the health care provider in the number. (b) Required and permitted uses for the...

75 FR 50731 - Federal Acquisition Regulation; Unique Procurement Instrument Identifiers (PIID)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-17

... accordance with FAR 4.605(a), agencies are required to have in place a process that ensures that each PIID... standardization of contract data beyond FPDS, thereby causing the potential for duplication of contract data... lack of specific policies and procedures necessary to ensure standardization of unique PIIDs identified...

Estimating avian population size using Bowden's estimator

USGS Publications Warehouse

Diefenbach, D.R.

2009-01-01

Avian researchers often uniquely mark birds, and multiple estimators could be used to estimate population size using individually identified birds. However, most estimators of population size require that all sightings of marked birds be uniquely identified, and many assume homogeneous detection probabilities. Bowden's estimator can incorporate sightings of marked birds that are not uniquely identified and relax assumptions required of other estimators. I used computer simulation to evaluate the performance of Bowden's estimator for situations likely to be encountered in bird studies. When the assumptions of the estimator were met, abundance and variance estimates and confidence-interval coverage were accurate. However, precision was poor for small population sizes (N < 50) unless a large percentage of the population was marked (>75%) and multiple (≥8) sighting surveys were conducted. If additional birds are marked after sighting surveys begin, it is important to initially mark a large proportion of the population (pm ≥ 0.5 if N ≤ 100 or pm > 0.1 if N ≥ 250) and minimize sightings in which birds are not uniquely identified; otherwise, most population estimates will be overestimated by >10%. Bowden's estimator can be useful for avian studies because birds can be resighted multiple times during a single survey, not all sightings of marked birds have to uniquely identify individuals, detection probabilities among birds can vary, and the complete study area does not have to be surveyed. I provide computer code for use with pilot data to design mark-resight surveys to meet desired precision for abundance estimates.

Comparing Unique Title Coverage of Web of Science and Scopus in Earth and Atmospheric Sciences

ERIC Educational Resources Information Center

Barnett, Philip; Lascar, Claudia

2012-01-01

The current journal titles in earth and atmospheric sciences, that are unique to each of two databases, Web of Science and Scopus, were identified using different methods. Comparing by subject category shows that Scopus has hundreds of unique titles, and Web of Science just 16. The titles unique to each database have low SCImago Journal Rank…

A Stratified Transcriptomics Analysis of Polygenic Fat and Lean Mouse Adipose Tissues Identifies Novel Candidate Obesity Genes

PubMed Central

Morton, Nicholas M.; Nelson, Yvonne B.; Michailidou, Zoi; Di Rollo, Emma M.; Ramage, Lynne; Hadoke, Patrick W. F.; Seckl, Jonathan R.; Bunger, Lutz; Horvat, Simon; Kenyon, Christopher J.; Dunbar, Donald R.

2011-01-01

Background Obesity and metabolic syndrome results from a complex interaction between genetic and environmental factors. In addition to brain-regulated processes, recent genome wide association studies have indicated that genes highly expressed in adipose tissue affect the distribution and function of fat and thus contribute to obesity. Using a stratified transcriptome gene enrichment approach we attempted to identify adipose tissue-specific obesity genes in the unique polygenic Fat (F) mouse strain generated by selective breeding over 60 generations for divergent adiposity from a comparator Lean (L) strain. Results To enrich for adipose tissue obesity genes a ‘snap-shot’ pooled-sample transcriptome comparison of key fat depots and non adipose tissues (muscle, liver, kidney) was performed. Known obesity quantitative trait loci (QTL) information for the model allowed us to further filter genes for increased likelihood of being causal or secondary for obesity. This successfully identified several genes previously linked to obesity (C1qr1, and Np3r) as positional QTL candidate genes elevated specifically in F line adipose tissue. A number of novel obesity candidate genes were also identified (Thbs1, Ppp1r3d, Tmepai, Trp53inp2, Ttc7b, Tuba1a, Fgf13, Fmr) that have inferred roles in fat cell function. Quantitative microarray analysis was then applied to the most phenotypically divergent adipose depot after exaggerating F and L strain differences with chronic high fat feeding which revealed a distinct gene expression profile of line, fat depot and diet-responsive inflammatory, angiogenic and metabolic pathways. Selected candidate genes Npr3 and Thbs1, as well as Gys2, a non-QTL gene that otherwise passed our enrichment criteria were characterised, revealing novel functional effects consistent with a contribution to obesity. Conclusions A focussed candidate gene enrichment strategy in the unique F and L model has identified novel adipose tissue-enriched genes contributing to obesity. PMID:21915269

A stratified transcriptomics analysis of polygenic fat and lean mouse adipose tissues identifies novel candidate obesity genes.

PubMed

Morton, Nicholas M; Nelson, Yvonne B; Michailidou, Zoi; Di Rollo, Emma M; Ramage, Lynne; Hadoke, Patrick W F; Seckl, Jonathan R; Bunger, Lutz; Horvat, Simon; Kenyon, Christopher J; Dunbar, Donald R

2011-01-01

Obesity and metabolic syndrome results from a complex interaction between genetic and environmental factors. In addition to brain-regulated processes, recent genome wide association studies have indicated that genes highly expressed in adipose tissue affect the distribution and function of fat and thus contribute to obesity. Using a stratified transcriptome gene enrichment approach we attempted to identify adipose tissue-specific obesity genes in the unique polygenic Fat (F) mouse strain generated by selective breeding over 60 generations for divergent adiposity from a comparator Lean (L) strain. To enrich for adipose tissue obesity genes a 'snap-shot' pooled-sample transcriptome comparison of key fat depots and non adipose tissues (muscle, liver, kidney) was performed. Known obesity quantitative trait loci (QTL) information for the model allowed us to further filter genes for increased likelihood of being causal or secondary for obesity. This successfully identified several genes previously linked to obesity (C1qr1, and Np3r) as positional QTL candidate genes elevated specifically in F line adipose tissue. A number of novel obesity candidate genes were also identified (Thbs1, Ppp1r3d, Tmepai, Trp53inp2, Ttc7b, Tuba1a, Fgf13, Fmr) that have inferred roles in fat cell function. Quantitative microarray analysis was then applied to the most phenotypically divergent adipose depot after exaggerating F and L strain differences with chronic high fat feeding which revealed a distinct gene expression profile of line, fat depot and diet-responsive inflammatory, angiogenic and metabolic pathways. Selected candidate genes Npr3 and Thbs1, as well as Gys2, a non-QTL gene that otherwise passed our enrichment criteria were characterised, revealing novel functional effects consistent with a contribution to obesity. A focussed candidate gene enrichment strategy in the unique F and L model has identified novel adipose tissue-enriched genes contributing to obesity.

Multivariate pattern analysis of MEG and EEG: A comparison of representational structure in time and space.

PubMed

Cichy, Radoslaw Martin; Pantazis, Dimitrios

2017-09-01

Multivariate pattern analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data can reveal the rapid neural dynamics underlying cognition. However, MEG and EEG have systematic differences in sampling neural activity. This poses the question to which degree such measurement differences consistently bias the results of multivariate analysis applied to MEG and EEG activation patterns. To investigate, we conducted a concurrent MEG/EEG study while participants viewed images of everyday objects. We applied multivariate classification analyses to MEG and EEG data, and compared the resulting time courses to each other, and to fMRI data for an independent evaluation in space. We found that both MEG and EEG revealed the millisecond spatio-temporal dynamics of visual processing with largely equivalent results. Beyond yielding convergent results, we found that MEG and EEG also captured partly unique aspects of visual representations. Those unique components emerged earlier in time for MEG than for EEG. Identifying the sources of those unique components with fMRI, we found the locus for both MEG and EEG in high-level visual cortex, and in addition for MEG in low-level visual cortex. Together, our results show that multivariate analyses of MEG and EEG data offer a convergent and complimentary view on neural processing, and motivate the wider adoption of these methods in both MEG and EEG research. Copyright © 2017 Elsevier Inc. All rights reserved.

Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome.

PubMed

Barrero, Roberto A; Guerrero, Felix D; Black, Michael; McCooke, John; Chapman, Brett; Schilkey, Faye; Pérez de León, Adalberto A; Miller, Robert J; Bruns, Sara; Dobry, Jason; Mikhaylenko, Galina; Stormo, Keith; Bell, Callum; Tao, Quanzhou; Bogden, Robert; Moolhuijzen, Paula M; Hunter, Adam; Bellgard, Matthew I

2017-08-01

The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0Gbp represented in 195,170 scaffolds with a N50 of 60,284bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, short interspersed elements, long interspersed elements and long terminal repeats. We identified 38,827 putative R. microplus gene loci, of which 24,758 were protein coding genes (≥100 amino acids). OrthoMCL comparative analysis against 11 selected species including insects and vertebrates identified 10,835 and 3,423 protein coding gene loci that are unique to R. microplus or common to both R. microplus and Ixodes scapularis ticks, respectively. We identified 191 microRNA loci, of which 168 have similarity to known miRNAs and 23 represent novel miRNA families. We identified the genomic loci of several highly divergent R. microplus esterases with sequence similarity to acetylcholinesterase. Additionally we report the finding of a novel cytochrome P450 CYP41 homolog that shows similar protein folding structures to known CYP41 proteins known to be involved in acaricide resistance. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Unique Outcomes in the Narratives of Young Adults Who Experienced Dating Violence as Adolescents.

PubMed

Draucker, Claire Burke; Smith, Carolyn; Mazurczyk, Jill; Thomas, Destini; Ramirez, Patricia; McNealy, Kim; Thomas, Jade; Martsolf, Donna S

2016-01-01

Narrative therapy, an approach based on the reauthoring of life narratives, may be a useful psychotherapeutic strategy for youth who have experienced dating violence. A cornerstone of narrative therapy is the concept of unique outcomes, which are moments that stand in contrast to a client's otherwise problem-saturated narratives. The purpose of this study was to identify and categorize unique outcomes embedded in narratives about adolescent dating violence. Text units representing unique outcomes were extracted from transcripts of interviews with 88 young adults who had experienced dating violence and were categorized using standard content analytic techniques. Six categories of unique outcome stories were identified: facing-facts stories, standing-up-for-myself stories, cutting-it-off stories, cutting-'em-loose stories, getting-back-on-track stories, and changing-it-up stories. This typology of unique outcomes can inform clinicians who work with clients who have a history of adolescent dating violence. © The Author(s) 2015.

Father involvement: Identifying and predicting family members' shared and unique perceptions.

PubMed

Dyer, W Justin; Day, Randal D; Harper, James M

2014-08-01

Father involvement research has typically not recognized that reports of involvement contain at least two components: 1 reflecting a view of father involvement that is broadly recognized in the family, and another reflecting each reporter's unique perceptions. Using a longitudinal sample of 302 families, this study provides a first examination of shared and unique views of father involvement (engagement and warmth) from the perspectives of fathers, children, and mothers. This study also identifies influences on these shared and unique perspectives. Father involvement reports were obtained when the child was 12 and 14 years old. Mother reports overlapped more with the shared view than father or child reports. This suggests the mother's view may be more in line with broadly recognized father involvement. Regarding antecedents, for fathers' unique view, a compensatory model partially explains results; that is, negative aspects of family life were positively associated with fathers' unique view. Children's unique view of engagement may partially reflect a sentiment override with father antisocial behaviors being predictive. Mothers' unique view of engagement was predicted by father and mother work hours and her unique view of warmth was predicted by depression and maternal gatekeeping. Taken, together finding suggests a far more nuanced view of father involvement should be considered.

Selective Mutism Questionnaire: measurement structure and validity.

PubMed

Letamendi, Andrea M; Chavira, Denise A; Hitchcock, Carla A; Roesch, Scott C; Shipon-Blum, Elisa; Stein, Murray B

2008-10-01

To evaluate the factor structure, reliability, and validity of the 17-item Selective Mutism Questionnaire (SMQ). Diagnostic interviews were administered via telephone to 102 parents of children identified with selective mutism (SM) and 43 parents of children without SM from varying U.S. geographic regions. Children were between the ages of 3 and 11 inclusive and comprised 58% girls and 42% boys. SM diagnoses were determined using the Anxiety Disorders Interview Schedule for Children-Parent Version; SM severity was assessed using the 17-item SMQ; and behavioral and affective symptoms were assessed using the Child Behavior Checklist. An exploratory factor analysis was conducted to investigate the dimensionality of the SMQ and a modified parallel analysis procedure was used to confirm exploratory factor analysis results. Internal consistency, construct validity, and incremental validity were also examined. The exploratory factor analysis yielded a 13-item solution consisting of three factors: social situations outside of school, school situations, and home and family situations. Internal consistency of SMQ factors and total scale ranged from moderate to high. Convergent and incremental validity was also well supported. Measure structure findings are consistent with the three-factor solution found in a previous psychometric evaluation of the SMQ. Results also suggest that the SMQ provides useful and unique information in the prediction of SM phenomena beyond other child anxiety measures.

Unique barriers and needs in weight management for obese women with fibromyalgia.

PubMed

Craft, Jennifer M; Ridgeway, Jennifer L; Vickers, Kristin S; Hathaway, Julie C; Vincent, Ann; Oh, Terry H

2015-01-01

The aim of this study was to identify barriers, needs, and preferences of weight management intervention for women with fibromyalgia (FM). Obesity appears in higher rates in women with fibromyalgia compared to the population at large, and no study to date has taken a qualitative approach to better understand how these women view weight management in relation to their disease and vice versa. We designed a qualitative interview study with women patients with FM and obesity. Women (N = 15) were recruited by their participation in a fibromyalgia treatment program (FTP) within the year prior. The women approached for the study met the following inclusion criteria: confirmed diagnosis of FM, age between 30 and 60 years (M = 51 ± 6.27), and body mass index (BMI) ≥ 30 (M = 37.88 ± 4.87). Patients completed questionnaire data prior to their participation in focus groups (N = 3), including weight loss history, physical activity data, the Revised Fibromyalgia Impact Questionnaire (FIQR), and the Patient Health Questionnaire 9-item (PHQ-9). Three focus group interviews were conducted to collect qualitative data. Consistent themes were revealed within and between groups. Patients expressed the complex relationships between FM symptoms, daily responsibilities, and weight management. Weight was viewed as an emotionally laden topic requiring compassionate delivery of programming from an empathetic leader who is knowledgeable about fibromyalgia. Patients view themselves as complex and different, requiring a specifically tailored weight management program for women with FM. Women with FM identify unique barriers to weight management, including the complex interrelationships between symptoms of FM and health behaviors, such as diet and exercise. They prefer a weight management program for women with FM that consists of an in-person, group-based approach with a leader but are open to a tailored conventional weight management program. Feasibility may be one of the biggest barriers to such a program both from an institutional and individual perspective. Copyright © 2015 Elsevier Inc. All rights reserved.

Upper- and mid-mantle interaction between the Samoan plume and the Tonga-Kermadec slabs

NASA Astrophysics Data System (ADS)

Chang, Sung-Joon; Ferreira, Ana M. G.; Faccenda, Manuele

2016-02-01

Mantle plumes are thought to play a key role in transferring heat from the core-mantle boundary to the lithosphere, where it can significantly influence plate tectonics. On impinging on the lithosphere at spreading ridges or in intra-plate settings, mantle plumes may generate hotspots, large igneous provinces and hence considerable dynamic topography. However, the active role of mantle plumes on subducting slabs remains poorly understood. Here we show that the stagnation at 660 km and fastest trench retreat of the Tonga slab in Southwestern Pacific are consistent with an interaction with the Samoan plume and the Hikurangi plateau. Our findings are based on comparisons between 3D anisotropic tomography images and 3D petrological-thermo-mechanical models, which self-consistently explain several unique features of the Fiji-Tonga region. We identify four possible slip systems of bridgmanite in the lower mantle that reconcile the observed seismic anisotropy beneath the Tonga slab (VSH>VSV) with thermo-mechanical calculations.

Determinants of propranolol’s selective effect on loss aversion

PubMed Central

Sokol-Hessner, Peter; Lackovic, Sandra F.; Tobe, Russell H.; Camerer, Colin F.; Leventhal, Bennett L.; Phelps, Elizabeth A.

2015-01-01

Research on emotion and decision-making has suggested that arousal mediates risky decisions (e.g., Bechara et al., 1997), but several distinct and often confounded processes drive such choices. Here, we used econometric modeling to separate and quantify the unique contributions of loss aversion, risk sensitivity and choice consistency to risky decision-making. We administered the beta-blocker propranolol in a double-blind, placebo-controlled within-subjects study, targeting the neurohormonal basis of physiological arousal. Matching our intervention’s pharmacological specificity with a quantitative model delineating decision-making components allowed us to identify the causal relationships between arousal and decision-making that do and do not exist. Propranolol selectively reduced loss aversion in a baseline- and dose-dependent manner (i.e. as a function of initial loss aversion and body-mass index), and did not affect risk sensitivity or choice consistency. These findings provide evidence for a specific, modulatory, and causal relationship between precise components of both emotion and risky decision-making. PMID:26063441

Collision of Ductal Carcinoma In Situ of Anogenital Mammary-like Glands and Vulvar Sarcomatoid Squamous Cell Carcinoma.

PubMed

Tran, Tien A N; Deavers, Michael T; Carlson, J Andrew; Malpica, Anais

2015-09-01

A spectrum of invasive adenocarcinomas presumably arising from the anogenital mammary-like glands of the vulva has been reported. Even rarer are the cases of pure ductal carcinoma in situ that originated from these unique glandular structures. Herein, we report an 81-yr-old woman presented with an invasive well-differentiated squamous cell carcinoma of the vulva. Unexpectedly, the underlying dermis demonstrated a cystically dilated structure that displayed a layer of malignant squamous cells in the periphery, and a second centrally located population of neoplastic cells exhibiting glandular differentiation. In addition, a spindle and pleomorphic malignant cell population consistent with a sarcomatoid carcinoma was identified around the cystic structure. Scattered benign anogenital mammary-like glands were present in the adjacent dermis. The histologic and immunohistochemical findings were consistent with those of vulvar squamous cell carcinoma that has undergone sarcomatoid transformation after spreading in a pagetoid fashion into an underlying focus of ductal carcinoma in situ of anogenital mammary-like gland origin.

Detection of arcing location on photovoltaic systems using filters

DOEpatents

Johnson, Jay

2018-02-20

The present invention relates to photovoltaic systems capable of identifying the location of an arc-fault. In particular, such systems include a unique filter connected to each photovoltaic (PV) string, thereby providing a unique filtered noise profile associated with a particular PV string. Also described herein are methods for identifying and isolating such arc-faults.

Identification and Classification of Player Types in Massive Multiplayer Online Games Using Avatar Behavior

DTIC Science & Technology

2011-08-01

display specific characteristics that can be used to identify the player behind the avatar. This kind of information can be used by game companies to...bring in players. This kind of information can also be used to identify deviant behaviors such as ‘gold farming.’ Gold farming refers to the practice...unique behaviors associated with a player controlling the avatar. Some of the observable information used to identify these unique behaviors are

A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf

PubMed Central

2010-01-01

Subtraction technique has been broadly applied for target gene discovery. However, most current protocols apply relative differential subtraction and result in great amount clone mixtures of unique and differentially expressed genes. This makes it more difficult to identify unique or target-orientated expressed genes. In this study, we developed a novel method for subtraction at mRNA level by integrating magnetic particle technology into driver preparation and tester–driver hybridization to facilitate uniquely expressed gene discovery between peanut immature pod and leaf through a single round subtraction. The resulting target clones were further validated through polymerase chain reaction screening using peanut immature pod and leaf cDNA libraries as templates. This study has resulted in identifying several genes expressed uniquely in immature peanut pod. These target genes can be used for future peanut functional genome and genetic engineering research. PMID:21406066

FY2007 Laboratory Directed Research and Development Annual Report

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

Craig, W W; Sketchley, J A; Kotta, P R

The Laboratory Directed Research and Development (LDRD) annual report for fiscal year 2007 (FY07) provides a summary of LDRD-funded projects for the fiscal year and consists of two parts: An introduction to the LDRD Program, the LDRD portfolio-management process, program statistics for the year, and highlights of accomplishments for the year. A summary of each project, submitted by the principal investigator. Project summaries include the scope, motivation, goals, relevance to Department of Energy (DOE)/National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laboratory (LLNL) mission areas, the technical progress achieved in FY07, and a list of publications that resulted frommore » the research in FY07. Summaries are organized in sections by research category (in alphabetical order). Within each research category, the projects are listed in order of their LDRD project category: Strategic Initiative (SI), Exploratory Research (ER), Laboratory-Wide Competition (LW), and Feasibility Study (FS). Within each project category, the individual project summaries appear in order of their project tracking code, a unique identifier that consists of three elements. The first is the fiscal year the project began, the second represents the project category, and the third identifies the serial number of the proposal for that fiscal year.« less

A Laminin G-EGF-Laminin G module in Neurexin IV is essential for the apico-lateral localization of Contactin and organization of septate junctions.

PubMed

Banerjee, Swati; Paik, Raehum; Mino, Rosa E; Blauth, Kevin; Fisher, Elizabeth S; Madden, Victoria J; Fanning, Alan S; Bhat, Manzoor A

2011-01-01

Septate junctions (SJs) display a unique ultrastructural morphology with ladder-like electron densities that are conserved through evolution. Genetic and molecular analyses have identified a highly conserved core complex of SJ proteins consisting of three cell adhesion molecules Neurexin IV, Contactin, and Neuroglian, which interact with the cytoskeletal FERM domain protein Coracle. How these individual proteins interact to form the septal arrays that create the paracellular barrier is poorly understood. Here, we show that point mutations that map to specific domains of neurexin IV lead to formation of fewer septae and disorganization of SJs. Consistent with these observations, our in vivo domain deletion analyses identified the first Laminin G-EGF-Laminin G module in the extracellular region of Neurexin IV as necessary for the localization of and association with Contactin. Neurexin IV protein that is devoid of its cytoplasmic region is able to create septae, but fails to form a full complement of SJs. These data provide the first in vivo evidence that specific domains in Neurexin IV are required for protein-protein interactions and organization of SJs. Given the molecular conservation of SJ proteins across species, our studies may provide insights into how vertebrate axo-glial SJs are organized in myelinated axons.

Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae.

PubMed

Li, Jia; Gao, Lei; Chen, Shanshan; Tao, Ke; Su, Yingjuan; Wang, Ting

2016-02-11

Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data.

A Laminin G-EGF-Laminin G Module in Neurexin IV Is Essential for the Apico-Lateral Localization of Contactin and Organization of Septate Junctions

PubMed Central

Banerjee, Swati; Paik, Raehum; Mino, Rosa E.; Blauth, Kevin; Fisher, Elizabeth S.; Madden, Victoria J.; Fanning, Alan S.; Bhat, Manzoor A.

2011-01-01

Septate junctions (SJs) display a unique ultrastructural morphology with ladder-like electron densities that are conserved through evolution. Genetic and molecular analyses have identified a highly conserved core complex of SJ proteins consisting of three cell adhesion molecules Neurexin IV, Contactin, and Neuroglian, which interact with the cytoskeletal FERM domain protein Coracle. How these individual proteins interact to form the septal arrays that create the paracellular barrier is poorly understood. Here, we show that point mutations that map to specific domains of neurexin IV lead to formation of fewer septae and disorganization of SJs. Consistent with these observations, our in vivo domain deletion analyses identified the first Laminin G-EGF-Laminin G module in the extracellular region of Neurexin IV as necessary for the localization of and association with Contactin. Neurexin IV protein that is devoid of its cytoplasmic region is able to create septae, but fails to form a full complement of SJs. These data provide the first in vivo evidence that specific domains in Neurexin IV are required for protein-protein interactions and organization of SJs. Given the molecular conservation of SJ proteins across species, our studies may provide insights into how vertebrate axo-glial SJs are organized in myelinated axons. PMID:22022470

Environmental correlates of physical activity and dietary behaviours among young people: a systematic review of reviews.

PubMed

de Vet, E; de Ridder, D T D; de Wit, J B F

2011-05-01

An extensive body of research exists on environmental influences on weight-related behaviours in young people. Existing reviews aimed to synthesize this body of work, but generally focused on specific samples, behaviours or environmental influences and integration of findings is lacking. Hereto, we reviewed 18 reviews representing 671 unique studies, aiming to identify what environmental factors do and do not affect physical activity and dietary behaviours in children and adolescents. Eleven reviews focused exclusively on physical activity, six on diet, and one review focused on both physical activity and dietary behaviours with only small overlap in included studies. Physical activity was more consistently related to school and neighbourhood characteristics than to interpersonal and societal environments. In contrast, interpersonal factors played a pronounced role in dietary behaviours; no school, neighbourhood or societal factors were consistently related to dietary behaviours. This review of reviews adds to the literature by providing a comprehensive synthesis of factors related to physical activity and dietary behaviours that could be targeted in interventions. Moreover, by identifying factors that are unrelated to physical activity and dietary behaviours, this review may help to narrow the scope of future studies and environmental interventions. © 2010 The Authors. obesity reviews © 2010 International Association for the Study of Obesity.

Identifying parameter regions for multistationarity

PubMed Central

Conradi, Carsten; Mincheva, Maya; Wiuf, Carsten

2017-01-01

Mathematical modelling has become an established tool for studying the dynamics of biological systems. Current applications range from building models that reproduce quantitative data to identifying systems with predefined qualitative features, such as switching behaviour, bistability or oscillations. Mathematically, the latter question amounts to identifying parameter values associated with a given qualitative feature. We introduce a procedure to partition the parameter space of a parameterized system of ordinary differential equations into regions for which the system has a unique or multiple equilibria. The procedure is based on the computation of the Brouwer degree, and it creates a multivariate polynomial with parameter depending coefficients. The signs of the coefficients determine parameter regions with and without multistationarity. A particular strength of the procedure is the avoidance of numerical analysis and parameter sampling. The procedure consists of a number of steps. Each of these steps might be addressed algorithmically using various computer programs and available software, or manually. We demonstrate our procedure on several models of gene transcription and cell signalling, and show that in many cases we obtain a complete partitioning of the parameter space with respect to multistationarity. PMID:28972969

Application of LANDSAT data to delimitation of avalanche hazards in Montane Colorado

NASA Technical Reports Server (NTRS)

Knepper, D. H., Jr. (Principal Investigator)

1977-01-01

The author has identified the following significant results. Many avalanche hazard zones can be identified on LANDSAT imagery, but not consistently over a large region. Therefore, regional avalanche hazard mapping, using LANDSAT imagery, must draw on additional sources of information. A method was devised that depicts three levels of avalanche hazards according to three corresponding levels of certainty that active avalanches occur. The lowest level, potential avalanche hazards, was defined by delineating slopes steep enough to support avalanches at elevations where snowfall was likely to be sufficient to produce a thick snowpack. The intermediate level of avalanche hazard was interpreted as avalanche hazard zones. These zones have direct and indirect indicators of active avalanche activity and were interpreted from LANDSAT imagery. The highest level of known or active avalanche hazards was compiled from existing maps. Some landslides in Colorado were identified and, to a degree, delimited on LANDSAT imagery, but the conditions of their identification were highly variable. Because of local topographic, geologic, structural, and vegetational variations, there was no unique landslide spectral appearance.

Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus.

PubMed

Nguyen, Thong T; Suryamohan, Kushal; Kuriakose, Boney; Janakiraman, Vasantharajan; Reichelt, Mike; Chaudhuri, Subhra; Guillory, Joseph; Divakaran, Neethu; Rabins, P E; Goel, Ridhi; Deka, Bhabesh; Sarkar, Suman; Ekka, Preety; Tsai, Yu-Chih; Vargas, Derek; Santhosh, Sam; Mohan, Sangeetha; Chin, Chen-Shan; Korlach, Jonas; Thomas, George; Babu, Azariah; Seshagiri, Somasekar

2018-06-12

We sequenced the Hyposidra talaca NPV (HytaNPV) double stranded circular DNA genome using PacBio single molecule sequencing technology. We found that the HytaNPV genome is 139,089 bp long with a GC content of 39.6%. It encodes 141 open reading frames (ORFs) including the 37 baculovirus core genes, 25 genes conserved among lepidopteran baculoviruses, 72 genes known in baculovirus, and 7 genes unique to the HytaNPV genome. It is a group II alphabaculovirus that codes for the F protein and lacks the gp64 gene found in group I alphabaculovirus viruses. Using RNA-seq, we confirmed the expression of the ORFs identified in the HytaNPV genome. Phylogenetic analysis showed HytaNPV to be closest to BusuNPV, SujuNPV and EcobNPV that infect other tea pests, Buzura suppressaria, Sucra jujuba, and Ectropis oblique, respectively. We identified repeat elements and a conserved non-coding baculovirus element in the genome. Analysis of the putative promoter sequences identified motif consistent with the temporal expression of the genes observed in the RNA-seq data.

Consistency of psychotropic drug-drug interactions listed in drug monographs.

PubMed

Liu, Xinyue; Hatton, Randy C; Zhu, Yanmin; Hincapie-Castillo, Juan M; Bussing, Regina; Barnicoat, Marie; Winterstein, Almut G

With an increasing prevalence of psychotropic polypharmacy, clinicians depend on drug-drug interaction (DDI) references to ensure safe regimens, but the consistency of such information is frequently questioned. To evaluate the consistency of psychotropic DDIs documented in Clinical Pharmacology (CP), Micromedex (MM), and Lexicomp (LC) and summarize consistent psychotropic DDIs. In May 2016, we extracted severe or major psychotropic DDIs for 102 psychotropic drugs, including central nervous system (CNS) stimulants, antidepressants, an antimanic agent (lithium), antipsychotics, anticonvulsants, and anxiolytics-sedatives-hypnotics from CP, MM, and LC. We then summarized the psychotropic DDIs that were included in all 3 references and with evidence quality of "excellent" or "good" based on MM. We identified 1496, 938, and 1006 unique severe or major psychotropic DDIs from CP, MM, and LC, respectively. Common adverse effects related to psychotropic DDIs include increased or decreased effectiveness, CNS depression, neurotoxicity, QT prolongation, serotonin syndrome, and multiple adverse effects. Among these interactions, only 371 psychotropic DDIs were documented in all 3 references, 59 of which had "excellent" or "good" quality of evidence based on MM. The consistency of psychotropic DDI documentation across CP, MM, and LC is poor. DDI documentations need standards that would encourage consistency among drug information references. The list of the 59 DDIs may be useful in the assessment of psychotropic polypharmacy and highlighting DDI alerts in clinical practice. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

HLA class I molecules consistently present internal influenza epitopes.

PubMed

Wahl, Angela; Schafer, Fredda; Bardet, Wilfried; Buchli, Rico; Air, Gillian M; Hildebrand, William H

2009-01-13

Cytotoxic T lymphocytes (CTL) limit influenza virus replication and prevent morbidity and mortality upon recognition of HLA class I presented epitopes on the surface of virus infected cells, yet the number and origin of the viral epitopes that decorate the infected cell are unknown. To understand the presentation of influenza virus ligands by human MHC class I molecules, HLA-B*0702-presented viral peptides were directly identified following influenza infection. After transfection with soluble class I molecules, peptide ligands unique to infected cells were eluted from isolated MHC molecules and identified by comparative mass spectrometry (MS). Then CTL were gathered following infection with influenza and viral peptides were tested for immune recognition. We found that the class I molecule B*0702 presents 3-6 viral ligands following infection with different strains of influenza. Peptide ligands derived from the internal viral nucleoprotein (NP(418-426) and NP(473-481)) and from the internal viral polymerase subunit PB1 (PB1(329-337)) were presented by B*0702 following infection with each of 3 different influenza strains; ligands NP(418-426), NP(473-481), and PB1(329-337) derived from internal viral proteins were consistently revealed by class I HLA. In contrast, ligands derived from hemagglutinin (HA) and matrix protein (M1) were presented intermittently on a strain-by-strain basis. When tested for immune recognition, HLA-B*0702 transgenic mice responded to NP(418-426) and PB1(329-337) consistently and NP(473-481) intermittently while ligands from HA and M1 were not recognized. These data demonstrate an emerging pattern whereby class I HLA reveal a handful of internal viral ligands and whereby CTL recognize consistently presented influenza ligands.

HLA class I molecules consistently present internal influenza epitopes

PubMed Central

Wahl, Angela; Schafer, Fredda; Bardet, Wilfried; Buchli, Rico; Air, Gillian M.; Hildebrand, William H.

2009-01-01

Cytotoxic T lymphocytes (CTL) limit influenza virus replication and prevent morbidity and mortality upon recognition of HLA class I presented epitopes on the surface of virus infected cells, yet the number and origin of the viral epitopes that decorate the infected cell are unknown. To understand the presentation of influenza virus ligands by human MHC class I molecules, HLA-B*0702-presented viral peptides were directly identified following influenza infection. After transfection with soluble class I molecules, peptide ligands unique to infected cells were eluted from isolated MHC molecules and identified by comparative mass spectrometry (MS). Then CTL were gathered following infection with influenza and viral peptides were tested for immune recognition. We found that the class I molecule B*0702 presents 3–6 viral ligands following infection with different strains of influenza. Peptide ligands derived from the internal viral nucleoprotein (NP418–426 and NP473–481) and from the internal viral polymerase subunit PB1 (PB1329–337) were presented by B*0702 following infection with each of 3 different influenza strains; ligands NP418–426, NP473–481, and PB1329–337 derived from internal viral proteins were consistently revealed by class I HLA. In contrast, ligands derived from hemagglutinin (HA) and matrix protein (M1) were presented intermittently on a strain-by-strain basis. When tested for immune recognition, HLA-B*0702 transgenic mice responded to NP418–426 and PB1329–337 consistently and NP473–481 intermittently while ligands from HA and M1 were not recognized. These data demonstrate an emerging pattern whereby class I HLA reveal a handful of internal viral ligands and whereby CTL recognize consistently presented influenza ligands. PMID:19122146

AST: A Simplified 3-item Tool for Managing Alcohol Withdrawal.

PubMed

Holzman, Samuel B; Rastegar, Darius A

2016-01-01

This study compared the Glasgow Modified Alcohol Withdrawal Scale (GMAWS) and a newly devised 3-item "Anxiety Sweats Tremor" Scale (AST) to the Revised Clinical Institute Withdrawal Assessment Scale (CIWA-Ar)-the standard of care for symptom-triggered management of alcohol withdrawal syndrome. Our study took place over 2 separate 1-week observational periods, and included 332 serial evaluations from 85 unique patients. All study participants were treated per hospital protocol based on CIWA-Ar, with supplemental scoring initially by GMAWS and later by AST in tandem. Internal consistency, interitem correlation, and operational characteristics were explored. Median CIWA-Ar score across both phases was 6 (range 0-13), with a median GMAWS score of 2 (range 0-5) and an AST score of 3 (range 0-7). The internal consistency of CIWA-Ar and GMAWS were both poor, with Cronbach alpha scores of 0.46 (n = 156) and 0.41 (n = 156), respectively. The internal consistency of the AST scale was significantly better, with a Cronbach alpha of 0.68 (n = 176). AST identified individuals with CIWA-Ar ≥8 with an area under the receiver-operating characteristic curve of 0.83 (95% confidence interval 0.77-0.89), compared with 0.81 (95% confidence interval 0.74-0.88) for GMAWS. An AST score of ≥3 (out of a possible 9) predicted CIWA-Ar ≥8, with a sensitivity of 93% and a specificity of 63%, whereas the GMAWS had a sensitivity and specificity of 100% and 12%, respectively, based on previously defined cut-offs. A simple 3-item scale demonstrated good internal consistency and reliably identified individuals experiencing significant alcohol withdrawal. This scale needs to be tested in other settings and among patients with a broader spectrum of withdrawal severity.

Fulminant sepsis is a cardinal sign of HP-PRRSV in pigs

USDA-ARS?s Scientific Manuscript database

In 2006 a unique syndrome with high morbidity and mortality was recognized in growing pigs in China that became known as porcine high fever disease (PHFD). One consistent finding in affected pigs was the detection of porcine reproductive and respiratory syndrome virus (PRRSV) that had unique nsp2 ge...

The Quality Control of Data in a Clinical Database System—The Patient Identification Problem *

PubMed Central

Lai, J. Chi-Sang; Covvey, H.D.; Sevcik, K.C.; Wigle, E.D.

1981-01-01

Ensuring the accuracy of patient identification and the linkage of records with the appropriate patient owner is the first level of quality control of data in a clinical database system. Without a unique patient identifier, the fact that patient identity may be recorded at different places and times means that multiple identities may be associated with a given patient and new records associated with any of these identities. Even when a unique patient identifier is utilized, errors introduced in the data handling process can result in the same problems. The outcome is that the retrieval request for a given record may fail, or an erroneously identified record may be retrieved. We have studied each of the ways this fundamental problem occurs and propose a solution based on record linkage techniques to detect errors of this type. Specifically, we propose a patient identification scheme for the situation where no unique health identifier is available and detail a method to find patient records with erroneous identifiers.

The impact of cigarette pack shape, size and opening: evidence from tobacco company documents.

PubMed

Kotnowski, Kathy; Hammond, David

2013-09-01

To use tobacco industry documents on cigarette pack shape, size and openings to identify industry findings on associations with brand imagery, product attributes, consumer perceptions and behaviour. Internal tobacco industry research and marketing documents obtained through court disclosure contained in the Legacy Tobacco Documents Library were searched using keywords related to pack shapes, sizes and opening methods. The search identified 66 documents related to consumer research and marketing plans on pack shape, size and openings, drawn from 1973 to 2002. Industry research consistently found that packs that deviated from the traditional flip-top box projected impressions of 'modern', 'elegant' and 'unique' brand imagery. Alternative pack shape and openings were identified as an effective means to communicate product attributes, particularly with regard to premium quality and smooth taste. Consumer studies consistently found that pack shape, size and opening style influenced perceptions of reduced product harm, and were often used to communicate a 'lighter' product. Slim, rounded, oval and booklet packs were found to be particularly appealing among young adults, and several studies demonstrated increased purchase interest for tobacco products presented in novel packaging shape or opening. Evidence from consumer tracking reports and company presentations indicate that pack innovations in shape or opening method increased market share of brands. Consumer research by the tobacco industry between 1973 and 2002 found that variations in packaging shape, size and opening method could influence brand appeal and risk perceptions and increase cigarette sales. © 2013 Society for the Study of Addiction.

The Classroom Environment Questionnaire (CEQ): Development and preliminary structural validity.

PubMed

Lyons, Carissa; Brown, Ted; Bourke-Taylor, Helen

2018-04-16

Occupational therapists offer a unique perspective regarding the contribution of the environment to occupational performance. Therefore, a scale that measures the unique characteristics of the primary school classroom environment where children complete their daily schoolwork occupations is needed. The aim of this study was to develop and psychometrically evaluate a new teacher-report questionnaire that measures a number of environmental characteristics of primary school classrooms. Participants (N = 117) completed the Classroom Environment Questionnaire (CEQ), which utilises a 4-point Likert scale where teachers rate 51 environmental characteristics of their classroom. Teachers also rate the extent to which they believe the physical, social, temporal, institutional and cultural classroom environmental domains contribute to students' schoolwork performance using a 10-point scale. The structural validity of the CEQ was examined using principal component analysis (PCA). Inter-item correlations were examined using Pearson r correlations, while the internal consistency of the CEQ was assessed using Cronbach's alpha. PCA revealed the CEQ to be multidimensional, with 31 items loading onto nine viable factors, representing the unique nature of classroom environments. Based on the PCA results, 20 items were removed from the CEQ. Cronbach's alpha and correlation analysis indicated that most CEQ subsections had acceptable internal consistency (alpha range 0.70-0.82), with four subsections demonstrating a lower level of internal consistency (alpha range 0.55-0.69). Preliminary structural validity and internal consistency analysis findings confirm that the CEQ has potential to be a useful scale for professionals wishing to examine the unique characteristics of primary school classrooms that influence the occupational performance of students. Ongoing analyses will be undertaken to further explore the CEQ's validity and reliability. © 2018 Occupational Therapy Australia.

Functional Proteomics to Identify Moderators of CD8+ T Cell Function in Melanoma

DTIC Science & Technology

2015-05-01

identified 17 phage that selectively bind TIL rather than effector cells. However, none of these phage influenced CD8+ TIL expansion or function in vitro...Using a novel NextGeneration sequencing approach, we have further defined another 1,000,000 phage that selectively bind TIL , of which 100,000 are unique...Using the original approach outlined in the application, we identified a total of 17 unique phage that selectively bind CD8+ TIL but not effector or

21 CFR 801.45 - Devices that must be directly marked with a unique device identifier.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Devices that must be directly marked with a unique device identifier. 801.45 Section 801.45 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... previously marked under paragraph (a) of this section. (e) Exception to be noted in design history file. A...

Children's concepts of physical illness: a review and critique of the cognitive-developmental literature.

PubMed

Burbach, D J; Peterson, L

1986-01-01

Cognitive-developmental studies relevant to children's concepts of physical illness are reviewed and critiqued. Although numerous methodological weaknesses make firm conclusions difficult, most data appear to suggest that children's concepts of illness do evolve in a systematic and predictable sequence consistent with Piaget's theory of cognitive development. Methodological weaknesses identified include poor description of samples, assessment instruments, and procedures; lack of control over potential observer bias, expectancy effects, and other confounding variables; and minimal attention to reliability and validity issues. Increased methodological rigor and a further explication of the specific and unique ways in which children's concepts of illness develop over the course of cognitive development could substantially increase the value of these studies for professionals in pediatric health care settings.

An Empirical Typology of Social Networks and Its Association With Physical and Mental Health: A Study With Older Korean Immigrants

PubMed Central

Jang, Yuri; Lee, Beom S.; Ko, Jung Eun; Haley, William E.; Chiriboga, David A.

2015-01-01

Objectives. In the context of social convoy theory, the purposes of the study were (a) to identify an empirical typology of the social networks evident in older Korean immigrants and (b) to examine its association with self-rated health and depressive symptoms. Method. The sample consisted of 1,092 community-dwelling older Korean immigrants in Florida and New York. Latent class analyses were conducted to identify the optimal social network typology based on 8 indicators of interpersonal relationships and activities. Bivariate and multivariate analyses were conducted to examine how the identified social network typology was associated with self-rating of health and depressive symptoms. Results. Results from the latent class analysis identified 6 clusters as being most optimal, and they were named diverse, unmarried/diverse, married/coresidence, family focused, unmarried/restricted, and restricted. Memberships in the clusters of diverse and married/coresidence were significantly associated with more favorable ratings of health and lower levels of depressive symptoms. Discussion. Notably, no distinct network solely composed of friends was identified in the present sample of older immigrants; this may reflect the disruptions in social convoys caused by immigration. The findings of this study promote our understanding of the unique patterns of social connectedness in older immigrants. PMID:23887929

Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations.

PubMed

Swings, Toon; Weytjens, Bram; Schalck, Thomas; Bonte, Camille; Verstraeten, Natalie; Michiels, Jan; Marchal, Kathleen

2017-11-01

Efficient production of ethanol for use as a renewable fuel requires organisms with a high level of ethanol tolerance. However, this trait is complex and increased tolerance therefore requires mutations in multiple genes and pathways. Here, we use experimental evolution for a system-level analysis of adaptation of Escherichia coli to high ethanol stress. As adaptation to extreme stress often results in complex mutational data sets consisting of both causal and noncausal passenger mutations, identifying the true adaptive mutations in these settings is not trivial. Therefore, we developed a novel method named IAMBEE (Identification of Adaptive Mutations in Bacterial Evolution Experiments). IAMBEE exploits the temporal profile of the acquisition of mutations during evolution in combination with the functional implications of each mutation at the protein level. These data are mapped to a genome-wide interaction network to search for adaptive mutations at the level of pathways. The 16 evolved populations in our data set together harbored 2,286 mutated genes with 4,470 unique mutations. Analysis by IAMBEE significantly reduced this number and resulted in identification of 90 mutated genes and 345 unique mutations that are most likely to be adaptive. Moreover, IAMBEE not only enabled the identification of previously known pathways involved in ethanol tolerance, but also identified novel systems such as the AcrAB-TolC efflux pump and fatty acids biosynthesis and even allowed to gain insight into the temporal profile of adaptation to ethanol stress. Furthermore, this method offers a solid framework for identifying the molecular underpinnings of other complex traits as well. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Systems and methods for an extensible business application framework

NASA Technical Reports Server (NTRS)

Bell, David G. (Inventor); Crawford, Michael (Inventor)

2012-01-01

Method and systems for editing data from a query result include requesting a query result using a unique collection identifier for a collection of individual files and a unique identifier for a configuration file that specifies a data structure for the query result. A query result is generated that contains a plurality of fields as specified by the configuration file, by combining each of the individual files associated with a unique identifier for a collection of individual files. The query result data is displayed with a plurality of labels as specified in the configuration file. Edits can be performed by querying a collection of individual files using the configuration file, editing a portion of the query result, and transmitting only the edited information for storage back into a data repository.

A History and Informal Assessment of the "Slacker Astronomy" Podcast

ERIC Educational Resources Information Center

Price, Aaron; Gay, Pamela; Searle, Travis; Brissenden, Gina

2007-01-01

"Slacker Astronomy" is a weekly podcast that covers a recent astronomical news event or discovery. The show has a unique style consisting of irreverent, over-the-top humor combined with a healthy dose of hard science. According to our demographic analysis, the combination of this style and the unique podcasting distribution mechanism allows the…

What Is Different about Deaf Education? The Effects of Child and Family Factors on Educational Services

ERIC Educational Resources Information Center

Luft, Pamela

2017-01-01

Deaf education is characterized by several distinctive aspects, beginning with qualities unique to deaf and hard-of-hearing (DHH) children and their families. Consisting of approximately 1.2% of the special education K-12 population, educational and disability systems often struggle to meet the unique challenges that these children and their…

Reduced Plasmodium Parasite Burden Associates with CD38+ CD4+ T Cells Displaying Cytolytic Potential and Impaired IFN-γ Production

PubMed Central

Burel, Julie G.; Apte, Simon H.; Groves, Penny L.; Klein, Kerenaftali; McCarthy, James S.; Doolan, Denise L.

2016-01-01

Using a unique resource of samples from a controlled human malaria infection (CHMI) study, we identified a novel population of CD4+ T cells whose frequency in the peripheral blood was inversely correlated with parasite burden following P. falciparum infection. These CD4+ T cells expressed the multifunctional ectoenzyme CD38 and had unique features that distinguished them from other CD4+ T cells. Specifically, their phenotype was associated with proliferation, activation and cytotoxic potential as well as significantly impaired production of IFN-γ and other cytokines and reduced basal levels of activated STAT1. A CD38+ CD4+ T cell population with similar features was identified in healthy uninfected individuals, at lower frequency. CD38+ CD4+ T cells could be generated in vitro from CD38- CD4+ T cells after antigenic or mitogenic stimulation. This is the first report of a population of CD38+ CD4+ T cells with a cytotoxic phenotype and markedly impaired IFN-γ capacity in humans. The expansion of this CD38+ CD4+ T population following infection and its significant association with reduced blood-stage parasite burden is consistent with an important functional role for these cells in protective immunity to malaria in humans. Their ubiquitous presence in humans suggests that they may have a broad role in host-pathogen defense. Trial Registration ClinicalTrials.gov clinical trial numbers ACTRN12612000814875, ACTRN12613000565741 and ACTRN12613001040752 PMID:27662621

The transcriptional PPARβ/δ network in human macrophages defines a unique agonist-induced activation state

PubMed Central

Adhikary, Till; Wortmann, Annika; Schumann, Tim; Finkernagel, Florian; Lieber, Sonja; Roth, Katrin; Toth, Philipp M.; Diederich, Wibke E.; Nist, Andrea; Stiewe, Thorsten; Kleinesudeik, Lara; Reinartz, Silke; Müller-Brüsselbach, Sabine; Müller, Rolf

2015-01-01

Peroxisome proliferator-activated receptor β/δ (PPARβ/δ) is a lipid ligand-inducible transcription factor with established metabolic functions, whereas its anti-inflammatory function is poorly understood. To address this issue, we determined the global PPARβ/δ-regulated signaling network in human monocyte-derived macrophages. Besides cell type-independent, canonical target genes with metabolic and immune regulatory functions we identified a large number of inflammation-associated NFκB and STAT1 target genes that are repressed by agonists. Accordingly, PPARβ/δ agonists inhibited the expression of multiple pro-inflammatory mediators and induced an anti-inflammatory, IL-4-like morphological phenotype. Surprisingly, bioinformatic analyses also identified immune stimulatory effects. Consistent with this prediction, PPARβ/δ agonists enhanced macrophage survival under hypoxic stress and stimulated CD8+ T cell activation, concomitantly with the repression of immune suppressive target genes and their encoded products CD274 (PD-1 ligand), CD32B (inhibitory Fcγ receptor IIB) and indoleamine 2,3-dioxygenase 1 (IDO-1), as well as a diminished release of the immune suppressive IDO-1 metabolite kynurenine. Comparison with published data revealed a significant overlap of the PPARβ/δ transcriptome with coexpression modules characteristic of both anti-inflammatory and pro-inflammatory cytokines. Our findings indicate that PPARβ/δ agonists induce a unique macrophage activation state with strong anti-inflammatory but also specific immune stimulatory components, pointing to a context-dependent function of PPARβ/δ in immune regulation. PMID:25934804

Classical pathology of sympathetic ophthalmia presented in a unique case.

PubMed

Chen, Shida; Aronow, Mary E; Wang, Charles; Shen, Defen; Chan, Chi-Chao

2014-01-01

The ocular pathology of sympathetic ophthalmia is demonstrated in a 10 year-old boy who sustained a penetrating left globe injury and subsequently developed sympathetic ophthalmia in the right eye two months later. Two and a half weeks following extensive surgical repair of the left ruptured globe, he developed endophthalmitis and was treated with oral and topical fortified antibiotics. One month after the initial injury, a progressive corneal ulcer of the left eye led to perforation and the need for emergent corneal transplantation. The surgical specimen revealed fungus, Scedosporium dehoogii. The boy received systemic and topical anti-fungal therapy. Two months following the penetrating globe injury of the left eye, a granulomatous uveitis developed in the right eye. Sympathetic ophthalmia was suspected and the patient began treatment with topical and oral corticosteroids. Given the concern of vision loss secondary to sympathetic ophthalmia in the right eye, as well as poor vision and hypotony in the injured eye, the left eye was enucleated. Microscopically, granulomatous inflammation with giant cells was noted within a cyclitic membrane which filled the anterior and posterior chamber of the left globe. Other classic features including Dalen-Fuchs nodules were identified. Small, choroidal, ill-defined granulomas and relative sparing of the choriocapillaris were present. Molecular analysis did not identify evidence of remaining fungal infection. The pathology findings were consistent with previously described features of sympathetic ophthalmia. The present case is unique in that co-existing fungal infection may have potentiated the risk for developing sympathetic ophthalmia in the fellow eye.

Using global unique identifiers to link autism collections.

PubMed

Johnson, Stephen B; Whitney, Glen; McAuliffe, Matthew; Wang, Hailong; McCreedy, Evan; Rozenblit, Leon; Evans, Clark C

2010-01-01

To propose a centralized method for generating global unique identifiers to link collections of research data and specimens. The work is a collaboration between the Simons Foundation Autism Research Initiative and the National Database for Autism Research. The system is implemented as a web service: an investigator inputs identifying information about a participant into a client application and sends encrypted information to a server application, which returns a generated global unique identifier. The authors evaluated the system using a volume test of one million simulated individuals and a field test on 2000 families (over 8000 individual participants) in an autism study. Inverse probability of hash codes; rate of false identity of two individuals; rate of false split of single individual; percentage of subjects for which identifying information could be collected; percentage of hash codes generated successfully. Large-volume simulation generated no false splits or false identity. Field testing in the Simons Foundation Autism Research Initiative Simplex Collection produced identifiers for 96% of children in the study and 77% of parents. On average, four out of five hash codes per subject were generated perfectly (only one perfect hash is required for subsequent matching). The system must achieve balance among the competing goals of distinguishing individuals, collecting accurate information for matching, and protecting confidentiality. Considerable effort is required to obtain approval from institutional review boards, obtain consent from participants, and to achieve compliance from sites during a multicenter study. Generic unique identifiers have the potential to link collections of research data, augment the amount and types of data available for individuals, support detection of overlap between collections, and facilitate replication of research findings.

Comprehensive Proteomic Analysis of Human Milk-derived Extracellular Vesicles Unveils a Novel Functional Proteome Distinct from Other Milk Components.

PubMed

van Herwijnen, Martijn J C; Zonneveld, Marijke I; Goerdayal, Soenita; Nolte-'t Hoen, Esther N M; Garssen, Johan; Stahl, Bernd; Maarten Altelaar, A F; Redegeld, Frank A; Wauben, Marca H M

2016-11-01

Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins. Because of the difficulty in separating EV from other milk components, an in-depth analysis of the proteome of human milk-derived EV is lacking. In this study, an extensive LC-MS/MS proteomic analysis was performed of EV that had been purified from breast milk of seven individual donors using a recently established, optimized density-gradient-based EV isolation protocol. A total of 1963 proteins were identified in milk-derived EV, including EV-associated proteins like CD9, Annexin A5, and Flotillin-1, with a remarkable overlap between the different donors. Interestingly, 198 of the identified proteins are not present in the human EV database Vesiclepedia, indicating that milk-derived EV harbor proteins not yet identified in EV of different origin. Similarly, the proteome of milk-derived EV was compared with that of other milk components. For this, data from 38 published milk proteomic studies were combined in order to construct the total milk proteome, which consists of 2698 unique proteins. Remarkably, 633 proteins identified in milk-derived EV have not yet been identified in human milk to date. Interestingly, these novel proteins include proteins involved in regulation of cell growth and controlling inflammatory signaling pathways, suggesting that milk-derived EVs could support the newborn's developing gastrointestinal tract and immune system. Overall, this study provides an expansion of the whole milk proteome and illustrates that milk-derived EV are macromolecular components with a unique functional proteome. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Novel Angiogenic Domains: Use in Identifying Unique Transforming and Tumor Promoting Pathways in Human Breast Cancer

DTIC Science & Technology

2004-10-01

Cancer PRINCIPAL INVESTIGATOR: Thomas F. Deuel, M.D. CONTRACTING ORGANIZATION: The Scripps Research Institute...NUMBER Novel Angiogenic Domains: Use in Identifying Unique Transforming and Tumor Promoting Pathways in Human Breast Cancer 5b. GRANT NUMBER DAMD17...SUPPLEMENTARY NOTES 14. ABSTRACT Breast cancers in humans often grow slowly or even remain undetectable for long periods of time only to

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

Schuffenhauer, S.; Daumer-Haas, C.; Murken, J.

Karyotypes with an interstitial deletion and a marker chromosome formed from the deleted segment are rare. We identified such a rearrangement in a newborn infant, who presented with macrocephaly, asymmetric square skull, minor facial anomalies, omphalocele, inguinal hernias, hypospadias, and club feet. The karyotype 46,XY,del(5)(pter{r_arrow}p13::cen{r_arrow}qter)/47,XY,+dicr(5)(:p13{r_arrow}cen::p13{r_arrow}cen),del(5)(pter{r_arrow}p13::cen{r_arrow}qter) was identified by banding studies and FISH analysis in the peripheral lymphocytes. One breakpoint on the del(5) maps distal to GDNF, and FISH analysis using an {alpha}-satellite probe suggests that the proximal breakpoint maps within the centromere. The dicentric r(5) consists of two copies of the segment deleted in the del(5), resulting in trisomy ofmore » proximal 5p (5p13-cen). The phenotype of the propositus is compared with other trisomy 5p cases and possible mechanisms for the generation of this unique chromosomal rearrangement are discussed. 27 refs., 3 figs.« less

Resting-state fMRI correlations: From link-wise unreliability to whole brain stability.

PubMed

Pannunzi, Mario; Hindriks, Rikkert; Bettinardi, Ruggero G; Wenger, Elisabeth; Lisofsky, Nina; Martensson, Johan; Butler, Oisin; Filevich, Elisa; Becker, Maxi; Lochstet, Martyna; Kühn, Simone; Deco, Gustavo

2017-08-15

The functional architecture of spontaneous BOLD fluctuations has been characterized in detail by numerous studies, demonstrating its potential relevance as a biomarker. However, the systematic investigation of its consistency is still in its infancy. Here, we analyze within- and between-subject variability and test-retest reliability of resting-state functional connectivity (FC) in a unique data set comprising multiple fMRI scans (42) from 5 subjects, and 50 single scans from 50 subjects. We adopt a statistical framework that enables us to identify different sources of variability in FC. We show that the low reliability of single links can be significantly improved by using multiple scans per subject. Moreover, in contrast to earlier studies, we show that spatial heterogeneity in FC reliability is not significant. Finally, we demonstrate that despite the low reliability of individual links, the information carried by the whole-brain FC matrix is robust and can be used as a functional fingerprint to identify individual subjects from the population. Copyright © 2017 Elsevier Inc. All rights reserved.

The auditory brain-stem response to complex sounds: a potential biomarker for guiding treatment of psychosis.

PubMed

Tarasenko, Melissa A; Swerdlow, Neal R; Makeig, Scott; Braff, David L; Light, Gregory A

2014-01-01

Cognitive deficits limit psychosocial functioning in schizophrenia. For many patients, cognitive remediation approaches have yielded encouraging results. Nevertheless, therapeutic response is variable, and outcome studies consistently identify individuals who respond minimally to these interventions. Biomarkers that can assist in identifying patients likely to benefit from particular forms of cognitive remediation are needed. Here, we describe an event-related potential (ERP) biomarker - the auditory brain-stem response (ABR) to complex sounds (cABR) - that appears to be particularly well-suited for predicting response to at least one form of cognitive remediation that targets auditory information processing. Uniquely, the cABR quantifies the fidelity of sound encoded at the level of the brainstem and midbrain. This ERP biomarker has revealed auditory processing abnormalities in various neurodevelopmental disorders, correlates with functioning across several cognitive domains, and appears to be responsive to targeted auditory training. We present preliminary cABR data from 18 schizophrenia patients and propose further investigation of this biomarker for predicting and tracking response to cognitive interventions.

The Equilibrium Allele Frequency Distribution for a Population with Reproductive Skew

PubMed Central

Der, Ricky; Plotkin, Joshua B.

2014-01-01

We study the population genetics of two neutral alleles under reversible mutation in a model that features a skewed offspring distribution, called the Λ-Fleming–Viot process. We describe the shape of the equilibrium allele frequency distribution as a function of the model parameters. We show that the mutation rates can be uniquely identified from this equilibrium distribution, but the form of the offspring distribution cannot itself always be so identified. We introduce an estimator for the mutation rate that is consistent, independent of the form of reproductive skew. We also introduce a two-allele infinite-sites version of the Λ-Fleming–Viot process, and we use it to study how reproductive skew influences standing genetic diversity in a population. We derive asymptotic formulas for the expected number of segregating sites as a function of sample size and offspring distribution. We find that the Wright–Fisher model minimizes the equilibrium genetic diversity, for a given mutation rate and variance effective population size, compared to all other Λ-processes. PMID:24473932

Weather conditions associated with autumn migration by mule deer in Wyoming.

PubMed

Rittenhouse, Chadwick D; Mong, Tony W; Hart, Thomas

2015-01-01

Maintaining ecological integrity necessitates a proactive approach of identifying and acquiring lands to conserve unfragmented landscapes, as well as evaluating existing mitigation strategies to increase connectivity in fragmented landscapes. The increased use of highway underpasses and overpasses to restore connectivity for wildlife species offers clear conservation benefits, yet also presents a unique opportunity to understand how weather conditions may impact movement of wildlife species. We used remote camera observations (19,480) from an existing wildlife highway underpass in Wyoming and daily meteorological observations to quantify weather conditions associated with autumn migration of mule deer in 2009 and 2010. We identified minimal daily temperature and snow depth as proximate cues associated with mule deer migration to winter range. These weather cues were consistent across does and bucks, but differed slightly by year. Additionally, extreme early season snow depth or cold temperature events appear to be associated with onset of migration. This information will assist wildlife managers and transportation officials as they plan future projects to maintain and enhance migration routes for mule deer.

In Silico Prediction and In Vitro Characterization of Multifunctional Human RNase3

PubMed Central

Kuo, Ping-Hsueh; Chen, Chien-Jung; Chang, Hsiu-Hui; Fang, Shun-lung; Wu, Wei-Shuo; Lai, Yiu-Kay; Pai, Tun-Wen; Chang, Margaret Dah-Tsyr

2013-01-01

Human ribonucleases A (hRNaseA) superfamily consists of thirteen members with high-structure similarities but exhibits divergent physiological functions other than RNase activity. Evolution of hRNaseA superfamily has gained novel functions which may be preserved in a unique region or domain to account for additional molecular interactions. hRNase3 has multiple functions including ribonucleolytic, heparan sulfate (HS) binding, cellular binding, endocytic, lipid destabilization, cytotoxic, and antimicrobial activities. In this study, three putative multifunctional regions, 34RWRCK38 (HBR1), 75RSRFR79 (HBR2), and 101RPGRR105 (HBR3), of hRNase3 have been identified employing in silico sequence analysis and validated employing in vitro activity assays. A heparin binding peptide containing HBR1 is characterized to act as a key element associated with HS binding, cellular binding, and lipid binding activities. In this study, we provide novel insights to identify functional regions of hRNase3 that may have implications for all hRNaseA superfamily members. PMID:23484086

SPIRIT: A seamless phase I/II randomized design for immunotherapy trials.

PubMed

Guo, Beibei; Li, Daniel; Yuan, Ying

2018-06-07

Immunotherapy-treatments that enlist the immune system to battle tumors-has received widespread attention in cancer research. Due to its unique features and mechanisms for treating cancer, immunotherapy requires novel clinical trial designs. We propose a Bayesian seamless phase I/II randomized design for immunotherapy trials (SPIRIT) to find the optimal biological dose (OBD) defined in terms of the restricted mean survival time. We jointly model progression-free survival and the immune response. Progression-free survival is used as the primary endpoint to determine the OBD, and the immune response is used as an ancillary endpoint to quickly screen out futile doses. Toxicity is monitored throughout the trial. The design consists of two seamlessly connected stages. The first stage identifies a set of safe doses. The second stage adaptively randomizes patients to the safe doses identified and uses their progression-free survival and immune response to find the OBD. The simulation study shows that the SPIRIT has desirable operating characteristics and outperforms the conventional design. Copyright © 2018 John Wiley & Sons, Ltd.

High-Throughput Assay and Discovery of Small Molecules that Interrupt Malaria Transmission

PubMed Central

Plouffe, David M.; Wree, Melanie; Du, Alan Y.; Meister, Stephan; Li, Fengwu; Patra, Kailash; Lubar, Aristea; Okitsu, Shinji L.; Flannery, Erika L.; Kato, Nobutaka; Tanaseichuk, Olga; Comer, Eamon; Zhou, Bin; Kuhen, Kelli; Zhou, Yingyao; Leroy, Didier; Schreiber, Stuart L.; Scherer, Christina A.; Vinetz, Joseph; Winzeler, Elizabeth A.

2016-01-01

Summary Preventing transmission is an important element of malaria control. However, most of the current available methods to assay for malaria transmission blocking are relatively low throughput and cannot be applied to large chemical libraries. We have developed a high-throughput and cost-effective assay, the Saponin-lysis Sexual Stage Assay (SaLSSA), for identifying small molecules with transmission-blocking capacity. SaLSSA analysis of 13,983 unique compounds uncovered that >90% of well-characterized antimalarials, including endoperoxides and 4-aminoquinolines, as well as compounds active against asexual blood stages, lost most of their killing activity when parasites developed into metabolically quiescent stage V gametocytes. On the other hand, we identified compounds with consistent low nanomolar transmission-blocking activity, some of which showed cross-reactivity against asexual blood and liver stages. The data clearly emphasize substantial physiological differences between sexual and asexual parasites and provide a tool and starting points for the discovery and development of transmission-blocking drugs. PMID:26749441

High-resolution Spectroscopic Abundances of Red Giant Branch Stars in NGC 6681

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

O’Malley, Erin M.; Chaboyer, Brian; Knaizev, Alexei

We obtain high-resolution spectra of nine red giant branch stars in NGC 6681 and perform the first detailed abundance analysis of stars in this cluster. We confirm cluster membership for these stars based on consistent radial velocities of 214.5 ± 3.7 km s{sup −1} and find a mean [Fe/H] = −1.63 ± 0.07 dex and [ α /Fe] = 0.42 ± 0.11 dex. Additionally, we confirm the existence of a Na–O anti-correlation in NGC 6681 and identify two populations of stars with unique abundance trends. With the use of HST photometry from Sarajedini et al. and Piotto et al. wemore » are able to identify these two populations as discrete sequences in the cluster CMD. Although we cannot confirm the nature of the polluter stars responsible for the abundance differences in these populations, these results do help put constraints on possible polluter candidates.« less

Transancestral mapping and genetic load in systemic lupus erythematosus.

PubMed

Langefeld, Carl D; Ainsworth, Hannah C; Cunninghame Graham, Deborah S; Kelly, Jennifer A; Comeau, Mary E; Marion, Miranda C; Howard, Timothy D; Ramos, Paula S; Croker, Jennifer A; Morris, David L; Sandling, Johanna K; Almlöf, Jonas Carlsson; Acevedo-Vásquez, Eduardo M; Alarcón, Graciela S; Babini, Alejandra M; Baca, Vicente; Bengtsson, Anders A; Berbotto, Guillermo A; Bijl, Marc; Brown, Elizabeth E; Brunner, Hermine I; Cardiel, Mario H; Catoggio, Luis; Cervera, Ricard; Cucho-Venegas, Jorge M; Dahlqvist, Solbritt Rantapää; D'Alfonso, Sandra; Da Silva, Berta Martins; de la Rúa Figueroa, Iñigo; Doria, Andrea; Edberg, Jeffrey C; Endreffy, Emőke; Esquivel-Valerio, Jorge A; Fortin, Paul R; Freedman, Barry I; Frostegård, Johan; García, Mercedes A; de la Torre, Ignacio García; Gilkeson, Gary S; Gladman, Dafna D; Gunnarsson, Iva; Guthridge, Joel M; Huggins, Jennifer L; James, Judith A; Kallenberg, Cees G M; Kamen, Diane L; Karp, David R; Kaufman, Kenneth M; Kottyan, Leah C; Kovács, László; Laustrup, Helle; Lauwerys, Bernard R; Li, Quan-Zhen; Maradiaga-Ceceña, Marco A; Martín, Javier; McCune, Joseph M; McWilliams, David R; Merrill, Joan T; Miranda, Pedro; Moctezuma, José F; Nath, Swapan K; Niewold, Timothy B; Orozco, Lorena; Ortego-Centeno, Norberto; Petri, Michelle; Pineau, Christian A; Pons-Estel, Bernardo A; Pope, Janet; Raj, Prithvi; Ramsey-Goldman, Rosalind; Reveille, John D; Russell, Laurie P; Sabio, José M; Aguilar-Salinas, Carlos A; Scherbarth, Hugo R; Scorza, Raffaella; Seldin, Michael F; Sjöwall, Christopher; Svenungsson, Elisabet; Thompson, Susan D; Toloza, Sergio M A; Truedsson, Lennart; Tusié-Luna, Teresa; Vasconcelos, Carlos; Vilá, Luis M; Wallace, Daniel J; Weisman, Michael H; Wither, Joan E; Bhangale, Tushar; Oksenberg, Jorge R; Rioux, John D; Gregersen, Peter K; Syvänen, Ann-Christine; Rönnblom, Lars; Criswell, Lindsey A; Jacob, Chaim O; Sivils, Kathy L; Tsao, Betty P; Schanberg, Laura E; Behrens, Timothy W; Silverman, Earl D; Alarcón-Riquelme, Marta E; Kimberly, Robert P; Harley, John B; Wakeland, Edward K; Graham, Robert R; Gaffney, Patrick M; Vyse, Timothy J

2017-07-17

Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (∼50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 × 10 -8 ), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.

Usability evaluation of Laboratory and Radiology Information Systems integrated into a hospital information system.

PubMed

Nabovati, Ehsan; Vakili-Arki, Hasan; Eslami, Saeid; Khajouei, Reza

2014-04-01

This study was conducted to evaluate the usability of widely used laboratory and radiology information systems. Three usability experts independently evaluated the user interfaces of Laboratory and Radiology Information Systems using heuristic evaluation method. They applied Nielsen's heuristics to identify and classify usability problems and Nielsen's severity rating to judge their severity. Overall, 116 unique heuristic violations were identified as usability problems. In terms of severity, 67 % of problems were rated as major and catastrophic. Among 10 heuristics, "consistency and standards" was violated most frequently. Moreover, mean severity of problems concerning "error prevention" and "help and documentation" heuristics was higher than of the others. Despite widespread use of specific healthcare information systems, they suffer from usability problems. Improving the usability of systems by following existing design standards and principles from the early phased of system development life cycle is recommended. Especially, it is recommended that the designers design systems that inhibit the initiation of erroneous actions and provide sufficient guidance to users.

Characterization of a New HIV-1 CRF01_AE/ CRF07_BC recombinant virus in Tianjin, China.

PubMed

Zhou, Zhehua; Ma, Ping; Feng, Yi; Ou, Weidong; Qian, Jing; Gao, Liying; Zhang, Defa; Shao, Yiming; Wei, Min

2018-05-04

Human immunodeficiency virus (HIV) is notorious for its rapid evolving since its transmissions from money to human. Currently, HIV contains multiple subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs). Here, from an HIV-positive mother and her child in Tianjin, China, we identified a novel HIV-1 second-generation recombinant virus (TJ20170316 and TJ20170317) between CRF01_AE and CRF07_BC. Near full-length genomes were obtained from both samples, and they shared very close sequences, except some point mutations. Phylogenetic analyses of the near full-length genomes showed that they consist of CRF01_AE backbone and part CRF07_BC sequences. Recombinant Identification Program (RIP) and Simplot software identified four breakpoints in gag, pol, vif, tat genes in TJ20170316, totally different from other reported CRFs and URFs. The emergence of such URF in Tianjin, China, highlights the complexity of HIV-1 epidemic and more measures should be taken to prevent HIV transmissions.

Transancestral mapping and genetic load in systemic lupus erythematosus

PubMed Central

Langefeld, Carl D.; Ainsworth, Hannah C.; Graham, Deborah S. Cunninghame; Kelly, Jennifer A.; Comeau, Mary E.; Marion, Miranda C.; Howard, Timothy D.; Ramos, Paula S.; Croker, Jennifer A.; Morris, David L.; Sandling, Johanna K.; Almlöf, Jonas Carlsson; Acevedo-Vásquez, Eduardo M.; Alarcón, Graciela S.; Babini, Alejandra M.; Baca, Vicente; Bengtsson, Anders A.; Berbotto, Guillermo A.; Bijl, Marc; Brown, Elizabeth E.; Brunner, Hermine I.; Cardiel, Mario H.; Catoggio, Luis; Cervera, Ricard; Cucho-Venegas, Jorge M.; Dahlqvist, Solbritt Rantapää; D’Alfonso, Sandra; Da Silva, Berta Martins; de la Rúa Figueroa, Iñigo; Doria, Andrea; Edberg, Jeffrey C.; Endreffy, Emőke; Esquivel-Valerio, Jorge A.; Fortin, Paul R.; Freedman, Barry I.; Frostegård, Johan; García, Mercedes A.; de la Torre, Ignacio García; Gilkeson, Gary S.; Gladman, Dafna D.; Gunnarsson, Iva; Guthridge, Joel M.; Huggins, Jennifer L.; James, Judith A.; Kallenberg, Cees G. M.; Kamen, Diane L.; Karp, David R.; Kaufman, Kenneth M.; Kottyan, Leah C.; Kovács, László; Laustrup, Helle; Lauwerys, Bernard R.; Li, Quan-Zhen; Maradiaga-Ceceña, Marco A.; Martín, Javier; McCune, Joseph M.; McWilliams, David R.; Merrill, Joan T.; Miranda, Pedro; Moctezuma, José F.; Nath, Swapan K.; Niewold, Timothy B.; Orozco, Lorena; Ortego-Centeno, Norberto; Petri, Michelle; Pineau, Christian A.; Pons-Estel, Bernardo A.; Pope, Janet; Raj, Prithvi; Ramsey-Goldman, Rosalind; Reveille, John D.; Russell, Laurie P.; Sabio, José M.; Aguilar-Salinas, Carlos A.; Scherbarth, Hugo R.; Scorza, Raffaella; Seldin, Michael F.; Sjöwall, Christopher; Svenungsson, Elisabet; Thompson, Susan D.; Toloza, Sergio M. A.; Truedsson, Lennart; Tusié-Luna, Teresa; Vasconcelos, Carlos; Vilá, Luis M.; Wallace, Daniel J.; Weisman, Michael H.; Wither, Joan E.; Bhangale, Tushar; Oksenberg, Jorge R.; Rioux, John D.; Gregersen, Peter K.; Syvänen, Ann-Christine; Rönnblom, Lars; Criswell, Lindsey A.; Jacob, Chaim O.; Sivils, Kathy L.; Tsao, Betty P.; Schanberg, Laura E.; Behrens, Timothy W.; Silverman, Earl D.; Alarcón-Riquelme, Marta E.; Kimberly, Robert P.; Harley, John B.; Wakeland, Edward K.; Graham, Robert R.; Gaffney, Patrick M.; Vyse, Timothy J.

2017-01-01

Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (∼50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 × 10−8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE. PMID:28714469

Development of the Functional Flow Block Diagram for the J-2X Rocket Engine System

NASA Technical Reports Server (NTRS)

White, Thomas; Stoller, Sandra L.; Greene, WIlliam D.; Christenson, Rick L.; Bowen, Barry C.

2007-01-01

The J-2X program calls for the upgrade of the Apollo-era Rocketdyne J-2 engine to higher power levels, using new materials and manufacturing techniques, and with more restrictive safety and reliability requirements than prior human-rated engines in NASA history. Such requirements demand a comprehensive systems engineering effort to ensure success. Pratt & Whitney Rocketdyne system engineers performed a functional analysis of the engine to establish the functional architecture. J-2X functions were captured in six major operational blocks. Each block was divided into sub-blocks or states. In each sub-block, functions necessary to perform each state were determined. A functional engine schematic consistent with the fidelity of the system model was defined for this analysis. The blocks, sub-blocks, and functions were sequentially numbered to differentiate the states in which the function were performed and to indicate the sequence of events. The Engine System was functionally partitioned, to provide separate and unique functional operators. Establishing unique functional operators as work output of the System Architecture process is novel in Liquid Propulsion Engine design. Each functional operator was described such that its unique functionality was identified. The decomposed functions were then allocated to the functional operators both of which were the inputs to the subsystem or component performance specifications. PWR also used a novel approach to identify and map the engine functional requirements to customer-specified functions. The final result was a comprehensive Functional Flow Block Diagram (FFBD) for the J-2X Engine System, decomposed to the component level and mapped to all functional requirements. This FFBD greatly facilitates component specification development, providing a well-defined trade space for functional trades at the subsystem and component level. It also provides a framework for function-based failure modes and effects analysis (FMEA), and a rigorous baseline for the functional architecture.

Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change.

PubMed

Maguire, Kaitlin C; Shinneman, Douglas J; Potter, Kevin M; Hipkins, Valerie D

2018-03-14

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change

USGS Publications Warehouse

Maguire, Kaitlin C.; Shinneman, Douglas; Potter, Kevin M.; Hipkins, Valerie D.

2018-01-01

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

Shared and Unique Risk Factors Underlying Mathematical Disability and Reading and Spelling Disability.

PubMed

Slot, Esther M; van Viersen, Sietske; de Bree, Elise H; Kroesbergen, Evelyn H

2016-01-01

High comorbidity rates have been reported between mathematical learning disabilities (MD) and reading and spelling disabilities (RSD). Research has identified skills related to math, such as number sense (NS) and visuospatial working memory (visuospatial WM), as well as to literacy, such as phonological awareness (PA), rapid automatized naming (RAN) and verbal short-term memory (Verbal STM). In order to explain the high comorbidity rates between MD and RSD, 7-11-year-old children were assessed on a range of cognitive abilities related to literacy (PA, RAN, Verbal STM) and mathematical ability (visuospatial WM, NS). The group of children consisted of typically developing (TD) children (n = 32), children with MD (n = 26), children with RSD (n = 29), and combined MD and RSD (n = 43). It was hypothesized that, in line with the multiple deficit view on learning disorders, at least one unique predictor for both MD and RSD and a possible shared cognitive risk factor would be found to account for the comorbidity between the symptom dimensions literacy and math. Secondly, our hypotheses were that (a) a probabilistic multi-factorial risk factor model would provide a better fit to the data than a deterministic single risk factor model and (b) that a shared risk factor model would provide a better fit than the specific multi-factorial model. All our hypotheses were confirmed. NS and visuospatial WM were identified as unique cognitive predictors for MD, whereas PA and RAN were both associated with RSD. Also, a shared risk factor model with PA as a cognitive predictor for both RSD and MD fitted the data best, indicating that MD and RSD might co-occur due to a shared underlying deficit in phonological processing. Possible explanations are discussed in the context of sample selection and composition. This study shows that different cognitive factors play a role in mathematics and literacy, and that a phonological processing deficit might play a role in the occurrence of MD and RSD.

Unique risk and protective factors for partner aggression in a large scale air force survey.

PubMed

Slep, Amy M Smith; Foran, Heather M; Heyman, Richard E; Snarr, Jeffery D

2010-08-01

The objective of this study is to examine risk factors of physical aggression against a partner in a large representative Active Duty Air Force sample. A stratified sample of 128,950 United States Active Duty members were invited to participate in an Air Force-wide anonymous online survey across 82 bases. The final sample (N = 52,780) was weighted to be representative of the United States Air Force. Backward stepwise regression analyses were conducted to identify unique predictors of partner physical aggression perpetration within and across different ecological levels (individual, family, organization, and community levels). Relationship satisfaction, alcohol problems, financial stress, and number of years in the military were identified as unique predictors of men's and women's perpetration of violence against their partner across ecological levels. Parental status, support from neighbors, personal coping, and support from formal agencies also uniquely predicted men's but not women's perpetration of violence across ecological levels. This study identified specific risk factors of partner violence that may be targeted by prevention and intervention efforts aimed at different levels of impact (e.g., family interventions, community-wide programs).

Thermal imaging as a biometrics approach to facial signature authentication.

PubMed

Guzman, A M; Goryawala, M; Wang, Jin; Barreto, A; Andrian, J; Rishe, N; Adjouadi, M

2013-01-01

A new thermal imaging framework with unique feature extraction and similarity measurements for face recognition is presented. The research premise is to design specialized algorithms that would extract vasculature information, create a thermal facial signature and identify the individual. The proposed algorithm is fully integrated and consolidates the critical steps of feature extraction through the use of morphological operators, registration using the Linear Image Registration Tool and matching through unique similarity measures designed for this task. The novel approach at developing a thermal signature template using four images taken at various instants of time ensured that unforeseen changes in the vasculature over time did not affect the biometric matching process as the authentication process relied only on consistent thermal features. Thirteen subjects were used for testing the developed technique on an in-house thermal imaging system. The matching using the similarity measures showed an average accuracy of 88.46% for skeletonized signatures and 90.39% for anisotropically diffused signatures. The highly accurate results obtained in the matching process clearly demonstrate the ability of the thermal infrared system to extend in application to other thermal imaging based systems. Empirical results applying this approach to an existing database of thermal images proves this assertion.

Community Reintegration Problems Among Veterans and Active Duty Service Members With Traumatic Brain Injury.

PubMed

McGarity, Suzanne; Barnett, Scott D; Lamberty, Greg; Kretzmer, Tracy; Powell-Cope, Gail; Patel, Nitin; Nakase-Richardson, Risa

To examine community reintegration problems among Veterans and military service members with mild or moderate/severe traumatic brain injury (TBI) at 1 year postinjury and to identify unique predictors that may contribute to these difficulties. VA Polytrauma Rehabilitation Centers. Participants were 154 inpatients enrolled in the VA TBI Model Systems Program with available injury severity data (mild = 28.6%; moderate/severe = 71.4%) and 1-year postinjury outcome data. Prospective, longitudinal cohort. Community reintegration outcomes included independent driving, employability, and general community participation. Additional measures assessed depression, posttraumatic stress, and cognitive and motor functioning. In the mild TBI (mTBI) group, posttraumatic stress disorder and depressive symptoms were associated with lower levels of various community reintegration outcomes. In the moderate/severe TBI group, cognition and motor skills were significantly associated with lower levels of community participation, independent driving, and employability. Community reintegration is problematic for Veterans and active duty service members with a history of TBI. Unique comorbidities across injury severity groups inhibit full reintegration into the community. These findings highlight the ongoing rehabilitation needs of persons with TBI, specifically evidence-based mental healthcare, in comprehensive rehabilitation programs consistent with a chronic disease management model.

Children's loneliness, sense of coherence, family climate, and hope: developmental risk and protective factors.

PubMed

Sharabi, Adi; Levi, Uzi; Margalit, Malka

2012-01-01

The study examined the contributions of individual and familial variables for the prediction of loneliness as a developmental risk and the sense of coherence as a protective factor. The sample consisted of 287 children from grades 5-6. Their loneliness, sense of coherence, hope, effort, and family climate were assessed. Separate hierarchical multiple regression analyses revealed that family cohesion and children's hope contributed to the explanation of the risk and protective outcomes. Yet, the contribution of the family adaptability was not significant. Cluster analysis of the family climate dimensions (i.e., cohesion and adaptability) was performed to clarify the interactive roles of family adaptability together with family cohesion. The authors identified 4 separate family profiles: Children in the 2 cohesive families' clusters (Cohesive Structured Families and Cohesive Adaptable Families) reported the lowest levels of loneliness and the highest levels of personal strengths. Children within rigid and noncohesive family cluster reported the highest levels of loneliness and the lowest levels of children's sense of coherence. The unique role of the family flexibility within nonsupportive family systems was demonstrated. The results further clarified the unique profiles' characteristics of the different family clusters and their adjustment indexes in terms of loneliness and personal strengths.

Female streetwalkers' perspectives on migration and HIV/STI risks in a changing economic and social environment: a qualitative study in Shanghai, China.

PubMed

Huang, Z Jennifer; Hu, Dier; Chang, Ruth; Zaccaro, Heather; Iguchi, Martin; Zheng, Huang; He, Na

2015-01-01

China's 30-year economic boom has created a unique social and economic market for commercial sex, as well as for a workforce of migrant women from rural China. This qualitative study explores the impact of the rapidly changing social and economic environment on migration patterns, knowledge of sexually transmitted infections (STIs), STI risk behaviours and health beliefs among female streetwalkers in Shanghai. Qualitative data were collected in 2010 through semi-structured in-depth interviews with 16 streetwalkers to characterise their migration passages, sexual health and behaviours, and peer networks. Many streetwalkers reported histories of childhood impoverishment, of family or partner violence or trauma, of migration consistent with the timeline and routes of economic development and of a scarcity in health, social or economic support. Their knowledge of the prevention and treatment of HIV and STIs was limited. They had little bargaining power on condom use and the majority resorted to vaginal douching and self-management with antibiotics as preventative measures. The study identifies streetwalkers' perspectives on the changing environment, their options and actions and, finally, HIV/STI risks that were unique to this hidden population.

Disclosure of Positive BRCA1/2-Mutation Status in Young Couples: The Journey From Uncertainty to Bonding Through Partner Support

PubMed Central

Hoskins, Lindsey M.; Roy, Kevin; Peters, June A.; Loud, Jennifer T.; Greene, Mark H.

2011-01-01

BRCA1/2-positive women who learn their mutation status early in the life-course face unique challenges related to navigating the tasks of young adulthood. Using qualitative methods and grounded theory, the authors analyzed in-depth interviews with 11 women aged 26 to 35 who learned their mutation status before marriage. Their narratives illustrate the complexity of relationship formation, and highlight the potential for relationship-bonding and intimacy-building in the course of sharing mutation information. Disclosing BRCA mutation status to dating partners is often preceded by feelings of fear and anxiety, yet many participants reported that doing so has positive effects on relationships. Partners’ abilities to respond with interest, empathy, and affection are associated with in creased future intimacy, consistent with generally accepted principles within the family/couple systems field. Individual cancer risk perception and familial cancer experiences may affect the disclosure experience, which can be understood via Attachment Theory. Our findings provide clinical insight, identify new areas for research, and suggest ways to assist this unique population in their adjustment to being BRCA mutation-positive. PMID:25132793

Toward a national fuels mapping strategy: Lessons from selected mapping programs

USGS Publications Warehouse

Loveland, Thomas R.

2001-01-01

The establishment of a robust national fuels mapping program must be based on pertinent lessons from relevant national mapping programs. Many large-area mapping programs are under way in numerous Federal agencies. Each of these programs follows unique strategies to achieve mapping goals and objectives. Implementation approaches range from highly centralized programs that use tightly integrated standards and dedicated staff, to dispersed programs that permit considerable flexibility. One model facilitates national consistency, while the other allows accommodation of locally relevant conditions and issues. An examination of the programmatic strategies of four national vegetation and land cover mapping initiatives can identify the unique approaches, accomplishments, and lessons of each that should be considered in the design of a national fuel mapping program. The first three programs are the U.S. Geological Survey Gap Analysis Program, the U.S. Geological Survey National Land Cover Characterization Program, and the U.S. Fish and Wildlife Survey National Wetlands Inventory. A fourth program, the interagency Multiresolution Land Characterization Program, offers insights in the use of partnerships to accomplish mapping goals. Collectively, the programs provide lessons, guiding principles, and other basic concepts that can be used to design a successful national fuels mapping initiative.

A Recessive Contiguous Gene Deletion of Chromosome 2p16 Associated with Cystinuria and a Mitochondrial Disease

PubMed Central

Parvari, Ruti; Brodyansky, Irena; Elpeleg, Orly; Moses, Shimon; Landau, Daniel; Hershkovitz, Eli

2001-01-01

Deletions ranging from 100 Kb to 1 Mb—too small to be detected under the microscope—may still involve dozens of genes, thus causing microdeletion syndromes. The vast majority of these syndromes are caused by haploinsufficiency of one or several genes and are transmitted as dominant traits. We identified seven patients originating from an extended family and presenting with a unique syndrome, inherited in a recessive mode, consisting of cystinuria, neonatal seizures, hypotonia, severe somatic and developmental delay, facial dysmorphism, and lactic acidemia. Reduced activity of all the respiratory chain enzymatic complexes that are encoded in the mitochondria was found in muscle biopsy specimens of the patients examined. The molecular basis of this disorder is a homozygous deletion of 179,311 bp on chromosome 2p16, which includes the type I cystinuria gene (SLC3A1), the protein phosphatase 2Cβ gene (PP2Cβ), an unidentified gene (KIAA0436), and several expressed sequence tags. The extent of the deletion suggests that this unique syndrome is related to the complete absence of these genes’ products, one of which may be essential for the synthesis of mitochondrial encoded proteins. PMID:11524703

A recessive contiguous gene deletion of chromosome 2p16 associated with cystinuria and a mitochondrial disease.

PubMed

Parvari, R; Brodyansky, I; Elpeleg, O; Moses, S; Landau, D; Hershkovitz, E

2001-10-01

Deletions ranging from 100 Kb to 1 Mb--too small to be detected under the microscope--may still involve dozens of genes, thus causing microdeletion syndromes. The vast majority of these syndromes are caused by haploinsufficiency of one or several genes and are transmitted as dominant traits. We identified seven patients originating from an extended family and presenting with a unique syndrome, inherited in a recessive mode, consisting of cystinuria, neonatal seizures, hypotonia, severe somatic and developmental delay, facial dysmorphism, and lactic acidemia. Reduced activity of all the respiratory chain enzymatic complexes that are encoded in the mitochondria was found in muscle biopsy specimens of the patients examined. The molecular basis of this disorder is a homozygous deletion of 179,311 bp on chromosome 2p16, which includes the type I cystinuria gene (SLC3A1), the protein phosphatase 2Cbeta gene (PP2Cbeta), an unidentified gene (KIAA0436), and several expressed sequence tags. The extent of the deletion suggests that this unique syndrome is related to the complete absence of these genes' products, one of which may be essential for the synthesis of mitochondrial encoded proteins.

Challenging the Metallothionein (MT) Gene of Biomphalaria glabrata: Unexpected Response Patterns Due to Cadmium Exposure and Temperature Stress.

PubMed

Niederwanger, Michael; Dvorak, Martin; Schnegg, Raimund; Pedrini-Martha, Veronika; Bacher, Katharina; Bidoli, Massimo; Dallinger, Reinhard

2017-08-11

Metallothioneins (MTs) are low-molecular-mass, cysteine-rich, metal binding proteins. In most animal species, they are involved in metal homeostasis and detoxification, and provide protection from oxidative stress. Gastropod MTs are highly diversified, exhibiting unique features and adaptations like metal specificity and multiplications of their metal binding domains. Here, we show that the MT gene of Biomphalaria glabrata , one of the largest MT genes identified so far, is composed in a unique way. The encoding for an MT protein has a three-domain structure and a C-terminal, Cys-rich extension. Using a bioinformatic approach involving structural and in silico analysis of putative transcription factor binding sites (TFBs), we found that this MT gene consists of five exons and four introns. It exhibits a regulatory promoter region containing three metal-responsive elements (MREs) and several TFBs with putative involvement in environmental stress response, and regulation of gene expression. Quantitative real-time polymerase chain reaction (qRT-PCR) data indicate that the MT gene is not inducible by cadmium (Cd) nor by temperature challenges (heat and cold), despite significant Cd uptake within the midgut gland and the high Cd tolerance of metal-exposed snails.

Challenging the Metallothionein (MT) Gene of Biomphalaria glabrata: Unexpected Response Patterns Due to Cadmium Exposure and Temperature Stress

PubMed Central

Dvorak, Martin; Schnegg, Raimund; Pedrini-Martha, Veronika; Bacher, Katharina; Bidoli, Massimo; Dallinger, Reinhard

2017-01-01

Metallothioneins (MTs) are low-molecular-mass, cysteine-rich, metal binding proteins. In most animal species, they are involved in metal homeostasis and detoxification, and provide protection from oxidative stress. Gastropod MTs are highly diversified, exhibiting unique features and adaptations like metal specificity and multiplications of their metal binding domains. Here, we show that the MT gene of Biomphalaria glabrata, one of the largest MT genes identified so far, is composed in a unique way. The encoding for an MT protein has a three-domain structure and a C-terminal, Cys-rich extension. Using a bioinformatic approach involving structural and in silico analysis of putative transcription factor binding sites (TFBs), we found that this MT gene consists of five exons and four introns. It exhibits a regulatory promoter region containing three metal-responsive elements (MREs) and several TFBs with putative involvement in environmental stress response, and regulation of gene expression. Quantitative real-time polymerase chain reaction (qRT-PCR) data indicate that the MT gene is not inducible by cadmium (Cd) nor by temperature challenges (heat and cold), despite significant Cd uptake within the midgut gland and the high Cd tolerance of metal-exposed snails. PMID:28800079

Dealing with an Unconventional Genetic Code in  Mitochondria: The Biogenesis and Pathogenic  Defects of the 5-Formylcytosine Modification in  Mitochondrial tRNAMet.

PubMed

Van Haute, Lindsey; Powell, Christopher A; Minczuk, Michal

2017-03-02

Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt-tRNAMet) also recognises AUA during translation initiation and elongation. Post-transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5-formylcytosine (f5C) modification of position 34 in mt-tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f5C have been identified only recently. The first step of the f5C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f5C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA modification and its involvement in human disease.

Minimum probe length for unique identification of all open reading frames in a microbial genome

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

Sokhansanj, B A; Ng, J; Fitch, J P

2000-03-05

In this paper, we determine the minimum hybridization probe length to uniquely identify at least 95% of the open reading frame (ORF) in an organism. We analyze the whole genome sequences of 17 species, 11 bacteria, 4 archaea, and 2 eukaryotes. We also present a mathematical model for minimum probe length based on assuming that all ORFs are random, of constant length, and contain an equal distribution of bases. The model accurately predicts the minimum probe length for all species, but it incorrectly predicts that all ORFs may be uniquely identified. However, a probe length of just 9 bases ismore » adequate to identify over 95% of the ORFs for all 15 prokaryotic species we studied. Using a minimum probe length, while accepting that some ORFs may not be identified and that data will be lost due to hybridization error, may result in significant savings in microarray and oligonucleotide probe design.« less

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

MicroRNA profiling of human kidney cancer subtypes.

PubMed

Petillo, David; Kort, Eric J; Anema, John; Furge, Kyle A; Yang, Ximing J; Teh, Bin Tean

2009-07-01

Although the functions of most of the identified microRNAs (miRNAs) have yet to be determined, their use as potential biomarkers has been considered in several human diseases and cancers. In order to understand their role in renal tumorigenesis, we screened the expression levels of miRNAs in four subtypes of human renal neoplasms: clear cell, papillary, and chromophobe renal cell carcinomas (RCC) as well as benign renal oncocytomas. We found a unique miRNA signature for each subtype of renal tumor. Furthermore, we identified unique patterns of miRNA expression distinguishing clear cell RCC cases with favorable vs. unfavorable outcome. Specifically, we documented the overexpression of miRs 424 and 203 in clear cell RCC relative to papillary RCC, as well as the inversion of expression of miR-203 in the benign oncocytomas (where it is underexpressed relative to normal kidney) as compared to the malignant chromophobe RCC (where it is overexpressed relative to normal kidney). Our results further suggest that overexpression of S-has-miR-32 is associated with poor outcome. While previous studies have identified unique miRNA expression pattern distinguishing tumors from different anatomical locations, here we extend this principle to demonstrate the utility of miRNA expression profiling to identify a signature unique to various tumor subtypes at a single anatomic locus.

HowTo - Easy use of global unique identifier

NASA Astrophysics Data System (ADS)

Czerniak, A.; Fleischer, D.; Schirnick, C.

2013-12-01

The GEOMAR sample- and core repository covers several thousands of samples and cores and was collected over the last decades. In the actual project, we bring this collection up to the new generation and tag every sample and core with a unique identifier, in our case the International Geo Sample Number (ISGN). This work is done with our digital Ink and hand writing recognition implementation. The Smart Pen technology was save time and resources to record the information on every sample or core. In the procedure of recording, there are several steps systematical are done: 1. Getting all information about the core or sample, such as cruise number, responsible person and so on. 2. Tag with unique identifiers, in our case a QR-Code. 3. Wrote down the location of sample or core. After transmitting the information from Smart Pen, actually via USB but wireless is a choice too, into our server infrastructure the link to other information began. As it linked in our Virtual Research Environment (VRE) with the unique identifier (ISGN) sample or core can be located and the QR-Code was simply linked back from core or sample to ISGN with additional scientific information. On the QR-Code all important information are on it and it was simple to produce thousand of it.

Conditional clustering of temporal expression profiles

PubMed Central

Wang, Ling; Montano, Monty; Rarick, Matt; Sebastiani, Paola

2008-01-01

Background Many microarray experiments produce temporal profiles in different biological conditions but common cluster techniques are not able to analyze the data conditional on the biological conditions. Results This article presents a novel technique to cluster data from time course microarray experiments performed across several experimental conditions. Our algorithm uses polynomial models to describe the gene expression patterns over time, a full Bayesian approach with proper conjugate priors to make the algorithm invariant to linear transformations, and an iterative procedure to identify genes that have a common temporal expression profile across two or more experimental conditions, and genes that have a unique temporal profile in a specific condition. Conclusion We use simulated data to evaluate the effectiveness of this new algorithm in finding the correct number of clusters and in identifying genes with common and unique profiles. We also use the algorithm to characterize the response of human T cells to stimulations of antigen-receptor signaling gene expression temporal profiles measured in six different biological conditions and we identify common and unique genes. These studies suggest that the methodology proposed here is useful in identifying and distinguishing uniquely stimulated genes from commonly stimulated genes in response to variable stimuli. Software for using this clustering method is available from the project home page. PMID:18334028

The Selective Mutism Questionnaire: Measurement Structure and Validity

PubMed Central

Letamendi, Andrea M.; Chavira, Denise A.; Hitchcock, Carla A.; Roesch, Scott C.; Shipon-Blum, Elisa; Stein, Murray B.; Roesch, Scott C.

2010-01-01

Objective To evaluate the factor structure, reliability, and validity of the 17-item Selective Mutism Questionnaire. Method Diagnostic interviews were administered via telephone to 102 parents of children identified with selective mutism (SM) and 43 parents of children without SM from varying U.S. geographic regions. Children were between the ages of 3 and 11 inclusive and comprised 58% girls and 42% boys. SM diagnoses were determined using the Anxiety Disorders Interview Schedule for Children - Parent Version (ADIS-C/P); SM severity was assessed using the 17-item Selective Mutism Questionnaire (SMQ); and behavioral and affective symptoms were assessed using the Child Behavior Checklist (CBCL). An exploratory factor analysis (EFA) was conducted to investigate the dimensionality of the SMQ and a modified parallel analysis procedure was used to confirm EFA results. Internal consistency, construct validity, and incremental validity were also examined. Results The EFA yielded a 13-item solution consisting of three factors: a) Social Situations Outside of School, b) School Situations, and c) Home and Family Situations. Internal consistency of SMQ factors and total scale ranged from moderate to high. Convergent and incremental validity were also well supported. Conclusions Measure structure findings are consistent with the 3-factor solution found in a previous psychometric evaluation of the SMQ. Results also suggest that the SMQ provides useful and unique information in the prediction of SM phenomenon beyond other child anxiety measures. PMID:18698268

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome

PubMed Central

2011-01-01

Background Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly. PMID:21554714

Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

PubMed

Ragupathy, Raja; Rathinavelu, Rajkumar; Cloutier, Sylvie

2011-05-09

Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

PubMed Central

Oakes, Theres; Heather, James M.; Best, Katharine; Byng-Maddick, Rachel; Husovsky, Connor; Ismail, Mazlina; Joshi, Kroopa; Maxwell, Gavin; Noursadeghi, Mahdad; Riddell, Natalie; Ruehl, Tabea; Turner, Carolin T.; Uddin, Imran; Chain, Benny

2017-01-01

The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3′ end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts. PMID:29075258

SEM/EDS and optical microscopy analyses of microplastics in ocean trawl and fish guts.

PubMed

Wang, Zhong-Min; Wagner, Jeff; Ghosal, Sutapa; Bedi, Gagandeep; Wall, Stephen

2017-12-15

Microplastic particles from Atlantic and Pacific Ocean trawls, lab-fed fish guts and ocean fish guts have been characterized using optical microscopy and SEM/EDS in terms of size, morphology, and chemistry. We assessed whether these measurements could serve as a rapid screening process for subsequent identification of the likely microplastic candidates by micro-spectroscopy. Optical microscopy enabled morphological classification of the types of particles or fibers present in the sample, as well as the quantification of particle size ranges and fiber lengths. SEM/EDS analysis was used to rule out non-plastic particles and screen the prepared samples for potential microplastic, based on their element signatures and surface characteristics. Chlorinated plastics such as polyvinyl chloride (PVC) could be easily identified with SEM/EDS due to their unique elemental signatures including chlorine, as could mineral species that are falsely identified as plastics by optical microscopy. Particle morphology determined by optical microscopy and SEM suggests the fish ingested particles contained both degradation fragments from larger plastic pieces and also manufactured microplastics. SEM images of microplastic particle surfaces revealed characteristic cracks consistent with environmental exposure, as well as pigment particles consistent with manufactured materials. Most of the microplastic surfaces in the fish guts and ocean trawls were covered with biofilms, radiolarians, and crustaceans. Many of the fish stomachs contained micro-shell pieces which visually resembled microplastics. Copyright © 2017 Elsevier B.V. All rights reserved.

A Meta-analysis of Cerebellar Contributions to Higher Cognition from PET and fMRI studies

PubMed Central

Keren-Happuch, E; Chen, Shen-Hsing Annabel; Ho, Moon-Ho Ringo; Desmond, John E.

2013-01-01

A growing interest in cerebellar function and its involvement in higher cognition have prompted much research in recent years. Cerebellar presence in a wide range of cognitive functions examined within an increasing body of neuroimaging literature has been observed. We applied a meta-analytic approach, which employed the activation likelihood estimate method, to consolidate results of cerebellar involvement accumulated in different cognitive tasks of interest and systematically identified similarities among the studies. The current analysis included 88 neuroimaging studies demonstrating cerebellar activations in higher cognitive domains involving emotion, executive function, language, music, timing and working memory. While largely consistent with a prior meta-analysis by Stoodley and Schmahmann (2009), our results extended their findings to include music and timing domains to provide further insights into cerebellar involvement and elucidate its role in higher cognition. In addition, we conducted inter- and intra-domain comparisons for the cognitive domains of emotion, language and working memory. We also considered task differences within the domain of verbal working memory by conducting a comparison of the Sternberg with the n-back task, as well as an analysis of the differential components within the Sternberg task. Results showed a consistent cerebellar presence in the timing domain, providing evidence for a role in time keeping. Unique clusters identified within the domain further refine the topographic organization of the cerebellum. PMID:23125108

Back to the basics: Identifying and addressing underlying challenges in achieving high quality and relevant health statistics for indigenous populations in Canada

PubMed Central

Smylie, Janet; Firestone, Michelle

2015-01-01

Canada is known internationally for excellence in both the quality and public policy relevance of its health and social statistics. There is a double standard however with respect to the relevance and quality of statistics for Indigenous populations in Canada. Indigenous specific health and social statistics gathering is informed by unique ethical, rights-based, policy and practice imperatives regarding the need for Indigenous participation and leadership in Indigenous data processes throughout the spectrum of indicator development, data collection, management, analysis and use. We demonstrate how current Indigenous data quality challenges including misclassification errors and non-response bias systematically contribute to a significant underestimate of inequities in health determinants, health status, and health care access between Indigenous and non-Indigenous people in Canada. The major quality challenge underlying these errors and biases is the lack of Indigenous specific identifiers that are consistent and relevant in major health and social data sources. The recent removal of an Indigenous identity question from the Canadian census has resulted in further deterioration of an already suboptimal system. A revision of core health data sources to include relevant, consistent, and inclusive Indigenous self-identification is urgently required. These changes need to be carried out in partnership with Indigenous peoples and their representative and governing organizations. PMID:26793283

Numerous Transitions of Sex Chromosomes in Diptera

PubMed Central

Vicoso, Beatriz; Bachtrog, Doris

2015-01-01

Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa. PMID:25879221

Measuring pediatric hematology-oncology fellows' skills in humanism and professionalism: A novel assessment instrument.

PubMed

Kesselheim, Jennifer C; Agrawal, Anurag K; Bhatia, Nita; Cronin, Angel; Jubran, Rima; Kent, Paul; Kersun, Leslie; Rao, Amulya Nageswara; Rose, Melissa; Savelli, Stephanie; Sharma, Mukta; Shereck, Evan; Twist, Clare J; Wang, Michael

2017-05-01

Educators in pediatric hematology-oncology lack rigorously developed instruments to assess fellows' skills in humanism and professionalism. We developed a novel 15-item self-assessment instrument to address this gap in fellowship training. Fellows (N = 122) were asked to assess their skills in five domains: balancing competing demands of fellowship, caring for the dying patient, confronting depression and burnout, responding to challenging relationships with patients, and practicing humanistic medicine. An expert focus group predefined threshold scores on the instrument that could be used as a cutoff to identify fellows who need support. Reliability and feasibility were assessed and concurrent validity was measured using three established instruments: Maslach Burnout Inventory (MBI), Flourishing Scale (FS), and Jefferson Scale of Physician Empathy (JSPE). For 90 participating fellows (74%), the self-assessment proved feasible to administer and had high internal consistency reliability (Cronbach's α = 0.81). It was moderately correlated with the FS and MBI (Pearson's r = 0.41 and 0.4, respectively) and weakly correlated with the JSPE (Pearson's r = 0.15). Twenty-eight fellows (31%) were identified as needing support. The self-assessment had a sensitivity of 50% (95% confidence interval [CI]: 31-69) and a specificity of 77% (95% CI: 65-87) for identifying fellows who scored poorly on at least one of the three established scales. We developed a novel assessment instrument for use in pediatric fellowship training. The new scale proved feasible and demonstrated internal consistency reliability. Its moderate correlation with other established instruments shows that the novel assessment instrument provides unique, nonredundant information as compared to existing scales. © 2016 Wiley Periodicals, Inc.

Uniqueness and Overlap: Characteristics and Longitudinal Correlates of Native Chinese Children’s Writing in English as a Foreign Language

PubMed Central

Zhang, Juan; McBride-Chang, Catherine; Wagner, Richard K.; Chan, Shingfong

2015-01-01

Longitudinal predictors of writing composition in Chinese and English written by the same 153 Hong Kong nine-year-old children were tested, and their production errors within the English essays across ten categories, focusing on punctuation, spelling, and grammar, were compared to errors made by ninety American nine-year-olds writing on the same topic. The correlation between quality of the compositions in Chinese and English was .53. In stepwise regression analyses examining early predictors at ages between five and nine years, tasks of speed or fluency were consistently uniquely associated with Chinese writing composition; measures of English vocabulary knowledge, word reading, or both were consistently uniquely associated with English writing quality. Compared to the American children, Chinese children’s writing reflected significantly higher proportions of errors in all grammatical categories but did not differ in punctuation or spelling. Findings underscore both similarities and differences in writing at different levels across languages. PMID:25729319

The complete chloroplast genome of Sinopodophyllum hexandrum (Berberidaceae).

PubMed

Li, Huie; Guo, Qiqiang

2016-07-01

The complete chloroplast (cp) genome of the Sinopodophyllum hexandrum (Berberidaceae) was determined in this study. The circular genome is 157,940 bp in size, and comprises a pair of inverted repeat (IR) regions of 26,077 bp each, a large single-copy (LSC) region of 86,460 bp and a small single-copy (SSC) region of 19,326 bp. The GC content of the whole cp genome was 38.5%. A total of 133 genes were identified, including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. The whole cp genome consists of 114 unique genes, and 19 genes are duplicated in the IR regions. The phylogenetic analysis revealed that S. hexandrum is closely related to Nandina domestica within the family Berberidaceae.

Historical Perspectives and Guidelines for Botulinum Neurotoxin Subtype Nomenclature

PubMed Central

Peck, Michael W.; Smith, Theresa J.; Anniballi, Fabrizio; Austin, John W.; Bano, Luca; Bradshaw, Marite; Cuervo, Paula; Cheng, Luisa W.; Derman, Yagmur; Dorner, Brigitte G.; Fisher, Audrey; Hill, Karen K.; Kalb, Suzanne R.; Korkeala, Hannu; Lindström, Miia; Lista, Florigio; Lúquez, Carolina; Mazuet, Christelle; Pirazzini, Marco; Popoff, Michel R.; Rossetto, Ornella; Rummel, Andreas; Sesardic, Dorothea; Singh, Bal Ram; Stringer, Sandra C.

2017-01-01

Botulinum neurotoxins are diverse proteins. They are currently represented by at least seven serotypes and more than 40 subtypes. New clostridial strains that produce novel neurotoxin variants are being identified with increasing frequency, which presents challenges when organizing the nomenclature surrounding these neurotoxins. Worldwide, researchers are faced with the possibility that toxins having identical sequences may be given different designations or novel toxins having unique sequences may be given the same designations on publication. In order to minimize these problems, an ad hoc committee consisting of over 20 researchers in the field of botulinum neurotoxin research was convened to discuss the clarification of the issues involved in botulinum neurotoxin nomenclature. This publication presents a historical overview of the issues and provides guidelines for botulinum neurotoxin subtype nomenclature in the future. PMID:28106761

Conformal higher spin theory and twistor space actions

NASA Astrophysics Data System (ADS)

Hähnel, Philipp; McLoughlin, Tristan

2017-12-01

We consider the twistor description of conformal higher spin theories and give twistor space actions for the self-dual sector of theories with spin greater than two that produce the correct flat space-time spectrum. We identify a ghost-free subsector, analogous to the embedding of Einstein gravity with cosmological constant in Weyl gravity, which generates the unique spin-s three-point anti-MHV amplitude consistent with Poincaré invariance and helicity constraints. By including interactions between the infinite tower of higher-spin fields we give a geometric interpretation to the twistor equations of motion as the integrability condition for a holomorphic structure on an infinite jet bundle. Finally, we conjecture anti-self-dual interaction terms which give an implicit definition of a twistor action for the full conformal higher spin theory.

Time-Dependent Hartree-Fock Approach to Nuclear Pasta at Finite Temperature

NASA Astrophysics Data System (ADS)

Schuetrumpf, B.; Klatt, M. A.; Iida, K.; Maruhn, J. A.; Mecke, K.; Reinhard, P.-G.

2013-03-01

We present simulations of neutron-rich matter at subnuclear densities, like supernova matter, with the time-dependent Hartree-Fock approximation at temperatures of several MeV. The initial state consists of α particles randomly distributed in space that have a Maxwell-Boltzmann distribution in momentum space. Adding a neutron background initialized with Fermi distributed plane waves the calculations reflect a reasonable approximation of astrophysical matter. This matter evolves into spherical, rod-like, and slab-like shapes and mixtures thereof. The simulations employ a full Skyrme interaction in a periodic three-dimensional grid. By an improved morphological analysis based on Minkowski functionals, all eight pasta shapes can be uniquely identified by the sign of only two valuations, namely the Euler characteristic and the integral mean curvature.

Immigrant sexual minority Latino men in rural North Carolina: an exploration of social context, social behaviors, and sexual outcomes.

PubMed

Gilbert, Paul A; Rhodes, Scott D

2014-01-01

Immigrant sexual minority Latino men-who may or may not self-identify as gay-constitute a minority within a minority. Often labeled "hidden" and "hard-to-reach," and marginalized along multiple dimensions, it is a subgroup about whom little is known. Informed by a social ecological framework, we sought to describe key social variables for 190 such men in rural North Carolina and to test associations with three sexual outcomes: consistent condom use, number of sex partners, and sexual compulsivity. Participants reported limited English-language use, predominantly Latino close friends, middle levels of social support despite numerous social ties, and frequent experiences of discrimination. There were unique sets of correlates for each sexual outcome. Findings may inform health promotion interventions and guide future research.

Historical Perspectives and Guidelines for Botulinum Neurotoxin Subtype Nomenclature.

PubMed

Peck, Michael W; Smith, Theresa J; Anniballi, Fabrizio; Austin, John W; Bano, Luca; Bradshaw, Marite; Cuervo, Paula; Cheng, Luisa W; Derman, Yagmur; Dorner, Brigitte G; Fisher, Audrey; Hill, Karen K; Kalb, Suzanne R; Korkeala, Hannu; Lindström, Miia; Lista, Florigio; Lúquez, Carolina; Mazuet, Christelle; Pirazzini, Marco; Popoff, Michel R; Rossetto, Ornella; Rummel, Andreas; Sesardic, Dorothea; Singh, Bal Ram; Stringer, Sandra C

2017-01-18

Botulinum neurotoxins are diverse proteins. They are currently represented by at least seven serotypes and more than 40 subtypes. New clostridial strains that produce novel neurotoxin variants are being identified with increasing frequency, which presents challenges when organizing the nomenclature surrounding these neurotoxins. Worldwide, researchers are faced with the possibility that toxins having identical sequences may be given different designations or novel toxins having unique sequences may be given the same designations on publication. In order to minimize these problems, an ad hoc committee consisting of over 20 researchers in the field of botulinum neurotoxin research was convened to discuss the clarification of the issues involved in botulinum neurotoxin nomenclature. This publication presents a historical overview of the issues and provides guidelines for botulinum neurotoxin subtype nomenclature in the future.

Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Characterizing Cellular Metabolism

PubMed Central

Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich

2010-01-01

Elementary Mode Analysis is a useful Metabolic Pathway Analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering. PMID:19015845

Recommendations of the National Heart, Lung, and Blood Institute Heart and Lung Xenotransplantation Working Group.

PubMed

Platt, Jeffrey; DiSesa, Verdi; Gail, Dorothy; Massicot-Fisher, Judith

2002-08-27

The National Heart, Lung, and Blood Institute (NHLBI) recently convened the Heart and Lung Xenotransplantation Working Group to identify hurdles to the clinical application of xenotransplantation, defined as the use of animal organs or tissue for transplantation, and to recommend possible solutions to these problems. The group consisted of experts in xenotransplantation from academia, industry, and federal agencies, and the discussions focused on those areas within the mission of the NHLBI. The areas covered included immunologic and physiological barriers to xenotransplantation, the limitations of the current animal models, the need for collaboration among groups, the high costs of studies using nonhuman primates and genetic engineering of pigs, and the unique problems of lung xenotransplantation. This report is a summary of those discussions.

Expression quantitative trait loci (eQTL) mapping in Puerto Rican children.

PubMed

Chen, Wei; Brehm, John M; Lin, Jerome; Wang, Ting; Forno, Erick; Acosta-Pérez, Edna; Boutaoui, Nadia; Canino, Glorisa; Celedón, Juan C

2015-01-01

Expression quantitative trait loci (eQTL) have been identified using tissue or cell samples from diverse human populations, thus enhancing our understanding of regulation of gene expression. However, few studies have attempted to identify eQTL in racially admixed populations such as Hispanics. We performed a systematic eQTL study to identify regulatory variants of gene expression in whole blood from 121 Puerto Rican children with (n = 63) and without (n = 58) asthma. Genome-wide genotyping was conducted using the Illumina Omni2.5M Bead Chip, and gene expression was assessed using the Illumina HT-12 microarray. After completing quality control, we performed a pair-wise genome analysis of ~15 K transcripts and ~1.3 M SNPs for both local and distal effects. This analysis was conducted under a regression framework adjusting for age, gender and principal components derived from both genotypic and mRNA data. We used a false discovery rate (FDR) approach to identify significant eQTL signals, which were next compared to top eQTL signals from existing eQTL databases. We then performed a pathway analysis for our top genes. We identified 36,720 local pairs in 3,391 unique genes and 1,851 distal pairs in 446 unique genes at FDR <0.05, corresponding to unadjusted P values lower than 1.5x10-4 and 4.5x10-9, respectively. A significant proportion of genes identified in our study overlapped with those identified in previous studies. We also found an enrichment of disease-related genes in our eQTL list. We present results from the first eQTL study in Puerto Rican children, who are members of a unique Hispanic cohort disproportionately affected with asthma, prematurity, obesity and other common diseases. Our study confirmed eQTL signals identified in other ethnic groups, while also detecting additional eQTLs unique to our study population. The identified eQTLs will help prioritize findings from future genome-wide association studies in Puerto Ricans.

Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

PubMed

Egorov, Evgeny S; Merzlyak, Ekaterina M; Shelenkov, Andrew A; Britanova, Olga V; Sharonov, George V; Staroverov, Dmitriy B; Bolotin, Dmitriy A; Davydov, Alexey N; Barsova, Ekaterina; Lebedev, Yuriy B; Shugay, Mikhail; Chudakov, Dmitriy M

2015-06-15

Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications. Copyright © 2015 by The American Association of Immunologists, Inc.

Giraffe genome sequence reveals clues to its unique morphology and physiology

PubMed Central

Agaba, Morris; Ishengoma, Edson; Miller, Webb C.; McGrath, Barbara C.; Hudson, Chelsea N.; Bedoya Reina, Oscar C.; Ratan, Aakrosh; Burhans, Rico; Chikhi, Rayan; Medvedev, Paul; Praul, Craig A.; Wu-Cavener, Lan; Wood, Brendan; Robertson, Heather; Penfold, Linda; Cavener, Douglas R.

2016-01-01

The origins of giraffe's imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe's closest relative and provides a useful comparison, to identify genetic variation underlying giraffe's long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe's unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe's stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions. PMID:27187213

Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae).

PubMed

Eckert, Andrew J; van Heerwaarden, Joost; Wegrzyn, Jill L; Nelson, C Dana; Ross-Ibarra, Jeffrey; González-Martínez, Santíago C; Neale, David B

2010-07-01

Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as F(ST) outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes.

Bartonella Infection in Hematophagous, Insectivorous, and Phytophagous Bat Populations of Central Mexico and the Yucatan Peninsula.

PubMed

Stuckey, Matthew J; Chomel, Bruno B; Galvez-Romero, Guillermo; Olave-Leyva, José Ignacio; Obregón-Morales, Cirani; Moreno-Sandoval, Hayde; Aréchiga-Ceballos, Nidia; Salas-Rojas, Mónica; Aguilar-Setién, Alvaro

2017-08-01

Although emerging nonviral pathogens remain relatively understudied in bat populations, there is an increasing focus on identifying bat-associated bartonellae around the world. Many novel Bartonella strains have been described from both bats and their arthropod ectoparasites, including Bartonella mayotimonensis , a zoonotic agent of human endocarditis. This cross-sectional study was designed to describe novel Bartonella strains isolated from bats sampled in Mexico and evaluate factors potentially associated with infection. A total of 238 bats belonging to seven genera were captured in five states of Central Mexico and the Yucatan Peninsula. Animals were screened by bacterial culture from whole blood and/or polymerase chain reaction of DNA extracted from heart tissue or blood. Bartonella spp. were isolated or detected in 54 (22.7%) bats, consisting of 41 (38%) hematophagous, 10 (16.4%) insectivorous, and three (4.3%) phytophagous individuals. This study also identified Balantiopteryx plicata as another possible bat reservoir of Bartonella . Univariate and multivariate logistic regression models suggested that Bartonella infection was positively associated with blood-feeding diet and ectoparasite burden. Phylogenetic analysis identified a number of genetic variants across hematophagous, phytophagous, and insectivorous bats that are unique from described bat-borne Bartonella species. However, these strains were closely related to those bartonellae previously identified in bat species from Latin America.

Using a distribution and conservation status weighted hotspot approach to identify areas in need of conservation action to benefit Idaho bird species

USGS Publications Warehouse

Haines, Aaron M.; Leu, Matthias; Svancara, Leona K.; Wilson, Gina; Scott, J. Michael

2010-01-01

Identification of biodiversity hotspots (hereafter, hotspots) has become a common strategy to delineate important areas for wildlife conservation. However, the use of hotspots has not often incorporated important habitat types, ecosystem services, anthropogenic activity, or consistency in identifying important conservation areas. The purpose of this study was to identify hotspots to improve avian conservation efforts for Species of Greatest Conservation Need (SGCN) in the state of Idaho, United States. We evaluated multiple approaches to define hotspots and used a unique approach based on weighting species by their distribution size and conservation status to identify hotspot areas. All hotspot approaches identified bodies of water (Bear Lake, Grays Lake, and American Falls Reservoir) as important hotspots for Idaho avian SGCN, but we found that the weighted approach produced more congruent hotspot areas when compared to other hotspot approaches. To incorporate anthropogenic activity into hotspot analysis, we grouped species based on their sensitivity to specific human threats (i.e., urban development, agriculture, fire suppression, grazing, roads, and logging) and identified ecological sections within Idaho that may require specific conservation actions to address these human threats using the weighted approach. The Snake River Basalts and Overthrust Mountains ecological sections were important areas for potential implementation of conservation actions to conserve biodiversity. Our approach to identifying hotspots may be useful as part of a larger conservation strategy to aid land managers or local governments in applying conservation actions on the ground.

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”

PubMed Central

Tettelin, Hervé; Masignani, Vega; Cieslewicz, Michael J.; Donati, Claudio; Medini, Duccio; Ward, Naomi L.; Angiuoli, Samuel V.; Crabtree, Jonathan; Jones, Amanda L.; Durkin, A. Scott; DeBoy, Robert T.; Davidsen, Tanja M.; Mora, Marirosa; Scarselli, Maria; Margarit y Ros, Immaculada; Peterson, Jeremy D.; Hauser, Christopher R.; Sundaram, Jaideep P.; Nelson, William C.; Madupu, Ramana; Brinkac, Lauren M.; Dodson, Robert J.; Rosovitz, Mary J.; Sullivan, Steven A.; Daugherty, Sean C.; Haft, Daniel H.; Selengut, Jeremy; Gwinn, Michelle L.; Zhou, Liwei; Zafar, Nikhat; Khouri, Hoda; Radune, Diana; Dimitrov, George; Watkins, Kisha; O'Connor, Kevin J. B.; Smith, Shannon; Utterback, Teresa R.; White, Owen; Rubens, Craig E.; Grandi, Guido; Madoff, Lawrence C.; Kasper, Dennis L.; Telford, John L.; Wessels, Michael R.; Rappuoli, Rino; Fraser, Claire M.

2005-01-01

The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for ≈80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes. PMID:16172379

New Manganese Silicide Mineral Phase in an Interplanetary Dust Particle

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Keller, L. P.; Clemett, S. J.; Jones, J. H.; Palma, R. L.; Pepin, R. O.; Kloeck, W.; Zolensky, M. E.; Messenger, S.

2008-01-01

Comet 26P/Grigg-Skjellerup was identified as a source of an Earth-crossing dust stream with low Earth-encounter velocities, with peak anticipated fluxes during April in 2003 and 2004 [1]. In response to this prediction, NASA performed dedicated stratospheric dust collections using high altitude aircraft to target potential interplanetary dust particles (IDPs) from this comet stream in April 2003. Several IDPs from this collection have shown unusually low noble gas abundances [2] consistent with the predicted short space exposure ages of Grigg-Skjellerup dust particles [1]. High abundances of large D enrichments [3] and presolar grains [4] in IDPs from this collection are also consistent with an origin from the comet Grigg-Skjellerup. Here we report a new mineral from one of the cluster IDPs of the "Grigg-Skjellerup" collection, L2055. Our report focuses on an unusual manganese-iron-chromium silicide phase that, to our knowledge, has not been observed previously in nature. This unique phase may also shed light on the genesis of the enigmatic low-Fe,Mn-enriched (LIME) olivine that has been previously reported in IDPs and meteorites [5].

NASA Astronaut Selection 2009: Behavioral Overview

NASA Technical Reports Server (NTRS)

Holland, A. W.; Sipes, W.; Beven, G.; Schmidt, L.; Slack, K.; Seaton, K.; Moomaw, R.; VanderArk, S.

2010-01-01

NASA's multi-phase U.S. astronaut selection process seeks to identify the most qualified astronaut candidates from a large number of applicants. With the approaching retirement of the Space Shuttle, NASA focused on selecting those individuals who were most suited to the unique demands of long-duration spaceflight. In total, NASA received 3,535 applications for the 2009 astronaut selection cycle. Of these, 123 were invited to NASA Johnson Space Center (JSC) for Round 1 initial screening and interviews, which consisted of an Astronaut Selection Board (ASB) preliminary interview, medical review, and psychological testing. Of these, 48 individuals were invited to return for Round 2. This round consisted of medical testing, further behavioral assessments, and a second ASB interview. Following this, nine astronaut candidates (ASCANs) were ultimately chosen to go forward to basic training. The contents, benefits, and lessons learned from implementing this phased process will be discussed. The lessons learned can benefit the future selection of space flyers, whether they are NASA or commercial. Learning Objective: 1) Familiarization with the 2009 NASA behavioral screening process for astronaut applicants.

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci

PubMed Central

Zubair, Niha; Luis Ambite, Jose; Bush, William S.; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H.; Absher, Devin; Assimes, Themistocles L.; Bielinski, Suzette J.; Bottinger, Erwin P.; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W.; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A.; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J.; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H.; Martin, Lisa W.; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P.; Robinson, Jennifer; Rotter, Jerome I.; Ryckman, Kelli K.; Schreiner, Pamela J.; Stahl, Eli; Tao, Ran; Tsai, Michael Y.; Waite, Lindsay L.; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C.; Loos, Ruth J.F.; Rich, Stephen S.; Fornage, Myriam; North, Kari E.; Kooperberg, Charles; Carty, Cara L.

2016-01-01

Abstract Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. PMID:28426890

Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes

PubMed Central

Hiller, Ekkehard; Istel, Fabian; Tscherner, Michael; Brunke, Sascha; Ames, Lauren; Firon, Arnaud; Green, Brian; Cabral, Vitor; Marcet-Houben, Marina; Jacobsen, Ilse D.; Quintin, Jessica; Seider, Katja; Frohner, Ingrid; Glaser, Walter; Jungwirth, Helmut; Bachellier-Bassi, Sophie; Chauvel, Murielle; Zeidler, Ute; Ferrandon, Dominique; Gabaldón, Toni; Hube, Bernhard; d'Enfert, Christophe; Rupp, Steffen; Cormack, Brendan; Haynes, Ken; Kuchler, Karl

2014-01-01

The opportunistic fungal pathogen Candida glabrata is a frequent cause of candidiasis, causing infections ranging from superficial to life-threatening disseminated disease. The inherent tolerance of C. glabrata to azole drugs makes this pathogen a serious clinical threat. To identify novel genes implicated in antifungal drug tolerance, we have constructed a large-scale C. glabrata deletion library consisting of 619 unique, individually bar-coded mutant strains, each lacking one specific gene, all together representing almost 12% of the genome. Functional analysis of this library in a series of phenotypic and fitness assays identified numerous genes required for growth of C. glabrata under normal or specific stress conditions, as well as a number of novel genes involved in tolerance to clinically important antifungal drugs such as azoles and echinocandins. We identified 38 deletion strains displaying strongly increased susceptibility to caspofungin, 28 of which encoding proteins that have not previously been linked to echinocandin tolerance. Our results demonstrate the potential of the C. glabrata mutant collection as a valuable resource in functional genomics studies of this important fungal pathogen of humans, and to facilitate the identification of putative novel antifungal drug target and virulence genes. PMID:24945925

Applications for unique identifiers in the geological sciences

NASA Astrophysics Data System (ADS)

Klump, J.; Lehnert, K. A.

2012-12-01

Even though geology has always been a generalist discipline in many parts, approaches towards questions about Earth's past have become increasingly interdisciplinary. At the same time, a wealth of samples has been collected, the resulting data have been stored in in disciplinary databases, the interpretations published in scientific literature. In the past these resources have existed alongside each other, semantically linked only by the knowledge of the researcher and his peers. One of the main drivers towards the inception of the world wide web was the ability to link scientific sources over the internet. The Uniform Resource Locator (URL) used to locate resources on the web soon turned out to be ephemeral in nature. A more reliable way of addressing objects was needed, a way of persistent identification to make digital objects, or digital representations of objects, part of the record of science. With their high degree of centralisation the scientific publishing houses were quick to implement and adopt a system for unique and persistent identification, the Digital Object Identifier (DOI) ®. At the same time other identifier systems exist alongside DOI, e.g. URN, ARK, handle ®, and others. There many uses for persistent identification in science, other than the identification of journal articles. DOI are already used for the identification of data, thus making data citable. There are several initiatives to assign identifiers to authors and institutions to allow unique identification. A recent development is the application of persistent identifiers for geological samples. As most data in the geosciences are derived from samples, it is crucial to be able to uniquely identify the samples from which a set of data were derived. Incomplete documentation of samples in publications, use of ambiguous sample names are major obstacles for synthesis studies and re-use of data. Access to samples for re-analysis and re-appraisal is limited due to the lack of a central catalogue that allows finding a sample's archiving location. The International Geo Sample Number (IGSN) provides solutions to the questions of unique sample identification and discovery. Use of the IGSN in digital data systems allows building linkages between the digital representation of samples in sample registries, e.g. SESAR, and their related data in the literature and in web accessible digital data repositories. Persistent identifiers are now available for literature, data, samples, and authors. More applications, e.g. identification of methods or instruments, will follow. In conjunction with semantic web technology the application of unique and persistent identifiers in the geosciences will aid discovery both through systematic data mining, exploratory data analysis, and serendipity effects. This talk will discuss existing and emerging applications for persistent identifiers in the geological sciences.

A methodology for generating a tailored implementation blueprint: an exemplar from a youth residential setting.

PubMed

Lewis, Cara C; Scott, Kelli; Marriott, Brigid R

2018-05-16

Tailored implementation approaches are touted as more likely to support the integration of evidence-based practices. However, to our knowledge, few methodologies for tailoring implementations exist. This manuscript will apply a model-driven, mixed methods approach to a needs assessment to identify the determinants of practice, and pilot a modified conjoint analysis method to generate an implementation blueprint using a case example of a cognitive behavioral therapy (CBT) implementation in a youth residential center. Our proposed methodology contains five steps to address two goals: (1) identify the determinants of practice and (2) select and match implementation strategies to address the identified determinants (focusing on barriers). Participants in the case example included mental health therapists and operations staff in two programs of Wolverine Human Services. For step 1, the needs assessment, they completed surveys (clinician N = 10; operations staff N = 58; other N = 7) and participated in focus groups (clinician N = 15; operations staff N = 38) guided by the domains of the Framework for Diffusion [1]. For step 2, the research team conducted mixed methods analyses following the QUAN + QUAL structure for the purpose of convergence and expansion in a connecting process, revealing 76 unique barriers. Step 3 consisted of a modified conjoint analysis. For step 3a, agency administrators prioritized the identified barriers according to feasibility and importance. For step 3b, strategies were selected from a published compilation and rated for feasibility and likelihood of impacting CBT fidelity. For step 4, sociometric surveys informed implementation team member selection and a meeting was held to identify officers and clarify goals and responsibilities. For step 5, blueprints for each of pre-implementation, implementation, and sustainment phases were generated. Forty-five unique strategies were prioritized across the 5 years and three phases representing all nine categories. Our novel methodology offers a relatively low burden collaborative approach to generating a plan for implementation that leverages advances in implementation science including measurement, models, strategy compilations, and methods from other fields.

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

PubMed

Benayoun, Bérénice A; Pollina, Elizabeth A; Ucar, Duygu; Mahmoudi, Salah; Karra, Kalpana; Wong, Edith D; Devarajan, Keerthana; Daugherty, Aaron C; Kundaje, Anshul B; Mancini, Elena; Hitz, Benjamin C; Gupta, Rakhi; Rando, Thomas A; Baker, Julie C; Snyder, Michael P; Cherry, J Michael; Brunet, Anne

2014-07-31

Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes. Copyright © 2014 Elsevier Inc. All rights reserved.

Proteomics and Deep Sequencing Comparison of Seasonally Active Venom Glands in the Platypus Reveals Novel Venom Peptides and Distinct Expression Profiles*

PubMed Central

Wong, Emily S. W.; Morgenstern, David; Mofiz, Ehtesham; Gombert, Sara; Morris, Katrina M.; Temple-Smith, Peter; Renfree, Marilyn B.; Whittington, Camilla M.; King, Glenn F.; Warren, Wesley C.; Papenfuss, Anthony T.; Belov, Katherine

2012-01-01

The platypus is a venomous monotreme. Male platypuses possess a spur on their hind legs that is connected to glands in the pelvic region. They produce venom only during the breeding season, presumably to fight off conspecifics. We have taken advantage of this unique seasonal production of venom to compare the transcriptomes of in- and out-of-season venom glands, in conjunction with proteomic analysis, to identify previously undiscovered venom genes. Comparison of the venom glands revealed distinct gene expression profiles that are consistent with changes in venom gland morphology and venom volumes in and out of the breeding season. Venom proteins were identified through shot-gun sequenced venom proteomes of three animals using RNA-seq-derived transcripts for peptide-spectral matching. 5,157 genes were expressed in the venom glands, 1,821 genes were up-regulated in the in-season gland, and 10 proteins were identified in the venom. New classes of platypus-venom proteins identified included antimicrobials, amide oxidase, serpin protease inhibitor, proteins associated with the mammalian stress response pathway, cytokines, and other immune molecules. Five putative toxins have only been identified in platypus venom: growth differentiation factor 15, nucleobindin-2, CD55, a CXC-chemokine, and corticotropin-releasing factor-binding protein. These novel venom proteins have potential biomedical and therapeutic applications and provide insights into venom evolution. PMID:22899769

Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.

PubMed

Wong, Emily S W; Morgenstern, David; Mofiz, Ehtesham; Gombert, Sara; Morris, Katrina M; Temple-Smith, Peter; Renfree, Marilyn B; Whittington, Camilla M; King, Glenn F; Warren, Wesley C; Papenfuss, Anthony T; Belov, Katherine

2012-11-01

The platypus is a venomous monotreme. Male platypuses possess a spur on their hind legs that is connected to glands in the pelvic region. They produce venom only during the breeding season, presumably to fight off conspecifics. We have taken advantage of this unique seasonal production of venom to compare the transcriptomes of in- and out-of-season venom glands, in conjunction with proteomic analysis, to identify previously undiscovered venom genes. Comparison of the venom glands revealed distinct gene expression profiles that are consistent with changes in venom gland morphology and venom volumes in and out of the breeding season. Venom proteins were identified through shot-gun sequenced venom proteomes of three animals using RNA-seq-derived transcripts for peptide-spectral matching. 5,157 genes were expressed in the venom glands, 1,821 genes were up-regulated in the in-season gland, and 10 proteins were identified in the venom. New classes of platypus-venom proteins identified included antimicrobials, amide oxidase, serpin protease inhibitor, proteins associated with the mammalian stress response pathway, cytokines, and other immune molecules. Five putative toxins have only been identified in platypus venom: growth differentiation factor 15, nucleobindin-2, CD55, a CXC-chemokine, and corticotropin-releasing factor-binding protein. These novel venom proteins have potential biomedical and therapeutic applications and provide insights into venom evolution.

A method for managing re-identification risk from small geographic areas in Canada

PubMed Central

2010-01-01

Background A common disclosure control practice for health datasets is to identify small geographic areas and either suppress records from these small areas or aggregate them into larger ones. A recent study provided a method for deciding when an area is too small based on the uniqueness criterion. The uniqueness criterion stipulates that an the area is no longer too small when the proportion of unique individuals on the relevant variables (the quasi-identifiers) approaches zero. However, using a uniqueness value of zero is quite a stringent threshold, and is only suitable when the risks from data disclosure are quite high. Other uniqueness thresholds that have been proposed for health data are 5% and 20%. Methods We estimated uniqueness for urban Forward Sortation Areas (FSAs) by using the 2001 long form Canadian census data representing 20% of the population. We then constructed two logistic regression models to predict when the uniqueness is greater than the 5% and 20% thresholds, and validated their predictive accuracy using 10-fold cross-validation. Predictor variables included the population size of the FSA and the maximum number of possible values on the quasi-identifiers (the number of equivalence classes). Results All model parameters were significant and the models had very high prediction accuracy, with specificity above 0.9, and sensitivity at 0.87 and 0.74 for the 5% and 20% threshold models respectively. The application of the models was illustrated with an analysis of the Ontario newborn registry and an emergency department dataset. At the higher thresholds considerably fewer records compared to the 0% threshold would be considered to be in small areas and therefore undergo disclosure control actions. We have also included concrete guidance for data custodians in deciding which one of the three uniqueness thresholds to use (0%, 5%, 20%), depending on the mitigating controls that the data recipients have in place, the potential invasion of privacy if the data is disclosed, and the motives and capacity of the data recipient to re-identify the data. Conclusion The models we developed can be used to manage the re-identification risk from small geographic areas. Being able to choose among three possible thresholds, a data custodian can adjust the definition of "small geographic area" to the nature of the data and recipient. PMID:20361870

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment

PubMed Central

Wong, Mabel T.; Wang, Weijun; Couturier, Marie; Razeq, Fakhria M.; Lombard, Vincent; Lapebie, Pascal; Edwards, Elizabeth A.; Terrapon, Nicolas; Henrissat, Bernard; Master, Emma R.

2017-01-01

To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron–sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization. PMID:29326667

The Use of Matrix Training to Promote Generative Language with Children with Autism

ERIC Educational Resources Information Center

Frampton, Sarah E.; Wymer, Sarah C.; Hansen, Bethany; Shillingsburg, M. Alice

2016-01-01

Matrix training consists of planning instruction by arranging components of desired skills across 2 axes. After training with diagonal targets that each combine 2 unique skill components, responses to nondiagonal targets, consisting of novel combinations of the components, may emerge. A multiple-probe design across participants was used to…

An Examination of Sampling Characteristics of Some Analytic Factor Transformation Techniques.

ERIC Educational Resources Information Center

Skakun, Ernest N.; Hakstian, A. Ralph

Two population raw data matrices were constructed by computer simulation techniques. Each consisted of 10,000 subjects and 12 variables, and each was constructed according to an underlying factorial model consisting of four major common factors, eight minor common factors, and 12 unique factors. The computer simulation techniques were employed to…

Targeted Metabolomics Demonstrates Distinct and Overlapping Maternal Metabolites Associated With BMI, Glucose, and Insulin Sensitivity During Pregnancy Across Four Ancestry Groups.

PubMed

Jacob, Saya; Nodzenski, Michael; Reisetter, Anna C; Bain, James R; Muehlbauer, Michael J; Stevens, Robert D; Ilkayeva, Olga R; Lowe, Lynn P; Metzger, Boyd E; Newgard, Christopher B; Scholtens, Denise M; Lowe, William L

2017-07-01

We used targeted metabolomics in pregnant mothers to compare maternal metabolite associations with maternal BMI, glycemia, and insulin sensitivity. Targeted metabolomic assays of clinical metabolites, amino acids, and acylcarnitines were performed on fasting and 1-h postglucose serum samples from European ancestry, Afro-Caribbean, Thai, and Mexican American mothers (400 from each ancestry group) who participated in the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study and underwent an oral glucose tolerance test at ∼28 weeks gestation. K-means clustering, which identified patterns of metabolite levels across ancestry groups, demonstrated that, at both fasting and 1-h, levels of the majority of metabolites were similar across ancestry groups. Meta-analyses demonstrated association of a broad array of fasting and 1-h metabolites, including lipids and amino acids and their metabolites, with maternal BMI, glucose levels, and insulin sensitivity before and after adjustment for the different phenotypes. At fasting and 1 h, a mix of metabolites was identified that were common across phenotypes or associated with only one or two phenotypes. Partial correlation estimates, which allowed comparison of the strength of association of different metabolites with maternal phenotypes, demonstrated that metabolites most strongly associated with different phenotypes included some that were common across as well as unique to each phenotype. Maternal BMI and glycemia have metabolic signatures that are both shared and unique to each phenotype. These signatures largely remain consistent across different ancestry groups and may contribute to the common and independent effects of these two phenotypes on adverse pregnancy outcomes. © 2017 by the American Diabetes Association.

Topology of Innovation Spaces in the Knowledge Networks Emerging through Questions-And-Answers

PubMed Central

Andjelković, Miroslav; Tadić, Bosiljka; Mitrović Dankulov, Marija; Rajković, Milan; Melnik, Roderick

2016-01-01

The communication processes of knowledge creation represent a particular class of human dynamics where the expertise of individuals plays a substantial role, thus offering a unique possibility to study the structure of knowledge networks from online data. Here, we use the empirical evidence from questions-and-answers in mathematics to analyse the emergence of the network of knowledge contents (or tags) as the individual experts use them in the process. After removing extra edges from the network-associated graph, we apply the methods of algebraic topology of graphs to examine the structure of higher-order combinatorial spaces in networks for four consecutive time intervals. We find that the ranking distributions of the suitably scaled topological dimensions of nodes fall into a unique curve for all time intervals and filtering levels, suggesting a robust architecture of knowledge networks. Moreover, these networks preserve the logical structure of knowledge within emergent communities of nodes, labeled according to a standard mathematical classification scheme. Further, we investigate the appearance of new contents over time and their innovative combinations, which expand the knowledge network. In each network, we identify an innovation channel as a subgraph of triangles and larger simplices to which new tags attach. Our results show that the increasing topological complexity of the innovation channels contributes to network’s architecture over different time periods, and is consistent with temporal correlations of the occurrence of new tags. The methodology applies to a wide class of data with the suitable temporal resolution and clearly identified knowledge-content units. PMID:27171149

International Metadata Standards and Enterprise Data Quality Metadata Systems

NASA Astrophysics Data System (ADS)

Habermann, T.

2016-12-01

Well-documented data quality is critical in situations where scientists and decision-makers need to combine multiple datasets from different disciplines and collection systems to address scientific questions or difficult decisions. Standardized data quality metadata could be very helpful in these situations. Many efforts at developing data quality standards falter because of the diversity of approaches to measuring and reporting data quality. The "one size fits all" paradigm does not generally work well in this situation. The ISO data quality standard (ISO 19157) takes a different approach with the goal of systematically describing how data quality is measured rather than how it should be measured. It introduces the idea of standard data quality measures that can be well documented in a measure repository and used for consistently describing how data quality is measured across an enterprise. The standard includes recommendations for properties of these measures that include unique identifiers, references, illustrations and examples. Metadata records can reference these measures using the unique identifier and reuse them along with details (and references) that describe how the measure was applied to a particular dataset. A second important feature of ISO 19157 is the inclusion of citations to existing papers or reports that describe quality of a dataset. This capability allows users to find this information in a single location, i.e. the dataset metadata, rather than searching the web or other catalogs. I will describe these and other capabilities of ISO 19157 with examples of how they are being used to describe data quality across the NASA EOS Enterprise and also compare these approaches with other standards.

Positive selection drives the evolution of a major histocompatibility complex gene in an endangered Mexican salamander species complex.

PubMed

Tracy, Karen E; Kiemnec-Tyburczy, Karen M; DeWoody, J Andrew; Parra-Olea, Gabriela; Zamudio, Kelly R

2015-06-01

Immune gene evolution can be critical to species survival in the face of infectious disease. In particular, polymorphism in the genes of the major histocompatibility complex (MHC) helps vertebrates combat novel and diverse pathogens by increasing the number of pathogen-derived proteins that can initiate the host's acquired immune response. In this study, we used a combination of presumably adaptive and neutral markers to investigate MHC evolution in populations of five salamander species within the Ambystoma velasci complex, a group consisting of 15 recently diverged species, several of which are endangered. We isolated 31 unique MHC class II β alleles from 75 total individuals from five species in this complex. MHC heterozygosity was significantly lower than expected for all five species, and we found no clear relationship between number of MHC alleles and species range, life history, or level of heterozygosity. We inferred a phylogeny representing the evolutionary history of Ambystoma MHC, with which we found signatures of positive selection on the overall gene, putative peptide-binding residues, and allelic lineages. We identified several instances of trans-species polymorphism, a hallmark of balancing selection observed in other groups of closely related species. In contrast, we did not detect comparable allelic diversity or signatures of selection on neutral loci. Additionally, we identified 17 supertypes among the 44 unique Ambystoma alleles, indicating that these sequences may encode functionally distinct MHC variants. We therefore have strong evidence that positive selection is a major evolutionary force driving patterns of MHC polymorphism in this recently radiated species complex.

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

Johannsen, Tim; Psaltis, Dimitrios, E-mail: timj@physics.arizona.edu, E-mail: dpsaltis@email.arizona.edu

According to the no-hair theorem, astrophysical black holes are uniquely described by their masses and spins. An observational test of the no-hair theorem can be performed by measuring at least three different multipole moments of the spacetime of a black hole and verifying whether their values are consistent with the unique combinations of the Kerr solution. In this paper, we study quasi-periodic variability observed in the emission from black holes across the electromagnetic spectrum as a test of the no-hair theorem. We derive expressions for the Keplerian and epicyclic frequencies in a quasi-Kerr spacetime, in which the quadrupole moment ismore » a free parameter in addition to mass and spin. We show that, for moderate spins, the Keplerian frequency is practically independent of small deviations of the quadrupole moment from the Kerr value, while the epicyclic frequencies exhibit significant variations. We apply this framework to quasi-periodic oscillations (QPOs) in black hole X-ray binaries in two different scenarios. In the case that a pair of QPOs can be identified as the fundamental g- and c-modes in the accretion disk, we show that the no-hair theorem can be tested in conjunction with an independent mass measurement. If pairs of oscillations are identified with non-parametric resonance of dynamical frequencies in the accretion disk, then testing the no-hair theorem also requires an independent measurement of the black hole spin. In addition, we argue that VLBI observations of Sgr A* may test the no-hair theorem through a combination of imaging observations and the detection of quasi-periodic variability.« less

Classical Pathology of Sympathetic Ophthalmia Presented in a Unique Case

PubMed Central

Chen, Shida; Aronow, Mary E; Wang, Charles; Shen, Defen; Chan, Chi-Chao

2014-01-01

The ocular pathology of sympathetic ophthalmia is demonstrated in a 10 year-old boy who sustained a penetrating left globe injury and subsequently developed sympathetic ophthalmia in the right eye two months later. Two and a half weeks following extensive surgical repair of the left ruptured globe, he developed endophthalmitis and was treated with oral and topical fortified antibiotics. One month after the initial injury, a progressive corneal ulcer of the left eye led to perforation and the need for emergent corneal transplantation. The surgical specimen revealed fungus, Scedosporium dehoogii. The boy received systemic and topical anti-fungal therapy. Two months following the penetrating globe injury of the left eye, a granulomatous uveitis developed in the right eye. Sympathetic ophthalmia was suspected and the patient began treatment with topical and oral corticosteroids. Given the concern of vision loss secondary to sympathetic ophthalmia in the right eye, as well as poor vision and hypotony in the injured eye, the left eye was enucleated. Microscopically, granulomatous inflammation with giant cells was noted within a cyclitic membrane which filled the anterior and posterior chamber of the left globe. Other classic features including Dalen-Fuchs nodules were identified. Small, choroidal, ill-defined granulomas and relative sparing of the choriocapillaris were present. Molecular analysis did not identify evidence of remaining fungal infection. The pathology findings were consistent with previously described features of sympathetic ophthalmia. The present case is unique in that co-existing fungal infection may have potentiated the risk for developing sympathetic ophthalmia in the fellow eye. PMID:25067979

Seasonal proteomic changes reveal molecular adaptations to preserve and replenish liver proteins during ground squirrel hibernation

PubMed Central

Epperson, L. Elaine; Rose, James C.; Carey, Hannah V.

2010-01-01

Hibernators are unique among mammals in their ability to survive extended periods of time with core body temperatures near freezing and with dramatically reduced heart, respiratory, and metabolic rates in a state known as torpor. To gain insight into the molecular events underlying this remarkable physiological phenotype, we applied a proteomic screening approach to identify liver proteins that differ between the summer active (SA) and the entrance (Ent) phase of winter hibernation in 13-lined ground squirrels. The relative abundance of 1,600 protein spots separated on two-dimensional gels was quantitatively determined using fluorescence difference gel electrophoresis, and 74 unique proteins exhibiting significant differences between the two states were identified using liquid chromatography followed by tandem mass spectrometry (LC-MS/MS). Proteins elevated in Ent hibernators included liver fatty acid-binding protein, fatty acid transporter, and 3-hydroxy-3-methylglutaryl-CoA synthase, which support the known metabolic fuel switch to lipid and ketone body utilization in winter. Several proteins involved in protein stability and protein folding were also elevated in the Ent phase, consistent with previous findings. In contrast to transcript screening results, there was a surprising increase in the abundance of proteins involved in protein synthesis during Ent hibernation, including several initiation and elongation factors. This finding, coupled with decreased abundance of numerous proteins involved in amino acid and nitrogen metabolism, supports the intriguing hypothesis that the mechanism of protein preservation and resynthesis is used by hibernating ground squirrels to help avoid nitrogen toxicity and ensure preservation of essential amino acids throughout the long winter fast. PMID:19923364

Can nanotechnology help advance glaciological research?

NASA Astrophysics Data System (ADS)

Dahlke, H. E.; McNew, C.; Wang, C.; McLaughlin, S.; Kocis, T. N.

2017-12-01

In a rapidly changing cryosphere, identifying sources, pathways, and residence times of snow and glacier meltwater is critical to developing improved understanding of watershed-stream connections and hydrological/glaciological melt models. Traditionally, glaciologists have used a variety of tracers, including chloride, microparticles, and dyes, to identify the structure and morphology of subglacial drainage systems. However, minimum detection limits, tracer expense, and the ability of watersheds to retain a memory of past tracer inputs have restricted both the scale of tracer application and the repeated or simultaneous use of most known tracers, thus limiting our ability to study complex glacial systems. These shortcomings in hydrologic tracers can be overcome by utilizing a tracer that allows for the unique identification between spatial and temporal inputs while maintaining identical transport characteristics. Here, we present the use of DNA-labeled nanoparticles, developed for nano-medicine and drug delivery, as environmental tracers. The DNA-labeled particle tracers consist of short DNA strands encapsulated within biodegradable polymer microspheres, which allow for repeatable production of numerous uniquely labelled tracers of pre-determined size and physical transport properties. Each batch of tracers are independently quantifiable; even a single DNA molecule can be detected with cost-effective quantitative polymerase chain reaction (qPCR). We have tested our tracer technology in complex systems such as valley glaciers in Sweden and Alaska and in both laboratory and field studies of channel flow, overland flow, and flow in porous media; these proof-of-concept studies indicate that nanotechnology allows for powerful characterization, description, and, ultimately, prediction of flow pathways in glacial systems and the environment.

Gene Expression Profiling of Development and Anthocyanin Accumulation in Kiwifruit (Actinidia chinensis) Based on Transcriptome Sequencing

PubMed Central

Zeng, Shaohua; Xiao, Gong; Wang, Gan; Wang, Ying; Peng, Ming; Huang, Hongwen

2015-01-01

Red-fleshed kiwifruit (Actinidia chinensis Planch. ‘Hongyang’) is a promising commercial cultivar due to its nutritious value and unique flesh color, derived from vitamin C and anthocyanins. In this study, we obtained transcriptome data of ‘Hongyang’ from seven developmental stages using Illumina sequencing. We mapped 39–54 million reads to the recently sequenced kiwifruit genome and other databases to define gene structure, to analyze alternative splicing, and to quantify gene transcript abundance at different developmental stages. The transcript profiles throughout red kiwifruit development were constructed and analyzed, with a focus on the biosynthesis and metabolism of compounds such as phytohormones, sugars, starch and L-ascorbic acid, which are indispensable for the development and formation of quality fruit. Candidate genes for these pathways were identified through MapMan and phylogenetic analysis. The transcript levels of genes involved in sucrose and starch metabolism were consistent with the change in soluble sugar and starch content throughout kiwifruit development. The metabolism of L-ascorbic acid was very active, primarily through the L-galactose pathway. The genes responsible for the accumulation of anthocyanin in red kiwifruit were identified, and their expression levels were investigated during kiwifruit development. This survey of gene expression during kiwifruit development paves the way for further investigation of the development of this uniquely colored and nutritious fruit and reveals which factors are needed for high quality fruit formation. This transcriptome data and its analysis will be useful for improving kiwifruit genome annotation, for basic fruit molecular biology research, and for kiwifruit breeding and improvement. PMID:26301713

Outbreak of Pneumocystis Pneumonia in Renal and Liver Transplant Patients Caused by Genotypically Distinct Strains of Pneumocystis jirovecii1

PubMed Central

Rostved, Andreas A.; Sassi, Monica; Kurtzhals, Jørgen A. L.; Sørensen, Søren Schwartz; Rasmussen, Allan; Ross, Christian; Gogineni, Emile; Huber, Charles; Kutty, Geetha; Kovacs, Joseph A.; Helweg-Larsen, Jannik

2013-01-01

Background An outbreak of 29 cases of Pneumocystis jirovecii pneumonia (PCP) occurred among renal and liver transplant recipients (RTR and LTR) in the largest Danish transplantation centre between 2007 and 2010, when routine PCP prophylaxis was not used. Methods P. jirovecii isolates from 22 transplant-cases, 2 colonized RTRs and 19 Pneumocystis-control samples were genotyped by restriction fragment length polymorphism and multi-locus sequence typing analysis. Contact tracing were used to investigate transmission. Potential risk factors were compared between PCP cases and matched non-PCP transplant patients. Results Three unique Pneumocystis genotypes were shared among 19 of the RTRs, LTRs and a colonized RTR in 3 distinct clusters, two of which overlapped temporally. In contrast, Pneumocystis-control samples harbored a wide range of genotypes. Evidence of possible nosocomial transmission was observed. Among several potential risk factors, only CMV viremia was consistently associated with PCP (P = 0.03; P = 0.009). Mycophenolate mofetile was associated with PCP risk only in the RTR population (P = 0.04). Conclusion We identified three large groups infected with unique strains of Pneumocystis and provide evidence of an outbreak profile and nosocomial transmission. LTRs may be infected in PCP outbreaks simultaneously with RTRs and by the same strains, most likely by inter-human transmission. Patients are at risk several years after transplantation, but the risk is highest during the first 6 months post-transplantation. Since patients at risk cannot be identified clinically and outbreaks cannot be predicted, six months of PCP chemoprophylaxis should be considered for all renal and liver transplant recipients. PMID:23903011

Outbreak of pneumocystis pneumonia in renal and liver transplant patients caused by genotypically distinct strains of Pneumocystis jirovecii.

PubMed

Rostved, Andreas A; Sassi, Monica; Kurtzhals, Jørgen A L; Sørensen, Søren Schwartz; Rasmussen, Allan; Ross, Christian; Gogineni, Emile; Huber, Charles; Kutty, Geetha; Kovacs, Joseph A; Helweg-Larsen, Jannik

2013-11-15

An outbreak of 29 cases of Pneumocystis jirovecii pneumonia (PCP) occurred among renal and liver transplant recipients (RTR and LTR) in the largest Danish transplantation centre between 2007 and 2010, when routine PCP prophylaxis was not used. P. jirovecii isolates from 22 transplant cases, 2 colonized RTRs, and 19 Pneumocystis control samples were genotyped by restriction fragment length polymorphism and multilocus sequence typing analysis. Contact tracing was used to investigate transmission. Potential risk factors were compared between PCP cases and matched non-PCP transplant patients. Three unique Pneumocystis genotypes were shared among 19 of the RTRs, LTRs, and a colonized RTR in three distinct clusters, two of which overlapped temporally. In contrast, Pneumocystis control samples harbored a wide range of genotypes. Evidence of possible nosocomial transmission was observed. Among several potential risk factors, only cytomegalovirus viremia was consistently associated with PCP (P=0.03; P=0.009). Mycophenolate mofetil was associated with PCP risk only in the RTR population (P=0.04). We identified three large groups infected with unique strains of Pneumocystis and provide evidence of an outbreak profile and nosocomial transmission. LTRs may be infected in PCP outbreaks simultaneously with RTRs and by the same strains, most likely by interhuman transmission. Patients are at risk several years after transplantation, but the risk is highest during the first 6 months after transplantation. Because patients at risk cannot be identified clinically and outbreaks cannot be predicted, 6 months of PCP chemoprophylaxis should be considered for all RTRs and LTRs.

Recent Acceleration of the Terrestrial Hydrologic Cycle in the U.S. Midwest

NASA Astrophysics Data System (ADS)

Yeh, Pat J.-F.; Wu, Chuanhao

2018-03-01

Most hydroclimatic trend studies considered only a subset of water budget variables; hence, the trend consistency and a holistic assessment of hydrologic changes across the entire water cycle cannot be evaluated. Here we use a unique 31 year (1983-2013) observed data set in Illinois (a representative region of the U.S. Midwest), including temperature (T), precipitation (P), evaporation (E), streamflow (R), soil moisture, and groundwater level (GWL), to estimate the trends and their sensitivity to different data periods and lengths. Both the Mann-Kendall trend test and the least squares linear method identify trends in close agreement. Despite no clear trends during 1983-2013, increasing trends are found in P (8.73-9.05 mm/year), E (6.87-7.47 mm/year), and R (1.57-3.54 mm/year) during 1992-2013, concurrently with a pronounced warming trend of 0.029-0.037 °C/year. However, terrestrial water storageis decreased by -2.0 mm/year (mainly due to declining GWL), suggesting that the increased R is caused by increased surface runoff rather than baseflow. Monthly analyses identify warming trends for all months except winter. In summer, P (E) exhibits an increasing (decreasing) trend, leading to increasing R, soil moisture, GWL, and terrestrial water storage. Most trends estimated for different subperiods are found to be sensitive to data lengths and periods. Overall, this study provides an internally consistent observed evidence on the intensification of the hydrologic cycle in response to recent climate warming in U.S. Midwest, in agreement with and well supported by several recent studies consistently reporting the increased P, R and E over the Midwest and Mississippi River basin.

DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of Cycads

PubMed Central

Sass, Chodon; Little, Damon P.; Stevenson, Dennis Wm.; Specht, Chelsea D.

2007-01-01

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation—especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants. PMID:17987130

Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.

PubMed

Fu, Cheng-Jie; Sheikh, Sanea; Miao, Wei; Andersson, Siv G E; Baldauf, Sandra L

2014-08-21

Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Distinguishing early and late brain aging from the Alzheimer's disease spectrum: consistent morphological patterns across independent samples.

PubMed

Doan, Nhat Trung; Engvig, Andreas; Zaske, Krystal; Persson, Karin; Lund, Martina Jonette; Kaufmann, Tobias; Cordova-Palomera, Aldo; Alnæs, Dag; Moberget, Torgeir; Brækhus, Anne; Barca, Maria Lage; Nordvik, Jan Egil; Engedal, Knut; Agartz, Ingrid; Selbæk, Geir; Andreassen, Ole A; Westlye, Lars T

2017-09-01

Alzheimer's disease (AD) is a debilitating age-related neurodegenerative disorder. Accurate identification of individuals at risk is complicated as AD shares cognitive and brain features with aging. We applied linked independent component analysis (LICA) on three complementary measures of gray matter structure: cortical thickness, area and gray matter density of 137 AD, 78 mild (MCI) and 38 subjective cognitive impairment patients, and 355 healthy adults aged 18-78 years to identify dissociable multivariate morphological patterns sensitive to age and diagnosis. Using the lasso classifier, we performed group classification and prediction of cognition and age at different age ranges to assess the sensitivity and diagnostic accuracy of the LICA patterns in relation to AD, as well as early and late healthy aging. Three components showed high sensitivity to the diagnosis and cognitive status of AD, with different relationships with age: one reflected an anterior-posterior gradient in thickness and gray matter density and was uniquely related to diagnosis, whereas the other two, reflecting widespread cortical thickness and medial temporal lobe volume, respectively, also correlated significantly with age. Repeating the LICA decomposition and between-subject analysis on ADNI data, including 186 AD, 395 MCI and 220 age-matched healthy controls, revealed largely consistent brain patterns and clinical associations across samples. Classification results showed that multivariate LICA-derived brain characteristics could be used to predict AD and age with high accuracy (area under ROC curve up to 0.93 for classification of AD from controls). Comparison between classifiers based on feature ranking and feature selection suggests both common and unique feature sets implicated in AD and aging, and provides evidence of distinct age-related differences in early compared to late aging. Copyright © 2017 Elsevier Inc. All rights reserved.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.

PubMed

Hankeln, Wolfgang; Buttigieg, Pier Luigi; Fink, Dennis; Kottmann, Renzo; Yilmaz, Pelin; Glöckner, Frank Oliver

2010-06-30

Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

PubMed Central

2010-01-01

Background Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft® Excel® spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data. PMID:20591175

45 CFR 164.312 - Technical safeguards.

Code of Federal Regulations, 2012 CFR

2012-10-01

... REQUIREMENTS SECURITY AND PRIVACY Security Standards for the Protection of Electronic Protected Health... that maintain electronic protected health information to allow access only to those persons or software... specifications: (i) Unique user identification (Required). Assign a unique name and/or number for identifying and...

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

PubMed Central

Wu, Guangxi; Zhao, He; Li, Chenhao; Rajapakse, Menaka Priyadarsani; Wong, Wing Cheong; Xu, Jun; Saunders, Charles W.; Reeder, Nancy L.; Reilman, Raymond A.; Scheynius, Annika; Sun, Sheng; Billmyre, Blake Robert; Li, Wenjun; Averette, Anna Floyd; Mieczkowski, Piotr; Heitman, Joseph; Theelen, Bart; Schröder, Markus S.; De Sessions, Paola Florez; Butler, Geraldine; Maurer-Stroh, Sebastian; Boekhout, Teun; Nagarajan, Niranjan; Dawson, Thomas L.

2015-01-01

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin. PMID:26539826

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

PubMed

Wu, Guangxi; Zhao, He; Li, Chenhao; Rajapakse, Menaka Priyadarsani; Wong, Wing Cheong; Xu, Jun; Saunders, Charles W; Reeder, Nancy L; Reilman, Raymond A; Scheynius, Annika; Sun, Sheng; Billmyre, Blake Robert; Li, Wenjun; Averette, Anna Floyd; Mieczkowski, Piotr; Heitman, Joseph; Theelen, Bart; Schröder, Markus S; De Sessions, Paola Florez; Butler, Geraldine; Maurer-Stroh, Sebastian; Boekhout, Teun; Nagarajan, Niranjan; Dawson, Thomas L

2015-11-01

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.

Investigation of basic cognitive predictors of reading and spelling abilities in Tunisian third-grade primary school children.

PubMed

Batnini, Soulef; Uno, Akira

2015-06-01

This study investigated first the main cognitive abilities; phonological processing, visual cognition, automatization and receptive vocabulary in predicting reading and spelling abilities in Arabic. Second, we compared good/poor readers and spellers to detect the characteristics of cognitive predictors which contribute to identifying reading and spelling difficulties in Arabic speaking children. A sample of 116 Tunisian third-grade children was tested on their abilities to read and spell, phonological processing, visual cognition, automatization and receptive vocabulary. For reading, phonological processing and automatization uniquely predicted Arabic word reading and paragraph reading abilities. Automatization uniquely predicted Arabic non-word reading ability. For spelling, phonological processing was a unique predictor for Arabic word spelling ability. Furthermore, poor readers had significantly lower scores on the phonological processing test and slower reading times on the automatization test as compared with good readers. Additionally, poor spellers showed lower scores on the phonological processing test as compared with good spellers. Visual cognitive processing and receptive vocabulary were not significant cognitive predictors of Arabic reading and spelling abilities for Tunisian third grade children in this study. Our results are consistent with previous studies in alphabetic orthographies and demonstrate that phonological processing and automatization are the best cognitive predictors in detecting early literacy problems. We suggest including phonological processing and automatization tasks in screening tests and in intervention programs may help Tunisian children with poor literacy skills overcome reading and spelling difficulties in Arabic. Copyright © 2014 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Parents' Attitudes about Adolescents' Premarital Sexual Activity: The Role of Inter-Parent Consistency/Inconsistency in Sexual Outcomes

ERIC Educational Resources Information Center

Somers, Cheryl L.; Anagurthi, Claudia

2014-01-01

Objective: Parents' values about sexuality and about premarital sex play unique roles in the development of adolescents' sexual attitudes and behaviours. However, research is scarce on the role of consistent versus inconsistent values transmission. The purpose of the present study was to examine the association between parental…

Management of the aging upper eyelid in the asian patient.

PubMed

Karam, Amir M; Lam, Samuel M

2010-08-01

Successful management of the aging upper eyelid region in the Asian patient requires a unique skill set and clinical experience. The surgeon must exhibit a thorough understanding of the unique anatomy of the Asian eyelid and its variations and of the cultural expectations of the patient and must possess a unique set of surgical skills such as de novo creation of the supratarsal crease as well as complementary procedures such as fat transfer used for volume augmentation of the periorbital region. The modern approach outlined here summarizes the key elements necessary to restore the youthful appearance of the upper eyelid region in a natural and ethnically consistent fashion.

NCI Launches Proteomics Assay Portal | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass spectrometry (MRM-MS) assays.  This community web-based repository for well-characterized quantitative proteomic assays currently consists of 456 unique peptide assays to 282 unique proteins and ser

SPATIALLY RESOLVED SPECTROSCOPY OF EUROPA: THE DISTINCT SPECTRUM OF LARGE-SCALE CHAOS

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

Fischer, P. D.; Brown, M. E.; Hand, K. P., E-mail: pfischer@caltech.edu

2015-11-15

We present a comprehensive analysis of spatially resolved moderate spectral resolution near-infrared spectra obtained with the adaptive optics system at the Keck Observatory. We identify three compositionally distinct end member regions: the trailing hemisphere bullseye, the leading hemisphere upper latitudes, and a third component associated with leading hemisphere chaos units. We interpret the composition of the three end member regions to be dominated by irradiation products, water ice, and evaporite deposits or salt brines, respectively. The third component is associated with geological features and distinct from the geography of irradiation, suggesting an endogenous identity. Identifying the endogenous composition is ofmore » particular interest for revealing the subsurface composition. However, its spectrum is not consistent with linear mixtures of the salt minerals previously considered relevant to Europa. The spectrum of this component is distinguished by distorted hydration features rather than distinct spectral features, indicating hydrated minerals but making unique identification difficult. In particular, it lacks features common to hydrated sulfate minerals, challenging the traditional view of an endogenous salty component dominated by Mg-sulfates. Chloride evaporite deposits are one possible alternative.« less

The Auditory Brain-Stem Response to Complex Sounds: A Potential Biomarker for Guiding Treatment of Psychosis

PubMed Central

Tarasenko, Melissa A.; Swerdlow, Neal R.; Makeig, Scott; Braff, David L.; Light, Gregory A.

2014-01-01

Cognitive deficits limit psychosocial functioning in schizophrenia. For many patients, cognitive remediation approaches have yielded encouraging results. Nevertheless, therapeutic response is variable, and outcome studies consistently identify individuals who respond minimally to these interventions. Biomarkers that can assist in identifying patients likely to benefit from particular forms of cognitive remediation are needed. Here, we describe an event-related potential (ERP) biomarker – the auditory brain-stem response (ABR) to complex sounds (cABR) – that appears to be particularly well-suited for predicting response to at least one form of cognitive remediation that targets auditory information processing. Uniquely, the cABR quantifies the fidelity of sound encoded at the level of the brainstem and midbrain. This ERP biomarker has revealed auditory processing abnormalities in various neurodevelopmental disorders, correlates with functioning across several cognitive domains, and appears to be responsive to targeted auditory training. We present preliminary cABR data from 18 schizophrenia patients and propose further investigation of this biomarker for predicting and tracking response to cognitive interventions. PMID:25352811

Polarization Behavior Across Profile Modes For B0329+54: What Consistent Non-RVM Polarization Tells About the Emission Processes

NASA Astrophysics Data System (ADS)

Brinkman-Traverse, Casey; Rankin, Joanna M.; Mitra, Dipanjan

2017-01-01

In this paper, we analyze the quirky polarization behavior across different profile modes for the pulsar B0329+54. We have multi-frequency observations in both the normal and abnormal profile modes, and have identified a non-RVM polarization kink in the core component of the emission. Mitra et al initially identified this kink in the normal profile mode of the pulsar in 2007, and a mirror analysis has been done here for abnormal profile modes at three different frequencies. This kink is intensity dependent, showing up only in the abberated/retarded high intensity pulses, and is frequency independent. This parallel between profile modes shows that the same geometric phenomenon—a height dependent amplifier—is responsible for the non-RVM polarization behavior in each. The question then arises: what can be the source of the profile change, which does not change the polarization characteristics of the pulsar. This pulsar gives us a unique opportunity to study the process of pulsar emission by showing what cannot be responsible for switches in profile mode, and thus profile shape.

The Genome of the Obligately Intracellular Bacterium Ehrlichia canis Reveals Themes of Complex Membrane Structure and Immune Evasion Strategies

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

Mavromatis, K; Doyle, C Kuyler; Lykidis, A

2006-01-01

Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, {alpha}-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associatedmore » with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7).« less

A Taxonomic Search Engine: Federating taxonomic databases using web services

PubMed Central

Page, Roderic DM

2005-01-01

Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

The genome of obligately intracellular Ehrlichia canis revealsthemes of complex membrane structure and immune evasion strategies

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

Mavromatis, K.; Kuyler Doyle, C.; Lykidis, A.

2005-09-01

Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, a-proteobacterium is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, and 17 putative pseudogenes, and a substantial proportion of non-coding sequence (27 percent). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences, and a unique serine-threonine bias associated with the potential for O-glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein familiesmore » associated with immune evasion were identified, one of which contains poly G:C tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Proteins associated with pathogen-host interactions were identified including a small group of proteins (12) with tandem repeats and another with eukaryotic-like ankyrin domains (7).« less

Genome mining of the sordarin biosynthetic gene cluster from Sordaria araneosa Cain ATCC 36386: characterization of cycloaraneosene synthase and GDP-6-deoxyaltrose transferase.

PubMed

Kudo, Fumitaka; Matsuura, Yasunori; Hayashi, Takaaki; Fukushima, Masayuki; Eguchi, Tadashi

2016-07-01

Sordarin is a glycoside antibiotic with a unique tetracyclic diterpene aglycone structure called sordaricin. To understand its intriguing biosynthetic pathway that may include a Diels-Alder-type [4+2]cycloaddition, genome mining of the gene cluster from the draft genome sequence of the producer strain, Sordaria araneosa Cain ATCC 36386, was carried out. A contiguous 67 kb gene cluster consisting of 20 open reading frames encoding a putative diterpene cyclase, a glycosyltransferase, a type I polyketide synthase, and six cytochrome P450 monooxygenases were identified. In vitro enzymatic analysis of the putative diterpene cyclase SdnA showed that it catalyzes the transformation of geranylgeranyl diphosphate to cycloaraneosene, a known biosynthetic intermediate of sordarin. Furthermore, a putative glycosyltransferase SdnJ was found to catalyze the glycosylation of sordaricin in the presence of GDP-6-deoxy-d-altrose to give 4'-O-demethylsordarin. These results suggest that the identified sdn gene cluster is responsible for the biosynthesis of sordarin. Based on the isolated potential biosynthetic intermediates and bioinformatics analysis, a plausible biosynthetic pathway for sordarin is proposed.

Improving Patient Safety, Health Data Accuracy, and Remote Self-Management of Health Through the Establishment of a Biometric-Based Global UHID.

PubMed

Hembroff, Guy

2016-01-01

Healthcare systems globally continue to face challenges surrounding patient identification. Consequences of misidentification include incomplete and inaccurate electronic patient health records potentially jeopardizing patients' safety, a significant amount of cases of medical fraud because of inadequate identification mechanisms, and difficulties affiliated with the value of remote health self-management application data being aggregated accurately into the user's Electronic Health Record (EHR). We introduce a new technique of user identification in healthcare capable of establishing a global identifier. Our research has developed algorithms capable of establishing a Unique Health Identifier (UHID) based on the user's fingerprint biometric, with the utilization of facial-recognition as a secondary validation step before health records can be accessed. Biometric captures are completed using standard smartphones and Web cameras in a touchless method. We present a series of experiments to demonstrate the formation of an accurate, consistent, and scalable UHID. We hope our solution will aid in the reduction of complexities associated with user misidentification in healthcare resulting in lowering costs, enhancing population health monitoring, and improving patient-safety.

A threshold gas Cerenkov detector for the spin asymmetries of the nucleon experiment

DOE PAGES

Armstrong, Whitney R.; Choi, Seonho; Kaczanowicz, Ed; ...

2015-09-26

In this study, we report on the design, construction, commissioning, and performance of a threshold gas Cerenkov counter in an open configuration, which operates in a high luminosity environment and produces a high photo-electron yield. Part of a unique open geometry detector package known as the Big Electron Telescope Array, this Cerenkov counter served to identify scattered electrons and reject produced pions in an inclusive scattering experiment known as the Spin Asymmetries of the Nucleon Experiment E07-003 at the Thomas Jefferson National Accelerator Facility (TJNAF) also known as Jefferson Lab. The experiment consisted of a measurement of double spin asymmetriesmore » A || and A ⊥ of a polarized electron beam impinging on a polarized ammonia target. The Cerenkov counter's performance is characterised by a yield of about 20 photoelectrons per electron or positron track. Thanks to this large number of photoelectrons per track, the Cerenkov counter had enough resolution to identify electron-positron pairs from the conversion of photons resulting mainly from π 0 decays.« less

Integration of two RAB5 groups during endosomal transport in plants

PubMed Central

Ebine, Kazuo; Choi, Seung-won; Ichinose, Sakura; Uemura, Tomohiro; Nakano, Akihiko

2018-01-01

RAB5 is a key regulator of endosomal functions in eukaryotic cells. Plants possess two different RAB5 groups, canonical and plant-unique types, which act via unknown counteracting mechanisms. Here, we identified an effector molecule of the plant-unique RAB5 in Arabidopsis thaliana, ARA6, which we designated PLANT-UNIQUE RAB5 EFFECTOR 2 (PUF2). Preferential colocalization with canonical RAB5 on endosomes and genetic interaction analysis indicated that PUF2 coordinates vacuolar transport with canonical RAB5, although PUF2 was identified as an effector of ARA6. Competitive binding of PUF2 with GTP-bound ARA6 and GDP-bound canonical RAB5, together interacting with the shared activating factor VPS9a, showed that ARA6 negatively regulates canonical RAB5-mediated vacuolar transport by titrating PUF2 and VPS9a. These results suggest a unique and unprecedented function for a RAB effector involving the integration of two RAB groups to orchestrate endosomal trafficking in plant cells. PMID:29749929

Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

PubMed

Hong, Jungeui; Gresham, David

2017-11-01

Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using RNA-Seq.

Leveraging Administrative Data for Program Evaluations: A Method for Linking Data Sets Without Unique Identifiers.

PubMed

Lorden, Andrea L; Radcliff, Tiffany A; Jiang, Luohua; Horel, Scott A; Smith, Matthew L; Lorig, Kate; Howell, Benjamin L; Whitelaw, Nancy; Ory, Marcia

2016-06-01

In community-based wellness programs, Social Security Numbers (SSNs) are rarely collected to encourage participation and protect participant privacy. One measure of program effectiveness includes changes in health care utilization. For the 65 and over population, health care utilization is captured in Medicare administrative claims data. Therefore, methods as described in this article for linking participant information to administrative data are useful for program evaluations where unique identifiers such as SSN are not available. Following fuzzy matching methodologies, participant information from the National Study of the Chronic Disease Self-Management Program was linked to Medicare administrative data. Linking variables included participant name, date of birth, gender, address, and ZIP code. Seventy-eight percent of participants were linked to their Medicare claims data. Linking program participant information to Medicare administrative data where unique identifiers are not available provides researchers with the ability to leverage claims data to better understand program effects. © The Author(s) 2014.

Joint-Attention and the Social Phenotype of School-Aged Children with ASD.

PubMed

Mundy, Peter; Novotny, Stephanie; Swain-Lerro, Lindsey; McIntyre, Nancy; Zajic, Matt; Oswald, Tasha

2017-05-01

The validity of joint attention assessment in school-aged children with ASD is unclear (Lord, Jones, Journal of Child Psychology and Psychiatry 53(5):490-509, 2012). This study examined the feasibility and validity of a parent-report measure of joint attention related behaviors in verbal children and adolescents with ASD. Fifty-two children with ASD and 34 controls were assessed with the Childhood Joint Attention Rating Scale (C-JARS). The C-JARS exhibited internally consistency, α = 0.88, and one factor explained 49% of the scale variance. Factor scores correctly identified between 88 and 94% of the children with ASD and 62-82% of controls. These scores were correlated with the ADOS-2, but not other parent-report symptom measures. The C-JARS appears to assess a unique dimension of the social-phenotype of children with ASD.

Characteristics of Subcooled Liquid Methane During Passage Through a Spray-Bar Joule-Thompson Thermodynamic Vent System

NASA Technical Reports Server (NTRS)

Hastings, L. J.; Bolshinskiy, L. G.; Hedayat, A.; Schnell, A.

2011-01-01

NASA s Marshall Space Flight Center (MSFC) conducted liquid methane (LCH4) testing in November 2006 using the multipurpose hydrogen test bed (MHTB) outfitted with a spray-bar thermodynamic vent system (TVS). The basic objective was to identify any unusual or unique thermodynamic characteristics associated with subcooled LCH4 that should be considered in the design of space-based TVSs. Thirteen days of testing were performed with total tank heat loads ranging from 720 W to 420 W at a fill level of approximately 90%. During an updated evaluation of the data, it was noted that as the fluid passed through the Joule Thompson expansion, thermodynamic conditions consistent with the pervasive presence of metastability were indicated. This paper describes the observed thermodynamic conditions that correspond with metastability and effects on TVS performance.

Spacecraft attitude determination using a second-order nonlinear filter

NASA Technical Reports Server (NTRS)

Vathsal, S.

1987-01-01

The stringent attitude determination accuracy and faster slew maneuver requirements demanded by present-day spacecraft control systems motivate the development of recursive nonlinear filters for attitude estimation. This paper presents the second-order filter development for the estimation of attitude quaternion using three-axis gyro and star tracker measurement data. Performance comparisons have been made by computer simulation of system models and filter mechanization. It is shown that the second-order filter consistently performs better than the extended Kalman filter when the performance index of the root sum square estimation error of the quaternion vector is compared. The second-order filter identifies the gyro drift rates faster than the extended Kalman filter. The uniqueness of this algorithm is the online generation of the time-varying process and measurement noise covariance matrices, derived as a function or the process and measurement nonlinearity, respectively.

Monolayer nanoparticle-covered liquid marbles derived from a sol-gel coating

NASA Astrophysics Data System (ADS)

Li, Xiaoguang; Wang, Yiqi; Huang, Junchao; Yang, Yao; Wang, Renxian; Geng, Xingguo; Zang, Duyang

2017-12-01

A sol-gel coating consisting of hydrophobic SiO2 nanoparticles (NPs) was used to produce monolayer NP-covered (mNPc) liquid marbles. The simplest approach was rolling a droplet on this coating, and an identifiable signet allowed determination of the coverage ratio of the resulting liquid marble. Alternatively, the particles were squeezed onto a droplet surface with two such coatings, generating surface buckling from interfacial NP jamming, and then a liquid marble was produced via a jamming-relief process in which water was added into the buckled droplet. This process revealed an ˜7% reduction in particle distance after interfacial jamming. The mNPc liquid marbles obtained by the two methods were transparent with smooth profiles, as naked droplets, and could be advantageously used in fundamental and applied researches for their unique functions.

NASA Developmental Biology Workshop: A summary

NASA Technical Reports Server (NTRS)

Souza, K. A. (Editor); Halstead, T. W. (Editor)

1985-01-01

The Life Sciences Division of the National Aeronautics and Space Administration (NASA) as part of its continuing assessment of its research program, convened a workshop on Developmental Biology to determine whether there are important scientific studies in this area which warrant continued or expanded NASA support. The workshop consisted of six panels, each of which focused on a single major phylogenetic group. The objectives of each panel were to determine whether gravity plays a role in the ontogeny of their subject group, to determine whether the microgravity of spaceflight can be used to help understand fundamental problems in developmental biology, to develop the rationale and hypotheses for conducting NASA-relevant research in development biology both on the ground and in space, and to identify any unique equipment and facilities that would be required to support both ground-based and spaceflight experiments.

Immigrant Sexual Minority Latino Men in Rural North Carolina: An Exploration of Social Context, Social Behaviors, and Sexual Outcomes

PubMed Central

Gilbert, Paul A.; Rhodes, Scott D.

2014-01-01

Immigrant Sexual minority Latino men—who may or may not self-identify as gay—constitute a minority within a minority. Often labeled “hidden” and “hard-to-reach,” and marginalized along multiple dimensions, it is a sub-group about whom little is known. Informed by a Social Ecological Framework, we sought to describe key social variables for 190 such men in rural North Carolina and to test associations with three sexual outcomes: consistent condom use, number of sex partners, and sexual compulsivity. Participants reported limited English-language use, predominantly Latino close friends, middle levels of social support despite numerous social ties, and frequent experiences of discrimination. There were unique sets of correlates for each sexual outcome. Findings may inform health promotion interventions and guide future research. PMID:24344629

Two-Dimensional VO2 Mesoporous Microarrays for High-Performance Supercapacitor

NASA Astrophysics Data System (ADS)

Fan, Yuqi; Ouyang, Delong; Li, Bao-Wen; Dang, Feng; Ren, Zongming

2018-05-01

Two-dimensional (2D) mesoporous VO2 microarrays have been prepared using an organic-inorganic liquid interface. The units of microarrays consist of needle-like VO2 particles with a mesoporous structure, in which crack-like pores with a pore size of about 2 nm and depth of 20-100 nm are distributed on the particle surface. The liquid interface acts as a template for the formation of the 2D microarrays, as identified from the kinetic observation. Due to the mesoporous structure of the units and high conductivity of the microarray, such 2D VO2 microarrays exhibit a high specific capacitance of 265 F/g at 1 A/g and excellent rate capability (182 F/g at 10 A/g) and cycling stability, suggesting the effect of unique microstructure for improving the electrochemical performance.

Application of person-centered analytic methodology in longitudinal research: exemplars from the Women's Health Initiative Clinical Trial data.

PubMed

Zaslavsky, Oleg; Cochrane, Barbara B; Herting, Jerald R; Thompson, Hilaire J; Woods, Nancy F; Lacroix, Andrea

2014-02-01

Despite the variety of available analytic methods, longitudinal research in nursing has been dominated by use of a variable-centered analytic approach. The purpose of this article is to present the utility of person-centered methodology using a large cohort of American women 65 and older enrolled in the Women's Health Initiative Clinical Trial (N = 19,891). Four distinct trajectories of energy/fatigue scores were identified. Levels of fatigue were closely linked to age, socio-demographic factors, comorbidities, health behaviors, and poor sleep quality. These findings were consistent regardless of the methodological framework. Finally, we demonstrated that energy/fatigue levels predicted future hospitalization in non-disabled elderly. Person-centered methods provide unique opportunities to explore and statistically model the effects of longitudinal heterogeneity within a population. © 2013 Wiley Periodicals, Inc.

Pharmacokinetics and PBPK Models

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

Corley, Richard A.

2010-07-01

Since the landmark report Pesticides in the Diets of Infants and Children (NRC 1993), children at all stages of development, from fertilization through postnatal maturation, have explicitly been identified as an area of emphasis in human health risk assessments. Exposure to drugs or chemicals at any point in development has the potential for causing irreversible changes that can be unique to each stage of development (Grabowski and Daston 1983; Rodier 1978; Wilson 1973). While exposures of a developing embryo or fetus are mediated by the mother, postnatal exposures consist of maternal influences via breastfeeding as well as environmental factors (Figuremore » 1). As a result, risk assessments for developmental toxicity must consider the sources as well as timing of potential exposures to adequately protect children when they may be the most exposed or the most sensitive to adverse consequences (NRC 1993).« less

Attention, motivation, and reading coherence failure: a neuropsychological perspective.

PubMed

Wasserman, Theodore

2012-01-01

Reading coherence, defined as the ability to create appropriate, meaningful connections between the elements within a specific text itself and between elements within a text and the reader's prior knowledge, is one of the key processes involved in reading comprehension. This article describes reading coherence within the context of a neuropsychological model combining recent research in motivation, attention, and working memory. Specifically, a unique neuropsychologically identifiable form of reading coherence failure arising from the attentional and motivational deficiencies, based in altered frontoventral striatal reward circuits associated with noradrenaline (NA) circuitry, consistent with the delay-aversion model (dual-pathway model) of Sonuga-Barke ( 2003 ) is postulated. This article provides a model for this subset of reading disorders of which etiology is based on the executive support processes for reading and not in the mechanics of actual reading such as decoding and phonetics.

A Novel Non-Invasive Selection Criterion for the Preservation of Primitive Dutch Konik Horses

PubMed Central

May-Davis, Sharon; Shorter, Kathleen; Vermeulen, Zefanja; Butler, Raquel; Koekkoek, Marianne

2018-01-01

The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed, particularly in height at the wither, colour (mouse to grey dun) and presence of primitive markings. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik (n = 47) and modern domesticated horses (n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed. PMID:29389896

Correlates of vitamin D in psychotic disorders: A comprehensive systematic review.

PubMed

Adamson, James; Lally, John; Gaughran, Fiona; Krivoy, Amir; Allen, Lauren; Stubbs, Brendon

2017-03-01

People with psychosis have high prevalence of low vitamin D levels but the correlates and relevance of this deficiency are unclear. A systematic search of major databases from inception to 03/2016 was undertaken investigating correlates of vitamin D in people with psychosis. Data was summarised with a best evidence synthesis. Across 23 included studies (n=1770 psychosis, n=8171 controls) a mean difference in vitamin D levels between both groups of -11.14ng/ml±0.59 was found. 53 unique correlations between vitamin D and outcomes in people with psychosis were identified. The evidence base was broadly equivocal although season of blood sampling (67% of studies found a positive correlation with warmer seasons) and parathyroid hormone (100% of studies found a negative correlation) were associated with vitamin D levels. The most commonly non-correlated variables were: BMI (83% found no correlation), age (73%), gender (86%), smoking (100%), duration of illness (100%) and general assessment of functioning score (100%). In conclusion, whilst many unique correlates have been investigated, there is weak and inconclusive evidence regarding the consistency and meaning of the correlates of vitamin D levels in people with psychosis. Future longitudinal studies should consider the correlates of vitamin D in people with psychosis. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Constraining Binary Asteroid Mass Distributions Based On Mutual Motion

NASA Astrophysics Data System (ADS)

Davis, Alex B.; Scheeres, Daniel J.

2017-06-01

The mutual gravitational potential and torques of binary asteroid systems results in a complex coupling of attitude and orbital motion based on the mass distribution of each body. For a doubly-synchronous binary system observations of the mutual motion can be leveraged to identify and measure the unique mass distributions of each body. By implementing arbitrary shape and order computation of the full two-body problem (F2BP) equilibria we study the influence of asteroid asymmetries on separation and orientation of a doubly-synchronous system. Additionally, simulations of binary systems perturbed from doubly-synchronous behavior are studied to understand the effects of mass distribution perturbations on precession and nutation rates such that unique behaviors can be isolated and used to measure asteroid mass distributions. We apply our investigation to the Trojan binary asteroid system 617 Patroclus and Menoetius (1906 VY), which will be the final flyby target of the recently announced LUCY Discovery mission in March 2033. This binary asteroid system is of particular interest due to the results of a recent stellar occultation study (DPS 46, id.506.09) that suggests the system to be doubly-synchronous and consisting of two-similarly sized oblate ellipsoids, in addition to suggesting the presence mass asymmetries resulting from an impact crater on the southern limb of Menoetius.

Psychometric properties of the Image of God Scale in breast cancer survivors.

PubMed

Schreiber, Judy A

2012-07-01

To examine the psychometric properties of the Image of God Scale (IGS) in a clinical population. Descriptive, cross-sectional. University and community oncology practices in the southeastern United States. 123 breast cancer survivors no more than two years from completion of treatment. Scale reliability was determined with the coefficient alpha. Instrument dimensionality was examined using principal component analysis. Construct validity was evaluated by examining correlations with other instruments used in the study. An individual's image of God. Internal consistency was strong (anger subscale = 0.8; engagement subscale = 0.89). The principle component analysis resulted in a two-factor solution with items loading uniquely on Factor 1-Engagement (8) and Factor 2-Anger (6). Significant correlations between the IGS and religious coping support convergence on a God concept. Correlations with psychological well-being, psychological distress, and concern about recurrence were nonsignificant (engagement) or inverse (anger), supporting discrimination between concepts of God and psychological adjustment. The IGS is a unique measure of how God is viewed by the depth and character of His involvement with the individual and the world. The IGS may be a measure that can transcend sects, denominations, and religions by identifying the image of God that underlies and defines an individuals' worldview, which influences their attitudes and behaviors.

Comparative Genomic Analyses of Clavibacter michiganensis subsp. insidiosus and Pathogenicity on Medicago truncatula.

PubMed

Lu, You; Ishimaru, Carol A; Glazebrook, Jane; Samac, Deborah A

2018-02-01

Clavibacter michiganensis is the most economically important gram-positive bacterial plant pathogen, with subspecies that cause serious diseases of maize, wheat, tomato, potato, and alfalfa. Much less is known about pathogenesis involving gram-positive plant pathogens than is known for gram-negative bacteria. Comparative genome analyses of C. michiganensis subspecies affecting tomato, potato, and maize have provided insights on pathogenicity. In this study, we identified strains of C. michiganensis subsp. insidiosus with contrasting pathogenicity on three accessions of the model legume Medicago truncatula. We generated complete genome sequences for two strains and compared these to a previously sequenced strain and genome sequences of four other subspecies. The three C. michiganensis subsp. insidiosus strains varied in gene content due to genome rearrangements, most likely facilitated by insertion elements, and plasmid number, which varied from one to three depending on strain. The core C. michiganensis genome consisted of 1,917 genes, with 379 genes unique to C. michiganensis subsp. insidiosus. An operon for synthesis of the extracellular blue pigment indigoidine, enzymes for pectin degradation, and an operon for inositol metabolism are among the unique features. Secreted serine proteases belonging to both the pat-1 and ppa families were present but highly diverged from those in other subspecies.

Remodeling of the Vibrio cholerae membrane by incorporation of exogenous fatty acids from host and aquatic environments

PubMed Central

Giles, David K.; Hankins, Jessica V.; Guan, Ziqiang; Trent, M. Stephen

2011-01-01

Summary The Gram-negative bacteria Vibrio cholerae poses significant public health concerns by causing an acute intestinal infection afflicting millions of people each year. V. cholerae motility, as well as virulence factor expression and outer membrane protein production, have been shown to be affected by bile (Childers & Klose, 2007). The current study examines the effects of bile on V. cholerae phospholipids. Bile exposure caused significant alterations to the phospholipid profile of V. cholerae but not of other enteric pathogens. These changes consisted of a quantitative increase and migratory difference in cardiolipin, decreases in phosphatidylglycerol and phosphatidylethanolamine, and the dramatic appearance of an unknown phospholipid determined to be lyso-phosphatidylethanolamine. Major components of bile were not responsible for the observed changes, but long chain polyunsaturated fatty acids, which are minor components of bile, were shown to be incorporated into phospholipids of V. cholerae. Although the bile-induced phospholipid profile was independent of the V. cholerae virulence cascade, we identified another relevant environment in which V. cholerae assimilates unique fatty acids into its membrane phospholipids—marine sediment. Our results suggest that Vibrio species possess unique machinery conferring the ability to take up a wider range of exogenous fatty acids than other enteric bacteria. PMID:21255114

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish.

PubMed

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-08-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change - an important component of biological conservation and ecosystem management.

Gender role, sexual orientation and suicide risk.

PubMed

Fitzpatrick, Kathleen Kara; Euton, Stephanie J; Jones, Jamie N; Schmidt, Norman B

2005-07-01

There has been interest in the relationship between homosexuality, gender role and suicide risk. Though homosexuals are more likely to identify as cross-gender, research has not simultaneously examined sexual orientation and gender role in assessing suicide risk. In the current study, the unique and interactive effects of sexual orientation and gender role were assessed in regard to suicidal ideation, related psychopathology and measures of coping. 77 participants were recruited from an undergraduate psychology subject pool (n=47) or from gay, lesbian and transgender student organizations (n=30) and assessed on measures of gender role, homosexuality, and psychopathology. Consistent with expectations, cross-gender role (i.e., personality traits associated with the opposite sex) is a unique predictor of suicidal symptoms. Moreover, gender role accounted for more of the overall variance in suicidal symptoms, positive problem orientation, peer acceptance and support, than sexual orientation. After accounting for gender role, sexual orientation contributed little to the variance in suicidal symptoms, associated pathology and problem-solving deficits. There was no support for gender role by sexual orientation interaction effects. The cross-sectional nature of the data limits statements regarding causality. Cross-gendered individuals, regardless of sexual orientation, appear to have higher risk for suicidal symptoms. Researchers and clinicians should assess gender role in evaluations of youth samples.

“It’s Not JUST Skin Cancer”: Understanding Their Cancer Experience From Melanoma Survivor Narratives Shared Online

PubMed Central

Banerjee, Smita C.; D’Agostino, Thomas A.; Gordon, Mallorie L.; Hay, Jennifer L.

2016-01-01

Cancer survivors narrate their experiences in unique ways, articulating different aspects of the cancer journey. The purpose of this study was to analyze the content of cancer narratives that melanoma survivors share online in order to present the ways that survivors narrate their cancer experience, to identify survivors’ motivations for sharing, and to better understand the ways in which survivors are impacted by and cope with the diagnosis and treatment of cancer. The sample consisted of 95 unique melanoma survivor narratives, accessed from the Melanoma Research Foundation in November 2015, that were inductively and deductively coded for key themes and subthemes. Emergent themes described different aspects of the melanoma experience during prediagnosis (identification of selfphenotype, searching for causes, suspicious findings, delay in diagnosis), diagnosis (communication of diagnosis, emotional responses), transition from diagnosis to beginning treatment (second opinion), treatment (positive reframing of attitude, proactive cancer management, side effects), and posttreatment phases (social support, vigilance behaviors posttreatment). Two themes that cut across all phases of the cancer journey included recognizing and dealing with uncertainty and survivors’ motive for sharing narrative. These findings have implications for understanding how melanoma survivors may benefit personally from sharing their cancer experience online and for the potential for survivor narratives to motivate behavior change and facilitate coping among readers. PMID:27982699

Peptide vaccine immunotherapy biomarkers and response patterns in pediatric gliomas

PubMed Central

Müller, Sören; Agnihotri, Sameer; Shoger, Karsen E.; Myers, Max I.; Chaparala, Srilakshmi; Villanueva, Clarence R.; Chattopadhyay, Ansuman; Butterfield, Lisa H.; Okada, Hideho; Pollack, Ian F.

2018-01-01

Low-grade gliomas (LGGs) are the most common brain tumor affecting children. We recently reported an early phase clinical trial of a peptide-based vaccine, which elicited consistent antigen-specific T cell responses in pediatric LGG patients. Additionally, we observed radiologic responses of stable disease (SD), partial response (PR), and near-complete/complete response (CR) following therapy. To identify biomarkers of clinical response in peripheral blood, we performed RNA sequencing on PBMC samples collected at multiple time points. Patients who showed CR demonstrated elevated levels of T cell activation markers, accompanied by a cytotoxic T cell response shortly after treatment initiation. At week 34, patients with CR demonstrated both IFN signaling and Poly-IC:LC adjuvant response patterns. Patients with PR demonstrated a unique, late monocyte response signature. Interestingly, HLA-V expression, before or during therapy, and an early monocytic hematopoietic response were strongly associated with SD. Finally, low IDO1 and PD-L1 expression before treatment and early elevated levels of T cell activation markers were associated with prolonged progression-free survival. Overall, our data support the presence of unique peripheral immune patterns in LGG patients associated with different radiographic responses to our peptide vaccine immunotherapy. Future clinical trials, including our ongoing phase II LGG vaccine immunotherapy, should monitor these response patterns. PMID:29618666

A Novel Non-Invasive Selection Criterion for the Preservation of Primitive Dutch Konik Horses.

PubMed

May-Davis, Sharon; Brown, Wendy Y; Shorter, Kathleen; Vermeulen, Zefanja; Butler, Raquel; Koekkoek, Marianne

2018-02-01

The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed, particularly in height at the wither, colour (mouse to grey dun) and presence of primitive markings. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik ( n = 47) and modern domesticated horses ( n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish

PubMed Central

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-01-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management. PMID:26240605

Impact of Huntington Disease Gene-Positive Status on Pre-Symptomatic Young Adults and Recommendations for Genetic Counselors.

PubMed

Gong, Ping; Fanos, Joanna H; Korty, Lauren; Siskind, Carly E; Hanson-Kahn, Andrea K

2016-12-01

Huntington disease (HD) is an autosomal dominant, progressive neurodegenerative disorder for which there is no cure. Predictive testing for HD is available to asymptomatic at-risk individuals. Approximately half of the population undergoing predictive testing for HD consists of young adults (≤35 years old). Finishing one's education, starting a career, engaging in romantic relationships and becoming a parent are key milestones of young adulthood. We conducted a qualitative study to explore how testing gene-positive for HD influences young adults' attainment of these milestones, and to identify major challenges that pre-symptomatic young adults face to aid the development of targeted genetic counseling. Results of our study demonstrate that 1) knowing one's gene-positive status results in an urgency to reach milestones and positively changes young adults' approach to life; 2) testing positive influences young adults' education and career choices, romantic relationships, and family planning; 3) young adults desire flexible and tailored genetic counseling to address needs and concerns unique to this population. Findings of this study contribute to the understanding of the impact of predictive testing for HD on young adults, and highlight issues unique to this population that call for further research, intervention and advocacy.

Application of Wavelet Transform for PDZ Domain Classification

PubMed Central

Daqrouq, Khaled; Alhmouz, Rami; Balamesh, Ahmed; Memic, Adnan

2015-01-01

PDZ domains have been identified as part of an array of signaling proteins that are often unrelated, except for the well-conserved structural PDZ domain they contain. These domains have been linked to many disease processes including common Avian influenza, as well as very rare conditions such as Fraser and Usher syndromes. Historically, based on the interactions and the nature of bonds they form, PDZ domains have most often been classified into one of three classes (class I, class II and others - class III), that is directly dependent on their binding partner. In this study, we report on three unique feature extraction approaches based on the bigram and trigram occurrence and existence rearrangements within the domain's primary amino acid sequences in assisting PDZ domain classification. Wavelet packet transform (WPT) and Shannon entropy denoted by wavelet entropy (WE) feature extraction methods were proposed. Using 115 unique human and mouse PDZ domains, the existence rearrangement approach yielded a high recognition rate (78.34%), which outperformed our occurrence rearrangements based method. The recognition rate was (81.41%) with validation technique. The method reported for PDZ domain classification from primary sequences proved to be an encouraging approach for obtaining consistent classification results. We anticipate that by increasing the database size, we can further improve feature extraction and correct classification. PMID:25860375

A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1

PubMed Central

Lidral, Andrew C.; Liu, Huan; Bullard, Steven A.; Bonde, Greg; Machida, Junichiro; Visel, Axel; Uribe, Lina M. Moreno; Li, Xiao; Amendt, Brad; Cornell, Robert A.

2015-01-01

Three common diseases, isolated cleft lip and cleft palate (CLP), hypothyroidism and thyroid cancer all map to the FOXE1 locus, but causative variants have yet to be identified. In patients with CLP, the frequency of coding mutations in FOXE1 fails to account for the risk attributable to this locus, suggesting that the common risk alleles reside in nearby regulatory elements. Using a combination of zebrafish and mouse transgenesis, we screened 15 conserved non-coding sequences for enhancer activity, identifying three that regulate expression in a tissue specific pattern consistent with endogenous foxe1 expression. These three, located −82.4, −67.7 and +22.6 kb from the FOXE1 start codon, are all active in the oral epithelium or branchial arches. The −67.7 and +22.6 kb elements are also active in the developing heart, and the −67.7 kb element uniquely directs expression in the developing thyroid. Within the −67.7 kb element is the SNP rs7850258 that is associated with all three diseases. Quantitative reporter assays in oral epithelial and thyroid cell lines show that the rs7850258 allele (G) associated with CLP and hypothyroidism has significantly greater enhancer activity than the allele associated with thyroid cancer (A). Moreover, consistent with predicted transcription factor binding differences, the −67.7 kb element containing rs7850258 allele G is significantly more responsive to both MYC and ARNT than allele A. By demonstrating that this common non-coding variant alters FOXE1 expression, we have identified at least in part the functional basis for the genetic risk of these seemingly disparate disorders. PMID:25652407

Spatial variation of volcanic rock geochemistry in the Virunga Volcanic Province: Statistical analysis of an integrated database

NASA Astrophysics Data System (ADS)

Barette, Florian; Poppe, Sam; Smets, Benoît; Benbakkar, Mhammed; Kervyn, Matthieu

2017-10-01

We present an integrated, spatially-explicit database of existing geochemical major-element analyses available from (post-) colonial scientific reports, PhD Theses and international publications for the Virunga Volcanic Province, located in the western branch of the East African Rift System. This volcanic province is characterised by alkaline volcanism, including silica-undersaturated, alkaline and potassic lavas. The database contains a total of 908 geochemical analyses of eruptive rocks for the entire volcanic province with a localisation for most samples. A preliminary analysis of the overall consistency of the database, using statistical techniques on sets of geochemical analyses with contrasted analytical methods or dates, demonstrates that the database is consistent. We applied a principal component analysis and cluster analysis on whole-rock major element compositions included in the database to study the spatial variation of the chemical composition of eruptive products in the Virunga Volcanic Province. These statistical analyses identify spatially distributed clusters of eruptive products. The known geochemical contrasts are highlighted by the spatial analysis, such as the unique geochemical signature of Nyiragongo lavas compared to other Virunga lavas, the geochemical heterogeneity of the Bulengo area, and the trachyte flows of Karisimbi volcano. Most importantly, we identified separate clusters of eruptive products which originate from primitive magmatic sources. These lavas of primitive composition are preferentially located along NE-SW inherited rift structures, often at distance from the central Virunga volcanoes. Our results illustrate the relevance of a spatial analysis on integrated geochemical data for a volcanic province, as a complement to classical petrological investigations. This approach indeed helps to characterise geochemical variations within a complex of magmatic systems and to identify specific petrologic and geochemical investigations that should be tackled within a study area.

Tick Haller's Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects.

PubMed

Carr, Ann L; Mitchell, Robert D; Dhammi, Anirudh; Bissinger, Brooke W; Sonenshine, Daniel E; Roe, R Michael

2017-07-18

Ticks are the vector of many human and animal diseases; and host detection is critical to this process. Ticks have a unique sensory structure located exclusively on the 1st pairs of legs; the fore-tarsal Haller's organ, not found in any other animals, presumed to function like the insect antennae in chemosensation but morphologically very different. The mechanism of tick chemoreception is unknown. Utilizing next-generation sequencing and comparative transcriptomics between the 1st and 4th legs (the latter without the Haller's organ), we characterized 1st leg specific and putative Haller's organ specific transcripts from adult American dog ticks, Dermacentor variabilis . The analysis suggested that the Haller's organ is involved in olfaction, not gustation. No known odorant binding proteins like those found in insects, chemosensory lipocalins or typical insect olfactory mechanisms were identified; with the transcriptomic data only supporting a possible olfactory G-protein coupled receptor (GPCR) signal cascade unique to the Haller's organ. Each component of the olfactory GPCR signal cascade was identified and characterized. The expression of GPCR, G αo and β-arrestin transcripts identified exclusively in the 1st leg transcriptome, and putatively Haller's organ specific, were examined in unfed and blood-fed adult female and male D. variabilis . Blood feeding to repletion in adult females down-regulated the expression of all three chemosensory transcripts in females but not in males; consistent with differences in post-feeding tick behavior between sexes and an expected reduced chemosensory function in females as they leave the host. Data are presented for the first time of the potential hormonal regulation of tick chemosensation; behavioral assays confirmed the role of the Haller's organ in N , N -diethyl-meta-toluamide (DEET) repellency but showed no role for the Haller's organ in host attachment. Further research is needed to understand the potential role of the GPCR cascade in olfaction.

A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes.

PubMed

Rokyta, Darin R; Wray, Kenneth P; Lemmon, Alan R; Lemmon, Emily Moriarty; Caudle, S Brian

2011-04-01

Despite causing considerable human mortality and morbidity, animal toxins represent a valuable source of pharmacologically active macromolecules, a unique system for studying molecular adaptation, and a powerful framework for examining structure-function relationships in proteins. Snake venoms are particularly useful in the latter regard as they consist primarily of a moderate number of proteins and peptides that have been found to belong to just a handful of protein families. As these proteins and peptides are produced in dedicated glands, transcriptome sequencing has proven to be an effective approach to identifying the expressed toxin genes. We generated a venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) using Roche 454 sequencing technology. In the current work, we focus on transcripts encoding toxins. We identified 40 unique toxin transcripts, 30 of which have full-length coding sequences, and 10 have only partial coding sequences. These toxins account for 24% of the total sequencing reads. We found toxins from 11 previously described families of snake-venom toxins and have discovered two putative, previously undescribed toxin classes. The most diverse and highly expressed toxin classes in the C. adamanteus venom-gland transcriptome are the serine proteinases, metalloproteinases, and C-type lectins. The serine proteinases are the most abundant class, accounting for 35% of the toxin sequencing reads. Metalloproteinases are the most diverse; 11 different forms have been identified. Using our sequences and those available in public databases, we detected positive selection in seven of the eight toxin families for which sufficient sequences were available for the analysis. We find that the vast majority of the genes that contribute directly to this vertebrate trait show evidence for a role for positive selection in their evolutionary history. Copyright © 2011 Elsevier Ltd. All rights reserved.

Injury-Dependent and Disability-Specific Lumbar Spinal Gene Regulation following Sciatic Nerve Injury in the Rat

PubMed Central

Denyer, Gareth S.; Keay, Kevin A.

2015-01-01

Allodynia, hyperalgesia and spontaneous pain are cardinal sensory signs of neuropathic pain. Clinically, many neuropathic pain patients experience affective-motivational state changes, including reduced familial and social interactions, decreased motivation, anhedonia and depression which are severely debilitating. In earlier studies we have shown that sciatic nerve chronic constriction injury (CCI) disrupts social interactions, sleep-wake-cycle and endocrine function in one third of rats, a subgroup reliably identified six days after injury. CCI consistently produces allodynia and hyperalgesia, the intensity of which was unrelated either to the altered social interactions, sleep-wake-cycle or endocrine changes. This decoupling of the sensory consequences of nerve injury from the affective-motivational changes is reported in both animal experiments and human clinical data. The sensory changes triggered by CCI are mediated primarily by functional changes in the lumbar dorsal horn, however, whether lumbar spinal changes may drive different affective-motivational states has never been considered. In these studies, we used microarrays to identify the unique transcriptomes of rats with altered social behaviours following sciatic CCI to determine whether specific patterns of lumbar spinal adaptations characterised this subgroup. Rats underwent CCI and on the basis of reductions in dominance behaviour in resident-intruder social interactions were categorised as having Pain & Disability, Pain & Transient Disability or Pain alone. We examined the lumbar spinal transcriptomes two and six days after CCI. Fifty-four ‘disability-specific’ genes were identified. Sixty-five percent were unique to Pain & Disability rats, two-thirds of which were associated with neurotransmission, inflammation and/or cellular stress. In contrast, 40% of genes differentially regulated in rats without disabilities were involved with more general homeostatic processes (cellular structure, transcription or translation). We suggest that these patterns of gene expression lead to either the expression of disability, or to resilience and recovery, by modifying local spinal circuitry at the origin of ascending supraspinal pathways. PMID:25905723

Injury-Dependent and Disability-Specific Lumbar Spinal Gene Regulation following Sciatic Nerve Injury in the Rat.

PubMed

Austin, Paul J; Bembrick, Alison L; Denyer, Gareth S; Keay, Kevin A

2015-01-01

Allodynia, hyperalgesia and spontaneous pain are cardinal sensory signs of neuropathic pain. Clinically, many neuropathic pain patients experience affective-motivational state changes, including reduced familial and social interactions, decreased motivation, anhedonia and depression which are severely debilitating. In earlier studies we have shown that sciatic nerve chronic constriction injury (CCI) disrupts social interactions, sleep-wake-cycle and endocrine function in one third of rats, a subgroup reliably identified six days after injury. CCI consistently produces allodynia and hyperalgesia, the intensity of which was unrelated either to the altered social interactions, sleep-wake-cycle or endocrine changes. This decoupling of the sensory consequences of nerve injury from the affective-motivational changes is reported in both animal experiments and human clinical data. The sensory changes triggered by CCI are mediated primarily by functional changes in the lumbar dorsal horn, however, whether lumbar spinal changes may drive different affective-motivational states has never been considered. In these studies, we used microarrays to identify the unique transcriptomes of rats with altered social behaviours following sciatic CCI to determine whether specific patterns of lumbar spinal adaptations characterised this subgroup. Rats underwent CCI and on the basis of reductions in dominance behaviour in resident-intruder social interactions were categorised as having Pain & Disability, Pain & Transient Disability or Pain alone. We examined the lumbar spinal transcriptomes two and six days after CCI. Fifty-four 'disability-specific' genes were identified. Sixty-five percent were unique to Pain & Disability rats, two-thirds of which were associated with neurotransmission, inflammation and/or cellular stress. In contrast, 40% of genes differentially regulated in rats without disabilities were involved with more general homeostatic processes (cellular structure, transcription or translation). We suggest that these patterns of gene expression lead to either the expression of disability, or to resilience and recovery, by modifying local spinal circuitry at the origin of ascending supraspinal pathways.

Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

PubMed Central

Carr, Ann L.; Mitchell III, Robert D.; Dhammi, Anirudh; Bissinger, Brooke W.; Sonenshine, Daniel E.; Roe, R. Michael

2017-01-01

Ticks are the vector of many human and animal diseases; and host detection is critical to this process. Ticks have a unique sensory structure located exclusively on the 1st pairs of legs; the fore-tarsal Haller’s organ, not found in any other animals, presumed to function like the insect antennae in chemosensation but morphologically very different. The mechanism of tick chemoreception is unknown. Utilizing next-generation sequencing and comparative transcriptomics between the 1st and 4th legs (the latter without the Haller’s organ), we characterized 1st leg specific and putative Haller’s organ specific transcripts from adult American dog ticks, Dermacentor variabilis. The analysis suggested that the Haller’s organ is involved in olfaction, not gustation. No known odorant binding proteins like those found in insects, chemosensory lipocalins or typical insect olfactory mechanisms were identified; with the transcriptomic data only supporting a possible olfactory G-protein coupled receptor (GPCR) signal cascade unique to the Haller’s organ. Each component of the olfactory GPCR signal cascade was identified and characterized. The expression of GPCR, Gαo and β-arrestin transcripts identified exclusively in the 1st leg transcriptome, and putatively Haller’s organ specific, were examined in unfed and blood-fed adult female and male D. variabilis. Blood feeding to repletion in adult females down-regulated the expression of all three chemosensory transcripts in females but not in males; consistent with differences in post-feeding tick behavior between sexes and an expected reduced chemosensory function in females as they leave the host. Data are presented for the first time of the potential hormonal regulation of tick chemosensation; behavioral assays confirmed the role of the Haller’s organ in N,N-diethyl-meta-toluamide (DEET) repellency but showed no role for the Haller’s organ in host attachment. Further research is needed to understand the potential role of the GPCR cascade in olfaction. PMID:28718821

Some Unique Causes of Black Suicide.

ERIC Educational Resources Information Center

Spaights, Ernest; Simpson, Gloria

1986-01-01

Aspects of suicide unique to blacks are: cultural expectations for males, which include repression of feelings and strict obedience to parents and elders; difficulty identifying with their race; gangs and drug abuse; poverty; and racism. These factors can cause depression, a known factor in suicidal behavior. (Author/ABB)

48 CFR 252.211-7003 - Item unique identification and valuation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... reader or interrogator, used to retrieve data encoded on machine-readable media. Concatenated unique item... identifier. Item means a single hardware article or a single unit formed by a grouping of subassemblies... manufactured under identical conditions. Machine-readable means an automatic identification technology media...

Antecedents of transition patterns of depressive symptom trajectories from adolescence to young adulthood.

PubMed

Lee, Tae Kyoung; Wickrama, Kandauda A S; Kwon, Josephine A; Lorenz, Frederick O; Oshri, Assaf

2017-11-01

This study examined (a) transition patterns from adolescent-specific depressive symptom trajectory classes to young adult-specific trajectory classes (N = 537; 15-26 years) and (b) identified risk factors associated with these transition patterns. The latent classes and transition analyses identified three transitional patterns of depressive symptom trajectories, including a deteriorating pattern (8.2%), a recovering pattern (22.5%), and a consistently low pattern (69.3%). Additionally, the results showed that contextual risk factors (i.e., negative economic events, negative romantic relationships, and low college enrolment rates) in the transition period to young adulthood were more positively associated with deteriorated or recovered transition patterns of depressive symptom trajectories than with the consistently low transition patterns even after taking into account the effects of adolescent risk factors. The identification of dynamic transition patterns in depressive symptom trajectories from adolescence to young adulthood and risk factors provide useful tools for preventive and intervention efforts. Statement of contribution What is already known on this subject? Heterogeneous trajectories of depressive symptoms across adolescence and young adulthood have been reported. Psychosocial characteristics differentiate trajectories of depressive symptoms from adolescence to young adulthood. What does this study add? Dynamic transition patterns of depressive symptom trajectories are found between adolescence and young adulthood. Life experiences in the transition period are uniquely associated with the transition patterns of depressive symptom trajectories even after adjusting the effects of adolescent characteristics. © 2017 The British Psychological Society.

Identification of a calmodulin-regulated Ca2+-ATPase in the endoplasmic reticulum

NASA Technical Reports Server (NTRS)

Hong, B.; Ichida, A.; Wang, Y.; Gens, J. S.; Pickard, B. G.; Harper, J. F.; Evans, M. L. (Principal Investigator)

1999-01-01

A unique subfamily of calmodulin-dependent Ca2+-ATPases was recently identified in plants. In contrast to the most closely related pumps in animals, plasma membrane-type Ca2+-ATPases, members of this new subfamily are distinguished by a calmodulin-regulated autoinhibitor located at the N-terminal instead of a C-terminal end. In addition, at least some isoforms appear to reside in non-plasma membrane locations. To begin delineating their functions, we investigated the subcellular localization of isoform ACA2p (Arabidopsis Ca2+-ATPase, isoform 2 protein) in Arabidopsis. Here we provide evidence that ACA2p resides in the endoplasmic reticulum (ER). In buoyant density sucrose gradients performed with and without Mg2+, ACA2p cofractionated with an ER membrane marker and a typical "ER-type" Ca2+-ATPase, ACA3p/ECA1p. To visualize its subcellular localization, ACA2p was tagged with a green fluorescence protein at its C terminus (ACA2-GFPp) and expressed in transgenic Arabidopsis. We collected fluorescence images from live root cells using confocal and computational optical-sectioning microscopy. ACA2-GFPp appeared as a fluorescent reticulum, consistent with an ER location. In addition, we observed strong fluorescence around the nuclei of mature epidermal cells, which is consistent with the hypothesis that ACA2p may also function in the nuclear envelope. An ER location makes ACA2p distinct from all other calmodulin-regulated pumps identified in plants or animals.

Assessing the influence of rater and subject characteristics on measures of agreement for ordinal ratings.

PubMed

Nelson, Kerrie P; Mitani, Aya A; Edwards, Don

2017-09-10

Widespread inconsistencies are commonly observed between physicians' ordinal classifications in screening tests results such as mammography. These discrepancies have motivated large-scale agreement studies where many raters contribute ratings. The primary goal of these studies is to identify factors related to physicians and patients' test results, which may lead to stronger consistency between raters' classifications. While ordered categorical scales are frequently used to classify screening test results, very few statistical approaches exist to model agreement between multiple raters. Here we develop a flexible and comprehensive approach to assess the influence of rater and subject characteristics on agreement between multiple raters' ordinal classifications in large-scale agreement studies. Our approach is based upon the class of generalized linear mixed models. Novel summary model-based measures are proposed to assess agreement between all, or a subgroup of raters, such as experienced physicians. Hypothesis tests are described to formally identify factors such as physicians' level of experience that play an important role in improving consistency of ratings between raters. We demonstrate how unique characteristics of individual raters can be assessed via conditional modes generated during the modeling process. Simulation studies are presented to demonstrate the performance of the proposed methods and summary measure of agreement. The methods are applied to a large-scale mammography agreement study to investigate the effects of rater and patient characteristics on the strength of agreement between radiologists. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Circuitry to explain how the relative number of L and M cones shapes color experience

PubMed Central

Schmidt, Brian P.; Touch, Phanith; Neitz, Maureen; Neitz, Jay

2016-01-01

The wavelength of light that appears unique yellow is surprisingly consistent across people even though the ratio of middle (M) to long (L) wavelength sensitive cones is strikingly variable. This observation has been explained by normalization to the mean spectral distribution of our shared environment. Our purpose was to reconcile the nearly perfect alignment of everyone's unique yellow through a normalization process with the striking variability in unique green, which varies by as much as 60 nm between individuals. The spectral location of unique green was measured in a group of volunteers whose cone ratios were estimated with a technique that combined genetics and flicker photometric electroretinograms. In contrast to unique yellow, unique green was highly dependent upon relative cone numerosity. We hypothesized that the difference in neural architecture of the blue-yellow and red-green opponent systems in the presence of a normalization process creates the surprising dependence of unique green on cone ratio. We then compared the predictions of different theories of color vision processing that incorporate L and M cone ratio and a normalization process. The results of this analysis reveal that—contrary to prevailing notions--postretinal contributions may not be required to explain the phenomena of unique hues. PMID:27366885

Contributions of identifiable neurons and neuron classes to lamprey vertebrate neurobiology.

PubMed

Buchanan, J T

2001-03-01

Among the advantages offered by the lamprey brainstem and spinal cord for studies of the structure and function of the nervous system is the unique identifiability of several pairs of reticulospinal neurons in the brainstem. These neurons have been exploited in investigations of the patterns of sensory input to these cells and the patterns of their outputs to spinal neurons, but no doubt these cells could be used much more effectively in exploring their roles in descending control of the spinal cord. The variability of cell positions of neurons in the spinal cord has precluded the recognition of unique spinal neurons. However, classes of nerve cells can be readily defined and characterized within the lamprey spinal cord and this has led to progress in understanding the cellular and synaptic mechanisms of locomotor activity. In addition, both the identifiable reticulospinal cells and the various spinal nerve cell classes and their known synaptic interactions have been used to demonstrate the degree and specificity of regeneration within the lamprey nervous system. The lack of uniquely identifiable cells within the lamprey spinal cord has hampered progress in these areas, especially in gaining a full understanding of the locomotor network and how neuromodulation of the network is accomplished.

The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia.

PubMed

Banker, Sarah E; Wade, Elizabeth J; Simon, Chris

2017-11-01

Phylogenetic studies of multiple independently inherited nuclear genes considered in combination with patterns of inheritance of organelle DNA have provided considerable insight into the history of species evolution. In particular, investigations of cicadas in the New Zealand genus Kikihia have identified interesting cases where mitochondrial DNA (mtDNA) crosses species boundaries in some species pairs but not others. Previous phylogenetic studies focusing on mtDNA largely corroborated Kikihia species groups identified by song, morphology and ecology with the exception of a unique South Island mitochondrial haplotype clade-the Westlandica group. This newly identified group consists of diverse taxa previously classified as belonging to three different sub-generic clades. We sequenced five nuclear loci from multiple individuals from every species of Kikihia to assess the nuclear gene concordance for this newly-identified mtDNA lineage. Bayes Factor analysis of the constrained phylogeny suggests some support for the mtDNA-based hypotheses, despite the fact that neither concatenation nor multiple species tree methods resolve the Westlandica group as monophyletic. The nuclear analyses suggest a geographic distinction between clearly defined monophyletic North Island clades and unresolved South Island clades. We suggest that more extreme habitat modification on South Island during the Pliocene and Pleistocene resulted in secondary contact and hybridization between species pairs and a series of mitochondrial capture events followed by subsequent lineage evolution. Copyright © 2017 Elsevier Inc. All rights reserved.

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

PubMed Central

Eckert, Andrew J.; van Heerwaarden, Joost; Wegrzyn, Jill L.; Nelson, C. Dana; Ross-Ibarra, Jeffrey; González-Martínez, Santíago C.; Neale, David. B.

2010-01-01

Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as FST outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes. PMID:20439779

Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry.

PubMed

Welham, Nathan V; Chang, Zhen; Smith, Lloyd M; Frey, Brian L

2013-01-01

Natural biologic scaffolds for tissue engineering are commonly generated by decellularization of tissues and organs. Despite some preclinical and clinical success, in vivo scaffold remodeling and functional outcomes remain variable, presumably due to the influence of unidentified bioactive molecules on the scaffold-host interaction. Here, we used 2D electrophoresis and high-resolution mass spectrometry-based proteomic analyses to evaluate decellularization effectiveness and identify potentially bioactive protein remnants in a human vocal fold mucosa model. We noted proteome, phosphoproteome and O-glycoproteome depletion post-decellularization, and identified >200 unique protein species within the decellularized scaffold. Gene ontology-based enrichment analysis revealed a dominant set of functionally-related ontology terms associated with extracellular matrix assembly, organization, morphology and patterning, consistent with preservation of a tissue-specific niche for later cell seeding and infiltration. We further identified a subset of ontology terms associated with bioactive (some of which are antigenic) cellular proteins, despite histological and immunohistochemical data indicating complete decellularization. These findings demonstrate the value of mass spectrometry-based proteomics in identifying agents potentially responsible for variation in host response to engineered tissues derived from decellularized scaffolds. This work has implications for the manufacturing of biologic scaffolds from any tissue or organ, as well as for prediction and monitoring of the scaffold-host interaction in vivo. Copyright © 2012 Elsevier Ltd. All rights reserved.

Method for identifying eligible individuals for a prevalence survey in the absence of a disease register or population register.

PubMed

Richardson, A K; Clarke, G; Sabel, C E; Pearson, J F; Mason, D F; Taylor, B V

2012-11-01

Identifying eligible individuals for a prevalence survey is difficult in the absence of a disease register or a national population register. To develop a method to identify and invite eligible individuals to participate in a national prevalence survey while maintaining confidentiality and complying with privacy legislation. A unique identifier (based on date of birth, sex and initials) was developed so that database holders could identify eligible individuals, notify us and invite them on our behalf to participate in a national multiple sclerosis prevalence survey while maintaining confidentiality and complying with privacy legislation. Several organisations (including central government, health and non-governmental organisations) used the method described to assign unique identifiers to individuals listed on their databases and to forward invitations and consent forms to them. The use of a unique identifier allowed us to recognise and record all the sources of identification for each individual. This prevented double counting or approaching the same individual more than once and facilitated the use of capture-recapture methods to improve the prevalence estimate. Capture-recapture analysis estimated that the method identified over 96% of eligible individuals in this prevalence survey. This method was developed and used successfully in a national prevalence survey of multiple sclerosis in New Zealand. The method may be useful for prevalence surveys of other diseases in New Zealand and for prevalence surveys in other countries with similar privacy legislation and lack of disease registers and population registers. © 2012 The Authors; Internal Medicine Journal © 2012 Royal Australasian College of Physicians.

Unique determination of stratified steady water waves from pressure

NASA Astrophysics Data System (ADS)

Chen, Robin Ming; Walsh, Samuel

2018-01-01

Consider a two-dimensional stratified solitary wave propagating through a body of water that is bounded below by an impermeable ocean bed. In this work, we study how such a wave can be recovered from data consisting of the wave speed, upstream and downstream density and velocity profile, and the trace of the pressure on the bed. In particular, we prove that this data uniquely determines the wave, both in the (real) analytic and Sobolev regimes.

The Uniqueness of Speech among Motor Systems

ERIC Educational Resources Information Center

Kent, Ray

2004-01-01

This paper considers evidence that the speech muscles are unique in their genetic, developmental, functional and phenotypical properties. The literature was reviewed using PubMed, ScienceDirect, ComDisDome and other literature-retrieval systems to identify studies reporting on the craniofacial and laryngeal muscles. Particular emphasis was given…

47 CFR 10.320 - Provider alert gateway requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... must be identified by a unique IP address or domain name. (b) Authentication and validation. The CMS... alert gateway if a validation fails. (c) Security. The CMS provider gateway must support standardized IP... CMSP Name Unique identification of CMSP. CMSP gateway Address IP address or Domain Name Alternate IP...

Cancer treatment model with the Caputo-Fabrizio fractional derivative

NASA Astrophysics Data System (ADS)

Ali Dokuyucu, Mustafa; Celik, Ercan; Bulut, Hasan; Mehmet Baskonus, Haci

2018-03-01

In this article, a model for cancer treatment is examined. The model is integrated into the Caputo-Fabrizio fractional derivative first, to examine the existence of the solution. Then, the uniqueness of the solution is investigated and we identified under which conditions the model provides a unique solution.

A Repeat Look at Repeating Patterns

ERIC Educational Resources Information Center

Markworth, Kimberly A.

2016-01-01

A "repeating pattern" is a cyclical repetition of an identifiable core. Children in the primary grades usually begin pattern work with fairly simple patterns, such as AB, ABC, or ABB patterns. The unique letters represent unique elements, whereas the sequence of letters represents the core that is repeated. Based on color, shape,…

Marketing the Uniqueness of Small Towns. Small Town Strategy.

ERIC Educational Resources Information Center

Hogg, David H.; Dunn, Douglas

A small town can strengthen its local economy as a result of business people and concerned citizens collectively identifying that community's uniqueness and then capitalizing on it via advertising, personal selling, sales promotion, or publicity. This publication relates the science of marketing to communities. Seven simple techniques are provided…

Measuring parent food practices: a systematic review of existing measures and examination of instruments

PubMed Central

2013-01-01

During the last decade, there has been a rapid increase in development of instruments to measure parent food practices. Because these instruments often measure different constructs, or define common constructs differently, an evaluation of these instruments is needed. A systematic review of the literature was conducted to identify existing measures of parent food practices and to assess the quality of their development. The initial search used terms capturing home environment, parenting behaviors, feeding practices and eating behaviors, and was performed in October of 2009 using PubMed/Medline, PsychInfo, Web of knowledge (ISI), and ERIC, and updated in July of 2012. A review of titles and abstracts was used to narrow results, after which full articles were retrieved and reviewed. Only articles describing development of measures of parenting food practices designed for families with children 2-12 years old were retained for the current review. For each article, two reviewers extracted data and appraised the quality of processes used for instrument development and evaluation. The initial search yielded 28,378 unique titles; review of titles and abstracts narrowed the pool to 1,352 articles; from which 57 unique instruments were identified. The review update yielded 1,772 new titles from which14 additional instruments were identified. The extraction and appraisal process found that 49% of instruments clearly identified and defined concepts to be measured, and 46% used theory to guide instrument development. Most instruments (80%) had some reliability testing, with internal consistency being the most common (79%). Test-retest or inter-rater reliability was reported for less than half the instruments. Some form of validity evidence was reported for 84% of instruments. Construct validity was most commonly presented (86%), usually with analysis of associations with child diet or weight/BMI. While many measures of food parenting practices have emerged, particularly in recent years, few have demonstrated solid development methods. Substantial variation in items across different scales/constructs makes comparison between instruments extremely difficult. Future efforts should be directed toward consensus development of food parenting practices constructs and measures. PMID:23688157

Factors Contributing to Single- and Dual-Task Timed "Up & Go" Test Performance in Middle-Aged and Older Adults Who Are Active and Dwell in the Community.

PubMed

Chen, Hui-Ya; Tang, Pei-Fang

2016-03-01

Dual-task Timed "Up & Go" (TUG) tests are likely to have applications different from those of a single-task TUG test and may have different contributing factors. The purpose of this study was to compare factors contributing to performance on single- and dual-task TUG tests. This investigation was a cross-sectional study. Sixty-four adults who were more than 50 years of age and dwelled in the community were recruited. Interviews and physical examinations were performed to identify potential contributors to TUG test performance. The time to complete the single-task TUG test (TUGsingle) or the dual-task TUG test, which consisted of completing the TUG test while performing a serial subtraction task (TUGcognitive) or while carrying water (TUGmanual), was measured. Age, hip extensor strength, walking speed, general mental function, and Stroop scores for word and color were significantly associated with performance on all TUG tests. Hierarchical multiple regression models, without the input of walking speed, revealed different independent factors contributing to TUGsingle performance (Mini-Mental Status Examination score, β=-0.32), TUGmanual performance (age, β=0.35), and TUGcognitive performance (Stroop word score, β=-0.40; Mini-Mental Status Examination score, β=-0.31). At least 40% of the variance in the performance on the 3 TUG tests was not explained by common clinical measures, even when the factor of walking speed was considered. However, this study successfully identified some important factors contributing to performance on different TUG tests, and other studies have reported similar findings for single-task TUG test and dual-task gait performance. Although the TUGsingle and the TUGcognitive shared general mental function as a common factor, the TUGmanual was uniquely influenced by age and the TUGcognitive was uniquely influenced by focused attention. These results suggest that both common and unique factors contribute to performance on single- and dual-task TUG tests and suggest important applications of the combined use of the 3 TUG tests. © 2016 American Physical Therapy Association.

An empirical typology of social networks and its association with physical and mental health: a study with older Korean immigrants.

PubMed

Park, Nan Sook; Jang, Yuri; Lee, Beom S; Ko, Jung Eun; Haley, William E; Chiriboga, David A

2015-01-01

In the context of social convoy theory, the purposes of the study were (a) to identify an empirical typology of the social networks evident in older Korean immigrants and (b) to examine its association with self-rated health and depressive symptoms. The sample consisted of 1,092 community-dwelling older Korean immigrants in Florida and New York. Latent class analyses were conducted to identify the optimal social network typology based on 8 indicators of interpersonal relationships and activities. Bivariate and multivariate analyses were conducted to examine how the identified social network typology was associated with self-rating of health and depressive symptoms. Results from the latent class analysis identified 6 clusters as being most optimal, and they were named diverse, unmarried/diverse, married/coresidence, family focused, unmarried/restricted, and restricted. Memberships in the clusters of diverse and married/coresidence were significantly associated with more favorable ratings of health and lower levels of depressive symptoms. Notably, no distinct network solely composed of friends was identified in the present sample of older immigrants; this may reflect the disruptions in social convoys caused by immigration. The findings of this study promote our understanding of the unique patterns of social connectedness in older immigrants. © The Author 2013. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quality Primary Care and Family Planning Services for LGBT Clients: A Comprehensive Review of Clinical Guidelines.

PubMed

Klein, David A; Malcolm, Nikita M; Berry-Bibee, Erin N; Paradise, Scott L; Coulter, Jessica S; Keglovitz Baker, Kristin; Schvey, Natasha A; Rollison, Julia M; Frederiksen, Brittni N

2018-04-01

LGBT clients have unique healthcare needs but experience a wide range of quality in the care that they receive. This study provides a summary of clinical guideline recommendations related to the provision of primary care and family planning services for LGBT clients. In addition, we identify gaps in current guidelines, and inform future recommendations and guidance for clinical practice and research. PubMed, Cochrane, and Agency for Healthcare Research and Quality electronic bibliographic databases, and relevant professional organizations' websites, were searched to identify clinical guidelines related to the provision of primary care and family planning services for LGBT clients. Information obtained from a technical expert panel was used to inform the review. Clinical guidelines meeting the inclusion criteria were assessed to determine their alignment with Institute of Medicine (IOM) standards for the development of clinical practice guidelines and content relevant to the identified themes. The search parameters identified 2,006 clinical practice guidelines. Seventeen clinical guidelines met the inclusion criteria. Two of the guidelines met all eight IOM criteria. However, many recommendations were consistent regarding provision of services to LGBT clients within the following themes: clinic environment, provider cultural sensitivity and awareness, communication, confidentiality, coordination of care, general clinical principles, mental health considerations, and reproductive health. Guidelines for the primary and family planning care of LGBT clients are evolving. The themes identified in this review may guide professional organizations during guideline development, clinicians when providing care, and researchers conducting LGBT-related studies.

Reconsidering Anonymization-Related Concepts and the Term “Identification” Against the Backdrop of the European Legal Framework

PubMed Central

Schlünder, Irene

2016-01-01

Sharing data in biomedical contexts has become increasingly relevant, but privacy concerns set constraints for free sharing of individual-level data. Data protection law protects only data relating to an identifiable individual, whereas “anonymous” data are free to be used by everybody. Usage of many terms related to anonymization is often not consistent among different domains such as statistics and law. The crucial term “identification” seems especially hard to define, since its definition presupposes the existence of identifying characteristics, leading to some circularity. In this article, we present a discussion of important terms based on a legal perspective that it is outlined before we present issues related to the usage of terms such as unique “identifiers,” “quasi-identifiers,” and “sensitive attributes.” Based on these terms, we have tried to circumvent a circular definition for the term “identification” by making two decisions: first, deciding which (natural) identifier should stand for the individual; second, deciding how to recognize the individual. In addition, we provide an overview of anonymization techniques/methods for preventing re-identification. The discussion of basic notions related to anonymization shows that there is some work to be done in order to achieve a mutual understanding between legal and technical experts concerning some of these notions. Using a dialectical definition process in order to merge technical and legal perspectives on terms seems important for enhancing mutual understanding. PMID:27104620

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.

PubMed

Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert

2018-02-20

Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

Space Station Furnace Facility. Experiment/Facility Requirements Document (E/FRD), volume 2, appendix 5

NASA Technical Reports Server (NTRS)

Kephart, Nancy

1992-01-01

The function of the Space Station Furnace Facility (SSFF) is to support materials research into the crystal growth and solidification processes of electronic and photonic materials, metals and alloys, and glasses and ceramics. To support this broad base of research requirements, the SSFF will employ a variety of furnace modules operated, regulated, and supported by a core of common subsystems. Furnace modules may be reconfigured or specifically developed to provide unique solidifcation conditions for each set of experiments. The SSFF modular approach permits the addition of new or scaled-up furnace modules to support the evolution of the facility as new science requirements are identified. The SSFF Core is of modular design to permit augmentation for enhanced capabilities. The fully integrated configuration of the SSFF will consist of three racks with the capability of supporting up to two furnace modules per rack. The initial configuration of the SSFF will consist of two of the three racks and one furnace module. This Experiment/Facility Requirements Document (E/FRD) describes the integrated facility requirements for the Space Station Freedom (SSF) Integrated Configuration-1 (IC1) mission. The IC1 SSFF will consist of two racks: the Core Rack, with the centralized subsystem equipment, and the Experiment Rack-1, with Furnace Module-1 and the distributed subsystem equipment to support the furnace.

Testing general relativity using gravitational wave signals from the inspiral, merger and ringdown of binary black holes

NASA Astrophysics Data System (ADS)

Ghosh, Abhirup; Johnson-McDaniel, Nathan K.; Ghosh, Archisman; Kant Mishra, Chandra; Ajith, Parameswaran; Del Pozzo, Walter; Berry, Christopher P. L.; Nielsen, Alex B.; London, Lionel

2018-01-01

Advanced LIGO’s recent observations of gravitational waves (GWs) from merging binary black holes have opened up a unique laboratory to test general relativity (GR) in the highly relativistic regime. One of the tests used to establish the consistency of the first LIGO event with a binary black hole merger predicted by GR was the inspiral-merger-ringdown consistency test. This involves inferring the mass and spin of the remnant black hole from the inspiral (low-frequency) part of the observed signal and checking for the consistency of the inferred parameters with the same estimated from the post-inspiral (high-frequency) part of the signal. Based on the observed rate of binary black hole mergers, we expect the advanced GW observatories to observe hundreds of binary black hole mergers every year when operating at their design sensitivities, most of them with modest signal to noise ratios (SNRs). Anticipating such observations, this paper shows how constraints from a large number of events with modest SNRs can be combined to produce strong constraints on deviations from GR. Using kludge modified GR waveforms, we demonstrate how this test could identify certain types of deviations from GR if such deviations are present in the signal waveforms. We also study the robustness of this test against reasonable variations of a variety of different analysis parameters.

Epithelial ovarian cancer and recreational physical activity: A review of the epidemiological literature and implications for exercise prescription.

PubMed

Cannioto, Rikki A; Moysich, Kirsten B

2015-06-01

Despite the publication of two dozen observational epidemiological studies investigating the association between recreational physical activity (RPA) and epithelial ovarian cancer (EOC) risk and survival over the past two decades, taken collectively, data from retrospective and prospective studies are mixed and remain inconclusive. Our primary purpose was to conduct a careful review and summary of the epidemiological literature depicting the association between EOC and RPA in the framework of identifying factors which may be impeding our ability to observe consistent associations in the literature. Secondly, in the backdrop of the more broad scientific evidence regarding the benefits of RPA, we provide a summary of guidelines for practitioners to utilize in the context of exercise prescription for cancer patients, including a discussion of special considerations and contraindications to exercise which are unique to EOC patients and survivors. We performed a comprehensive literature search via PubMed to identify epidemiologic investigations focused on the association between RPA and EOC. To be included in the review, studies had to assess RPA independently of occupational or household activities. In total, 26 studies were identified for inclusion. Evidence of a protective effect of RPA relative to EOC risk is more consistent among-case control studies, with the majority of studies demonstrating significant risk reductions between 30 and 60% among the most active women. Among cohort studies, half yielded no significant associations, while the remaining studies provided mixed evidence of an association. Given the limitations identified in the current body of literature, practitioners should not rely on inconclusive evidence to dissuade women from participating in moderate or vigorous RPA. Rather, emphasis should be placed on the greater body of scientific evidence which has demonstrated that RPA results in a plethora of health benefits that can be achieved in all populations, including those with cancer. Copyright © 2015 Elsevier Inc. All rights reserved.

Insight into dementia care management using social-behavioral theory and mixed methods.

PubMed

Connor, Karen; McNeese-Smith, Donna; van Servellen, Gwen; Chang, Betty; Lee, Martin; Cheng, Eric; Hajar, Abdulrahman; Vickrey, Barbara G

2009-01-01

For health organizations (private and public) to advance their care-management programs, to use resources effectively and efficiently, and to improve patient outcomes, it is germane to isolate and quantify care-management activities and to identify overarching domains. The aims of this study were to identify and report on an application of mixed methods of qualitative statistical techniques, based on a theoretical framework, and to construct variables for factor analysis and exploratory factor analytic steps for identifying domains of dementia care management. Care-management activity data were extracted from the care plans of 181 pairs of individuals (with dementia and their informal caregivers) who had participated in the intervention arm of a randomized controlled trial of a dementia care-management program. Activities were organized into types, using card-sorting methods, influenced by published theoretical constructs on self-efficacy and general strain theory. These activity types were mapped in the initial data set to construct variables for exploratory factor analysis. Principal components extraction with varimax and promax rotations was used to estimate the number of factors. Cronbach's alpha was calculated for the items in each factor to assess internal consistency reliability. The two-phase card-sorting technique yielded 45 activity types out of 450 unique activities. Exploratory factor analysis produced four care-management domains (factors): behavior management, clinical strategies and caregiver support, community agency, and safety. Internal consistency reliability (Cronbach's alpha) of items for each factor ranged from.63 for the factor "safety" to.89 for the factor "behavior management" (Factor 1). Applying a systematic method to a large set of care-management activities can identify a parsimonious number of higher order categories of variables and factors to guide the understanding of dementia care-management processes. Further application of this methodology in outcome analyses and to other data sets is necessary to test its practicality.

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci.

PubMed

Zubair, Niha; Graff, Mariaelisa; Luis Ambite, Jose; Bush, William S; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H; Absher, Devin; Assimes, Themistocles L; Bielinski, Suzette J; Bottinger, Erwin P; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H; Martin, Lisa W; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P; Robinson, Jennifer; Rotter, Jerome I; Ryckman, Kelli K; Schreiner, Pamela J; Stahl, Eli; Tao, Ran; Tsai, Michael Y; Waite, Lindsay L; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C; Loos, Ruth J F; Rich, Stephen S; Fornage, Myriam; North, Kari E; Kooperberg, Charles; Carty, Cara L

2016-12-15

Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Novel Cell Wall Lipopeptide Is Important for Biofilm Formation and Pathogenicity of Mycobacterium avium subspecies paratuberculosis

PubMed Central

Wu, Chia-wei; Schmoller, Shelly K.; Bannantine, John P.; Eckstein, Torsten M.; Inamine, Julie M.; Livesey, Michael; Albrecht, Ralph; Talaat, Adel M.

2009-01-01

Biofilm formation by pathogenic bacteria plays a key role in their pathogenesis. Previously, the pstA gene was shown to be involved in the virulence of Mycobacterium avium subspecies paratuberculosis (M. ap), the causative agent of Johne's disease in cattle and a potential risk factor for Crohn's disease. Scanning electron microscopy and colonization levels of the M. ap mutant indicated that the pstA gene significantly contributes to the ability of M. ap to form biofilms. Digital measurements taken during electron microscopy identified a unique morphology for the ΔpstA mutant, which consisted of significantly shorter bacilli than the wild type. Analysis of the lipid profiles of the mycobacterial strains identified a novel lipopeptide that was present in the cell wall extracts of wild-type M. ap, but missing from the ΔpstA mutant. Interestingly, the calf infection model suggested that pstA contributes to intestinal invasion of M. ap. Furthermore, immunoblot analysis of peptides encoded by pstA identified a specific and significant level of immunogenicity. Taken together, our analysis revealed a novel cell wall component that could contribute to biofilm formation and to the virulence and immunogenicity of M. ap. Molecular tools to better control M. ap infections could be developed utilizing the presented findings. PMID:19490829

Postnatal Microstructural Developmental Trajectory of Corpus Callosum Subregions and Relationship to Clinical Factors in Very Preterm Infants.

PubMed

Teli, Radhika; Hay, Margaret; Hershey, Alexa; Kumar, Manoj; Yin, Han; Parikh, Nehal A

2018-05-15

Our objectives were to define the microstructural developmental trajectory of six corpus callosum subregions and identify perinatal clinical factors that influence early development of these subregions in very preterm infants. We performed a longitudinal cohort study of very preterm infants (32 weeks gestational age or younger) (N = 36) who underwent structural MRI and diffusion tensor imaging serially at four time points - before 32, 32, 38, and 52 weeks postmenstrual age. We divided the corpus callosum into six subregions, performed probabilistic tractography, and used linear mixed effects models to evaluate the influence of antecedent clinical factors on its microstructural growth trajectory. The genu and splenium demonstrated the most rapid developmental maturation, exhibited by a steep increase in fractional anisotropy. We identified several factors that favored greater corpus callosum microstructural development, including advancing postmenstrual age, higher birth weight, and college level or higher maternal education. Bronchopulmonary dysplasia, low 5-minute Apgar scores, caffeine therapy/apnea of prematurity and male sex were associated with reduced corpus callosum microstructural integrity/development over the first six months after very preterm birth. We identified a unique postnatal microstructural growth trajectory and associated clinical factor profile for each of the six corpus callosum subregions that is consistent with the heterogeneous functional role of these white matter subregions.

Measuring management's perspective of data quality in Pakistan's Tuberculosis control programme: a test-based approach to identify data quality dimensions.

PubMed

Ali, Syed Mustafa; Anjum, Naveed; Kamel Boulos, Maged N; Ishaq, Muhammad; Aamir, Javariya; Haider, Ghulam Rasool

2018-01-16

Data quality is core theme of programme's performance assessment and many organizations do not have any data quality improvement strategy, wherein data quality dimensions and data quality assessment framework are important constituents. As there is limited published research about the data quality specifics that are relevant to the context of Pakistan's Tuberculosis control programme, this study aims at identifying the applicable data quality dimensions by using the 'fitness-for-purpose' perspective. Forty-two respondents pooled a total of 473 years of professional experience, out of which 223 years (47%) were in TB control related programmes. Based on the responses against 11 practical cases, adopted from the routine recording and reporting system of Pakistan's TB control programme (real identities of patient were masked), completeness, accuracy, consistency, vagueness, uniqueness and timeliness are the applicable data quality dimensions relevant to the programme's context, i.e. work settings and field of practice. Based on a 'fitness-for-purpose' approach to data quality, this study used a test-based approach to measure management's perspective and identified data quality dimensions pertinent to the programme and country specific requirements. Implementation of a data quality improvement strategy and achieving enhanced data quality would greatly help organizations in promoting data use for informed decision making.

Radiation-induced hydroxyl addition to purine molecules: EPR and ENDOR study of hypoxanthine hydrochloride monohydrate single crystals.

PubMed

Tokdemir, Sibel; Nelson, William H

2005-06-01

Three radical species were detected in an EPR/ENDOR study of X-irradiated hypoxanthine.HCl.H2O single crystals at room temperature: RI was identified as the product of net H addition to C8, RII was identified as the product of net H addition to C2, and RIII was identified as the product of OH addition to C8. The observed set of radicals was the same for room-temperature irradiation as for irradiation at 10 K followed by warming the crystals to room temperature; however, the C2 H-addition and C8 OH-addition radicals were not detectable after storage of the crystals for about 2 months at room temperature. Use of selectively deuterated crystals permitted unique assignment of the observed hyperfine couplings, and results of density functional theory calculations on each of the radical structures were consistent with the experimental results. Comparison of these experimental results with others from previous crystal-based systems and model system computations provides insight into the mechanisms by which the biologically important purine C8 hydroxyl addition products are formed. The evidence from solid systems supports the mechanism of net water addition to one-electron oxidized purine bases and demonstrates the importance of a facial approach between the reactants.

Characterization and comparison of proteomes of albino sea cucumber Apostichopus japonicus (Selenka) by iTRAQ analysis.

PubMed

Xia, Chang-Ge; Zhang, Dijun; Ma, Chengnv; Zhou, Jun; He, Shan; Su, Xiu-Rong

2016-04-01

Sea cucumber is a commercially important marine organism in China. Of the different colored varieties sold in China, albino sea cucumber has the greatest appeal among consumers. Identification of factors contributing to albinism in sea cucumber is therefore likely to provide a scientific basis for improving the cultivability of these strains. In this study, two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification labeling was used for the first time to quantitatively define the proteome of sea cucumbers and reveal proteomic characteristics unique to albino sea cucumbers. A total of 549 proteins were identified and quantified in albino sea cucumber and the functional annotations of 485 proteins have been exhibited based on COG database. Compared with green sea cucumber, 12 proteins were identified as differentially expressed in the intestine and 16 proteins in the body wall of albino sea cucumber. Among them, 5 proteins were up-regulated in the intestine and 8 proteins were down-regulated in body wall. Gene ontology annotations of these differentially expressed proteins consisted mostly of 'biological process'. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying albinism in sea cucumber. Copyright © 2015 Elsevier Ltd. All rights reserved.

Unique Family Living Situations

MedlinePlus

... on children of divorce. Co-parent with your ex-spouse to develop consistent routines for bedtime, meals, ... about the symptoms and cause of, and risk factors and treatments for, nasopharyngeal cancer. About Support Us ...

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling*

PubMed Central

Boersema, Paul J.; Foong, Leong Yan; Ding, Vanessa M. Y.; Lemeer, Simone; van Breukelen, Bas; Philp, Robin; Boekhorst, Jos; Snel, Berend; den Hertog, Jeroen; Choo, Andre B. H.; Heck, Albert J. R.

2010-01-01

Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated. PMID:19770167

Forensic Tools to Track and Connect Physical Samples to Related Data

NASA Astrophysics Data System (ADS)

Molineux, A.; Thompson, A. C.; Baumgardner, R. W.

2016-12-01

Identifiers, such as local sample numbers, are critical to successfully connecting physical samples and related data. However, identifiers must be globally unique. The International Geo Sample Number (IGSN) generated when registering the sample in the System for Earth Sample Registration (SESAR) provides a globally unique alphanumeric code associated with basic metadata, related samples and their current physical storage location. When registered samples are published, users can link the figured samples to the basic metadata held at SESAR. The use cases we discuss include plant specimens from a Permian core, Holocene corals and derived powders, and thin sections with SEM stubs. Much of this material is now published. The plant taxonomic study from the core is a digital pdf and samples can be directly linked from the captions to the SESAR record. The study of stable isotopes from the corals is not yet digitally available, but individual samples are accessible. Full data and media records for both studies are located in our database where higher quality images, field notes, and section diagrams may exist. Georeferences permit mapping in current and deep time plate configurations. Several aspects emerged during this study. The first, ensure adequate and consistent details are registered with SESAR. Second, educate and encourage the researcher to obtain IGSNs. Third, publish the archive numbers, assigned prior to publication, alongside the IGSN. This provides access to further data through an Integrated Publishing Toolkit (IPT)/aggregators/or online repository databases, thus placing the initial sample in a much richer context for future studies. Fourth, encourage software developers to customize community software to extract data from a database and use it to register samples in bulk. This would improve workflow and provide a path for registration of large legacy collections.

Mrt, a Gene Unique to Fungi, Encodes an Oligosaccharide Transporter and Facilitates Rhizosphere Competency in Metarhizium robertsii1[C][W

PubMed Central

Fang, Weiguo; St. Leger, Raymond J.

2010-01-01

The symbiotic associations between rhizospheric fungi and plants have enormous environmental impact. Fungi are crucial to plant health as antagonists of pathogens and herbivores and facilitate the uptake of soil nutrients. However, little is known about the plant products obtained by fungi in exchange or how they are transported through the symbiotic interface. Here, we demonstrate that sucrose and raffinose family oligosaccharides in root exudates are important for rhizosphere competence in the insect pathogen Metarhizium robertsii (formerly known as Metarhizium anisopliae). We identified mutants in the Metarhizium raffinose transporter (Mrt) gene of M. robertsii that grew poorly in root exudate and were greatly reduced in rhizosphere competence on grass roots. Studies on sugar uptake, including competition assays, revealed that MRT was a sucrose and galactoside transporter. Disrupting MRT resulted in greatly reduced or no growth on sucrose and galactosides but did not affect growth on monosaccharides or oligosaccharides composed entirely of glucose subunits. Consistent with this, expression of Mrt is exclusively up-regulated by galactosides and sucrose. Expressing a green fluorescent protein gene under the control of the Mrt promoter confirmed that MRT was expressed by germlings in the vicinity of grass roots but not in surrounding bulk soil. Disrupting Mrt did not reduce virulence to insects, demonstrating that Mrt is exclusively involved in M. robertsii’s interactions with plants. To our knowledge, MRT is the first oligosaccharide transporter identified and characterized in a fungus and is unique to filamentous fungi, but homologous genes in Magnaporthe, Ustilago, Aspergillus, Fusarium, Epichloe, and Penicillium species indicate that oligosaccharide transport is of widespread significance. PMID:20837701

Reliability and Validity of Survey Instruments to Measure Work-Related Fatigue in the Emergency Medical Services Setting: A Systematic Review.

PubMed

Patterson, P Daniel; Weaver, Matthew D; Fabio, Anthony; Teasley, Ellen M; Renn, Megan L; Curtis, Brett R; Matthews, Margaret E; Kroemer, Andrew J; Xun, Xiaoshuang; Bizhanova, Zhadyra; Weiss, Patricia M; Sequeira, Denisse J; Coppler, Patrick J; Lang, Eddy S; Higgins, J Stephen

2018-02-15

This study sought to systematically search the literature to identify reliable and valid survey instruments for fatigue measurement in the Emergency Medical Services (EMS) occupational setting. A systematic review study design was used and searched six databases, including one website. The research question guiding the search was developed a priori and registered with the PROSPERO database of systematic reviews: "Are there reliable and valid instruments for measuring fatigue among EMS personnel?" (2016:CRD42016040097). The primary outcome of interest was criterion-related validity. Important outcomes of interest included reliability (e.g., internal consistency), and indicators of sensitivity and specificity. Members of the research team independently screened records from the databases. Full-text articles were evaluated by adapting the Bolster and Rourke system for categorizing findings of systematic reviews, and the rated data abstracted from the body of literature as favorable, unfavorable, mixed/inconclusive, or no impact. The Grading of Recommendations, Assessment, Development and Evaluation (GRADE) methodology was used to evaluate the quality of evidence. The search strategy yielded 1,257 unique records. Thirty-four unique experimental and non-experimental studies were determined relevant following full-text review. Nineteen studies reported on the reliability and/or validity of ten different fatigue survey instruments. Eighteen different studies evaluated the reliability and/or validity of four different sleepiness survey instruments. None of the retained studies reported sensitivity or specificity. Evidence quality was rated as very low across all outcomes. In this systematic review, limited evidence of the reliability and validity of 14 different survey instruments to assess the fatigue and/or sleepiness status of EMS personnel and related shift worker groups was identified.

Development of the PROMIS positive emotional and sensory expectancies of smoking item banks.

PubMed

Tucker, Joan S; Shadel, William G; Edelen, Maria Orlando; Stucky, Brian D; Li, Zhen; Hansen, Mark; Cai, Li

2014-09-01

The positive emotional and sensory expectancies of cigarette smoking include improved cognitive abilities, positive affective states, and pleasurable sensorimotor sensations. This paper describes development of Positive Emotional and Sensory Expectancies of Smoking item banks that will serve to standardize the assessment of this construct among daily and nondaily cigarette smokers. Data came from daily (N = 4,201) and nondaily (N =1,183) smokers who completed an online survey. To identify a unidimensional set of items, we conducted item factor analyses, item response theory analyses, and differential item functioning analyses. Additionally, we evaluated the performance of fixed-item short forms (SFs) and computer adaptive tests (CATs) to efficiently assess the construct. Eighteen items were included in the item banks (15 common across daily and nondaily smokers, 1 unique to daily, 2 unique to nondaily). The item banks are strongly unidimensional, highly reliable (reliability = 0.95 for both), and perform similarly across gender, age, and race/ethnicity groups. A SF common to daily and nondaily smokers consists of 6 items (reliability = 0.86). Results from simulated CATs indicated that, on average, less than 8 items are needed to assess the construct with adequate precision using the item banks. These analyses identified a new set of items that can assess the positive emotional and sensory expectancies of smoking in a reliable and standardized manner. Considerable efficiency in assessing this construct can be achieved by using the item bank SF, employing computer adaptive tests, or selecting subsets of items tailored to specific research or clinical purposes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Contributions of Phonological and Morphological Awareness to Literacy Skills In the Adult Basic Education Population

PubMed Central

Fracasso, Lucille E.; Bangs, Kathryn; Binder, Katherine S.

2014-01-01

The Adult Basic Education (ABE) population consists of a wide range of abilities with needs that may be unique to this set of learners. The purpose of this study was to better understand the relative contributions of phonological decoding and morphological awareness to spelling, vocabulary, and comprehension across a sample of ABE students. In this study, phonological decoding was a unique predictor of spelling ability, listening comprehension and reading comprehension. We also found that morphological awareness was a unique predictor of spelling ability, vocabulary, and listening comprehension. Morphological awareness indirectly contributed to reading comprehension through vocabulary. These findings suggest the need for morphological interventions for this group of learners. PMID:24935886

Detecting photovoltaic solar panels using hyperspectral imagery and estimating solar power production

NASA Astrophysics Data System (ADS)

Czirjak, Daniel

2017-04-01

Remote sensing platforms have consistently demonstrated the ability to detect, and in some cases identify, specific targets of interest, and photovoltaic solar panels are shown to have a unique spectral signature that is consistent across multiple manufacturers and construction methods. Solar panels are proven to be detectable in hyperspectral imagery using common statistical target detection methods such as the adaptive cosine estimator, and false alarms can be mitigated through the use of a spectral verification process that eliminates pixels that do not have the key spectral features of photovoltaic solar panel reflectance spectrum. The normalized solar panel index is described and is a key component in the false-alarm mitigation process. After spectral verification, these solar panel arrays are confirmed on openly available literal imagery and can be measured using numerous open-source algorithms and tools. The measurements allow for the assessment of overall solar power generation capacity using an equation that accounts for solar insolation, the area of solar panels, and the efficiency of the solar panels conversion of solar energy to power. Using a known location with readily available information, the methods outlined in this paper estimate the power generation capabilities within 6% of the rated power.

Medication adherence communications in community pharmacies: A naturalistic investigation.

PubMed

Rickles, Nathaniel M; Young, Gary J; Hall, Judith A; Noland, Carey; Kim, Ayoung; Peterson, Conner; Hong, Mina; Hale, John

2016-03-01

To describe the extent of pharmacy detection and monitoring of medication non-adherence, and solutions offered to improve adherence. Participants were 60 residents of the Boston area who had a generic chronic medication with 30 day supplies from their usual pharmacy. Participants received a duplicate prescription which they filled at a different pharmacy. For 5 months, participants alternated between the two pharmacies, creating gaps in their refill records at both pharmacies but no gaps in their medication adherence. Participants followed a scripted protocol and after each pharmacy visit reported their own and the pharmacy staff's behavior. Across 78 unique community pharmacies and 260 pharmacy visits, pharmacies were inconsistent and inadequate in asking if participants had questions, discussing the importance of adherence, providing adequate consultations with new medication, and detecting and intervening on non-adherence. Insurers rarely contacted the participants about adherence concerns. There is a need for more structured intervention systems to ensure pharmacists are consistently and adequately educating patients and detecting/managing potential medication non-adherence. The present study calls for more attention to building infrastructure in pharmacy practice that helps pharmacists more consistently identify, monitor, and intervene on medication adherence. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Validating Dimensions of Psychosis Symptomatology: Neural Correlates and 20-year Outcomes

PubMed Central

Kotov, Roman; Foti, Dan; Li, Kaiqiao; Bromet, Evelyn J.; Hajcak, Greg; Ruggero, Camilo J.

2016-01-01

Heterogeneity of psychosis presents significant challenges for classification. Between two and 12 symptom dimensions have been proposed, and consensus is lacking. The present study sought to identify uniquely informative models by comparing the validity of these alternatives. An epidemiologic cohort of 628 first-admission inpatients with psychosis was interviewed 6 times over two decades and completed an electrophysiological assessment of error processing at year 20. We first analyzed a comprehensive set of 49 symptoms rated by interviewers at baseline, progressively extracting from one to 12 factors. Next, we compared the ability of resulting factor solutions to (a) account for concurrent neural dysfunction and (b) predict 20-year role, social, residential, and global functioning, and life satisfaction. A four-factor model showed incremental validity with all outcomes, and more complex models did not improve explanatory power. The four dimensions—reality distortion, disorganization, inexpressivity, and apathy/asociality—were replicable in 5 follow-ups, internally consistent, stable across assessments, and showed strong discriminant validity. These results reaffirm the value of separating disorganization and reality distortion, are consistent with recent findings distinguishing inexpressivity and apathy/asociality, and suggest that these four dimensions are fundamental to understanding neural abnormalities and long-term outcomes in psychosis. PMID:27819471

Nuclear Pasta at Finite Temperature with the Time-Dependent Hartree-Fock Approach

NASA Astrophysics Data System (ADS)

Schuetrumpf, B.; Klatt, M. A.; Iida, K.; Maruhn, J. A.; Mecke, K.; Reinhard, P.-G.

2016-01-01

We present simulations of neutron-rich matter at sub-nuclear densities, like supernova matter. With the time-dependent Hartree-Fock approximation we can study the evolution of the system at temperatures of several MeV employing a full Skyrme interaction in a periodic three-dimensional grid [1]. The initial state consists of α particles randomly distributed in space that have a Maxwell-Boltzmann distribution in momentum space. Adding a neutron background initialized with Fermi distributed plane waves the calculations reflect a reasonable approximation of astrophysical matter. The matter evolves into spherical, rod-like, connected rod-like and slab-like shapes. Further we observe gyroid-like structures, discussed e.g. in [2], which are formed spontaneously choosing a certain value of the simulation box length. The ρ-T-map of pasta shapes is basically consistent with the phase diagrams obtained from QMD calculations [3]. By an improved topological analysis based on Minkowski functionals [4], all observed pasta shapes can be uniquely identified by only two valuations, namely the Euler characteristic and the integral mean curvature. In addition we propose the variance in the cell-density distribution as a measure to distinguish pasta matter from uniform matter.

Study of structural active cooling and heat sink systems for space shuttle

NASA Technical Reports Server (NTRS)

1972-01-01

This technology investigation was conducted to evaluate the feasibility of a number of thermal protection systems (TPS) concepts which are alternate candidates to the space shuttle baseline TPS. Four independent tasks were performed. Task 1 consisted of an in-depth evaluation of active structural cooling of the space shuttle orbiter. In Task 2, heat sink concepts for the booster were studied to identify and postulate solutions for design problems unique to heat sink TPS. Task 3 consisted of a feasibility demonstration test of a phase change material (PCM) incorporated into a reusable surface insulation (RSI) thermal protection system for the shuttle orbiter. In Task 4 the feasibility of heat pipes for stagnation region cooling was studied for the booster and the orbiter. Designs were developed for the orbiter leading edge and used in trade studies of leading edge concepts. At the time this program was initiated, a 2-stage fully reusable shuttle system was envisioned; therefore, the majority of the tasks were focused on the fully reusable system environments. Subsequently, a number of alternate shuttle system approaches, with potential for reduced shuttle system development funding requirements, were proposed. Where practicable, appropriate shifts in emphasis and task scoping were made to reflect these changes.

Face to (face)book: the two faces of social behavior?

PubMed

Ivcevic, Zorana; Ambady, Nalini

2013-06-01

Social networking sites such as Facebook represent a unique and dynamic social environment. This study addresses three theoretical issues in personality psychology in the context of online social networking sites: (a) the temporal consistency of Facebook activity, (b) people's awareness of their online behavior, and (c) comparison of social behavior on Facebook with self- and informant-reported behavior in real life. Facebook Wall pages of 99 college students (mean age = 19.72) were downloaded six times during 3 weeks and coded for quantity and quality of activity. Everyday social interactions were assessed by self- and friend report. Facebook activity showed significant consistency across time, and people demonstrated awareness of their online behavior. There was significant similarity between everyday traits and interactions and Facebook behavior (e.g., more posts by friends are related to Agreeableness). Some differences between online and everyday interactions warrant further research (e.g., individuals with more positive offline relationships are less likely to engage in back-and-forth conversations on Facebook). The results indicate substantial similarity between online and offline social behavior and identify avenues for future research on the possible use of Facebook to compensate for difficulty in everyday interactions. © 2012 Wiley Periodicals, Inc.

Data-driven inference of network connectivity for modeling the dynamics of neural codes in the insect antennal lobe

PubMed Central

Shlizerman, Eli; Riffell, Jeffrey A.; Kutz, J. Nathan

2014-01-01

The antennal lobe (AL), olfactory processing center in insects, is able to process stimuli into distinct neural activity patterns, called olfactory neural codes. To model their dynamics we perform multichannel recordings from the projection neurons in the AL driven by different odorants. We then derive a dynamic neuronal network from the electrophysiological data. The network consists of lateral-inhibitory neurons and excitatory neurons (modeled as firing-rate units), and is capable of producing unique olfactory neural codes for the tested odorants. To construct the network, we (1) design a projection, an odor space, for the neural recording from the AL, which discriminates between distinct odorants trajectories (2) characterize scent recognition, i.e., decision-making based on olfactory signals and (3) infer the wiring of the neural circuit, the connectome of the AL. We show that the constructed model is consistent with biological observations, such as contrast enhancement and robustness to noise. The study suggests a data-driven approach to answer a key biological question in identifying how lateral inhibitory neurons can be wired to excitatory neurons to permit robust activity patterns. PMID:25165442

18 CFR 390.3 - Waiver applications.

Code of Federal Regulations, 2012 CFR

2012-04-01

... register pursuant to paragraph (a) of this section will receive a unique numeric identifier that must... for filing. If the waiver is granted, the Secretary will add the assigned numeric identifier to the...

18 CFR 390.3 - Waiver applications.

Code of Federal Regulations, 2011 CFR

2011-04-01

... register pursuant to paragraph (a) of this section will receive a unique numeric identifier that must... for filing. If the waiver is granted, the Secretary will add the assigned numeric identifier to the...

18 CFR 390.3 - Waiver applications.

Code of Federal Regulations, 2010 CFR

2010-04-01

... register pursuant to paragraph (a) of this section will receive a unique numeric identifier that must... for filing. If the waiver is granted, the Secretary will add the assigned numeric identifier to the...

18 CFR 390.3 - Waiver applications.

Code of Federal Regulations, 2013 CFR

2013-04-01

... register pursuant to paragraph (a) of this section will receive a unique numeric identifier that must... for filing. If the waiver is granted, the Secretary will add the assigned numeric identifier to the...

18 CFR 390.3 - Waiver applications.

Code of Federal Regulations, 2014 CFR

2014-04-01

... register pursuant to paragraph (a) of this section will receive a unique numeric identifier that must... for filing. If the waiver is granted, the Secretary will add the assigned numeric identifier to the...

Conducting an Efficient Proactive Risk Assessment Prior to CPOE Implementation in an Intensive Care Unit

PubMed Central

Hundt, Ann Schoofs; Adams, Jean A.; Schmid, J. Andrew; Musser, Linda M.; Walker, James M.; Wetterneck, Tosha B; Douglas, Stephen V.; Paris, Bonnie L.; Carayon, Pascale

2012-01-01

Purpose To develop, conduct, and evaluate a proactive risk assessment (PRA) of the design and implementation of CPOE in an ICU. Methods We developed a PRA method based on issues identified from documented experience with conventional PRA methods and the constraints of an organization about to implement CPOE in an intensive care unit. The PRA method consists of three phases: planning (three months), team (one five-hour meeting), and evaluation (short- and long-term). Results Sixteen unique relevant vulnerabilities were identified as a result of the PRA team’s efforts. Negative consequences resulting from the vulnerabilities included potential patient safety and quality of care issues, non-compliance with regulatory requirements, increases in cognitive burden on CPOE users, and/or worker inconvenience or distress. Actions taken to address the vulnerabilities included redesign of the technology, process (workflow) redesign, user training, and/or ongoing monitoring. Verbal and written evaluation by the team members indicated that the PRA method was useful and that participants were willing to participate in future PRAs. Long-term evaluation was accomplished by monitoring an ongoing “issues list” of CPOE problems identified by or reported to IT staff. Vulnerabilities identified by the team were either resolved prior to CPOE implementation (n = 7) or shortly thereafter (n = 9). No other issues were identified beside those identified by the team. Conclusions Generally positive results from the various evaluations including a long-term evaluation demonstrate the value of developing an efficient PRA method that meets organizational and contextual requirements and constraints. PMID:22608242

Method for the unique identification of hyperelastic material properties using full-field measures. Application to the passive myocardium material response.

PubMed

Perotti, Luigi E; Ponnaluri, Aditya V S; Krishnamoorthi, Shankarjee; Balzani, Daniel; Ennis, Daniel B; Klug, William S

2017-11-01

Quantitative measurement of the material properties (eg, stiffness) of biological tissues is poised to become a powerful diagnostic tool. There are currently several methods in the literature to estimating material stiffness, and we extend this work by formulating a framework that leads to uniquely identified material properties. We design an approach to work with full-field displacement data-ie, we assume the displacement field due to the applied forces is known both on the boundaries and also within the interior of the body of interest-and seek stiffness parameters that lead to balanced internal and external forces in a model. For in vivo applications, the displacement data can be acquired clinically using magnetic resonance imaging while the forces may be computed from pressure measurements, eg, through catheterization. We outline a set of conditions under which the least-square force error objective function is convex, yielding uniquely identified material properties. An important component of our framework is a new numerical strategy to formulate polyconvex material energy laws that are linear in the material properties and provide one optimal description of the available experimental data. An outcome of our approach is the analysis of the reliability of the identified material properties, even for material laws that do not admit unique property identification. Lastly, we evaluate our approach using passive myocardium experimental data at the material point and show its application to identifying myocardial stiffness with an in silico experiment modeling the passive filling of the left ventricle. Copyright © 2017 John Wiley & Sons, Ltd.

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

PubMed Central

Du, Pan; Kibbe, Warren A; Lin, Simon M

2007-01-01

Background Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe. Results We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers. Reviewers This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman). PMID:17540033

Experimental investigations of weak definite and weak indefinite noun phrases

PubMed Central

Klein, Natalie M.; Gegg-Harrison, Whitney M.; Carlson, Greg N.; Tanenhaus, Michael K.

2013-01-01

Definite noun phrases typically refer to entities that are uniquely identifiable in the speaker and addressee’s common ground. Some definite noun phrases (e.g. the hospital in Mary had to go the hospital and John did too) seem to violate this uniqueness constraint. We report six experiments that were motivated by the hypothesis that these “weak definite” interpretations arise in “incorporated” constructions. Experiments 1-3 compared nouns that seem to allow for a weak definite interpretation (e.g. hospital, bank, bus, radio) with those that do not (e.g. farm, concert, car, book). Experiments 1 and 2 used an instruction-following task and picture-judgment task, respectively, to demonstrate that a weak definite need not uniquely refer. In Experiment 3 participants imagined scenarios described by sentences such as The Federal Express driver had to go to the hospital/farm. The imagined scenarios following weak definite noun phrases were more likely to include conventional activities associated with the object, whereas following regular nouns, participants were more likely to imagine scenarios that included typical activities associated with the subject; similar effects were observed with weak indefinites. Experiment 4 found that object-related activities were reduced when the same subject and object were used with a verb that does not license weak definite interpretations. In Experiment 5, a science fiction story introduced an artificial lexicon for novel concepts. Novel nouns that shared conceptual properties with English weak definite nouns were more likely to allow weak reference in a judgment task. Experiment 6 demonstrated that familiarity for definite articles and anti- familiarity for indefinite articles applies to the activity associated with the noun, consistent with predictions made by the incorporation analysis. PMID:23685208

Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress.

PubMed

Chen, Chi-Chien; Fu, Shih-Feng; Norikazu, Monma; Yang, Yau-Wen; Liu, Yu-Ju; Ikeo, Kazuho; Gojobori, Takashi; Huang, Hao-Jen

2015-12-01

MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited. In this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress. By deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes. This large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity.

Identical mitochondrial somatic mutations unique to chronic periodontitis and coronary artery disease

PubMed Central

Pallavi, Tokala; Chandra, Rampalli Viswa; Reddy, Aileni Amarender; Reddy, Bavigadda Harish; Naveen, Anumala

2016-01-01

Context: The inflammatory processes involved in chronic periodontitis and coronary artery diseases (CADs) are similar and produce reactive oxygen species that may result in similar somatic mutations in mitochondrial deoxyribonucleic acid (mtDNA). Aims: The aims of the present study were to identify somatic mtDNA mutations in periodontal and cardiac tissues from subjects undergoing coronary artery bypass surgery and determine what fraction was identical and unique to these tissues. Settings and Design: The study population consisted of 30 chronic periodontitis subjects who underwent coronary artery surgery after an angiogram had indicated CAD. Materials and Methods: Gingival tissue samples were taken from the site with deepest probing depth; coronary artery tissue samples were taken during the coronary artery bypass grafting procedures, and blood samples were drawn during this surgical procedure. These samples were stored under aseptic conditions and later transported for mtDNA analysis. Statistical Analysis Used: Complete mtDNA sequences were obtained and aligned with the revised Cambridge reference sequence (NC_012920) using sequence analysis and auto assembler tools. Results: Among the complete mtDNA sequences, a total of 162 variations were spread across the whole mitochondrial genome and present only in the coronary artery and the gingival tissue samples but not in the blood samples. Among the 162 variations, 12 were novel and four of the 12 novel variations were found in mitochondrial NADH dehydrogenase subunit 5 complex I gene (33.3%). Conclusions: Analysis of mtDNA mutations indicated 162 variants unique to periodontitis and CAD. Of these, 12 were novel and may have resulted from destructive oxidative forces common to these two diseases. PMID:27041832

HIV integration sites in latently infected cell lines: evidence of ongoing replication.

PubMed

Symons, Jori; Chopra, Abha; Malatinkova, Eva; De Spiegelaere, Ward; Leary, Shay; Cooper, Don; Abana, Chike O; Rhodes, Ajantha; Rezaei, Simin D; Vandekerckhove, Linos; Mallal, Simon; Lewin, Sharon R; Cameron, Paul U

2017-01-13

Assessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding of how HIV persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate HIV integration sites in latently infected cell lines to determine whether there was virus replication or clonal expansion in these cell lines observed as multiple integration events at the same position. We modified a previously reported method using random DNA shearing and PCR to allow for high throughput robotic processing to identify the site and frequency of HIV integration in latently infected cell lines. Latently infected cell lines infected with intact virus demonstrated multiple distinct HIV integration sites (28 different sites in U1, 110 in ACH-2 and 117 in J1.1 per 150,000 cells). In contrast, cell lines infected with replication-incompetent viruses (J-Lat cells) demonstrated single integration sites. Following in vitro passaging of the ACH-2 cell line, we observed a significant increase in the frequency of unique HIV integration sites and there were multiple mutations and large deletions in the proviral DNA. When the ACH-2 cell line was cultured with the integrase inhibitor raltegravir, there was a significant decrease in the number of unique HIV integration sites and a transient increase in the frequency of 2-LTR circles consistent with virus replication in these cells. Cell lines latently infected with intact HIV demonstrated multiple unique HIV integration sites indicating that these cell lines are not clonal and in the ACH-2 cell line there was evidence of low level virus replication. These findings have implications for the use of latently infected cell lines as models of HIV latency and for the use of these cells as standards.

The Unique Morgue Ubiquitination Protein Is Conserved in a Diverse but Restricted Set of Invertebrates

PubMed Central

Zhou, Ying; Carpenter, Zachary W.; Brennan, Gregory

2009-01-01

Drosophila Morgue is a unique ubiquitination protein that facilitates programmed cell death and associates with DIAP1, a critical cell death inhibitor with E3 ubiquitin ligase activity. Morgue possesses a unique combination of functional domains typically associated with distinct types of ubiquitination enzymes. This includes an F box characteristic of the substrate-binding subunit in Skp, Cullin, and F box (SCF)-type ubiquitin E3 ligase complexes and a variant ubiquitin E2 conjugase domain where the active site cysteine is replaced by a glycine. Morgue also contains a single C4-type zinc finger motif. This architecture suggests potentially novel ubiquitination activities for Morgue. In this study, we address the evolutionary origins of this distinctive protein utilizing a combination of bioinformatics and molecular biology approaches. We find that Morgue exhibits widespread but restricted phylogenetic distribution among metazoans. Morgue proteins were identified in a wide range of Protostome phyla, including Arthropoda, Annelida, Mollusca, Nematoda, and Platyhelminthes. However, with one potential exception, Morgue was not detected in Deuterostomes, including Chordates, Hemichordates, or Echinoderms. Morgue was also not found in Ctenophora, Cnidaria, Placozoa, or Porifera. Characterization of Morgue sequences within specific animal lineages suggests that gene deletion or acquisition has occurred during divergence of nematodes and that at least one arachnid expresses an atypical form of Morgue consisting only of the variant E2 conjugase domain. Analysis of the organization of several morgue genes suggests that exon-shuffling events have contributed to the evolution of the Morgue protein. These results suggest that Morgue mediates conserved and distinctive ubiquitination functions in specific cell death pathways. PMID:19602541

An OmpA family protein, a target of the GinI/GinR quorum-sensing system in Gluconacetobacter intermedius, controls acetic acid fermentation.

PubMed

Iida, Aya; Ohnishi, Yasuo; Horinouchi, Sueharu

2008-07-01

Via N-acylhomoserine lactones, the GinI/GinR quorum-sensing system in Gluconacetobacter intermedius NCI1051, a gram-negative acetic acid bacterium, represses acetic acid and gluconic acid fermentation. Two-dimensional polyacrylamide gel electrophoretic analysis of protein profiles of strain NCI1051 and ginI and ginR mutants identified a protein that was produced in response to the GinI/GinR regulatory system. Cloning and nucleotide sequencing of the gene encoding this protein revealed that it encoded an OmpA family protein, named GmpA. gmpA was a member of the gene cluster containing three adjacent homologous genes, gmpA to gmpC, the organization of which appeared to be unique to vinegar producers, including "Gluconacetobacter polyoxogenes." In addition, GmpA was unique among the OmpA family proteins in that its N-terminal membrane domain forming eight antiparallel transmembrane beta-strands contained an extra sequence in one of the surface-exposed loops. Transcriptional analysis showed that only gmpA of the three adjacent gmp genes was activated by the GinI/GinR quorum-sensing system. However, gmpA was not controlled directly by GinR but was controlled by an 89-amino-acid protein, GinA, a target of this quorum-sensing system. A gmpA mutant grew more rapidly in the presence of 2% (vol/vol) ethanol and accumulated acetic acid and gluconic acid in greater final yields than strain NCI1051. Thus, GmpA plays a role in repressing oxidative fermentation, including acetic acid fermentation, which is unique to acetic acid bacteria and allows ATP synthesis via ethanol oxidation. Consistent with the involvement of gmpA in oxidative fermentation, its transcription was also enhanced by ethanol and acetic acid.

Toward a Comprehensive System of Personnel Development in Deafblind Education

ERIC Educational Resources Information Center

Parker, Amy T.; Nelson, Catherine

2016-01-01

Students who are deafblind are a unique population with unique needs for learning, communication, and environmental access. Two roles have been identified as important to their education: teacher of the deafblind and intervener. However, these roles are not officially recognized in most states. Because of this lack of recognition and the low…

Exploring the Feminine Journey of Gifted Women Regarding Career Self-Efficacy and Emotional Well-Being

ERIC Educational Resources Information Center

Penny, Heather Elizabeth Dean

2013-01-01

Highly capable and intelligent individuals identified as gifted and talented (GATE) in educational settings require support for their unique needs associated with their giftedness. Unique needs for gifted girls include high emotional sensitivities including anxiety, depression, and frustration. These needs can impede the positive development of…

Is There a Unique Black Personality?

ERIC Educational Resources Information Center

Mosby, Doris P.

This article reviews research from the 1940's, 1950's and 1960's on the effects of discrimination on blacks. Data from these studies indicate that adverse cultural restrictions have fostered a unique and distinctive black personality. Among traits identified are: a negative or inferior self-image, pessimism about the future, attachment to the…

Girls with Emotional Disturbance and a History of Arrest: Characteristics and School-Based Predictors of Arrest

ERIC Educational Resources Information Center

Gage, Nicholas A.; Josephs, Nikki L.; Lunde, Kimberly

2012-01-01

Research suggests that girls receiving special education services for Emotional Disturbance (ED) may have unique characteristics and needs. Similarly, juvenile justice research has identified unique characteristics of court-involved girls. This study examined characteristics of girls with ED and a history of arrest. Additionally, classroom-based…

Mineralogy of Tagish Lake, a Unique Type 2 Carbonaceous Chondrite

NASA Technical Reports Server (NTRS)

Gounelle, M.; Zolensky, M. E.; Tonui, E.; Mikouchi, T.

2001-01-01

We have identified in Tagish Lake an abondant carbonate-poor lithology and a less common carbonate-rich lithology. Tagish Lake shows similarities and differences with CMs and CI1s. It is a unique carbonaceous chondrite recording specific aqueous alteration conditions. Additional information is contained in the original extended abstract.

Cognitive Abilities, Social Adaptation, and Externalizing Behavior Problems in Childhood and Adolescence: Specific Cascade Effects Across Development.

PubMed

Racz, Sarah Jensen; Putnick, Diane L; Suwalsky, Joan T D; Hendricks, Charlene; Bornstein, Marc H

2017-08-01

Children's and adolescents' cognitive abilities, social adaptation, and externalizing behaviors are broadly associated with each other at the bivariate level; however, the direction, ordering, and uniqueness of these associations have yet to be identified. Developmental cascade models are particularly well-suited to (1) discern unique pathways among psychological domains and (2) model stability in and covariation among constructs, allowing for conservative tests of longitudinal associations. The current study aimed to identify specific cascade effects among children's cognitive abilities, social adaptation, and externalizing behaviors, beginning in preschool and extending through adolescence. Children (46.2 % female) and mothers (N = 351 families) provided data when children were 4, 10, and 14 years old. Cascade effects highlighted significant stability in these domains. Unique longitudinal associations were identified between (1) age-10 cognitive abilities and age-14 social adaptation, (2) age-4 social adaptation and age-10 externalizing behavior, and (3) age-10 externalizing behavior and age-14 social adaptation. These findings suggest that children's social adaptation in preschool and externalizing behavior in middle childhood may be ideal intervention targets to enhance adolescent well-being.

Using the Theory of Planned Behavior to Identify Predictors of Oral Hygiene: A Collection of Unique Behaviors.

PubMed

Brein, Daniel J; Fleenor, Thomas J; Kim, Soo-Woo; Krupat, Edward

2016-03-01

This study aims to identify predictors of performed oral hygiene behaviors (OHBs) based on the Theory of Planned Behavior (TPB), oral health knowledge, and demographic factors. Using a questionnaire, 381 participants in three general dental offices and one hospital dental department in York, Pennsylvania, were surveyed regarding performed OHB, attitudes, subjective norms, perceived behavioral control, oral health knowledge, income, age, and sex. Three unique elements of OHB were identified for analysis: brushing, interdental cleaning, and tongue cleaning. Regression analysis revealed that attitude was the strongest predictor of brushing behavior, followed by oral health knowledge, perceived behavior control, subjective norms, and income. Perceived behavior control was the strongest predictor of interdental cleaning, followed by increased age and attitude. Female sex was the strongest predictor of tongue cleaning, followed by subjective norms, decreased age, and perceived behavior control. Respectively, these three groups of predictive variables explained 22.5% of brushing behavior, 22.7% of interdental cleaning behavior, and 9.5% of tongue cleaning behavior. The present findings highlight the utility of viewing OHB as a set of unique behaviors with unique predictive variables and provide additional support for use of TPB in predicting OHB. Periodontal practitioners should consider the strong associations of attitude and perceived behavioral control with brushing and interdental cleaning behaviors when designing interventional efforts to improve patient home care.

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.

PubMed

Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

2013-01-07

Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata

PubMed Central

Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

2013-01-01

Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem–loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping–pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration. PMID:23166307

Classifying threats with a 14-MeV neutron interrogation system.

PubMed

Strellis, Dan; Gozani, Tsahi

2005-01-01

SeaPODDS (Sea Portable Drug Detection System) is a non-intrusive tool for detecting concealed threats in hidden compartments of maritime vessels. This system consists of an electronic neutron generator, a gamma-ray detector, a data acquisition computer, and a laptop computer user-interface. Although initially developed to detect narcotics, recent algorithm developments have shown that the system is capable of correctly classifying a threat into one of four distinct categories: narcotic, explosive, chemical weapon, or radiological dispersion device (RDD). Detection of narcotics, explosives, and chemical weapons is based on gamma-ray signatures unique to the chemical elements. Elements are identified by their characteristic prompt gamma-rays induced by fast and thermal neutrons. Detection of RDD is accomplished by detecting gamma-rays emitted by common radioisotopes and nuclear reactor fission products. The algorithm phenomenology for classifying threats into the proper categories is presented here.

Forming, changing, and acting on attitude toward affirmative action programs in employment: a theory-driven approach.

PubMed

Bell, M P; Harrison, D A; McLaughlin, M E

2000-10-01

A model of attitude toward affirmative action programs (AAPs) was applied in 4 studies involving 1,622 participants. In Study 1, attributes people tacitly associate with AAPs were identified by open-ended elicitation. Using those attributes, an instrument was developed and administered in Studies 2, 3, and 4. In those studies, a multiplicative composite of beliefs and evaluations about the AAP attributes predicted AAP attitude, consistent with M. Fishbein and I. Ajzen's (1975) theory of reasoned action. Demographic effects on AAP attitude were partially mediated by this composite. In Studies 3 and 4, an experimental manipulation of AAP information was successful in changing AAP attitude, but in a way that polarized existing demographic differences. Study 4 also showed that AAP attitude and subjective norm jointly and uniquely predicted intentions to perform AAP-related behaviors. Intentions predicted the actual behavior of mailing postcards to political representatives reflecting participants' support for AAPs.

Solar burst with millimetre-wave emission at high frequency only

NASA Technical Reports Server (NTRS)

Kaufmann, P.; Correia, E.; Costa, J. E. R.; Vaz, A. M. Z.; Dennis, B. R.

1985-01-01

The first high sensitivity and high time-resolution observations of a solar burst taken simultaneously at 90 GHz and at 30 GHz are presented. These identify a unique impulsive burst on May 21, 1984 with fast pulsed emission that was considerably more intense at 90 GHz than at lower frequencies. Hard X-ray time structures at energies above 25 keV were almost identical to the 90 GHz structures to better than 1 s. The structure of the onset of the major 90 GHz burst coincided with the hard X-ray structure to within 128 ms. All 90 GHz major time structures consisted of trains of multiple subsecond pulses with rise times as short as 0.03 s and amplitudes that were large compared with the mean flux. When detectable, the 30 GHz subsecond pulses had smaller relative amplitude and were in phase with the corresponding 90 GHz pulses.

Piezoelectric modulation of surface voltage in GaN and AlGaN/GaN: charge screening effects and 2DEG

NASA Astrophysics Data System (ADS)

Wilson, Marshall; Schrayer, Bret; Savtchouk, Alexandre; Hillard, Bob; Lagowski, Jacek

2017-02-01

Surface voltage response to pulses of piezoelectric polarization is measured with a Kelvin-probe providing a unique means for investigation of the dynamics of polarization induced sheet charge and 2DEG. Combined with biasing of the surface with a corona-deposited charge from accumulation to deep depletion and corresponding non-contact C-V type characterization, the technique identifies surface band bending and interface traps as key factors that affect the magnitude and time decay of piezoelectric polarization. For 2DEG structures, surface potential pinning is observed when the 2DEG is fully populated. Pinning is released by negative corona charging to fully deplete the 2DEG. These results are consistent with the role of surface states. Presently demonstrated polarization modulation and wafer scale measurements shall impact the in-depth characterization and fundamental understanding of AlGaN/GaN 2DEG structures.

Selective detection of vapor phase hydrogen peroxide with phthalocyanine chemiresistors.

PubMed

Bohrer, Forest I; Colesniuc, Corneliu N; Park, Jeongwon; Schuller, Ivan K; Kummel, Andrew C; Trogler, William C

2008-03-26

The use of hydrogen peroxide as a precursor to improvised explosives has made its detection a topic of critical importance. Chemiresistor arrays comprised of 50 nm thick films of metallophthalocyanines (MPcs) are redox selective vapor sensors of hydrogen peroxide. Hydrogen peroxide is shown to decrease currents in cobalt phthalocyanine sensors while it increases currents in nickel, copper, and metal-free phthalocyanine sensors; oxidation and reduction of hydrogen peroxide via catalysis at the phthalocyanine surface are consistent with the pattern of sensor responses. This represents the first example of MPc vapor sensors being oxidized and reduced by the same analyte by varying the metal center. Consequently, differential analysis by redox contrast with catalytic amplification using a small array of sensors may be used to uniquely identify peroxide vapors. Metallophthalocyanine chemiresistors represent an improvement over existing peroxide vapor detection technologies in durability and selectivity in a greatly decreased package size.

Application of enhanced modern structured analysis techniques to Space Station Freedom electric power system requirements

NASA Technical Reports Server (NTRS)

Biernacki, John; Juhasz, John; Sadler, Gerald

1991-01-01

A team of Space Station Freedom (SSF) system engineers are in the process of extensive analysis of the SSF requirements, particularly those pertaining to the electrical power system (EPS). The objective of this analysis is the development of a comprehensive, computer-based requirements model, using an enhanced modern structured analysis methodology (EMSA). Such a model provides a detailed and consistent representation of the system's requirements. The process outlined in the EMSA methodology is unique in that it allows the graphical modeling of real-time system state transitions, as well as functional requirements and data relationships, to be implemented using modern computer-based tools. These tools permit flexible updating and continuous maintenance of the models. Initial findings resulting from the application of EMSA to the EPS have benefited the space station program by linking requirements to design, providing traceability of requirements, identifying discrepancies, and fostering an understanding of the EPS.

Equine welfare: risk of horses falling in the Grand National.

PubMed

Proudman, Christopher; Pinchbeck, Gina; Clegg, Peter; French, Nigel

2004-03-25

As in other competitive sports, the famous Grand National steeplechase, which is held at Aintree in the United Kingdom and is watched by 600 million people worldwide, sometimes results in injury. By analysing data from the past 15 Grand National races (consisting of 560 starts by horses), we are able to identify several factors that are significantly associated with failure to complete the race: no previous experience of the course and its unique obstacles, unfavourable ground conditions (too soft or too hard), a large number of runners, and the length of the odds ('starting price'). We also find that there is an increased risk of falling at the first fence and at the jump known as Becher's Brook, which has a ditch on the landing side. Our findings indicate ways in which the Grand National could be made safer for horses and illustrate how epidemiological analysis might contribute to preventing injury in competitive sport.

Future property damage from flooding: sensitivities to economy and climate change

DOE PAGES

Liu, Jing; Hertel, Thomas; Diffenbaugh, Noah; ...

2015-08-09

Using a unique dataset for Indiana counties during the period 1995-2012, we estimate the effects of flood hazard, asset exposure, and social vulnerability on property damage. This relationship then is combined with the expected level of future flood risks to project property damage from flooding in 2030 under various scenarios. We compare these scenario projections to identify which risk management strategy offers the greatest potential to mitigate flooding loss. Results show that by 2030, county level flooding hazard measured by extreme flow volume and frequency will increase by an average of 16.2% and 7.4%, respectively. The total increase in propertymore » damages projected under different model specifications range from 13.3% to 20.8%. Across models future damages consistently exhibit the highest sensitivity to future increases in asset exposure, reinforcing the importance of non-structural measures in managing floodplain development.« less

Psychological Distress in Afghan Refugees: A Mixed-Method Systematic Review

PubMed Central

Alemi, Qais; James, Sigrid; Cruz, Romalene; Zepeda, Veronica; Racadio, Michael

2013-01-01

Mental health problems disproportionately affect Afghan refugees and asylum seekers who continue to seek international protection with prolonged exposure to war. We performed a systematic review aimed at synthesizing peer-reviewed literature pertaining to mental health problems among Afghans resettled in industrialized nations. We used five databases to identify studies published between 1979 and 2013 that provided data on distress levels, and subjective experiences with distress. Seventeen studies met our inclusion criteria consisting of 1 mixed-method, 7 qualitative, and 9 quantitative studies. Themes from our qualitative synthesis described antecedents for distress being rooted in cultural conflicts and loss, and also described unique coping mechanisms. Quantitative findings indicated moderate to high prevalence of depressive and posttraumatic symptomatology. These findings support the need for continued mental health research with Afghans that accounts for: distress among newly resettled groups, professional help-seeking utilization patterns, and also culturally relevant strategies for mitigating distress and engaging Afghans in research. PMID:23784146

Multitemporal diurnal AVIRIS images of a forested ecosystem

NASA Technical Reports Server (NTRS)

Ustin, Susan L.; Smith, Milton O.; Adams, John B.

1992-01-01

Both physiological and ecosystem structural information may be derived from diurnal images. Structural information may be inferred from changes in canopy shadows between images and from changes in spectral composition due to changes in proportions of subpixel mixing resulting from the differences in sun/view angles. Physiological processes having diurnal scales also may be measurable if a stable basis for spectral comparison can be established. Six diurnal images of an area east of Mt. Shasta, CA were acquired on 22 Sep. 1989. This unique diurnal data set provided an opportunity to test the consistency of endmember fractions and residuals. It was expected that shade endmember abundances would show the greatest change as lighting geometry changed and less change in the normalized fractional proportion of other endmembers. Diurnal changes in spectral features related to physiological characteristics may be identifiable as changes in wavelength specific residuals.

Liquid Methane Testing With a Large-Scale Spray Bar Thermodynamic Vent System

NASA Technical Reports Server (NTRS)

Hastings, L. J.; Bolshinskiy, L. G.; Hedayat, A.; Flachbart, R. H.; Sisco, J. D.; Schnell. A. R.

2014-01-01

NASA's Marshall Space Flight Center conducted liquid methane testing in November 2006 using the multipurpose hydrogen test bed outfitted with a spray bar thermodynamic vent system (TVS). The basic objective was to identify any unusual or unique thermodynamic characteristics associated with densified methane that should be considered in the design of space-based TVSs. Thirteen days of testing were performed with total tank heat loads ranging from 720 to 420 W at a fill level of approximately 90%. It was noted that as the fluid passed through the Joule-Thompson expansion, thermodynamic conditions consistent with the pervasive presence of metastability were indicated. This Technical Publication describes conditions that correspond with metastability and its detrimental effects on TVS performance. The observed conditions were primarily functions of methane densification and helium pressurization; therefore, assurance must be provided that metastable conditions have been circumvented in future applications of thermodynamic venting to in-space methane storage.

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi

PubMed Central

Chibucos, Marcus C.; Soliman, Sameh; Gebremariam, Teclegiorgis; Lee, Hongkyu; Daugherty, Sean; Orvis, Joshua; Shetty, Amol C.; Crabtree, Jonathan; Hazen, Tracy H.; Etienne, Kizee A.; Kumari, Priti; O'Connor, Timothy D.; Rasko, David A.; Filler, Scott G.; Fraser, Claire M.; Lockhart, Shawn R.; Skory, Christopher D.; Ibrahim, Ashraf S.; Bruno, Vincent M.

2016-01-01

Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets. PMID:27447865

Occupational safety and health management in the construction industry: a review.

PubMed

Jaafar, Mohd Hafiidz; Arifin, Kadir; Aiyub, Kadaruddin; Razman, Muhammad Rizal; Ishak, Muhammad Izzuddin Syakir; Samsurijan, Mohamad Shaharudin

2017-09-11

The construction industry plays a significant role in contributing to the economy and development globally. During the process of construction, various hazards coupled with the unique nature of the industry contribute to high fatality rates. This review refers to previous published studies and related Malaysian legislation documents. Four main elements consisting of human, worksite, management and external elements which cause occupational accidents and illnesses were identified. External and management elements are the underlying causes contributing to occupational safety and health (OSH), while human and worksite elements are more apparent causes of occupational accidents and illnesses. An effective OSH management approach is required to contain all hazards at construction sites. An approach to OSH management constructed by elements of policy, process, personnel and incentive developed in previous work is explored. Changes to the sub-elements according to previous studies and the related Malaysian legislation are also covered in this review.

Patient Characteristics Predicting Readmission Among Individuals Hospitalized for Heart Failure.

PubMed

O'Connor, Melissa; Murtaugh, Christopher M; Shah, Shivani; Barrón-Vaya, Yolanda; Bowles, Kathryn H; Peng, Timothy R; Zhu, Carolyn W; Feldman, Penny H

2016-02-01

Heart failure is difficult to manage and increasingly common with many individuals experiencing frequent hospitalizations. Little is known about patient factors consistently associated with hospital readmission. A literature review was conducted to identify heart failure patient characteristics, measured before discharge, that contribute to variation in hospital readmission rates. Database searches yielded 950 potential articles, of which 34 studies met inclusion criteria. Patient characteristics generally have a very modest effect on all-cause or heart failure-related readmission within 7 to 180 days of index hospital discharge. A range of cardiac diseases and other comorbidities only minimally increase readmission rates. No single patient characteristic stands out as a key contributor across multiple studies underscoring the challenge of developing successful interventions to reduce readmissions. Interventions may need to be general in design with the specific intervention depending on each patient's unique clinical profile. © The Author(s) 2015.

Patient Characteristics Predicting Readmission Among Individuals Hospitalized for Heart Failure

PubMed Central

O'Connor, Melissa; Murtaugh, Christopher M.; Shah, Shivani; Barrón-Vaya, Yolanda; Bowles, Kathryn H.; Peng, Timothy R.; Zhu, Carolyn W.; Feldman, Penny H.

2015-01-01

Heart failure is difficult to manage and increasingly common with many individuals experiencing frequent hospitalizations. Little is known about patient factors consistently associated with hospital readmission. A literature review was conducted to identify heart failure patient characteristics, measured before discharge, that contribute to variation in hospital readmission rates. Database searches yielded 950 potential articles, of which 34 studies met inclusion criteria. Patient characteristics generally have a very modest effect on all-cause or heart failure–related readmission within 7 to 180 days of index hospital discharge. A range of cardiac diseases and other comorbidities only minimally increase readmission rates. No single patient characteristic stands out as a key contributor across multiple studies underscoring the challenge of developing successful interventions to reduce readmissions. Interventions may need to be general in design with the specific intervention depending on each patient's unique clinical profile. PMID:26180045

Improving Voluntary Environmental Management Programs: Facilitating Learning and Adaptation

NASA Astrophysics Data System (ADS)

Genskow, Kenneth D.; Wood, Danielle M.

2011-05-01

Environmental planners and managers face unique challenges understanding and documenting the effectiveness of programs that rely on voluntary actions by private landowners. Programs, such as those aimed at reducing nonpoint source pollution or improving habitat, intend to reach those goals by persuading landowners to adopt behaviors and management practices consistent with environmental restoration and protection. Our purpose with this paper is to identify barriers for improving voluntary environmental management programs and ways to overcome them. We first draw upon insights regarding data, learning, and adaptation from the adaptive management and performance management literatures, describing three key issues: overcoming information constraints, structural limitations, and organizational culture. Although these lessons are applicable to a variety of voluntary environmental management programs, we then present the issues in the context of on-going research for nonpoint source water quality pollution. We end the discussion by highlighting important elements for advancing voluntary program efforts.

The Marriage Wealth Premium Revisited: Gender Disparities and Within-Individual Changes in Personal Wealth in Germany.

PubMed

Lersch, Philipp M

2017-06-01

This study examines the association between marriage and economic wealth of women and men. Going beyond previous research that focused on household wealth, I examine personal wealth, which allows identifying gender disparities in the association between marriage and wealth. Using unique data from the German Socio-Economic Panel Study (2002, 2007, and 2012), I apply random-effects and fixed-effects regression models to test my expectations. I find that both women and men experience substantial marriage wealth premiums not only in household wealth but also in personal wealth. However, I do not find consistent evidence for gender disparities in these general marriage premiums. Additional analyses indicate, however, that women's marriage premiums are substantially lower than men's premiums in older cohorts and when only nonhousing wealth is considered. Overall, this study provides new evidence that women and men gain unequally in their wealth attainment through marriage.

The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life

PubMed Central

Bains, William; Schulze-Makuch, Dirk

2016-01-01

Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe. PMID:27376334

A Simple Sequence Repeat- and Single-Nucleotide Polymorphism-Based Genetic Linkage Map of the Brown Planthopper, Nilaparvata lugens

PubMed Central

Jairin, Jirapong; Kobayashi, Tetsuya; Yamagata, Yoshiyuki; Sanada-Morimura, Sachiyo; Mori, Kazuki; Tashiro, Kosuke; Kuhara, Satoru; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Yamamoto, Kimiko; Matsumura, Masaya; Yasui, Hideshi

2013-01-01

In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH. PMID:23204257

Physical Justification for Negative Remanent Magnetization in Homogeneous Nanoparticles

PubMed Central

Gu, Shuo; He, Weidong; Zhang, Ming; Zhuang, Taisen; Jin, Yi; ElBidweihy, Hatem; Mao, Yiwu; Dickerson, James H.; Wagner, Michael J.; Torre, Edward Della; Bennett, Lawrence H.

2014-01-01

The phenomenon of negative remanent magnetization (NRM) has been observed experimentally in a number of heterogeneous magnetic systems and has been considered anomalous. The existence of NRM in homogenous magnetic materials is still in debate, mainly due to the lack of compelling support from experimental data and a convincing theoretical explanation for its thermodynamic validation. Here we resolve the long-existing controversy by presenting experimental evidence and physical justification that NRM is real in a prototype homogeneous ferromagnetic nanoparticle, an europium sulfide nanoparticle. We provide novel insights into major and minor hysteresis behavior that illuminate the true nature of the observed inverted hysteresis and validate its thermodynamic permissibility and, for the first time, present counterintuitive magnetic aftereffect behavior that is consistent with the mechanism of magnetization reversal, possessing unique capability to identify NRM. The origin and conditions of NRM are explained quantitatively via a wasp-waist model, in combination of energy calculations. PMID:25183061

Conserved and variable domains of RNase MRP RNA.

PubMed

Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

2009-01-01

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

On the relative motions of long-lived Pacific mantle plumes.

PubMed

Konrad, Kevin; Koppers, Anthony A P; Steinberger, Bernhard; Finlayson, Valerie A; Konter, Jasper G; Jackson, Matthew G

2018-02-27

Mantle plumes upwelling beneath moving tectonic plates generate age-progressive chains of volcanos (hotspot chains) used to reconstruct plate motion. However, these hotspots appear to move relative to each other, implying that plumes are not laterally fixed. The lack of age constraints on long-lived, coeval hotspot chains hinders attempts to reconstruct plate motion and quantify relative plume motions. Here we provide 40 Ar/ 39 Ar ages for a newly identified long-lived mantle plume, which formed the Rurutu hotspot chain. By comparing the inter-hotspot distances between three Pacific hotspots, we show that Hawaii is unique in its strong, rapid southward motion from 60 to 50 Myrs ago, consistent with paleomagnetic observations. Conversely, the Rurutu and Louisville chains show little motion. Current geodynamic plume motion models can reproduce the first-order motions for these plumes, but only when each plume is rooted in the lowermost mantle.

Representation of Nursing Terminologies in UMLS

PubMed Central

Kim, Tae Youn; Coenen, Amy; Hardiker, Nicholas; Bartz, Claudia C.

2011-01-01

There are seven nursing terminologies or classifications that are considered a standard to support nursing practice in the U.S. Harmonizing these terminologies will enhance the interoperability of clinical data documented across nursing practice. As a first step to harmonize the nursing terminologies, the purpose of this study was to examine how nursing problems or diagnostic concepts from select terminologies were cross-mapped in Unified Medical Language System (UMLS). A comparison analysis was conducted by examining whether cross-mappings available in UMLS through concept unique identifiers were consistent with cross-mappings conducted by human experts. Of 423 concepts from three terminologies, 411 (97%) were manually cross-mapped by experts to the International Classification for Nursing Practice. The UMLS semantic mapping among the 411 nursing concepts presented 33.6% accuracy (i.e., 138 of 411 concepts) when compared to expert cross-mappings. Further research and collaboration among experts in this field are needed for future enhancement of UMLS. PMID:22195127

Maternal interaction style in affective disordered, physically ill, and normal women.

PubMed

Hamilton, E B; Jones, M; Hammen, C

1993-09-01

Affective style (AS) and communication deviance (CD) have been suggested as markers of dysfunctional family environments that may be associated with psychiatric illness. Studies have focused mainly on parental responses during family interactions when an offspring is the identified patient. The present study is unique in examining AS and CD in mothers with unipolar depression, bipolar disorder, or chronic physical illness, and in normal controls. The sample consisted of 64 mothers with children ages 8 to 16. Unipolar mothers were more likely to show negative AS than were any other maternal group. There were no group differences for CD. Chronic stress, few positive life events, and single parenting were associated with AS. CD was associated solely with lower socioeconomic status. Results suggest that dysfunctional interactions are determined not only by maternal psychopathology, but also by an array of contextual factors that are related to the quality of the family environment.

Time-dependent Hartree-Fock approach to nuclear ``pasta'' at finite temperature

NASA Astrophysics Data System (ADS)

Schuetrumpf, B.; Klatt, M. A.; Iida, K.; Maruhn, J. A.; Mecke, K.; Reinhard, P.-G.

2013-05-01

We present simulations of neutron-rich matter at subnuclear densities, like supernova matter, with the time-dependent Hartree-Fock approximation at temperatures of several MeV. The initial state consists of α particles randomly distributed in space that have a Maxwell-Boltzmann distribution in momentum space. Adding a neutron background initialized with Fermi distributed plane waves the calculations reflect a reasonable approximation of astrophysical matter. This matter evolves into spherical, rod-like, and slab-like shapes and mixtures thereof. The simulations employ a full Skyrme interaction in a periodic three-dimensional grid. By an improved morphological analysis based on Minkowski functionals, all eight pasta shapes can be uniquely identified by the sign of only two valuations, namely the Euler characteristic and the integral mean curvature. In addition, we propose the variance in the cell density distribution as a measure to distinguish pasta matter from uniform matter.

Discrimination, religious and cultural factors, and Middle Eastern/Arab Americans' psychological distress.

PubMed

Ikizler, Ayse S; Szymanski, Dawn M

2018-01-11

We investigated (1) the moderating role of religiosity in the link between religious affiliation and ethnic discrimination and (2) the moderating roles of religiosity, ethnic identity, and family connectedness in the relations between ethnic discrimination and psychological distress. Our sample consisted of 122 (60% women, 40% men) Middle Eastern/Arab Americans (MEAAs), ranging in age from 18 to 82 years old, who completed an online survey. Muslim identification predicted discrimination for MEAAs with high but not low religiosity. Higher levels of discrimination, more family connectedness, the interaction of discrimination and religiosity, and the interaction of discrimination and family connectedness were unique predictors of psychological distress. Religiosity is a risk factor for experiencing ethnic discrimination among Muslim identified MEAAs. MEAAs who have high religiosity and low to moderate levels of family connectedness are vulnerable to psychological distress associated with ethnic discrimination. © 2018 Wiley Periodicals, Inc.