The association between cecal insertion time and colorectal neoplasm detection

PubMed Central

2013-01-01

Background Information on the impact of cecal insertion time on colorectal neoplasm detection is limited. Our objective was to determine the association between cecal insertion time and colorectal neoplasm detection rate in colonoscopy screening. Methods We performed a cross-sectional study of 12,679 consecutive subjects aged 40–79 years undergoing screening colonoscopy in routine health check-ups at the Center for Health Promotion of the Samsung Medical Center from December 2007 to June 2009. Fixed effects logistic regression conditioning on colonoscopist was used to eliminate confounding due to differences in technical ability and other characteristics across colonoscopists. Results The mean cecal insertion time was 5.9 (SD, 4.4 minutes). We identified 4,249 (33.5%) participants with colorectal neoplasms, of whom 1,956 had small single adenomas (<5 mm), 595 had medium single adenomas (5–9 mm), and 1,699 had multiple adenomas or advanced colorectal neoplasms. The overall rates of colorectal neoplasm detection by quartiles of cecal insertion time were 36.8%, 33.4%, 32.7%, and 31.0%, respectively (p trend <0.001).The odds for small single colorectal adenoma detection was 16% lower (adjusted OR 0.84; 95% CI 0.71 to 0.99) in the fourth compared to the first quartile of insertion time (p trend 0.005). Insertion time was not associated with the detection rate of single adenomas ≥5 mm, multiple adenomas or advanced colorectal neoplasms. Conclusion Shorter insertion times were associated with increased rates of detection of small colorectal adenomas <5 mm. Cecal insertion time may be clinically relevant as missed small colorectal adenomas may progress to more advanced lesions. PMID:23915303

Random insertion and gene disruption via transposon mutagenesis of Ureaplasma parvum using a mini-transposon plasmid

PubMed Central

Aboklaish, Ali F.; Dordet-Frisoni, Emilie; Citti, Christine; Toleman, Mark A; Glass, John I.; Spiller, O. Brad

2015-01-01

While transposon mutagenesis has been successfully used for Mycoplasma spp. to disrupt and determine non-essential genes, previous attempts with Ureaplasma spp. have been unsuccessful. Using a polyethylene glycol-transformation enhancing protocol, we were able to transform three separate serovars of Ureaplasma parvum with a Tn4001-based mini-transposon plasmid containing a gentamicin resistance selection marker. Despite the large degree of homology between Ureaplasma parvum and Ureaplasma urealyticum, all attempts to transform the latter in parallel failed, with the exception of a single clinical U. urealyticum isolate. PCR probing and sequencing were used to confirm transposon insertion into the bacterial genome and identify disrupted genes. Transformation of prototype serovar 3 consistently resulted in transfer only of sequence between the mini-transposon inverted repeats, but some strains showed additional sequence transfer. Transposon insertion occurred randomly in the genome resulting in unique disruption of genes UU047, UU390, UU440, UU450, UU520, UU526, UU582 for single clones from a panel of screened clones. An intergenic insertion between genes UU187 and UU188 was also characterised. Two phenotypic alterations were observed in the mutated strains: Disruption of a DEAD-box RNA helicase (UU582) altered growth kinetics, while the U. urealyticum strain lost resistance to serum attack coincident with disruption of gene UUR10_137 and loss of expression of a 41 kDa protein. Transposon mutagenesis was used successfully to insert single copies of a mini-transposon into the genome and disrupt genes leading to phenotypic changes in Ureaplasma parvum strains. This method can now be used to deliver exogenous genes for expression and determine essential genes for Ureaplasma parvum replication in culture and experimental models. PMID:25444567

Random insertion and gene disruption via transposon mutagenesis of Ureaplasma parvum using a mini-transposon plasmid.

PubMed

Aboklaish, Ali F; Dordet-Frisoni, Emilie; Citti, Christine; Toleman, Mark A; Glass, John I; Spiller, O Brad

2014-11-01

While transposon mutagenesis has been successfully used for Mycoplasma spp. to disrupt and determine non-essential genes, previous attempts with Ureaplasma spp. have been unsuccessful. Using a polyethylene glycol-transformation enhancing protocol, we were able to transform three separate serovars of Ureaplasma parvum with a Tn4001-based mini-transposon plasmid containing a gentamicin resistance selection marker. Despite the large degree of homology between Ureaplasma parvum and Ureaplasma urealyticum, all attempts to transform the latter in parallel failed, with the exception of a single clinical U. urealyticum isolate. PCR probing and sequencing were used to confirm transposon insertion into the bacterial genome and identify disrupted genes. Transformation of prototype serovar 3 consistently resulted in transfer only of sequence between the mini-transposon inverted repeats, but some strains showed additional sequence transfer. Transposon insertion occurred randomly in the genome resulting in unique disruption of genes UU047, UU390, UU440, UU450, UU520, UU526, UU582 for single clones from a panel of screened clones. An intergenic insertion between genes UU187 and UU188 was also characterised. Two phenotypic alterations were observed in the mutated strains: Disruption of a DEAD-box RNA helicase (UU582) altered growth kinetics, while the U. urealyticum strain lost resistance to serum attack coincident with disruption of gene UUR10_137 and loss of expression of a 41 kDa protein. Transposon mutagenesis was used successfully to insert single copies of a mini-transposon into the genome and disrupt genes leading to phenotypic changes in Ureaplasma parvum strains. This method can now be used to deliver exogenous genes for expression and determine essential genes for Ureaplasma parvum replication in culture and experimental models. Copyright © 2014 Elsevier GmbH. All rights reserved.

Definitive airway management after pre-hospital supraglottic airway insertion: Outcomes and a management algorithm for trauma patients.

PubMed

Hernandez, Matthew C; Aho, Johnathon M; Zielinski, Martin D; Zietlow, Scott P; Kim, Brian D; Morris, David S

2018-01-01

Prehospital airway management increasingly involves supraglottic airway insertion and a paucity of data evaluates outcomes in trauma populations. We aim to describe definitive airway management in traumatically injured patients who necessitated prehospital supraglottic airway insertion. We performed a single institution retrospective review of multisystem injured patients (≥15years) that received prehospital supraglottic airway insertion during 2009 to 2016. Baseline demographics, number and type of: supraglottic airway insertion attempts, definitive airway and complications were recorded. Primary outcome was need for tracheostomy. Univariate and multivariable statistics were performed. 56 patients met inclusion criteria and were reviewed, 78% were male. Median age [IQR] was 36 [24-56] years. Injuries comprised blunt (94%), penetrating (4%) and burns (2%). Median ISS was 26 [22-41]. Median number of prehospital endotracheal intubation (PETI) attempts was 2 [1-3]. Definitive airway management included: (n=20, 36%, tracheostomy), (n=10, 18%, direct laryngoscopy), (n=6, 11%, bougie), (n=9, 15%, Glidescope), (n=11, 20%, bronchoscopic assistance). 24-hour mortality was 41%. Increasing number of PETI was associated with increasing facial injury. On regression, increasing cervical and facial injury patterns as well as number of PETI were associated with definitive airway control via surgical tracheostomy. After supraglottic airway insertion, operative or non-operative approaches can be utilized to obtain a definitive airway. Patients with increased craniofacial injuries have an increased risk for airway complications and need for tracheostomy. We used these factors to generate an evidence based algorithm that requires prospective validation. Level IV - Retrospective study. Retrospective single institution study. Copyright © 2017 Elsevier Inc. All rights reserved.

Monitoring oxygen movement by Raman spectroscopy of resistive random access memory with a graphene-inserted electrode.

PubMed

Tian, He; Chen, Hong-Yu; Gao, Bin; Yu, Shimeng; Liang, Jiale; Yang, Yi; Xie, Dan; Kang, Jinfeng; Ren, Tian-Ling; Zhang, Yuegang; Wong, H-S Philip

2013-02-13

In this paper, we employed Ramen spectroscopy to monitor oxygen movement at the electrode/oxide interface by inserting single-layer graphene (SLG). Raman area mapping and single-point measurements show noticeable changes in the D-band, G-band, and 2D-band signals of the SLG during consecutive electrical programming repeated for nine cycles. In addition, the inserted SLG enables the reduction of RESET current by 22 times and programming power consumption by 47 times. Collectively, our results show that monitoring the oxygen movement by Raman spectroscopy for a resistive random access memory (RRAM) is made possible by inserting a single-layer graphene at electrode/oxide interface. This may open up an important analysis tool for investigation of switching mechanism of RRAM.

Concealed Accessory Pathways with a Single Ventricular and Two Discrete Atrial Insertion Sites.

PubMed

Kipp, Ryan T; Abu Sham'a, Raed; Hiroyuki, Ito; Han, Frederick T; Refaat, Marwan; Hsu, Jonathan C; Field, Michael E; Kopp, Douglas E; Marcus, Gregory M; Scheinman, Melvin M; Hoffmayer, Kurt S

2017-03-01

Atrioventricular reciprocating tachycardia (AVRT) utilizing a concealed accessory pathway is common. It is well appreciated that some patients may have multiple accessory pathways with separate atrial and ventricular insertion sites. We present three cases of AVRT utilizing concealed pathways with evidence that each utilizing a single ventricular insertion and two discrete atrial insertion sites. In case one, two discrete atrial insertion sites were mapped in two separate procedures, and only during the second ablation was the Kent potential identified. Ablation of the Kent potential at this site remote from the two atrial insertion sites resulted in the termination of the retrograde conduction in both pathways. Case two presented with supraventricular tachycardia (SVT) with alternating eccentric atrial activation patterns without alteration in the tachycardia cycle length. The two distinct atrial insertion sites during orthodromic AVRT and ventricular pacing were targeted and each of the two atrial insertion sites were successfully mapped and ablated. In case three, retrograde decremental conduction utilizing both atrial insertion sites was identified prior to ablation. After mapping and ablation of the first discrete atrial insertion site, tachycardia persisted utilizing the second atrial insertion site. Only after ablation of the second atrial insertion site was SVT noninducible, and VA conduction was no longer present. Concealed retrograde accessory pathways with discrete atrial insertion sites may have a common ventricular insertion site. Identification and ablation of the ventricular insertion site or the separate discrete atrial insertion sites result in successful treatment. © 2017 Wiley Periodicals, Inc.

Practice-based clinical evaluation of ceramic single crowns after at least five years.

PubMed

Dhima, Matilda; Paulusova, Vladimira; Carr, Alan B; Rieck, Kevin L; Lohse, Christine; Salinas, Thomas J

2014-02-01

Long-term practice-based clinical evaluations of various contemporary ceramic crown restorations from multiple practitioners are limited. The aims of this study were to evaluate the clinical performance of ceramic single crowns and to identify factors that influence their clinical performance. Ceramic single crowns that had been placed at the Mayo Clinic and in function since 2005 were identified and included in the study. The restorations were examined clinically, radiographically, and with photographs. Modified United States Public Health Services criteria were used for the clinical evaluation. The ceramic systems evaluated were bilayer and monolayer. Fifty-nine patients (41 women, 18 men) with 226 single teeth and implants restored with single ceramic crowns were identified. The mean duration from insertion date to study examination date was 6.1 years. Thirteen restorations (6%) were replaced at a mean 3.3 years after insertion date (range, 0.1-6.1 years). Estimated replacement-free survival rates (95% confidence interval [CI]; number of teeth/implants still at risk) at 5 years after insertion date were 95.1% (95% CI, 92.2-98.1; 153) and at 10 years were 92.8% (95% CI, 89.1-96.8; 8). The most common reason for replacement was fracture to the core of posterior layered ceramic crowns. The most commonly used luting agent was resin-modified ionomer cement. Most restorations exhibited clinically acceptable marginal integrity, shade, no caries recurrence, and no periapical pathology. The clinical performance of ceramic single crowns at 5 and 10 years supports their application in all areas of the mouth. With the majority of fractures to the core occurring early in the lifetime of layered ceramic posterior crowns, consideration of other monolithic ceramic systems for posterior crowns is advised. Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Immediate functional loading of single implants: a multicenter study with 4 years of follow-up

PubMed Central

Raes, Filiep; Eccellente, Tammaro; Lenzi, Carolina; Ortolani, Michele; Luongo, Giuseppe; Mangano, Carlo; Mangano, Francesco

2018-01-01

Background. In the current scientific literature there are only few studies on the immediate functional loading of single implants. The aim of the present present study was to evaluate the 4-year survival rate, complication rate and peri-implant marginal bone loss (PIMBL) of immediately loaded single implants inserted in healed ridges and fresh post-extraction sites. Methods. Six centers were involved in this prospective study. The surgical and prosthetic protocol was defined in detail, before the start of recruiting patients. Recruitment of patients and performance of surgeries took place between February 2012 and February 2013. Criteria for inclusion were single-tooth gaps in healed ridges and fresh post-extraction sockets. All the fixtures (Anyridge®, Megagen Corporation, Gyeongbuk, South Korea) were functionally loaded immediately after insertion and followed for a period of 4 years. Outcome measures were implant survival, complications and PIMBL. Results. Forty-six patients (18‒73 years of age) were selected. In total, 57 fixtures were placed (10 in fresh post-extraction sockets). After 4 years of functional loading, only one fixture was lost; therefore, high survival rates (97.6% patient-based; 98.1% implant-based) were reported. In addition, a limited incidence of biologic (4.8% patient-based; 3.8% implant-based) and prosthetic (9.7% patient-based; 7.6% implant-based) complications was reported. The overall 4-year PIMBL amounted to 0.38±0.21 mm (healed ridges: 0.4±0.21 mm; fresh post-extraction sockets: 0.33±0.20 mm). Conclusion. Loading single implants immediately seems to be a highly successful treatment modality. However, long-term data are needed to confirm these positive outcomes. PMID:29732018

Organ-specific SPECT activity calibration using 3D printed phantoms for molecular radiotherapy dosimetry.

PubMed

Robinson, Andrew P; Tipping, Jill; Cullen, David M; Hamilton, David; Brown, Richard; Flynn, Alex; Oldfield, Christopher; Page, Emma; Price, Emlyn; Smith, Andrew; Snee, Richard

2016-12-01

Patient-specific absorbed dose calculations for molecular radiotherapy require accurate activity quantification. This is commonly derived from Single-Photon Emission Computed Tomography (SPECT) imaging using a calibration factor relating detected counts to known activity in a phantom insert. A series of phantom inserts, based on the mathematical models underlying many clinical dosimetry calculations, have been produced using 3D printing techniques. SPECT/CT data for the phantom inserts has been used to calculate new organ-specific calibration factors for (99m) Tc and (177)Lu. The measured calibration factors are compared to predicted values from calculations using a Gaussian kernel. Measured SPECT calibration factors for 3D printed organs display a clear dependence on organ shape for (99m) Tc and (177)Lu. The observed variation in calibration factor is reproduced using Gaussian kernel-based calculation over two orders of magnitude change in insert volume for (99m) Tc and (177)Lu. These new organ-specific calibration factors show a 24, 11 and 8 % reduction in absorbed dose for the liver, spleen and kidneys, respectively. Non-spherical calibration factors from 3D printed phantom inserts can significantly improve the accuracy of whole organ activity quantification for molecular radiotherapy, providing a crucial step towards individualised activity quantification and patient-specific dosimetry. 3D printed inserts are found to provide a cost effective and efficient way for clinical centres to access more realistic phantom data.

The insertion products of 2-picolyl lithium salt with benzonitrile and terephthalonitrile

NASA Astrophysics Data System (ADS)

Zhang, Yihao; Xiao, Xia; Bai, Jianliang; Cao, Wei; Chen, Xia

2018-02-01

Treatment of 2-picoline with BunLi in THF affords its corresponding 2-picolyl lithium salt in a high yield. The insertion of benzonitrile into the Lisbnd C bond of 2-picolyl lithium followed by acidic hydrolysis yields the corresponding β-pyridyl ketone (1), and diketone compounds (2) is obtained from 1 by intermolecular elimination of proton under the base condition. Similarly, the insertion of terephthalonitrile into 2-picolyl lithium leads to a 1,4-phenyl-linked pyridyl-azaalyl dilithium complex 4, followed by acidic hydrolysis yields corresponding 1,4-phenyl-linked dipyridylketone 3. The probable reaction pathway for the formation of 2 has been investigated. Compound 2 and 4 have been characterized by single-crystal X-ray crystallography.

Inferior vena cava filter insertion through the popliteal vein: enabling the percutaneous endovenous intervention of deep vein thrombosis with a single venous access approach in a single session

PubMed Central

Kim, Hyoung Ook; Kim, Jae Kyu; Park, Jin Gyoon; Yim, Nam Yeol; Kang, Yang Jun; Jung, Hye Doo

2016-01-01

PURPOSE We aimed to evaluate the efficiency of placing an inferior vena cava (IVC) filter through the same popliteal vein access site used for percutaneous endovenous intervention in patients with extensive lower extremity deep vein thrombosis. METHODS This retrospective study included 21 patients who underwent IVC filter insertion through the popliteal vein over a three-year period. Patient medical records were reviewed for the location of the deep vein thrombosis, result of filter removal, and total number of endovascular procedures needed for filter insertion and recanalization of the lower extremity venous system. Follow-up lower extremity computed tomography (CT) venography was also reviewed in each patient to assess the degree of filter tilt in the IVC. RESULTS All patients had extensive lower extremity deep vein thrombosis involving the iliac vein and/or femoral vein. Seventeen patients showed deep vein thrombosis of the calf veins. In all patients, IVC filter insertion and the recanalization procedure were performed during a single procedure through the single popliteal vein access site. In the 17 patients undergoing follow-up CT, the mean tilt angle of the filter was 7.14°±4.48° in the coronal plane and 8.77°±5.49° in the sagittal plane. Filter retrieval was successful in 16 of 17 patients (94.1%) in whom filter retrieval was attempted. CONCLUSION Transpopliteal IVC filter insertion is an efficient technique that results in low rates of significant filter tilt and enables a single session procedure using a single venous access site for filter insertion and percutaneous endovenous intervention. PMID:27559713

Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish.

PubMed

Albadri, Shahad; Del Bene, Filippo; Revenu, Céline

2017-05-15

With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish. Copyright © 2017 Elsevier Inc. All rights reserved.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexander E; Gschwind, Michael K; Gunnels, John A

2013-10-29

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Optimized scalar promotion with load and splat SIMD instructions

DOEpatents

Eichenberger, Alexandre E [Chappaqua, NY; Gschwind, Michael K [Chappaqua, NY; Gunnels, John A [Yorktown Heights, NY

2012-08-28

Mechanisms for optimizing scalar code executed on a single instruction multiple data (SIMD) engine are provided. Placement of vector operation-splat operations may be determined based on an identification of scalar and SIMD operations in an original code representation. The original code representation may be modified to insert the vector operation-splat operations based on the determined placement of vector operation-splat operations to generate a first modified code representation. Placement of separate splat operations may be determined based on identification of scalar and SIMD operations in the first modified code representation. The first modified code representation may be modified to insert or delete separate splat operations based on the determined placement of the separate splat operations to generate a second modified code representation. SIMD code may be output based on the second modified code representation for execution by the SIMD engine.

Mechanism of hole injection enhancement in light-emitting diodes by inserting multiple hole-reservoir layers in electron blocking layer

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

Zhao, Yukun; Wang, Shuai; Feng, Lungang

In this study, gallium nitride (GaN) based light-emitting diodes (LEDs) with single and multiple hole-reservoir layers (HRLs) inserted in the electron-blocking layer (EBL) have been investigated numerically and experimentally. According to simulation results, a better electron confinement and a higher hole injection level can be achieved by the multiple HRLs inserted in the EBL region. To further reveal the underlying mechanism of hole injection enhancement experimentally, the active regions were intentionally designed to emit photons with three different wavelengths of 440 nm, 460 nm, and 480 nm, respectively. Based on the experimental results of photoluminescence (PL) and time-resolved PL (TRPL) measurements conducted atmore » 298 K, the remarkable enhancement (148%) of PL intensities and significant increase in the decay times of the quantum wells close to p-GaN can be obtained. Therefore, the mechanism is proposed that carriers are able to reserve in the EBL region with multiple HRLs for a much longer time. Meanwhile, carriers could diffuse into the active region by tunnelling and/or thermo-electronic effect and then recombine efficiently, leading to the better carrier reservoir effect and higher hole injection in LEDs. As a result, by inserting multiple HRLs in the EBL region instead of single HRL, the experimental external quantum efficiency is enhanced by 19.8%, while the serious droop ratio is markedly suppressed from 37.0% to 27.6% at the high current injection of 100 A/cm{sup 2}.« less

Radio Frequency (RF) Micro-Electromechanical Systems (MEMS) Switches for Space Communications

NASA Technical Reports Server (NTRS)

Simons, Rainee N.; Ponchak, George E.; Scardelletti, Maximillian C.; Varaljay, Nicholas C.

2000-01-01

Micro-electromechanical systems (MEMS) is an emerging technology for radio frequency (RF) systems because it has the potential to dramatically decrease loss and improve efficiency. In this paper, we address the design and fabrication of novel MEMS switches being developed at NASA Glenn Research Center. Two types of switches are being developed: a microstrip series single pole single throw (SPST) switch and a coplanar waveguide (CPW) series SPST and single pole double throw (SPDT) switches. These are being fabricated as an integral part of 50 Ohm microstrip and CPW RF integrated circuits using microfabrication techniques. The construction of the switch relies on a cantilever beam that is partially supported by a dielectric post. The cantilever beam is electro-magnetically actuated. To decrease stiction, a Si3N4 thin film is deposited over the contact area. Thus, when the switch is closed, the ON-state insertion loss is governed by the parallel plate capacitance formed by the two contacts. The isolation in the OFF-state is governed by the parasitic capacitance when the cantilever is in the up position. RF MEMS switches have been demonstrated with 80% lower insertion loss than conventional solid state devices (GaAs Metal Semiconductor Field Effect Transistors (MESFETs) and Silicon PIN diodes) based switches. For example, a conventional GaAs five-bit phase shifter which is required for beam steering in a phased array antenna has approximately 7 dB of insertion loss at 26.5 GHz where as a comparable MEMS based phase shifter is expected to have only 2 dB of insertion loss. This translates into 56% lower power dissipation and therefore decreases the thermal load on the spacecraft and also reduces the power amplifier requirements. These benefits will enable NASA to build the next generation of deep space science crafts and micro/nano satellites.

Development of a 20-MHz wide-bandwidth PMN-PT single crystal phased-array ultrasound transducer.

PubMed

Wong, Chi-Man; Chen, Yan; Luo, Haosu; Dai, Jiyan; Lam, Kwok-Ho; Chan, Helen Lai-Wa

2017-01-01

In this study, a 20-MHz 64-element phased-array ultrasound transducer with a one-wavelength pitch is developed using a PMN-30%PT single crystal and double-matching layer scheme. High piezoelectric (d 33 >1000pC/N) and electromechanical coupling (k 33 >0.8) properties of the single crystal with an optimized fabrication process involving the photolithography technique have been demonstrated to be suitable for wide-bandwidth (⩾70%) and high-sensitivity (insertion loss ⩽30dB) phased-array transducer application. A -6dBbandwidth of 91% and an insertion loss of 29dBfor the 20-MHz 64-element phased-array transducer were achieved. This result shows that the bandwidth is improved comparing with the investigated high-frequency (⩾20MHz) ultrasound transducers using piezoelectric ceramic and single crystal materials. It shows that this phased-array transducer has potential to improve the resolution of biomedical imaging, theoretically. Based on the hypothesis of resolution improvement, this phased-array transducer is capable for small animal (i.e. mouse and zebrafish) studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Linkage disequilibrium and signatures of positive selection around LINE-1 retrotransposons in the human genome.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Cheng, Ching-Yu; Wong, Tien Yin; Quake, Stephen R; Burkholder, William F

2014-06-03

Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium with their surrounding genomic regions and that they were well tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity was detected around several L1 insertions. This finding suggests that some of these L1 insertions may have been the target of recent positive selection.

Single shot trajectory design for region-specific imaging using linear and nonlinear magnetic encoding fields.

PubMed

Layton, Kelvin J; Gallichan, Daniel; Testud, Frederik; Cocosco, Chris A; Welz, Anna M; Barmet, Christoph; Pruessmann, Klaas P; Hennig, Jürgen; Zaitsev, Maxim

2013-09-01

It has recently been demonstrated that nonlinear encoding fields result in a spatially varying resolution. This work develops an automated procedure to design single-shot trajectories that create a local resolution improvement in a region of interest. The technique is based on the design of optimized local k-space trajectories and can be applied to arbitrary hardware configurations that employ any number of linear and nonlinear encoding fields. The trajectories designed in this work are tested with the currently available hardware setup consisting of three standard linear gradients and two quadrupolar encoding fields generated from a custom-built gradient insert. A field camera is used to measure the actual encoding trajectories up to third-order terms, enabling accurate reconstructions of these demanding single-shot trajectories, although the eddy current and concomitant field terms of the gradient insert have not been completely characterized. The local resolution improvement is demonstrated in phantom and in vivo experiments. Copyright © 2012 Wiley Periodicals, Inc.

Single-cell manipulation and DNA delivery technology using atomic force microscopy and nanoneedle.

PubMed

Han, Sung-Woong; Nakamura, Chikashi; Miyake, Jun; Chang, Sang-Mok; Adachi, Taiji

2014-01-01

The recent single-cell manipulation technology using atomic force microscopy (AFM) not only allows high-resolution visualization and probing of biomolecules and cells but also provides spatial and temporal access to the interior of living cells via the nanoneedle technology. Here we review the development and application of single-cell manipulations and the DNA delivery technology using a nanoneedle. We briefly describe various DNA delivery methods and discuss their advantages and disadvantages. Fabrication of the nanoneedle, visualization of nanoneedle insertion into living cells, DNA modification on the nanoneedle surface, and the invasiveness of nanoneedle insertion into living cells are described. Different methods of DNA delivery into a living cell, such as lipofection, microinjection, and nanoneedles, are then compared. Finally, single-cell diagnostics using the nanoneedle and the perspectives of the nanoneedle technology are outlined. The nanoneedle-based DNA delivery technology provides new opportunities for efficient and specific introduction of DNA and other biomolecules into precious living cells with a high spatial resolution within a desired time frame. This technology has the potential to be applied for many basic cellular studies and for clinical studies such as single-cell diagnostics.

Institute for High Heat Flux Removal (IHHFR). Phases I, II, and III

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

Boyd, Ronald D.

2014-08-31

The IHHFR focused on interdisciplinary applications as it relates to high heat flux engineering issues and problems which arise due to engineering systems being miniaturized, optimized, or requiring increased high heat flux performance. The work in the IHHFR focused on water as a coolant and includes: (1) the development, design, and construction of the high heat flux flow loop and facility; (2) test section development, design, and fabrication; and, (3) single-side heat flux experiments to produce 2-D boiling curves and 3-D conjugate heat transfer measurements for single-side heated test sections. This work provides data for comparisons with previously developed andmore » new single-side heated correlations and approaches that address the single-side heated effect on heat transfer. In addition, this work includes the addition of single-side heated circular TS and a monoblock test section with a helical wire insert. Finally, the present work includes: (1) data base expansion for the monoblock with a helical wire insert (only for the latter geometry), (2) prediction and verification using finite element, (3) monoblock model and methodology development analyses, and (4) an alternate model development for a hypervapotron and related conjugate heat transfer controlling parameters.« less

High Isolation Single-Pole Four-Throw RF MEMS Switch Based on Series-Shunt Configuration

PubMed Central

Khaira, Navjot

2014-01-01

This paper presents a novel design of single-pole four-throw (SP4T) RF-MEMS switch employing both capacitive and ohmic switches. It is designed on high-resistivity silicon substrate and has a compact area of 1.06 mm2. The series or ohmic switches have been designed to provide low insertion loss with good ohmic contact. The pull-in voltage for ohmic switches is calculated to be 7.19 V. Shunt or capacitive switches have been used in each port to improve the isolation for higher frequencies. The proposed SP4T switch provides excellent RF performances with isolation better than 70.64 dB and insertion loss less than 0.72 dB for X-band between the input port and each output port. PMID:24711730

Lambda Red Mediated Gap Repair Utilizes a Novel Replicative Intermediate in Escherichia coli

PubMed Central

Reddy, Thimma R.; Fevat, Léna M. S.; Munson, Sarah E.; Stewart, A. Francis; Cowley, Shaun M.

2015-01-01

The lambda phage Red recombination system can mediate efficient homologous recombination in Escherichia coli, which is the basis of the DNA engineering technique termed recombineering. Red mediated insertion of DNA requires DNA replication, involves a single-stranded DNA intermediate and is more efficient on the lagging strand of the replication fork. Lagging strand recombination has also been postulated to explain the Red mediated repair of gapped plasmids by an Okazaki fragment gap filling model. Here, we demonstrate that gap repair involves a different strand independent mechanism. Gap repair assays examining the strand asymmetry of recombination did not show a lagging strand bias. Directly testing an ssDNA plasmid showed lagging strand recombination is possible but dsDNA plasmids did not employ this mechanism. Insertional recombination combined with gap repair also did not demonstrate preferential lagging strand bias, supporting a different gap repair mechanism. The predominant recombination route involved concerted insertion and subcloning though other routes also operated at lower frequencies. Simultaneous insertion of DNA resulted in modification of both strands and was unaffected by mutations to DNA polymerase I, responsible for Okazaki fragment maturation. The lower efficiency of an alternate Red mediated ends-in recombination pathway and the apparent lack of a Holliday junction intermediate suggested that gap repair does not involve a different Red recombination pathway. Our results may be explained by a novel replicative intermediate in gap repair that does not involve a replication fork. We exploited these observations by developing a new recombineering application based on concerted insertion and gap repair, termed SPI (subcloning plus insertion). SPI selected against empty vector background and selected for correct gap repair recombinants. We used SPI to simultaneously insert up to four different gene cassettes in a single recombineering reaction. Consequently, our findings have important implications for the understanding of E. coli replication and Red recombination. PMID:25803509

Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity

PubMed Central

Traverse, Charles C.

2017-01-01

ABSTRACT Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola, which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. PMID:28851848

1.5 W high efficiency and tunable single-longitudinal-mode Ho:YLF ring laser based on Faraday effect.

PubMed

Wu, Jing; Ju, Youlun; Dai, Tongyu; Yao, Baoquan; Wang, Yuezhu

2017-10-30

We demonstrated an efficient and tunable single-longitudinal-mode Ho:YLF ring laser based on Faraday effect for application to measure atmospheric carbon dioxide (CO 2 ). Single-longitudinal-mode power at 2051.65 nm achieved 528 mW with the slope efficiency of 39.5% and the M 2 factor of 1.07, and the tunable range of about 178 GHz was obtained by inserting a Fabry-Perot (F-P) etalon with the thickness of 0.5 mm. In addition, the maximum single-longitudinal-mode power reached 1.5 W with the injected power of 528 mW at 2051.65 nm by master oscillator power amplifier (MOPA) technique. High efficiency and tunable single-longitudinal-mode based on Faraday effect around 2 μm has not been reported yet to the best of our knowledge.

PIP silicone breast implants: rupture rates based on the explantation of 676 implants in a single surgeon series.

PubMed

Quaba, Omar; Quaba, Awf

2013-09-01

To determine the true rupture rates of PIP implants from a large single surgeon cohort and to assess whether rupture rates varied depending on time of implant insertion. In addition, the efficacy of ultra sound scanning (USS) in determining rupture is examined. Predominantly prospectively based analysis of patient records, investigations and surgical findings. 338 patients (676 implants) were included in the study and they all had removal of their implants. The senior author operated on all patients at some stage of their treatment. 160 patients were imaged pre-operatively with USS. Patients had implants inserted between 1999 and 2007 for cosmetic breast augmentation. A total of 144 ruptured implants were removed from 119 patients, giving a rupture rate of 35.2% per patient and 21.3% per implant over a mean implantation period of 7.8 years. A statistical difference (P < 0.001) in rupture rates between implants inserted prior to 2003 and those inserted from 2003 was demonstrated, with higher failure rates in the latter group. There was a significant difference in rupture rates depending on pocket placement of the implants. The sensitivity and specificity of USS at detecting rupture was 90.6% and 98.3% respectively. A proportion of patients (29.4%) demonstrated loco-regional spread of silicone to the axilla on scanning. Our paper has confirmed high rates of PIP implant failure in the largest published series to date. The significant difference in rupture rates between implants inserted prior to 2003 and those after this time supports the view that industrial silicone was used in the devices after 2003. Implants are more likely to rupture if inserted in the sub muscular plane compared to the sub glandular plane. USS is highly effective at detecting rupture in PIP implants and loco-regional spread is high compared to other devices. We believe this paper provides hard data enabling more informed decision making for patients, clinicians and providers in what remains an active issue affecting thousands of women. Copyright © 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Dynamic study of (De)sodiation in alpha-MnO 2 nanowires

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

Yuan, Yifei; Ma, Lu; He, Kun

2016-01-01

In this report, the electrochemical sodiation and desodiation in single crystalline alpha-MnO 2 nanowires are studied dynamically at both single particle level using in situ transmission electron microscopy (TEM) and bulk level using in situ synchrotron X-ray. The TEM results suggest that the first sodiation process starts with tunnel-based Na + intercalation, experiences the formation of Na 0.5MnO 2 as a result of tunnel degradation, and ends with the Mn 2O 3 phase. The inserted Na + can be partially extracted out of the sodiated products, and the following cycles are dominated by the reversible conversion reaction between Na 0.5MnOmore » 2 and Mn 2O 3. The Mn valence evolution inside a cycling coin using alpha-MnO 2 nanowire electrode also exhibits partially reversible characteristic, agreeing well with the in situ TEM analysis. The sodiation is compared with lithiation in the same alpha-MnO 2 nanowires. Both Na + and Li + interact with the tunneled structure via a similar tunnel -driven intercalation mechanism before Mn 4+ is reduced to Mn 3.5+. For the following deep insertion, the tunnels survive up. to LiMnO 2 (Mn3+) during lithiation, while the sodiation proceeds via a different mechanism that involves obvious phase transition and fast tunnel degradation after Mn's valence is below 3.5+. The difference in charge carrier insertion mechanisms can be ascribed to the strong interaction between the tunnel frame and inserted Na + possessing a larger ionic size than inserted Li +.« less

Ultra-wide bandpass filter based on long-period fiber gratings and the evanescent field coupling between two fibers.

PubMed

Kim, Myoung Jin; Jung, Yong Min; Kim, Bok Hyeon; Han, Won-Taek; Lee, Byeong Ha

2007-08-20

We demonstrate a fiber-based bandpass filter with an ultra-wide spectral bandwidth. The ultra-wide band feature is achieved by inscribing a long-period fiber grating (LPG) in a specially-designed low index core single mode fiber. To get the bandpass function, the evanescent field coupling between two attached fibers is utilized. By applying strain, the spectral shape of the pass-band is adjusted to flat-top and Gaussian shapes. For the flat-top case, the bandwidth is obtained ~ 160 nm with an insertion loss of ~ 2 dB. With strain, the spectral shape is switched into a Gaussian one, which has ~ 120 nm FWHM and ~ 4.18 dB insertion loss at the peak.

Clinical outcomes of VNS therapy with AspireSR® (including cardiac-based seizure detection) at a large complex epilepsy and surgery centre.

PubMed

Hamilton, Preci; Soryal, Imad; Dhahri, Prince; Wimalachandra, Welege; Leat, Anna; Hughes, Denise; Toghill, Nicole; Hodson, James; Sawlani, Vijay; Hayton, Tom; Samarasekera, Shanika; Bagary, Manny; McCorry, Dougall; Chelvarajah, Ramesh

2018-05-01

To compare the efficacy of AspireSR ® to preceding VNS battery models for battery replacements, and to determine the efficacy of the AspireSR ® for new implants. Data were collected retrospectively from patients with epilepsy who had VNS AspireSR ® implanted over a three-year period between June 2014 and June 2017 by a single surgeon. Cases were divided into two cohorts, those in whom the VNS was a new insertion, and those in whom the VNS battery was changed from a previous model to AspireSR ® . Within each group, the seizure burden was compared between the periods before and after insertion of AspireSR ® . Fifty-one patients with a newly inserted AspireSR ® VNS model had a significant reduction in seizure frequency (p < 0.001), with 59% (n = 30) reporting ≥50% reduction. Of the 62 patients who had an existing VNS, 53% (n = 33) reported ≥50% reduction in seizure burden when the original VNS was inserted. After the battery was changed to the AspireSR ® , 71% (n = 44) reported a further reduction of ≥50% in their seizure burden. The size of this reduction was at least as large as that resulting from the insertion of their existing VNS in 98% (61/62) of patients. The results suggest that approximately 70% of patients with existing VNS insertions could have significant additional benefit from cardiac based seizure detection and closed loop stimulation from the AspireSR ® device. For new insertions, the AspireSR ® device has efficacy in 59% of patients. The 'rule of thirds' used in counseling patients may need to be modified accordingly. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Evaluation of dual-tip micromanometers during 21-day implantation in goats

NASA Technical Reports Server (NTRS)

Reister, C. A.; Koenig, S. C.; Schaub, J. D.; Ewert, D. L.; Swope, R. D.; Latham, R. D.; Fanton, J. W.; Convertino, V. A. (Principal Investigator)

1998-01-01

Investigative research efforts using a cardiovascular model required the determination of central circulatory haemodynamic and arterial system parameters for the evaluation of cardiovascular performance. These calculations required continuous beat-to-beat measurement of pressure within the four chambers of the heart and great vessels. Sensitivity and offset drift, longevity, and sources of error for eight 3F dual-tipped micromanometers were determined during 21 days of implantation in goats. Subjects were instrumented with pairs of chronically implanted fluid-filled access catheters in the left and right ventricles, through which dual-tipped (test) micromanometers were chronically inserted and single-tip (standard) micromanometers were acutely inserted. Acutely inserted sensors were calibrated daily and measured pressures were compared in vivo to the chronically inserted sensors. Comparison of the pre- and post-gain calibration of the chronically inserted sensors showed a mean sensitivity drift of 1.0 +/- 0.4% (99% confidence, n = 9 sensors) and mean offset drift of 5.0 +/- 1.5 mmHg (99% confidence, n = 9 sensors). Potential sources of error for these drifts were identified, and included measurement system inaccuracies, temperature drift, hydrostatic column gradients, and dynamic pressure changes. Based upon these findings, we determined that these micromanometers may be chronically inserted in high-pressure chambers for up to 17 days with an acceptable error, but should be limited to acute (hours) insertions in low-pressure applications.

Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

PubMed Central

Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

2013-01-01

We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

Expression of a putative dioxygenase gene adjacent to an insertion mutation is involved in the short internodes of columnar apples (Malus × domestica).

PubMed

Okada, Kazuma; Wada, Masato; Moriya, Shigeki; Katayose, Yuichi; Fujisawa, Hiroko; Wu, Jianzhong; Kanamori, Hiroyuki; Kurita, Kanako; Sasaki, Harumi; Fujii, Hiroshi; Terakami, Shingo; Iwanami, Hiroshi; Yamamoto, Toshiya; Abe, Kazuyuki

2016-11-01

Determining the molecular mechanism of fruit tree architecture is important for tree management and fruit production. An apple mutant 'McIntosh Wijcik', which was discovered as a bud mutation from 'McIntosh', exhibits a columnar growth phenotype that is controlled by a single dominant gene, Co. In this study, the mutation and the Co gene were analyzed. Fine mapping narrowed the Co region to a 101 kb region. Sequence analysis of the Co region and the original wild-type co region identified an insertion mutation of an 8202 bp long terminal repeat (LTR) retroposon in the Co region. Segregation analysis using a DNA marker based on the insertion polymorphism showed that the LTR retroposon was closely associated with the columnar growth phenotype. RNA-seq and RT-PCR analysis identified a promising Co candidate gene (91071-gene) within the Co region that is specifically expressed in 'McIntosh Wijcik' but not in 'McIntosh'. The 91071-gene was located approximately 16 kb downstream of the insertion mutation and is predicted to encode a 2-oxoglutarate-dependent dioxygenase involved in an unknown reaction. Overexpression of the 91071-gene in transgenic tobaccos and apples resulted in phenotypes with short internodes, like columnar apples. These data suggested that the 8202 bp retroposon insertion in 'McIntosh Wijcik' is associated with the short internodes of the columnar growth phenotype via upregulated expression of the adjacent 91071-gene. Furthermore, the DNA marker based on the insertion polymorphism could be useful for the marker-assisted selection of columnar apples.

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.

PubMed

Anton, Brian P; Mongodin, Emmanuel F; Agrawal, Sonia; Fomenkov, Alexey; Byrd, Devon R; Roberts, Richard J; Raleigh, Elisabeth A

2015-01-01

We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

PubMed Central

Anton, Brian P.; Mongodin, Emmanuel F.; Agrawal, Sonia; Fomenkov, Alexey; Byrd, Devon R.; Roberts, Richard J.; Raleigh, Elisabeth A.

2015-01-01

We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems. PMID:26010885

Insertion Process of Ceramic Nanoporous Microneedles by Means of a Novel Mechanical Applicator Design.

PubMed

Hartmann, Xavier H M; van der Linde, Peter; Homburg, Erik F G A; van Breemen, Lambert C A; de Jong, Arthur M; Luttge, Regina

2015-11-18

Arrays of microneedles (MNAs) are integrated in an out-of-plane fashion with a base plate and can serve as patches for the release of drugs and vaccines. We used soft-lithography and micromolding to manufacture ceramic nanoporous (np)MNAs. Failure modes of ceramic npMNAs are as yet poorly understood and the question remained: is our npMNA platform technology ready for microneedle (MN) assembly into patches? We investigated npMNAs by microindentation, yielding average crack fracture forces above the required insertion force for a single MN to penetrate human skin. We further developed a thumb pressure-actuated applicator-assisted npMNA insertion method, which enables anchoring of MNs in the skin by an adhesive in one handling step. Using a set of simple artificial skin models, we found a puncture efficiency of this insertion method a factor three times higher than by applying thumb pressure on the npMNA base plate directly. In addition, this new method facilitated zero MN-breakage due to a well-defined force distribution exerted onto the MNs and the closely surrounding area prior to bringing the adhesive into contact with the skin. Owing to the fact that such parameter space exists, we can conclude that npMNAs by soft lithography are a platform technology for MN assembly into a patch.

Silicon-based highly-efficient fiber-to-waveguide coupler for high index contrast systems

NASA Astrophysics Data System (ADS)

Nguyen, Victor; Montalbo, Trisha; Manolatou, Christina; Agarwal, Anu; Hong, Ching-yin; Yasaitis, John; Kimerling, L. C.; Michel, Jurgen

2006-02-01

A coupler to efficiently transfer broadband light from a single-mode optical fiber to a single-mode high-index contrast waveguide has been fabricated on a silicon substrate. We utilized a novel coupling scheme, with a vertically asymmetric design consisting of a stepwise parabolic graded index profile combined with a horizontal taper, to simultaneously confine light in both directions. Coupling efficiency has been measured as a function of the device dimensions. The optimal coupling efficiency is achieved for structures whose length equals the focal distance of the graded index and whose input width is close to the mode field diameter of the fiber. The fabricated structure is compact, robust and highly efficient, with an insertion loss of 2.2dB at 1550nm. The coupler exhibits less than 1dB variation in coupling efficiency in the measured spectral range from 1520nmto1620nm. The lowest insertion loss of 1.9dB is measured at 1540nm. The coupler design offers highly efficient coupling for single mode waveguides of core indices up to 2.2.

Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange

PubMed Central

Hmelo, Laura R.; Borlee, Bradley R.; Almblad, Henrik; Love, Michelle E.; Randall, Trevor E.; Tseng, Boo Shan; Lin, Chuyang; Irie, Yasuhiko; Storek, Kelly M.; Yang, Jaeun Jane; Siehnel, Richard J.; Howell, P. Lynne; Singh, Pradeep K.; Tolker-Nielsen, Tim; Parsek, Matthew R.; Schweizer, Herbert P.; Harrison, Joe J.

2016-01-01

Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knockins, as well as single nucleotide insertions, deletions and substitutions in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selection are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ~2 weeks. PMID:26492139

Thermomicrocapillaries as temperature biosensors in single cells

NASA Astrophysics Data System (ADS)

Herth, Simone; Giesguth, Miriam; Wedel, Waldemar; Reiss, Günther; Dietz, Karl-Josef

2013-03-01

Temperature is an important physical parameter in biology and its deviation from optimum can cause damage in biosystems. Thermocouples based on the Seebeck effect can be structured on glass microcapillaries to obtain thermomicrocapillaries (TMCs) usable in a micromanipulation setup. The suitability of the setup was proven by monitoring the temperature increase upon illumination of leaves and single cells following insertion of the TMC. The increase was 1.5 K in green tissue and 0.75 K in white leaf sections due to lower absorption. In single cells of trichomes, the increase was 0.5 K due to heat dissipation to the surrounding air.

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

The "bench-presser's shoulder": an overuse insertional tendinopathy of the pectoralis minor muscle.

PubMed

Bhatia, Deepak N; de Beer, Joe F; van Rooyen, Karin S; Lam, Francis; du Toit, Donald F

2007-08-01

Tendinopathies of the rotator cuff muscles, biceps tendon and pectoralis major muscle are common causes of shoulder pain in athletes. Overuse insertional tendinopathy of pectoralis minor is a previously undescribed cause of shoulder pain in weightlifters/sportsmen. To describe the clinical features, diagnostic tests and results of an overuse insertional tendinopathy of the pectoralis minor muscle. To also present a new technique of ultrasonographic evaluation and injection of the pectoralis minor muscle/tendon based on use of standard anatomical landmarks (subscapularis, coracoid process and axillary artery) as stepwise reference points for ultrasonographic orientation. Between 2005 and 2006, seven sportsmen presenting with this condition were diagnosed and treated at the Cape Shoulder Institute, Cape Town, South Africa. In five patients, the initiating and aggravating factor was performance of the bench-press exercise (hence the term "bench-presser's shoulder"). Medial juxta-coracoid tenderness, a painful active-contraction test and bench-press manoeuvre, and decrease in pain after ultrasound-guided injection of a local anaesthetic agent into the enthesis, in the absence of any other clinically/radiologically apparent pathology, were diagnostic of pectoralis minor insertional tendinopathy. All seven patients were successfully treated with a single ultrasound-guided injection of a corticosteroid into the enthesis of pectoralis minor followed by a period of rest and stretching exercises. This study describes the clinical features and management of pectoralis minor insertional tendinopathy, secondary to the bench-press type of weightlifting. A new pain site-based classification of shoulder pathology in weightlifters is suggested.

The insertion of human dynamics models in the flight control loops of V/STOL research aircraft. Appendix 2: The optimal control model of a pilot in V/STOL aircraft control loops

NASA Technical Reports Server (NTRS)

Zipf, Mark E.

1989-01-01

An overview is presented of research work focussed on the design and insertion of classical models of human pilot dynamics within the flight control loops of V/STOL aircraft. The pilots were designed and configured for use in integrated control system research and design. The models of human behavior that were considered are: McRuer-Krendel (a single variable transfer function model); and Optimal Control Model (a multi-variable approach based on optimal control and stochastic estimation theory). These models attempt to predict human control response characteristics when confronted with compensatory tracking and state regulation tasks. An overview, mathematical description, and discussion of predictive limitations of the pilot models is presented. Design strategies and closed loop insertion configurations are introduced and considered for various flight control scenarios. Models of aircraft dynamics (both transfer function and state space based) are developed and discussed for their use in pilot design and application. Pilot design and insertion are illustrated for various flight control objectives. Results of pilot insertion within the control loops of two V/STOL research aricraft (Sikorski Black Hawk UH-60A, McDonnell Douglas Harrier II AV-8B) are presented and compared against actual pilot flight data. Conclusions are reached on the ability of the pilot models to adequately predict human behavior when confronted with similar control objectives.

Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins.

PubMed

Quadros, Rolen M; Miura, Hiromi; Harms, Donald W; Akatsuka, Hisako; Sato, Takehito; Aida, Tomomi; Redder, Ronald; Richardson, Guy P; Inagaki, Yutaka; Sakai, Daisuke; Buckley, Shannon M; Seshacharyulu, Parthasarathy; Batra, Surinder K; Behlke, Mark A; Zeiner, Sarah A; Jacobi, Ashley M; Izu, Yayoi; Thoreson, Wallace B; Urness, Lisa D; Mansour, Suzanne L; Ohtsuka, Masato; Gurumurthy, Channabasavaiah B

2017-05-17

Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes. Transgenic mice generated by random genomic insertion approaches pose problems of unreliable expression, and thus there is a need for targeted-insertion models. Although CRISPR-based strategies were reported to create conditional and targeted-insertion alleles via one-step delivery of targeting components directly to zygotes, these strategies are quite inefficient. Here we describe Easi-CRISPR (Efficient additions with ssDNA inserts-CRISPR), a targeting strategy in which long single-stranded DNA donors are injected with pre-assembled crRNA + tracrRNA + Cas9 ribonucleoprotein (ctRNP) complexes into mouse zygotes. We show for over a dozen loci that Easi-CRISPR generates correctly targeted conditional and insertion alleles in 8.5-100% of the resulting live offspring. Easi-CRISPR solves the major problem of animal genome engineering, namely the inefficiency of targeted DNA cassette insertion. The approach is robust, succeeding for all tested loci. It is versatile, generating both conditional and targeted insertion alleles. Finally, it is highly efficient, as treating an average of only 50 zygotes is sufficient to produce a correctly targeted allele in up to 100% of live offspring. Thus, Easi-CRISPR offers a comprehensive means of building large-scale Cre-LoxP animal resources.

Novel polarization diversity without switch duplication of a Si-wire PILOSS optical switch.

PubMed

Tanizawa, Ken; Suzuki, Keijiro; Ikeda, Kazuhiro; Namiki, Shu; Kawashima, Hitoshi

2016-04-04

We demonstrate the compact polarization diversity based on the bidirectional full-port use of a path-independent-insertion-loss (PILOSS) optical switch. A polarization-diversity 4 × 4 strictly non-blocking optical switch is developed using a single thermooptic PILOSS Si-wire switch and fiber-based polarization beam splitters (PBSs) and combiners (PBCs). We measure characteristics of the switch and confirm that the proposed configuration demonstrates the performance in the insertion loss, polarization-dependent loss (PDL), and differential group delay (DGD) comparable with that of a conventional polarization-diversity 4 × 4 PILOSS switch using double switch elements. On the other hand, higher crosstalk is observed. The crosstalk increase is associated with the backward crosstalk at a waveguide intersection based on a directional coupler. The effect of the backward crosstalk on the total crosstalk is estimated, and future prospects are discussed.

Single-step generation of gene knockout-rescue system in pluripotent stem cells by promoter insertion with CRISPR/Cas9.

PubMed

Matsunaga, Taichi; Yamashita, Jun K

2014-02-07

Specific gene knockout and rescue experiments are powerful tools in developmental and stem cell biology. Nevertheless, the experiments require multiple steps of molecular manipulation for gene knockout and subsequent rescue procedures. Here we report an efficient and single step strategy to generate gene knockout-rescue system in pluripotent stem cells by promoter insertion with CRISPR/Cas9 genome editing technology. We inserted a tetracycline-regulated inducible gene promoter (tet-OFF/TRE-CMV) upstream of the endogenous promoter region of vascular endothelial growth factor receptor 2 (VEGFR2/Flk1) gene, an essential gene for endothelial cell (EC) differentiation, in mouse embryonic stem cells (ESCs) with homologous recombination. Both homo- and hetero-inserted clones were efficiently obtained through a simple selection with a drug-resistant gene. The insertion of TRE-CMV promoter disrupted endogenous Flk1 expression, resulting in null mutation in homo-inserted clones. When the inserted TRE-CMV promoter was activated with doxycycline (Dox) depletion, Flk1 expression was sufficiently recovered from the downstream genomic Flk1 gene. Whereas EC differentiation was almost completely perturbed in homo-inserted clones, Flk1 rescue with TRE-CMV promoter activation restored EC appearance, indicating that phenotypic changes in EC differentiation can be successfully reproduced with this knockout-rescue system. Thus, this promoter insertion strategy with CRISPR/Cas9 would be a novel attractive method for knockout-rescue experiments. Copyright © 2014 Elsevier Inc. All rights reserved.

Single-row versus double-row capsulolabral repair: a comparative evaluation of contact pressure and surface area in the capsulolabral complex-glenoid bone interface.

PubMed

Kim, Doo-Sup; Yoon, Yeo-Seung; Chung, Hoi-Jeong

2011-07-01

Despite the attention that has been paid to restoration of the capsulolabral complex anatomic insertion onto the glenoid, studies comparing the pressurized contact area and mean interface pressure at the anatomic insertion site between a single-row repair and a double-row labral repair have been uncommon. The purpose of our study was to compare the mean interface pressure and pressurized contact area at the anatomic insertion site of the capsulolabral complex between a single-row repair and a double-row repair technique. Controlled laboratory study. Thirty fresh-frozen cadaveric shoulders (mean age, 61 ± 8 years; range, 48-71 years) were used for this study. Two types of repair were performed on each specimen: (1) a single-row repair and (2) a double-row repair. Using pressure-sensitive films, we examined the interface contact area and contact pressure. The mean interface pressure was greater for the double-row repair technique (0.29 ± 0.04 MPa) when compared with the single-row repair technique (0.21 ± 0.03 MPa) (P = .003). The mean pressurized contact area was also significantly greater for the double-row repair technique (211.8 ± 18.6 mm(2), 78.4% footprint) compared with the single-row repair technique (106.4 ± 16.8 mm(2), 39.4% footprint) (P = .001). The double-row repair has significantly greater mean interface pressure and pressurized contact area at the insertion site of the capsulolabral complex than the single-row repair. The double-row repair may be advantageous compared with the single-row repair in restoring the native footprint area of the capsulolabral complex.

Many P-Element Insertions Affect Wing Shape in Drosophila melanogaster

PubMed Central

Weber, Kenneth; Johnson, Nancy; Champlin, David; Patty, April

2005-01-01

A screen of random, autosomal, homozygous-viable P-element insertions in D. melanogaster found small effects on wing shape in 11 of 50 lines. The effects were due to single insertions and remained stable and significant for over 5 years, in repeated, high-resolution measurements. All 11 insertions were within or near protein-coding transcription units, none of which were previously known to affect wing shape. Many sites in the genome can affect wing shape. PMID:15545659

Many P-element insertions affect wing shape in Drosophila melanogaster.

PubMed

Weber, Kenneth; Johnson, Nancy; Champlin, David; Patty, April

2005-03-01

A screen of random, autosomal, homozygous-viable P-element insertions in D. melanogaster found small effects on wing shape in 11 of 50 lines. The effects were due to single insertions and remained stable and significant for over 5 years, in repeated, high-resolution measurements. All 11 insertions were within or near protein-coding transcription units, none of which were previously known to affect wing shape. Many sites in the genome can affect wing shape.

Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity.

PubMed

Traverse, Charles C; Ochman, Howard

2017-08-29

Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola , which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. IMPORTANCE The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions-errors that potentially have more dire effects on protein function-is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions. Knowledge of the full extent of sequences subject to transcription indels supports a new model of bacterial transcription slippage, one that relies on the number of complementary bases between the transcript and the DNA template to which it slipped. Copyright © 2017 Traverse and Ochman.

Sequential cooling insert for turbine stator vane

DOEpatents

Jones, Russel B

2017-04-04

A sequential flow cooling insert for a turbine stator vane of a small gas turbine engine, where the impingement cooling insert is formed as a single piece from a metal additive manufacturing process such as 3D metal printing, and where the insert includes a plurality of rows of radial extending impingement cooling air holes alternating with rows of radial extending return air holes on a pressure side wall, and where the insert includes a plurality of rows of chordwise extending second impingement cooling air holes on a suction side wall. The insert includes alternating rows of radial extending cooling air supply channels and return air channels that form a series of impingement cooling on the pressure side followed by the suction side of the insert.

Effect of insertion torque on bone screw pullout strength.

PubMed

Lawson, K J; Brems, J

2001-05-01

The effect of insertion torque on the holding strength of 4.5-mm ASIF/AO cortical bone screws was studied in vitro. Screw holding strength was determined using an Instron materials testing machine (Bristol, United Kingdom) on 55 lamb femora and 30 human tibiocortical bone sections. Holding strength was defined as tensile stress at pullout with rapid loading to construct failure. Different insertion torques were tested, normalizing to the thickness of cortical bone specimen engaged. These represented low, intermediate, high, and thread-damaging insertion torque. All screws inserted with thread-damaging torque and single cortex engaging screws inserted to high torque tightening moments showed diminished holding strength. This loss of strength amounted to 40%-50% less than screws inserted with less torque.

EUVL back-insertion layout optimization

NASA Astrophysics Data System (ADS)

Civay, D.; Laffosse, E.; Chesneau, A.

2018-03-01

Extreme ultraviolet lithography (EUVL) is targeted for front-up insertion at advanced technology nodes but will be evaluated for back insertion at more mature nodes. EUVL can put two or more mask levels back on one mask, depending upon what level(s) in the process insertion occurs. In this paper, layout optimization methods are discussed that can be implemented when EUVL back insertion is implemented. The layout optimizations can be focused on improving yield, reliability or density, depending upon the design needs. The proposed methodology modifies the original two or more colored layers and generates an optimized single color EUVL layout design.

The P gene of bovine parainfluenza virus 3 expresses all three reading frames from a single mRNA editing site.

PubMed Central

Pelet, T; Curran, J; Kolakofsky, D

1991-01-01

The P gene of bovine parainfluenza virus 3 (bPIV3) contains two downstream overlapping ORFs, called V and D. By comparison with the mRNA editing sites of other paramyxoviruses, two editing sites were predicted for bPIV3; site a to express the D protein, and site b to express the V protein. Examination of the bPIV3 mRNAs, however, indicates that site b is non-functional whereas site a operates frequently. Insertions at site a give rise to both V and D protein mRNAs, because a very broad distribution of Gs is added when insertions occur. This broad distribution is very different from the editing sites of Sendai virus or SV5, where predominantly one form of edited mRNA containing either a one or two G insertion respectively is created, to access the single overlapping ORF of these viruses. A model is proposed to explain how paramyxoviruses control the range of G insertions on that fraction of the mRNAs where insertions occur. The bPIV3 P gene is unique as far as we know, in that a sizeable portion of the gene expresses all 3 reading frames as protein. bPIV3 apparently does this from a single editing site by removing the constraints which control the number of slippage rounds which take place. Images PMID:1846805

Buckling behaviors of single-walled carbon nanotubes inserted with a linear carbon-atom chain.

PubMed

Zhu, Chunhua; Chen, Yinfeng; Liu, Rumeng; Zhao, Junhua

2018-08-17

Buckling behaviors of single-walled carbon nanotubes (SWCNTs) inserted with a linear carbon-atom chain (CAC) (the composite structures are also called carbon nanowires (CNWs)) under torsion and bending as well as compression are studied using molecular dynamics (MD) simulations, respectively. Our MD results show that the critical buckling angles (or strains) of CNWs under the three presented kinds of loading patterns can be two times those of corresponding independent SWCNTs for long CNWs, while the buckling improvement is not obvious for short ones. The main reason is that the radial van der Waals force between the CAC and the SWCNT is very small for a short CNW, while it increases with increasing length and then tends to a constant for a long CNW. The obtained MD results agree well with those from available theoretical models. These findings will be a great help towards understanding the stability and reliability of the special CNT structures, and designing flexible CNT-based devices.

Low-Power Consumption InGaAs PIN Diode Switches for V-band Applications

NASA Astrophysics Data System (ADS)

Ziegler, Volker; Berg, Michael; Tobler, Hans; Woelk, Claus; Deufel, Reinhard; Trasser, Andreas; Schumacher, Hermann; Alekseev, Egor; Pavlidis, Dimitris; Dickmann, Juergen

1999-02-01

In this paper, we present the measurement results of two InP-based coplanar SPST (single pole single throw) PIN diode switches operating at V-band frequencies. The switches show excellent mm-wave performance combined with a very low DC-power consumption. The SPST with on-chip biasing and DC-blocking capacitors demonstrates an insertion loss as low as 0.84 dB and a high isolation value of 21.8 dB at a center frequency of 53 GHz with only 0.8 mW of DC-power consumption. A more simple SPST exhibits under equivalent conditions (0.9 mW) an excellent insertion loss of 0.52 dB and an isolation of 21.7 dB. Furthermore the power-handling capability of the InGaAs PIN diodes, which are used as active switching elements, is investigated in this paper and found to exceed 25 dBm at a reverse voltage of -5 V.

Maximum powers of low-loss series-shunt FET RF switches

NASA Astrophysics Data System (ADS)

Yang, Z.; Hu, X.; Yang, J.; Simin, G.; Shur, M.; Gaska, R.

2009-02-01

Low-loss high-power single pole single throw (SPST) monolithic RF switch based on AlGaN/GaN heterojunction field effect transistors (HFETs) demonstrate the insertion loss and isolation of 0.15 dB and 45.9 dB at 0.5 GHz and 0.23 dB and 34.3 dB at 2 GHz. Maximum switching powers are estimated +47 dBm or higher. Factors determining the maximum switching powers are analyzed. Design principles to obtain equally high switching powers in the ON and OFF-states are developed.

Transposon-mediated generation of BCR-ABL1-expressing transgenic cell lines for unbiased sensitivity testing of tyrosine kinase inhibitors.

PubMed

Byrgazov, Konstantin; Lucini, Chantal Blanche; Berkowitsch, Bettina; Koenig, Margit; Haas, Oskar A; Hoermann, Gregor; Valent, Peter; Lion, Thomas

2016-11-22

Point mutations in the ABL1 kinase domain are an important mechanism of resistance to tyrosine kinase inhibitors (TKI) in BCR-ABL1-positive and, as recently shown, BCR-ABL1-like leukemias. The cell line Ba/F3 lentivirally transduced with mutant BCR-ABL1 constructs is widely used for in vitro sensitivity testing and response prediction to tyrosine kinase inhibitors. The transposon-based Sleeping Beauty system presented offers several advantages over lentiviral transduction including the absence of biosafety issues, faster generation of transgenic cell lines, and greater efficacy in introducing large gene constructs. Nevertheless, both methods can mediate multiple insertions in the genome. Here we show that multiple BCR-ABL1 insertions result in elevated IC50 levels for individual TKIs, thus overestimating the actual resistance of mutant subclones. We have therefore established flow-sorting-based fractionation of BCR-ABL1-transformed Ba/F3 cells facilitating efficient enrichment of cells carrying single-site insertions, as demonstrated by FISH-analysis. Fractions of unselected Ba/F3 cells not only showed a greater number of BCR-ABL1 hybridization signals, but also revealed higher IC50 values for the TKIs tested. The data presented highlight the need to carefully select transfected cells by flow-sorting, and to control the insertion numbers by FISH and real-time PCR to permit unbiased in vitro testing of drug resistance.

Evidence from the structure and function of cytochromes c(2) that nonsulfur purple bacterial photosynthesis followed the evolution of oxygen respiration.

PubMed

Meyer, Terry; Van Driessche, Gonzalez; Ambler, Richard; Kyndt, John; Devreese, Bart; Van Beeumen, Jozef; Cusanovich, Michael

2010-10-01

Cytochromes c(2) are the nearest bacterial homologs of mitochondrial cytochrome c. The sequences of the known cytochromes c(2) can be placed in two subfamilies based upon insertions and deletions, one subfamily is most like mitochondrial cytochrome c (the small C2s, without significant insertions and deletions), and the other, designated large C2, shares 3- and 8-residue insertions as well as a single-residue deletion. C2s generally function between cytochrome bc(1) and cytochrome oxidase in respiration (ca 80 examples known to date) and between cytochrome bc(1) and the reaction center in nonsulfur purple bacterial photosynthesis (ca 21 examples). However, members of the large C2 subfamily are almost always involved in photosynthesis (12 of 14 examples). In addition, the gene for the large C2 (cycA) is associated with those for the photosynthetic reaction center (pufBALM). We hypothesize that the insertions in the large C2s, which were already functioning in photosynthesis, allowed them to replace the membrane-bound tetraheme cytochrome, PufC, that otherwise mediates between the small C2 or other redox proteins and photosynthetic reaction centers. Based upon our analysis, we propose that the involvement of C2 in nonsulfur purple bacterial photosynthesis was a metabolic feature subsequent to the evolution of oxygen respiration.

Stable transfection of babesia bigemina and babesia bovis using a single plasmid containing homologous and heterologous insertion and gene regulatory sequences

USDA-ARS?s Scientific Manuscript database

Bovine babesiosis caused by Babesia bovis and B. bigemina is a severe, often fatal, tick-borne disease of cattle for which improved methods for control are urgently needed. One of our long term goals is to develop effective vaccines based on genetically modfied B. bigemina and B. bovis parasites. Al...

Survival rates and bone loss after immediate loading of implants in fresh extraction sockets (single gaps). A clinical prospective study with 4 year follow-up

PubMed Central

Wojtovicz, Eduardo; España-Lopez, Antonio; Jimenez-Guerra, Alvaro; Monsalve-Guil, Loreto; Ortiz-Garcia, Ivan; Serrera-Figallo, Maria-Angeles

2018-01-01

Background The aim of this prospective study was to report the outcome of treatment with implants inserted after tooth extraction and immediately loaded. Material and Methods Fifty-six patients with single tooth loss were treated with 116 IPX Galimplant® implants with internal connections and a sandblasted, acid-etched surface. All implants were placed after tooth extraction using a flapless approach without bone regeneration, and they were then immediately loaded with cemented acrylic prostheses. After a period of three months, definitive cemented ceramic prostheses were placed. Patients were examined throughout a total of 4 years of follow-up. Marginal bone loss and survival rates were evaluated using digital periapical radiographs, taking into account clinical variables such as age, gender, smoking, history of periodontitis, etiology of extraction, placement site, diameter, and implant length. The Mann-Whitney U and Kruskal-Wallis non-parametric tests were used to compare differences between subgroups created based on the different clinical variables identified. Results Clinical results indicate an implant survival and success rate of 97.4%. Three implants were lost. Of the 116 immediate acrylic single crowns initially placed, 113 were replaced with definitive ceramic crowns after 3 months. A total of 77.8% of implants were inserted in the maxilla, while 22.2% were inserted in the mandible. No further complications were reported after the follow-up period (4 years). The mean marginal bone loss was 0.67 mm ± 0.40 mm. No differences were found among the subgroups of study patients. Conclusions This study indicates that dental implants that are inserted after tooth extraction and immediately loaded may constitute a successful and predictable alternative implant treatment. Key words:Dental implants, post-extraction implants, fresh sockets, immediate loading, immediate prostheses, implant dentistry. PMID:29476669

Evaluation of PET Imaging Resolution Using 350 mu{m} Pixelated CZT as a VP-PET Insert Detector

NASA Astrophysics Data System (ADS)

Yin, Yongzhi; Chen, Ximeng; Li, Chongzheng; Wu, Heyu; Komarov, Sergey; Guo, Qingzhen; Krawczynski, Henric; Meng, Ling-Jian; Tai, Yuan-Chuan

2014-02-01

A cadmium-zinc-telluride (CZT) detector with 350 μm pitch pixels was studied in high-resolution positron emission tomography (PET) imaging applications. The PET imaging system was based on coincidence detection between a CZT detector and a lutetium oxyorthosilicate (LSO)-based Inveon PET detector in virtual-pinhole PET geometry. The LSO detector is a 20 ×20 array, with 1.6 mm pitches, and 10 mm thickness. The CZT detector uses ac 20 ×20 ×5 mm substrate, with 350 μm pitch pixelated anodes and a coplanar cathode. A NEMA NU4 Na-22 point source of 250 μm in diameter was imaged by this system. Experiments show that the image resolution of single-pixel photopeak events was 590 μm FWHM while the image resolution of double-pixel photopeak events was 640 μm FWHM. The inclusion of double-pixel full-energy events increased the sensitivity of the imaging system. To validate the imaging experiment, we conducted a Monte Carlo (MC) simulation for the same PET system in Geant4 Application for Emission Tomography. We defined LSO detectors as a scanner ring and 350 μm pixelated CZT detectors as an insert ring. GATE simulated coincidence data were sorted into an insert-scanner sinogram and reconstructed. The image resolution of MC-simulated data (which did not factor in positron range and acolinearity effect) was 460 μm at FWHM for single-pixel events. The image resolutions of experimental data, MC simulated data, and theoretical calculation are all close to 500 μm FWHM when the proposed 350 μm pixelated CZT detector is used as a PET insert. The interpolation algorithm for the charge sharing events was also investigated. The PET image that was reconstructed using the interpolation algorithm shows improved image resolution compared with the image resolution without interpolation algorithm.

Insertion of linear 8.4 μm diameter 16 channel carbon fiber electrode arrays for single unit recordings

PubMed Central

Patel, Paras R.; Na, Kyounghwan; Zhang, Huanan; Kozai, Takashi D. Y.; Kotov, Nicholas A.; Yoon, Euisik; Chestek, Cynthia A.

2016-01-01

Objective Single carbon fiber electrodes (d=8.4 μm) insulated with parylene-c and functionalized with PEDOT:pTS have been shown to record single unit activity but manual implantation of these devices with forceps can be difficult. Without an improvement in the insertion method any increase in the channel count by fabricating carbon fiber arrays would be impractical. In this study, we utilize a water soluble coating and structural backbones that allow us to create, implant, and record from fully functionalized arrays of carbon fibers with ~150 μm pitch. Approach Two approaches were tested for the insertion of carbon fiber arrays. The first method used a PEG coating that temporarily stiffened the fibers while leaving a small portion at the tip exposed. The small exposed portion (500 μm – 1 mm) readily penetrated the brain allowing for an insertion that did not require the handling of each fiber by forceps. The second method involved the fabrication of silicon support structures with individual shanks spaced 150 μm apart. Each shank consisted of a small groove that held an individual carbon fiber. Main results Our results showed that the PEG coating allowed for the chronic implantation of carbon fiber arrays in 5 rats with unit activity detected at 31 days post-implant. The silicon support structures recorded single unit activity in 3 acute rat surgeries. In one of those surgeries a stacked device with 3 layers of silicon support structures and carbon fibers was built and shown to readily insert into the brain with unit activity on select sites. Significance From these studies we have found that carbon fibers spaced at ~150 μm readily insert into the brain. This greatly increases the recording density of chronic neural probes and paves the way for even higher density devices that have a minimal scarring response. PMID:26035638

[Brief introduction of acupuncture needling and teaching keypoint].

PubMed

Hou, Shu-wei; Guo, Li; Kong, Su-ping

2014-09-01

We summarized our accumulated clinical and teaching experiences and explored the regularity of acupuncture needling and teaching. It is of great importance in pressing hand during inserting needle. Stroking and pressing are two crucial parts which deserve more attention, and seldom useage of pressing hand should be abolished. Operating hand needs practice before inserting needle, while it should fully relaxed during inserting. Blending "touching", "stretch" "gathering" "erupting" and "advancing" in single moment, applying appropriate dynamic mode of inserting needle such as "join 3 forces as one" "3 points in a line" expertly and naturally. In addition, enough attention should be paid on "altering direction" and "shifting point". Inserting deftly and powerfully, no/slight sensation, deqi when inserting needle are the highest reflection as an acupuncturist.

Masking as an effective quality control method for next-generation sequencing data analysis.

PubMed

Yun, Sajung; Yun, Sijung

2014-12-13

Next generation sequencing produces base calls with low quality scores that can affect the accuracy of identifying simple nucleotide variation calls, including single nucleotide polymorphisms and small insertions and deletions. Here we compare the effectiveness of two data preprocessing methods, masking and trimming, and the accuracy of simple nucleotide variation calls on whole-genome sequence data from Caenorhabditis elegans. Masking substitutes low quality base calls with 'N's (undetermined bases), whereas trimming removes low quality bases that results in a shorter read lengths. We demonstrate that masking is more effective than trimming in reducing the false-positive rate in single nucleotide polymorphism (SNP) calling. However, both of the preprocessing methods did not affect the false-negative rate in SNP calling with statistical significance compared to the data analysis without preprocessing. False-positive rate and false-negative rate for small insertions and deletions did not show differences between masking and trimming. We recommend masking over trimming as a more effective preprocessing method for next generation sequencing data analysis since masking reduces the false-positive rate in SNP calling without sacrificing the false-negative rate although trimming is more commonly used currently in the field. The perl script for masking is available at http://code.google.com/p/subn/. The sequencing data used in the study were deposited in the Sequence Read Archive (SRX450968 and SRX451773).

Optimizing the specificity of nucleic acid hybridization.

PubMed

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2012-01-22

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed 'toehold exchange' probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg(2+) to 47 mM Mg(2+), and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.

A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis.

PubMed

Namouchi, Amine; Mardassi, Helmi

2006-11-01

Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band.

Recombining overlapping BACs into a single larger BAC.

PubMed

Kotzamanis, George; Huxley, Clare

2004-01-06

BAC clones containing entire mammalian genes including all the transcribed region and long range controlling elements are very useful for functional analysis. Sequenced BACs are available for most of the human and mouse genomes and in many cases these contain intact genes. However, large genes often span more than one BAC, and single BACs covering the entire region of interest are not available. Here we describe a system for linking two or more overlapping BACs into a single clone by homologous recombination. The method was used to link a 61-kb insert carrying the final 5 exons of the human CFTR gene onto a 160-kb BAC carrying the first 22 exons. Two rounds of homologous recombination were carried out in the EL350 strain of bacteria which can be induced for the Red genes. In the first round, the inserts of the two overlapping BACs were subcloned into modified BAC vectors using homologous recombination. In the second round, the BAC to be added was linearised with the very rare-cutting enzyme I-PpoI and electroporated into recombination efficient EL350 bacteria carrying the other BAC. Recombined BACs were identified by antibiotic selection and PCR screening and 10% of clones contained the correctly recombined 220-kb BAC. The system can be used to link the inserts from any overlapping BAC or PAC clones. The original orientation of the inserts is not important and desired regions of the inserts can be selected. The size limit for the fragments recombined may be larger than the 61 kb used here and multiple BACs in a contig could be combined by alternating use of the two pBACLink vectors. This system should be of use to many investigators wishing to carry out functional analysis on large mammalian genes which are not available in single BAC clones.

A subtraction scheme for computing QCD jet cross sections at NNLO: integrating the iterated singly-unresolved subtraction terms

NASA Astrophysics Data System (ADS)

Bolzoni, Paolo; Somogyi, Gábor; Trócsányi, Zoltán

2011-01-01

We perform the integration of all iterated singly-unresolved subtraction terms, as defined in ref. [1], over the two-particle factorized phase space. We also sum over the unresolved parton flavours. The final result can be written as a convolution (in colour space) of the Born cross section and an insertion operator. We spell out the insertion operator in terms of 24 basic integrals that are defined explicitly. We compute the coefficients of the Laurent expansion of these integrals in two different ways, with the method of Mellin-Barnes representations and sector decomposition. Finally, we present the Laurent-expansion of the full insertion operator for the specific examples of electron-positron annihilation into two and three jets.

Lineages of Streptococcus equi ssp. equi in the Irish equine industry.

PubMed

Moloney, Emma; Kavanagh, Kerrie S; Buckley, Tom C; Cooney, Jakki C

2013-01-01

Streptococcus equi ssp. equi is the causative agent of 'Strangles' in horses. This is a debilitating condition leading to economic loss, yard closures and cancellation of equestrian events. There are multiple genotypes of S. equi ssp. equi which can cause disease, but to date there has been no systematic study of strains which are prevalent in Ireland. This study identified and classified Streptococcus equi ssp. equi strains isolated from within the Irish equine industry. Two hundred veterinary isolates were subjected to SLST (single locus sequence typing) based on an internal sequence from the seM gene of Streptococcus equi ssp equi. Of the 171 samples which successfully gave an amplicon, 162 samples (137 Irish and 24 UK strains) gave robust DNA sequence information. Analysis of the sequences allowed division of the isolates into 19 groups, 13 of which contain at least 2 isolates and 6 groups containing single isolates. There were 19 positions where a DNA SNP (single nucleotide polymorphism) occurs, and one 3 bp insertion. All groups had multiple (2-8) SNPs. Of the SNPs 17 would result in an amino acid change in the encoded protein. Interestingly, the single isolate EI8, which has 6 SNPs, has the three base pair insertion which is not seen in any other isolate, this would result in the insertion of an Ile residue at position 62 in that protein sequence. Comparison of the relevant region in the determined sequences with the UK Streptococcus equi seM MLST database showed that Group B (15 isolates) and Group I (2 isolates), as well as the individual isolates EI3 and EI8, are unique to Ireland, and some groups are most likely of UK origin (Groups F and M), but many more probably passed back and forth between the two countries. The strains occurring in Ireland are not clonal and there is a considerable degree of sequence variation seen in the seM gene. There are two major clades causing infection in Ireland and these strains are also common in the UK.

20 Gbit/s error free transmission with ~850 nm GaAs-based vertical cavity surface emitting lasers (VCSELs) containing InAs-GaAs submonolayer quantum dot insertions

NASA Astrophysics Data System (ADS)

Lott, J. A.; Shchukin, V. A.; Ledentsov, N. N.; Stinz, A.; Hopfer, F.; Mutig, A.; Fiol, G.; Bimberg, D.; Blokhin, S. A.; Karachinsky, L. Y.; Novikov, I. I.; Maximov, M. V.; Zakharov, N. D.; Werner, P.

2009-02-01

We report on the modeling, epitaxial growth, fabrication, and characterization of 830-845 nm vertical cavity surface emitting lasers (VCSELs) that employ InAs-GaAs quantum dot (QD) gain elements. The GaAs-based VCSELs are essentially conventional in design, grown by solid-source molecular beam epitaxy, and include top and bottom gradedheterointerface AlGaAs distributed Bragg reflectors, a single selectively-oxidized AlAs waveguiding/current funneling aperture layer, and a quasi-antiwaveguiding microcavity. The active region consists of three sheets of InAs-GaAs submonolayer insertions separated by AlGaAs matrix layers. Compared to QWs the InAs-GaAs insertions are expected to offer higher exciton-dominated modal gain and improved carrier capture and retention, thus resulting in superior temperature stability and resilience to degradation caused by operating at the larger switching currents commonly employed to increase the data rates of modern optical communication systems. We investigate the robustness and temperature performance of our QD VCSEL design by fabricating prototype devices in a high-frequency ground-sourceground contact pad configuration suitable for on-wafer probing. Arrays of VCSELs are produced with precise variations in top mesa diameter from 24 to 36 μm and oxide aperture diameter from 1 to 12 μm resulting in VCSELs that operate in full single-mode, single-mode to multi-mode, and full multi-mode regimes. The single-mode QD VCSELs have room temperature threshold currents below 0.5 mA and peak output powers near 1 mW, whereas the corresponding values for full multi-mode devices range from about 0.5 to 1.5 mA and 2.5 to 5 mW. At 20°C we observe optical transmission at 20 Gb/s through 150 m of OM3 fiber with a bit error ratio better than 10-12, thus demonstrating the great potential of our QD VCSELs for applications in next-generation short-distance optical data communications and interconnect systems.

Lineages of Streptococcus equi ssp. equi in the Irish equine industry

PubMed Central

2013-01-01

Background Streptococcus equi ssp. equi is the causative agent of ‘Strangles’ in horses. This is a debilitating condition leading to economic loss, yard closures and cancellation of equestrian events. There are multiple genotypes of S. equi ssp. equi which can cause disease, but to date there has been no systematic study of strains which are prevalent in Ireland. This study identified and classified Streptococcus equi ssp. equi strains isolated from within the Irish equine industry. Results Two hundred veterinary isolates were subjected to SLST (single locus sequence typing) based on an internal sequence from the seM gene of Streptococcus equi ssp equi. Of the 171 samples which successfully gave an amplicon, 162 samples (137 Irish and 24 UK strains) gave robust DNA sequence information. Analysis of the sequences allowed division of the isolates into 19 groups, 13 of which contain at least 2 isolates and 6 groups containing single isolates. There were 19 positions where a DNA SNP (single nucleotide polymorphism) occurs, and one 3 bp insertion. All groups had multiple (2–8) SNPs. Of the SNPs 17 would result in an amino acid change in the encoded protein. Interestingly, the single isolate EI8, which has 6 SNPs, has the three base pair insertion which is not seen in any other isolate, this would result in the insertion of an Ile residue at position 62 in that protein sequence. Comparison of the relevant region in the determined sequences with the UK Streptococcus equi seM MLST database showed that Group B (15 isolates) and Group I (2 isolates), as well as the individual isolates EI3 and EI8, are unique to Ireland, and some groups are most likely of UK origin (Groups F and M), but many more probably passed back and forth between the two countries. Conclusions The strains occurring in Ireland are not clonal and there is a considerable degree of sequence variation seen in the seM gene. There are two major clades causing infection in Ireland and these strains are also common in the UK. PMID:23731628

Novel insertion mutation of ABCB1 gene in an ivermectin-sensitive Border Collie.

PubMed

Han, Jae-Ik; Son, Hyoung-Won; Park, Seung-Cheol; Na, Ki-Jeong

2010-12-01

P-glycoprotein (P-gp) is encoded by the ABCB1 gene and acts as an efflux pump for xenobiotics. In the Border Collie, a nonsense mutation caused by a 4-base pair deletion in the ABCB1 gene is associated with a premature stop to P-gp synthesis. In this study, we examined the full-length coding sequence of the ABCB1 gene in an ivermectin-sensitive Border Collie that lacked the aforementioned deletion mutation. The sequence was compared to the corresponding sequences of a wild-type Beagle and seven ivermectin-tolerant family members of the Border Collie. When compared to the wild-type Beagle sequence, that of the ivermectin-sensitive Border Collie was found to have one insertion mutation and eight single nucleotide polymorphisms (SNPs) in the coding sequence of the ABCB1 gene. While the eight SNPs were also found in the family members' sequences, the insertion mutation was found only in the ivermectin-sensitive dog. These results suggest the possibility that the SNPs are species-specific features of the ABCB1 gene in Border Collies, and that the insertion mutation may be related to ivermectin intolerance.

Novel insertion mutation of ABCB1 gene in an ivermectin-sensitive Border Collie

PubMed Central

Han, Jae-Ik; Son, Hyoung-Won; Park, Seung-Cheol

2010-01-01

P-glycoprotein (P-gp) is encoded by the ABCB1 gene and acts as an efflux pump for xenobiotics. In the Border Collie, a nonsense mutation caused by a 4-base pair deletion in the ABCB1 gene is associated with a premature stop to P-gp synthesis. In this study, we examined the full-length coding sequence of the ABCB1 gene in an ivermectin-sensitive Border Collie that lacked the aforementioned deletion mutation. The sequence was compared to the corresponding sequences of a wild-type Beagle and seven ivermectin-tolerant family members of the Border Collie. When compared to the wild-type Beagle sequence, that of the ivermectin-sensitive Border Collie was found to have one insertion mutation and eight single nucleotide polymorphisms (SNPs) in the coding sequence of the ABCB1 gene. While the eight SNPs were also found in the family members' sequences, the insertion mutation was found only in the ivermectin-sensitive dog. These results suggest the possibility that the SNPs are species-specific features of the ABCB1 gene in Border Collies, and that the insertion mutation may be related to ivermectin intolerance. PMID:21113104

Rates and patterns of great ape retrotransposition.

PubMed

Hormozdiari, Fereydoun; Konkel, Miriam K; Prado-Martinez, Javier; Chiatante, Giorgia; Herraez, Irene Hernando; Walker, Jerilyn A; Nelson, Benjamin; Alkan, Can; Sudmant, Peter H; Huddleston, John; Catacchio, Claudia R; Ko, Arthur; Malig, Maika; Baker, Carl; Marques-Bonet, Tomas; Ventura, Mario; Batzer, Mark A; Eichler, Evan E

2013-08-13

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.

CRISPR-Cas9D10A Nickase-Assisted Genome Editing in Lactobacillus casei

PubMed Central

Song, Xin; Huang, He; Xiong, Zhiqiang

2017-01-01

ABSTRACT Lactobacillus casei has drawn increasing attention as a health-promoting probiotic, while effective genetic manipulation tools are often not available, e.g., the single-gene knockout in L. casei still depends on the classic homologous recombination-dependent double-crossover strategy, which is quite labor-intensive and time-consuming. In the present study, a rapid and precise genome editing plasmid, pLCNICK, was established for L. casei genome engineering based on CRISPR-Cas9D10A. In addition to the P23-Cas9D10A and Pldh-sgRNA (single guide RNA) expression cassettes, pLCNICK includes the homologous arms of the target gene as repair templates. The ability and efficiency of chromosomal engineering using pLCNICK were evaluated by in-frame deletions of four independent genes and chromosomal insertion of an enhanced green fluorescent protein (eGFP) expression cassette at the LC2W_1628 locus. The efficiencies associated with in-frame deletions and chromosomal insertion is 25 to 62%. pLCNICK has been proved to be an effective, rapid, and precise tool for genome editing in L. casei, and its potential application in other lactic acid bacteria (LAB) is also discussed in this study. IMPORTANCE The lack of efficient genetic tools has limited the investigation and biotechnological application of many LAB. The CRISPR-Cas9D10A nickase-based genome editing in Lactobacillus casei, an important food industrial microorganism, was demonstrated in this study. This genetic tool allows efficient single-gene deletion and insertion to be accomplished by one-step transformation, and the cycle time is reduced to 9 days. It facilitates a rapid and precise chromosomal manipulation in L. casei and overcomes some limitations of previous methods. This editing system can serve as a basic technological platform and offers the possibility to start a comprehensive investigation on L. casei. As a broad-host-range plasmid, pLCNICK has the potential to be adapted to other Lactobacillus species for genome editing. PMID:28864652

[The Predictive Factors of Stent Failure in the Treatment of Malignant Extrinsc Ureteral Obstruction Using Internal Ureteral Stents].

PubMed

Matsuura, Hiroshi; Arase, Shigeki; Hori, Yasuhide; Tochigi, Hiromi

2017-12-01

In this study, we retrospectively reviewed the experiences at our single institute in the treatment of malignant extrinsic ureteral obstruction (MUO) using ureteral stents to investigate the clinical outcomes and the predictive factors of stent failure. In 52 ureters of 38 patients who had radiologically significant hydronephrosis due to MUO, internal ureteral stents (The BARD(R) INLAY(TM) ureteral stent set) were inserted. The median follow-up interval after the initial stent insertion was 124.5 days (4-1,120). Stent failure occurred in 8 ureters (15.4%) of the 7 patients. The median interval from the first stent insertion to stent failure was 88 days (1-468). A Cox regression multivariate analysis showed that the significant predictors of stent failure were bladder invasion. Based on the possibility of stent failure, the adaptation of the internal ureteral stent placement should be considered especially in a patient with MUO combined with bladder invasion.

Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors.

PubMed

Miura, Hiromi; Quadros, Rolen M; Gurumurthy, Channabasavaiah B; Ohtsuka, Masato

2018-01-01

CRISPR/Cas9-based genome editing can easily generate knockout mouse models by disrupting the gene sequence, but its efficiency for creating models that require either insertion of exogenous DNA (knock-in) or replacement of genomic segments is very poor. The majority of mouse models used in research involve knock-in (reporters or recombinases) or gene replacement (e.g., conditional knockout alleles containing exons flanked by LoxP sites). A few methods for creating such models have been reported that use double-stranded DNA as donors, but their efficiency is typically 1-10% and therefore not suitable for routine use. We recently demonstrated that long single-stranded DNAs (ssDNAs) serve as very efficient donors, both for insertion and for gene replacement. We call this method efficient additions with ssDNA inserts-CRISPR (Easi-CRISPR) because it is a highly efficient technology (efficiency is typically 30-60% and reaches as high as 100% in some cases). The protocol takes ∼2 months to generate the founder mice.

Effective oligonucleotide-mediated gene disruption in ES cells lacking the mismatch repair protein MSH3.

PubMed

Dekker, M; Brouwers, C; Aarts, M; van der Torre, J; de Vries, S; van de Vrugt, H; te Riele, H

2006-04-01

We have previously demonstrated that site-specific insertion, deletion or substitution of one or two nucleotides in mouse embryonic stem cells (ES cells) by single-stranded deoxyribo-oligonucleotides is several hundred-fold suppressed by DNA mismatch repair (MMR) activity. Here, we have investigated whether compound mismatches and larger insertions escape detection by the MMR machinery and can be effectively introduced in MMR-proficient cells. We identified several compound mismatches that escaped detection by the MMR machinery to some extent, but could not define general rules predicting the efficacy of complex base-pair substitutions. In contrast, we found that four-nucleotide insertions were largely subject to suppression by the MSH2/MSH3 branch of MMR and could be effectively introduced in Msh3-deficient cells. As these cells have no overt mutator phenotype and Msh3-deficient mice do not develop cancer, Msh3-deficient ES cells can be used for oligonucleotide-mediated gene disruption. As an example, we present disruption of the Fanconi anemia gene Fancf.

Control of indium tin oxide anode work function modified using Langmuir-Blodgett monolayer for high-efficiency organic photovoltaics

NASA Astrophysics Data System (ADS)

Yokokura, Yuya; Dogase, Tomomichi; Shinbo, Tatsuki; Nakayashiki, Yuya; Takagi, Yusuke; Ueda, Kazuyoshi; Sarangerel, Khayankhyarvaa; Delgertsetseg, Byambasuren; Ganzorig, Chimed; Sakomura, Masaru

2017-08-01

The use of Langmuir-Blodgett (LB) monolayers to modify the indium tin oxide (ITO) work function and thus improve the performance of zinc phthalocyanine (ZnPc)/fullerene (C60)-based and boron subphthalocyanine chloride (SubPc)/C60-based small molecule organic photovoltaic devices (OPVs) was examined. In general, LB precursor compounds contain one or more long alkyl chain substituents that can act as spacers to prevent electrical contact with adjoining electrode surfaces. As one example of such a compound, arachidic acid (CH3(CH2)18COOH) was inserted in the forms of one-layer, three-layer or five-layer LB films between the anode ITO layer and the p-type layer in ZnPc-C60-based OPVs to investigate the effects of the long alkyl chain group when it acts as an electrically insulating spacer. The short-circuit current density (Jsc) values of the OPVs with the three- and five-layer inserts (1.78 mA.cm-2 and 0.61 mA.cm-2, respectively) were reduced dramatically, whereas the Jsc value for the OPV with the single-layer insertion (2.88 mA.cm-2) was comparable to that of the OPV without any insert (3.14 mA.cm-2). The ITO work function was shifted positively by LB deposition of a surfactant compound, C9F19C2H4-O-C2H4-COOH (PFECA), which contained a fluorinated head group. This positive effect was maintained even after formation of an upper p-type organic layer. The Jsc and open-circuit voltage (Voc) of the SubPc-C60-based OPV with the LB-modified ITO layers were effectively enhanced. As a result, a 42% increase in device efficiency was achieved.

Double layered tailorable advanced blanket insulation

NASA Technical Reports Server (NTRS)

Falstrup, D.

1983-01-01

An advanced flexible reusable surface insulation material for future space shuttle flights was investigated. A conventional fly shuttle loom with special modifications to weave an integral double layer triangular core fabric from quartz yarn was used. Two types of insulating material were inserted into the cells of the fabric, and a procedure to accomplish this was developed. The program is follow up of a program in which single layer rectangular cell core fabrics are woven and a single type of insulating material was inserted into the cells.

Monte Carlo dosimetry for {sup 103}Pd, {sup 125}I, and {sup 131}Cs ocular brachytherapy with various plaque models using an eye phantom

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

Lesperance, Marielle; Martinov, M.; Thomson, R. M., E-mail: rthomson@physics.carleton.ca

Purpose: To investigate dosimetry for ocular brachytherapy for a range of eye plaque models containing{sup 103}Pd, {sup 125}I, or {sup 131}Cs seeds with model-based dose calculations. Methods: Five representative plaque models are developed based on a literature review and are compared to the standardized COMS plaque, including plaques consisting of a stainless steel backing and acrylic insert, and gold alloy backings with: short collimating lips and acrylic insert, no lips and silicone polymer insert, no lips and a thin acrylic layer, and individual collimating slots for each seed within the backing and no insert. Monte Carlo simulations are performed usingmore » the EGSnrc user-code BrachyDose for single and multiple seed configurations for the plaques in water and within an eye model (including nonwater media). Simulations under TG-43 assumptions are also performed, i.e., with the same seed configurations in water, neglecting interseed and plaque effects. Maximum and average doses to ocular structures as well as isodose contours are compared for simulations of each radionuclide within the plaque models. Results: The presence of the plaque affects the dose distribution substantially along the plaque axis for both single seed and multiseed simulations of each plaque design in water. Of all the plaque models, the COMS plaque generally has the largest effect on the dose distribution in water along the plaque axis. Differences between doses for single and multiple seed configurations vary between plaque models and radionuclides. Collimation is most substantial for the plaque with individual collimating slots. For plaques in the full eye model, average dose in the tumor region differs from those for the TG-43 simulations by up to 10% for{sup 125}I and {sup 131}Cs, and up to 17% for {sup 103}Pd, and in the lens region by up to 29% for {sup 125}I, 34% for {sup 103}Pd, and 28% for {sup 131}Cs. For the same prescription dose to the tumor apex, the lowest doses to critical ocular structures are generally delivered with plaques containing {sup 103}Pd seeds. Conclusions: The combined effects of ocular and plaque media on dose are significant and vary with plaque model and radionuclide, suggesting the importance of model-based dose calculations employing accurate ocular and plaque media and geometries for eye plaque brachytherapy.« less

P-Element Insertion Alleles of Essential Genes on the Third Chromosome of Drosophila Melanogaster: Correlation of Physical and Cytogenetic Maps in Chromosomal Region 86e-87f

PubMed Central

Deak, P.; Omar, M. M.; Saunders, RDC.; Pal, M.; Komonyi, O.; Szidonya, J.; Maroy, P.; Zhang, Y.; Ashburner, M.; Benos, P.; Savakis, C.; Siden-Kiamos, I.; Louis, C.; Bolshakov, V. N.; Kafatos, F. C.; Madueno, E.; Modolell, J.; Glover, D. M.

1997-01-01

We have established a collection of 2460 lethal or semi-lethal mutant lines using a procedure thought to insert single P elements into vital genes on the third chromosome of Drosophila melanogaster. More than 1200 randomly selected lines were examined by in situ hybridization and 90% found to contain single insertions at sites that mark 89% of all lettered subdivisions of the Bridges' map. A set of chromosomal deficiencies that collectively uncover ~25% of the euchromatin of chromosome 3 reveal lethal mutations in 468 lines corresponding to 145 complementation groups. We undertook a detailed analysis of the cytogenetic interval 86E-87F and identified 87 P-element-induced mutations falling into 38 complementation groups, 16 of which correspond to previously known genes. Twenty-one of these 38 complementation groups have at least one allele that has a P-element insertion at a position consistent with the cytogenetics of the locus. We have rescued P elements and flanking chromosomal sequences from the 86E-87F region in 35 lines with either lethal or genetically silent P insertions, and used these as probes to identify cosmids and P1 clones from the Drosophila genome projects. This has tied together the physical and genetic maps and has linked 44 previously identified cosmid contigs into seven ``supercontigs'' that span the interval. STS data for sequences flanking one side of the P-element insertions in 49 lines has identified insertions in the αγ element at 87C, two known transposable elements, and the open reading frames of seven putative single copy genes. These correspond to five known genes in this interval, and two genes identified by the homology of their predicted products to known proteins from other organisms. PMID:9409831

Polymorphic amplified typing sequences (PATS) and pulsed-field gel electrophoresis (PFGE) yield comparable results in the strain typing of a diverse set of bovine Escherichia coli O157 isolates

USDA-ARS?s Scientific Manuscript database

The PCR-based Escherichia coli O157 (O157) strain typing system, Polymorphic Amplified Typing Sequences (PATS), targets insertions-deletions (Indels) and single nucleotide polymorphisms (SNPs) at the XbaI and AvrII(BlnI) restriction enzyme sites, respectively, besides amplifying four known virulenc...

Comparison of the Proseal LMA and intersurgical I-gel during gynecological laparoscopy

PubMed Central

Jeon, Woo Jae; Baek, Seong Jin; Kim, Kyoung Hun

2012-01-01

Background The relatively recently developed I-gel (Intersurgical Ltd., Workingham, England) is a supraglottic airway device designed for single-use that, unlike conventional LMAs, does not require an inflatable cuff. In addition, the I-gel, much like the Proseal LMA (PLMA), has a gastric drainage tube associated with an upper tube for decompression of the stomach, thereby avoiding acid reflux and decreasing the risk of pulmonary absorption. The purpose of this study was to compare PLMA and I-gel devices in patients undergoing gynecological laparoscopy based on sealing pressure before and during pneumoperitoneum, insertion time, and gas exchange. Methods Following Institutional Review Board approval and written informed consent, 30 adult patients were randomly allocated to one of two groups (the PLMA or I-gel group). In each case, insertion time and number of attempts were recorded. After successful insertion, airway leak pressure was measured. Results Successful insertion and mechanical ventilation with both supraglottic airway devices was achieved on the first attempt in all 30 patients, and there were no significant differences with respect to insertion time. Likewise, leak pressure did not vary significantly either between or within groups after CO2 insufflation. In addition, differences between leak volume and leak fraction between groups were not significant. Conclusions The results of our study indicate that the I-gel is a reasonable alternative to the PLMA for controlled ventilation during laparoscopic gynecologic surgery. PMID:23277811

Effects on Subtalar Joint Stress Distribution After Cannulated Screw Insertion at Different Positions and Directions.

PubMed

Yuan, Cheng-song; Chen, Wan; Chen, Chen; Yang, Guang-hua; Hu, Chao; Tang, Kang-lai

2015-01-01

We investigated the effects on subtalar joint stress distribution after cannulated screw insertion at different positions and directions. After establishing a 3-dimensional geometric model of a normal subtalar joint, we analyzed the most ideal cannulated screw insertion position and approach for subtalar joint stress distribution and compared the differences in loading stress, antirotary strength, and anti-inversion/eversion strength among lateral-medial antiparallel screw insertion, traditional screw insertion, and ideal cannulated screw insertion. The screw insertion approach allowing the most uniform subtalar joint loading stress distribution was lateral screw insertion near the border of the talar neck plus medial screw insertion close to the ankle joint. For stress distribution uniformity, antirotary strength, and anti-inversion/eversion strength, lateral-medial antiparallel screw insertion was superior to traditional double-screw insertion. Compared with ideal cannulated screw insertion, slightly poorer stress distribution uniformity and better antirotary strength and anti-inversion/eversion strength were observed for lateral-medial antiparallel screw insertion. Traditional single-screw insertion was better than double-screw insertion for stress distribution uniformity but worse for anti-rotary strength and anti-inversion/eversion strength. Lateral-medial antiparallel screw insertion was slightly worse for stress distribution uniformity than was ideal cannulated screw insertion but superior to traditional screw insertion. It was better than both ideal cannulated screw insertion and traditional screw insertion for anti-rotary strength and anti-inversion/eversion strength. Lateral-medial antiparallel screw insertion is an approach with simple localization, convenient operation, and good safety. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Comparison of Single-Stick and Double-Stick Techniques for Percutaneous Nephrostomy

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

Funaki, Brian, E-mail: bfunaki@midway.uchicago.edu; Vatakencherry, Geogi

2004-01-15

We compared single- and double-stick techniques of percutaneous nephrostomy insertion by retrospectively reviewing 140 percutaneous nephrostomy procedures in 101 patients. All procedures were performed by residents or fellows with direct attending supervision. Either the single-stick or double-stick technique was used based solely on personal attending preference. There were no significant differences in groups in terms of age, sex, or degree of hydronephrosis. In the single-stick technique, the kidney was punctured with sonographic guidance and the tract was serially dilated to accept an 8.5 Fr. nephrostomy catheter. In the double-stick technique, the kidney was punctured with sonographic guidance and a mixturemore » of air and contrast were injected into the collecting system. The affected side was then elevated and a posterior calyx was punctured using fluoroscopic guidance. Both groups were compared in terms of complications and early tube dysfunction using the chi-squared test. All procedures were successful without immediate complications. Bleeding requiring transfusion occurred in 4.7% (4/86) procedures in the single stick group and 3.7% (2/54) in the double stick group (p-value not significant). None of these patients required further interventions for bleeding. Tube dysfunction leading to premature tube exchange occurred in 3.5% (3/86) of catheters in the single stick group and 3.7% (2/54) of catheters in the double- stick group (p-value not significant). We found no significant difference between the single and double- stick methods of percutaneous nephrostomy in terms of success rates, complications, or tube function. We believe that the single-stick method should be adopted as the insertion technique of choice.« less

Remifentanil dose for laryngeal mask airway insertion with a single standard dose of propofol during emergency airway management in elderly patients.

PubMed

Ryu, Junghee; Oh, Ah Young; Baek, Ji-Seok; Kim, Jin-Hee; Park, Sang-Heon; Noh, Jae-Mun

2014-04-01

This study determined the dose of remifentanil to use during insertion of a Classic™ laryngeal mask airway (LMA, The Laryngeal Mask Co., Nicosia, Cyprus) in elderly patients during emergency airway management when combined with a single dose of propofol. Patients aged 65-80 years were enrolled. Anesthesia was induced with propofol 1 mg/kg, and then a blinded dose of remifentanil was infused over 30 s after confirming the patient's loss of consciousness. The dose of remifentanil was determined using Dixon's up-and-down method, starting at 0.5 µg/kg (a step size of 0.1 µg/kg). Insertion of the LMA was attempted 60 s after loss of consciousness. In total, 23 patients were recruited and the mean age ± standard deviation was 72 ± 3 years. The effective dose for successful LMA insertion in 50% of the patients (ED50) was 0.20 ± 0.05 µg/kg. No patient needed more than 0.3 µg/kg. Remifentanil 0.20 ± 0.05 µg/kg with propofol 1 mg/kg resulted in excellent LMA insertion in 50% of elderly patients without significant hemodynamic changes during emergency airway management.

High aspect ratio catalytic reactor and catalyst inserts therefor

DOEpatents

Lin, Jiefeng; Kelly, Sean M.

2018-04-10

The present invention relates to high efficient tubular catalytic steam reforming reactor configured from about 0.2 inch to about 2 inch inside diameter high temperature metal alloy tube or pipe and loaded with a plurality of rolled catalyst inserts comprising metallic monoliths. The catalyst insert substrate is formed from a single metal foil without a central supporting structure in the form of a spiral monolith. The single metal foil is treated to have 3-dimensional surface features that provide mechanical support and establish open gas channels between each of the rolled layers. This unique geometry accelerates gas mixing and heat transfer and provides a high catalytic active surface area. The small diameter, high aspect ratio tubular catalytic steam reforming reactors loaded with rolled catalyst inserts can be arranged in a multi-pass non-vertical parallel configuration thermally coupled with a heat source to carry out steam reforming of hydrocarbon-containing feeds. The rolled catalyst inserts are self-supported on the reactor wall and enable efficient heat transfer from the reactor wall to the reactor interior, and lower pressure drop than known particulate catalysts. The heat source can be oxygen transport membrane reactors.

Achievable accuracy of hip screw holding power estimation by insertion torque measurement.

PubMed

Erani, Paolo; Baleani, Massimiliano

2018-02-01

To ensure stability of proximal femoral fractures, the hip screw must firmly engage into the femoral head. Some studies suggested that screw holding power into trabecular bone could be evaluated, intraoperatively, through measurement of screw insertion torque. However, those studies used synthetic bone, instead of trabecular bone, as host material or they did not evaluate accuracy of predictions. We determined prediction accuracy, also assessing the impact of screw design and host material. We measured, under highly-repeatable experimental conditions, disregarding clinical procedure complexities, insertion torque and pullout strength of four screw designs, both in 120 synthetic and 80 trabecular bone specimens of variable density. For both host materials, we calculated the root-mean-square error and the mean-absolute-percentage error of predictions based on the best fitting model of torque-pullout data, in both single-screw and merged dataset. Predictions based on screw-specific regression models were the most accurate. Host material impacts on prediction accuracy: the replacement of synthetic with trabecular bone decreased both root-mean-square errors, from 0.54 ÷ 0.76 kN to 0.21 ÷ 0.40 kN, and mean-absolute-percentage errors, from 14 ÷ 21% to 10 ÷ 12%. However, holding power predicted on low insertion torque remained inaccurate, with errors up to 40% for torques below 1 Nm. In poor-quality trabecular bone, tissue inhomogeneities likely affect pullout strength and insertion torque to different extents, limiting the predictive power of the latter. This bias decreases when the screw engages good-quality bone. Under this condition, predictions become more accurate although this result must be confirmed by close in-vitro simulation of the clinical procedure. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Manually Operated, Advance Off-Stylet Insertion Tool for Minimally Invasive Cochlear Implantation Surgery

PubMed Central

Kratchman, Louis B.; Schurzig, Daniel; McRackan, Theodore R.; Balachandran, Ramya; Noble, Jack H.; Webster, Robert J.; Labadie, Robert F.

2014-01-01

The current technique for cochlear implantation (CI) surgery requires a mastoidectomy to gain access to the cochlea for electrode array insertion. It has been shown that microstereotactic frames can enable an image-guided, minimally invasive approach to CI surgery called percutaneous cochlear implantation (PCI) that uses a single drill hole for electrode array insertion, avoiding a more invasive mastoidectomy. Current clinical methods for electrode array insertion are not compatible with PCI surgery because they require a mastoidectomy to access the cochlea; thus, we have developed a manually operated electrode array insertion tool that can be deployed through a PCI drill hole. The tool can be adjusted using a preoperative CT scan for accurate execution of the advance off-stylet (AOS) insertion technique and requires less skill to operate than is currently required to implant electrode arrays. We performed three cadaver insertion experiments using the AOS technique and determined that all insertions were successful using CT and microdissection. PMID:22851233

Structural Mechanism of Replication Stalling on a Bulky Amino-Polycyclic Aromatic Hydrocarbon DNA Adduct by a Y Family DNA Polymerase

PubMed Central

Kirouac, Kevin N.; Basu, Ashis K.; Ling, Hong

2013-01-01

Polycyclic aromatic hydrocarbons and their nitro derivatives are culprits of the detrimental health effects of environmental pollution. These hydrophobic compounds metabolize to reactive species and attach to DNA producing bulky lesions, such as N-[deoxyguanosine-8-yl]-1-aminopyrene (APG), in genomic DNA. The bulky adducts block DNA replication by high-fidelity polymerases and compromise replication fidelities and efficiencies by specialized lesion bypass polymerases. Here we present three crystal structures of the DNA polymerase Dpo4, a model translesion DNA polymerase of the Y family, in complex with APG-lesion-containing DNA in pre-insertion and extension stages. APG is captured in two conformations in the pre-insertion complex; one is highly exposed to the solvent, whereas the other is harbored in a shallow cleft between the finger and unique Y family little finger domain. In contrast, APG is in a single conformation at the extension stage, in which the pyrene ring is sandwiched between the little finger domain and a base from the turning back single-stranded template strand. Strikingly, a nucleotide intercalates the DNA helix to form a quaternary complex with Dpo4, DNA, and an incoming nucleotide, which stabilizes the distorted DNA structure at the extension stage. The unique APG DNA conformations in Dpo4 inhibit DNA translocation through the polymerase active site for APG bypass. We also modeled an insertion complex that illustrates a solvent-exposed pyrene ring contributing to an unstable insertion state. The structural work combined with our lesion replication assays provides a novel structural mechanism on bypass of DNA adducts containing polycyclic aromatic hydrocarbon moieties. PMID:23876706

Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase.

PubMed

Kirouac, Kevin N; Basu, Ashis K; Ling, Hong

2013-11-15

Polycyclic aromatic hydrocarbons and their nitro derivatives are culprits of the detrimental health effects of environmental pollution. These hydrophobic compounds metabolize to reactive species and attach to DNA producing bulky lesions, such as N-[deoxyguanosine-8-yl]-1-aminopyrene (APG), in genomic DNA. The bulky adducts block DNA replication by high-fidelity polymerases and compromise replication fidelities and efficiencies by specialized lesion bypass polymerases. Here we present three crystal structures of the DNA polymerase Dpo4, a model translesion DNA polymerase of the Y family, in complex with APG-lesion-containing DNA in pre-insertion and extension stages. APG is captured in two conformations in the pre-insertion complex; one is highly exposed to the solvent, whereas the other is harbored in a shallow cleft between the finger and unique Y family little finger domain. In contrast, APG is in a single conformation at the extension stage, in which the pyrene ring is sandwiched between the little finger domain and a base from the turning back single-stranded template strand. Strikingly, a nucleotide intercalates the DNA helix to form a quaternary complex with Dpo4, DNA, and an incoming nucleotide, which stabilizes the distorted DNA structure at the extension stage. The unique APG DNA conformations in Dpo4 inhibit DNA translocation through the polymerase active site for APG bypass. We also modeled an insertion complex that illustrates a solvent-exposed pyrene ring contributing to an unstable insertion state. The structural work combined with our lesion replication assays provides a novel structural mechanism on bypass of DNA adducts containing polycyclic aromatic hydrocarbon moieties. © 2013.

[The application of Y-shaped self-expandable covered metal stents in the thoracostomach-airway fistula: a single center, 11 years experience].

PubMed

Fang, Yi; Li, Tengfei; Han, Xinwei; Wu, Gang; Ren, Jianzhuang; Ren, Kewei; Lu, Huibin; Zhang, Quanhui; Li, Zongming

2015-08-01

To investigate the clinical feasibility and efficacy of Y-shaped self-expandable covered metal stents (Y-stents) in the management of thoracostomach-airway fistula. Retrospective analysis was performed for 108 patients treated for thoracostomach-airway fistula with Y-shaped self-expandable coated metal stents between April 2003 and October 2014. Y-stents were designed based on the dimensions of trachea and bronchus and sites of the fistula and then were inserted under DSA monitoring. There were 65 cases with single big Y-stent placement, 26 cases with single small Y-stent placement, 23 cases with double Y-stents placement, and 1 case with 3 Y-stents placement. Stent implantation was successfully accomplished with single manipulation in all patients. Complete occlusion of the fistula was obtained in 104 patients after the primary manipulation, and 4 patients required a secondary manipulation where a double Y-stents was inserted because of failure of primary manipulate. Ninety-two patients completed the follow-up , while 16 were lost. Fifty-nine patients died while 33 were alive with marked improvement in their quality of life. The placement of Y-stents can effectively occlude the thoracostomach-airway fistula in patients who had had the esophageal tumors resected. The technique is not only feasible but reliable to improve the quality of life of the patients.

Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110.

PubMed

Fomukong, N G; Tang, T H; al-Maamary, S; Ibrahim, W A; Ramayah, S; Yates, M; Zainuddin, Z F; Dale, J W

1994-12-01

DNA fingerprinting with the insertion sequence IS6110 (also known as IS986) has become established as a major tool for investigating the spread of tuberculosis. Most strains of Mycobacterium tuberculosis have multiple copies of IS6110, but a small minority carry a single copy only. We have examined selected strains from Malaysia, Tanzania and Oman, in comparison with M. bovis isolates and BCG strains carrying one or two copies of IS6110. The insertion sequence appears to be present in the same position in all these strains, which suggests that in these organisms the element is defective in transposition and that the loss of transposability may have occurred at an early stage in the evolution of the M. tuberculosis complex.

Transposon-mediated generation of BCR-ABL1-expressing transgenic cell lines for unbiased sensitivity testing of tyrosine kinase inhibitors

PubMed Central

Berkowitsch, Bettina; Koenig, Margit; Haas, Oskar A.; Hoermann, Gregor; Valent, Peter; Lion, Thomas

2016-01-01

Point mutations in the ABL1 kinase domain are an important mechanism of resistance to tyrosine kinase inhibitors (TKI) in BCR-ABL1-positive and, as recently shown, BCR-ABL1-like leukemias. The cell line Ba/F3 lentivirally transduced with mutant BCR-ABL1 constructs is widely used for in vitro sensitivity testing and response prediction to tyrosine kinase inhibitors. The transposon-based Sleeping Beauty system presented offers several advantages over lentiviral transduction including the absence of biosafety issues, faster generation of transgenic cell lines, and greater efficacy in introducing large gene constructs. Nevertheless, both methods can mediate multiple insertions in the genome. Here we show that multiple BCR-ABL1 insertions result in elevated IC50 levels for individual TKIs, thus overestimating the actual resistance of mutant subclones. We have therefore established flow-sorting-based fractionation of BCR-ABL1-transformed Ba/F3 cells facilitating efficient enrichment of cells carrying single-site insertions, as demonstrated by FISH-analysis. Fractions of unselected Ba/F3 cells not only showed a greater number of BCR-ABL1 hybridization signals, but also revealed higher IC50 values for the TKIs tested. The data presented highlight the need to carefully select transfected cells by flow-sorting, and to control the insertion numbers by FISH and real-time PCR to permit unbiased in vitro testing of drug resistance. PMID:27801667

Mucoadhesive ocular insert based on thiolated poly(acrylic acid): development and in vivo evaluation in humans.

PubMed

Hornof, Margit; Weyenberg, Wim; Ludwig, Annick; Bernkop-Schnürch, Andreas

2003-05-20

The aim of the study was to develop a mucoadhesive ocular insert for the controlled delivery of ophthalmic drugs and to evaluate its efficacy in vivo. The inserts tested were based either on unmodified or thiolated poly(acrylic acid). Water uptake and swelling behavior of the inserts as well as the drug release rates of the model drugs fluorescein and two diclofenac salts with different solubility properties were evaluated in vitro. Fluorescein was used as fluorescent tracer to study the drug release from the insert in humans. The mean fluorescein concentration in the cornea/tearfilm compartment as a function of time was determined after application of aqueous eye drops and inserts composed of unmodified and of thiolated poly(acrylic acid). The acceptability of the inserts by the volunteers was also evaluated. Inserts based on thiolated poly(acrylic acid) were not soluble and had good cohesive properties. A controlled release was achieved for the incorporated model drugs. The in vivo study showed that inserts based on thiolated poly(acrylic acid) provide a fluorescein concentration on the eye surface for more than 8 h, whereas the fluorescein concentration rapidly decreased after application of aqueous eye drops or inserts based on unmodified poly(acrylic acid). Moreover, these inserts were well accepted by the volunteers. The present study indicates that ocular inserts based on thiolated poly(acrylic acid) are promising new solid devices for ocular drug delivery.

Body Piercing

MedlinePlus

... is piercing performed? A single-use, sterilized piercing gun is typically used to insert an earring into ... of jewelry into the hole. The safest piercing guns are single-use guns. It means that it ...

Atomic force microscopy captures length phenotypes in single proteins

PubMed Central

Carrion-Vazquez, Mariano; Marszalek, Piotr E.; Oberhauser, Andres F.; Fernandez, Julio M.

1999-01-01

We use single-protein atomic force microscopy techniques to detect length phenotypes in an Ig module. To gain amino acid resolution, we amplify the mechanical features of a single module by engineering polyproteins composed of up to 12 identical repeats. We show that on mechanical unfolding, mutant polyproteins containing five extra glycine residues added to the folded core of the module extend 20 Å per module farther than the wild-type polyproteins. By contrast, similar insertions near the N or C termini have no effect. Hence, our atomic force microscopy measurements readily discriminate the location of the insert and measure its size with a resolution similar to that of NMR and x-ray crystallography. PMID:10500169

W-band integrated circuit PIN switches

NASA Astrophysics Data System (ADS)

Tahim, R. S.; Pham, T.; Chang, K.

1986-12-01

Both single-pole single-throw (SPST) and single-pole double-throw (SPDT) PIN switches have been developed at W band using microstrip integrated circuits. In SPST configurations, these switches have less than 1 dB of insertion loss under forward-voltage conditions from 90 to 108 GHz. Isolation greater than 20 dB over 3 GHz and greater than 10 dB over 7 GHz has been achieved. In SPDT configurations, insertion loss of less than 2 dB and isolation of more than 15 dB over 10 GHz (90 to 110 GHz) have been achieved. Beam-lead PIN diodes were used. Major features included mechanical ruggedness, light weight, small size and low-cost manufacturing.

Intelligent switches of integrated lightwave circuits with core telecommunication functions

NASA Astrophysics Data System (ADS)

Izhaky, Nahum; Duer, Reuven; Berns, Neil; Tal, Eran; Vinikman, Shirly; Schoenwald, Jeffrey S.; Shani, Yosi

2001-05-01

We present a brief overview of a promising switching technology based on Silica on Silicon thermo-optic integrated circuits. This is basically a 2D solid-state optical device capable of non-blocking switching operation. Except of its excellent performance (insertion loss<5dB, switching time<2ms...), the switch enables additional important build-in functionalities. It enables single-to- single channel switching and single-to-multiple channel multicasting/broadcasting. In addition, it has the capability of channel weighting and variable output power control (attenuation), for instance, to equalize signal levels and compensate for unbalanced different optical input powers, or to equalize unbalanced EDFA gain curve. We examine the market segments appropriate for the switch size and technology, followed by a discussion of the basic features of the technology. The discussion is focused on important requirements from the switch and the technology (e.g., insertion loss, power consumption, channel isolation, extinction ratio, switching time, and heat dissipation). The mechanical design is also considered. It must take into account integration of optical fiber, optical planar wafer, analog electronics and digital microprocessor controls, embedded software, and heating power dissipation. The Lynx Photon.8x8 switch is compared to competing technologies, in terms of typical market performance requirements.

0.8 mJ quasi-continuously pumped sub-nanosecond highly doped Nd:YAG oscillator-amplifier laser system in bounce geometry

NASA Astrophysics Data System (ADS)

Jelínek, M.; Kubeček, V.; Čech, M.; Hiršl, P.

2011-03-01

A quasi-continuously pumped picosecond oscillator-amplifier laser system based on two identical 2.4% Nd:YAG slabs in a single bounce geometry was developed and investigated. The oscillator was passively mode locked by the multiple quantum well saturable absorber inserted into the resonator in transmission mode. Output train containing 7 pulses with total energy of 900 μJ was generated directly from the oscillator. Single pulse with energy of 75 μJ, duration of 113 ps and Gaussian spatial profile was cavity dumped from the resonator and amplified by the single pass amplifier to the energy of 830 μJ. Comparison with our previously reported data obtained with similar system based on Nd:GdVO4 shows advantage of using highly doped Nd:YAG for generation of sub-millijoule pulses in one hundred picoseconds range, which might be interesting in many applications.

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Rates and patterns of great ape retrotransposition

PubMed Central

Hormozdiari, Fereydoun; Konkel, Miriam K.; Prado-Martinez, Javier; Chiatante, Giorgia; Herraez, Irene Hernando; Walker, Jerilyn A.; Nelson, Benjamin; Alkan, Can; Sudmant, Peter H.; Huddleston, John; Catacchio, Claudia R.; Ko, Arthur; Malig, Maika; Baker, Carl; Genome Project, Great Ape; Marques-Bonet, Tomas; Ventura, Mario; Batzer, Mark A.; Eichler, Evan E.

2013-01-01

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r2 = 0.65) in contrast to Alu repeats, which show little correlation (r2 = 0.07). We estimate that the “rate” of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation—the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human–great ape evolution, with increases and decreases occurring over very short periods of evolutionary time. PMID:23884656

Submillisecond Dynamics of Mastoparan X Insertion into Lipid Membranes.

PubMed

Schuler, Erin E; Nagarajan, Sureshbabu; Dyer, R Brian

2016-09-01

The mechanism of protein insertion into a lipid bilayer is poorly understood because the kinetics of this process is difficult to measure. We developed a new approach to study insertion of the antimicrobial peptide Mastoparan X into zwitterionic lipid vesicles, using a laser-induced temperature-jump to initiate insertion on the microsecond time scale and infrared and fluorescence spectroscopies to follow the kinetics. Infrared probes the desolvation of the peptide backbone and yields biphasic kinetics with relaxation lifetimes of 12 and 117 μs, whereas fluorescence probes the intrinsic tryptophan residue located near the N-terminus and yields a single exponential phase with a lifetime of 440 μs. Arrhenius analysis of the temperature-dependent rates yields an activation energy for insertion of 96 kJ/mol. These results demonstrate the complexity of the insertion process and provide mechanistic insight into the interplay between peptides and the lipid bilayer required for peptide transport across cellular membranes.

Optimizing the specificity of nucleic acid hybridization

PubMed Central

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2014-01-01

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed ‘toehold exchange’ probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg2+ to 47 mM Mg2+, and with nucleic acid concentrations from 1 nM to 5 μM. Experiments with RNA also showed effective single-base change discrimination. PMID:22354435

Nano-oxide-layer insertion and specular effects in spin valves: Experiment and theory

NASA Astrophysics Data System (ADS)

Wang, L.; Qiu, J. J.; McMahon, W. J.; Li, K. B.; Wu, Y. H.

2004-06-01

We report a systematic study of NOL (nano-oxide-layer) insertion and specular effects on the giant magnetoresistance (GMR) of single, synthetic, and dual spin valves, using a semiclassical Boltzmann theory. It is confirmed that the GMR ratio is enhanced by NOL insertion inside the pinned layer or after the free layer. The enhancements are primarily due to the contribution of the majority carriers. The NOL insertions inside the inactive layers of spin valves such as the seed, under, and capping layers reduce the GMR ratio. Though introducing a NOL before or after the Cu spacer would, in principle, significantly suppress the GMR ratio due to the blocking effect or the average effect of different spin channels, large positive or negative (inverse) GMR is found by assuming spin-dependent NOL specular reflections. We have also demonstrated that specular reflection, even beyond a capping layer, may result in reduction of GMR. Upon appropriate NOL insertion, the amplitude of curve of GMR versus thickness of individual layer of spin valves may be generally enhanced, but the shape may change, depending on whether the distance of the NOL to the layer is small or large (distance effect). Finally, it is found that most results obtained for the single realistic spin valves are applicable to synthetic and dual spin valves.

Toward dynamic lumbar punctures guidance based on single element synthetic tracked aperture ultrasound imaging

NASA Astrophysics Data System (ADS)

Zhang, Haichong K.; Lin, Melissa; Kim, Younsu; Paredes, Mateo; Kannan, Karun; Patel, Nisu; Moghekar, Abhay; Durr, Nicholas J.; Boctor, Emad M.

2017-03-01

Lumbar punctures (LPs) are interventional procedures used to collect cerebrospinal fluid (CSF), a bodily fluid needed to diagnose central nervous system disorders. Most lumbar punctures are performed blindly without imaging guidance. Because the target window is small, physicians can only accurately palpate the appropriate space about 30% of the time and perform a successful procedure after an average of three attempts. Although various forms of imaging based guidance systems have been developed to aid in this procedure, these systems complicate the procedure by including independent image modalities and requiring image-to-needle registration to guide the needle insertion. Here, we propose a simple and direct needle insertion platform utilizing a single ultrasound element within the needle through dynamic sensing and imaging. The needle-shaped ultrasound transducer can not only sense the distance between the tip and a potential obstacle such as bone, but also visually locate structures by combining transducer location tracking and back projection based tracked synthetic aperture beam-forming algorithm. The concept of the system was validated through simulation first, which revealed the tolerance to realistic error. Then, the initial prototype of the single element transducer was built into a 14G needle, and was mounted on a holster equipped with a rotation tracking encoder. We experimentally evaluated the system using a metal wire phantom mimicking high reflection bone structures and an actual spine bone phantom with both the controlled motion and freehand scanning. An ultrasound image corresponding to the model phantom structure was reconstructed using the beam-forming algorithm, and the resolution was improved compared to without beam-forming. These results demonstrated the proposed system has the potential to be used as an ultrasound imaging system for lumbar puncture procedures.

Double emulsions from a capillary array injection microfluidic device.

PubMed

Shang, Luoran; Cheng, Yao; Wang, Jie; Ding, Haibo; Rong, Fei; Zhao, Yuanjin; Gu, Zhongze

2014-09-21

A facile microfluidic device was developed by inserting an annular capillary array into a collection channel for single-step emulsification of double emulsions. By inserting multiple inner-phase solutions into the capillary array, multicomponent double emulsions or microcapsules with inner droplets of different content could also be obtained from the device.

Tunable single frequency fiber laser based on FP-LD injection locking.

PubMed

Zhang, Aiqin; Feng, Xinhuan; Wan, Minggui; Li, Zhaohui; Guan, Bai-ou

2013-05-20

We propose and demonstrate a tunable single frequency fiber laser based on Fabry Pérot laser diode (FP-LD) injection locking. The single frequency operation principle is based on the fact that the output from a FP-LD injection locked by a multi-longitudinal-mode (MLM) light can have fewer longitudinal-modes number and narrower linewidth. By inserting a FP-LD in a fiber ring laser cavity, single frequency operation can be possibly achieved when stable laser oscillation established after many roundtrips through the FP-LD. Wavelength switchable single frequency lasing can be achieved by adjusting the tunable optical filter (TOF) in the cavity to coincide with different mode of the FP-LD. By adjustment of the drive current of the FP-LD, the lasing modes would shift and wavelength tunable operation can be obtained. In experiment, a wavelength tunable range of 32.4 nm has been obtained by adjustment of the drive current of the FP-LD and a tunable filter in the ring cavity. Each wavelength has a side-mode suppression ratio (SMSR) of at least 41 dB and a linewidth of about 13 kHz.

A backing device based on an embedded stiffener and retractable insertion tool for thin-film cochlear arrays

NASA Astrophysics Data System (ADS)

Tewari, Radheshyam

Intracochlear trauma from surgical insertion of bulky electrode arrays and inadequate pitch perception are areas of concern with current hand-assembled commercial cochlear implants. Parylene thin-film arrays with higher electrode densities and lower profiles are a potential solution, but lack rigidity and hence depend on manually fabricated permanently attached polyethylene terephthalate (PET) tubing based bulky backing devices. As a solution, we investigated a new backing device with two sub-systems. The first sub-system is a thin poly(lactic acid) (PLA) stiffener that will be embedded in the parylene array. The second sub-system is an attaching and detaching mechanism, utilizing a poly(N-vinylpyrrolidone)-block-poly(d,l-lactide) (PVP-b-PDLLA) copolymer-based biodegradable and water soluble adhesive, that will help to retract the PET insertion tool after implantation. As a proof-of-concept of sub-system one, a microfabrication process for patterning PLA stiffeners embedded in parylene has been developed. Conventional hot-embossing, mechanical micromachining, and standard cleanroom processes were integrated for patterning fully released and discrete stiffeners coated with parylene. The released embedded stiffeners were thermoformed to demonstrate that imparting perimodiolar shapes to stiffener-embedded arrays will be possible. The developed process when integrated with the array fabrication process will allow fabrication of stiffener-embedded arrays in a single process. As a proof-of-concept of sub-system two, the feasibility of the attaching and detaching mechanism was demonstrated by adhering 1x and 1.5x scale PET tube-based insertion tools and PLA stiffeners embedded in parylene using the copolymer adhesive. The attached devices survived qualitative adhesion tests, thermoforming, and flexing. The viability of the detaching mechanism was tested by aging the assemblies in-vitro in phosphate buffer solution. The average detachment times, 2.6 minutes and 10 minutes for 1x and 1.5x scale devices respectively, were found to be clinically relevant with respect to the reported array insertion times during surgical implantation. Eventually, the stiffener-embedded arrays would not need to be permanently attached to current insertion tools which are left behind after implantation and congest the cochlear scala tympani chamber. Finally, a simulation-based approach for accelerated failure analysis of PLA stiffeners and characterization of PVP-b-PDLLA copolymer adhesive has been explored. The residual functional life of embedded PLA stiffeners exposed to body-fluid and thereby subjected to degradation and erosion has been estimated by simulating PLA stiffeners with different parylene coating failure types and different PLA types for a given parylene coating failure type. For characterizing the PVP-b-PDLLA copolymer adhesive, several formulations of the copolymer adhesive were simulated and compared based on the insertion tool detachment times that were predicted from the dissolution, degradation, and erosion behavior of the simulated adhesive formulations. Results indicate that the simulation-based approaches could be used to reduce the total number of time consuming and expensive in-vitro tests that must be conducted.

Patient satisfaction and masticatory efficiency of single implant-retained mandibular overdentures using the stud and magnetic attachments.

PubMed

Cheng, Tao; Sun, Guifeng; Huo, Jingyu; He, Xiaoji; Wang, Yining; Ren, Yan-Fang

2012-11-01

To study patient satisfaction and masticatory efficiency of single implant-retained mandibular overdentures using the stud and magnetic attachments in a randomized clinical trial with a crossover design. Patients received a single implant placed in the midline of the mandible and either a stud (Locator) or a magnetic (Magfit) attachment, assigned at random. Patient satisfaction, including patient comfort, speech, chewing ability and retention, and masticatory efficiency measured by chewing peanuts, were assessed before and 3 months after attachment insertion. Patient satisfaction and masticatory efficiency were evaluated again 3 months after insertion of the alternate attachment bodies. The outcomes were compared before and after insertion of the attachments and between the two types of attachments using Wilcoxon signed rank tests. Patient overall satisfaction, comfort, speech, chewing ability, and retention improved significantly after insertion of both types of attachment bodies (p<0.05). Masticatory efficiencies also increased in both the Locator and the Magfit groups (p<0.05). There were no statistically significant differences in patient overall satisfaction, comfort, speech, and retention between the two types of attachments (p>0.05). The Locator attachments performed better in perceived chewing ability than the Magfit (p<0.05), but there was no statistically significant difference in masticatory efficiency between the two attachment types (p>0.05). Clinical outcomes were significantly improved in single implant-retained mandibular overdentures using either the Locator or the Magfit magnetic attachments. There was no difference in masticatory efficiency between the two attachment types. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cell-free formation and interactome analysis of caveolae.

PubMed

Jung, WooRam; Sierecki, Emma; Bastiani, Michele; O'Carroll, Ailis; Alexandrov, Kirill; Rae, James; Johnston, Wayne; Hunter, Dominic J B; Ferguson, Charles; Gambin, Yann; Ariotti, Nicholas; Parton, Robert G

2018-06-04

Caveolae have been linked to the regulation of signaling pathways in eukaryotic cells through direct interactions with caveolins. Here, we describe a cell-free system based on Leishmania tarentolae ( Lt ) extracts for the biogenesis of caveolae and show its use for single-molecule interaction studies. Insertion of expressed caveolin-1 (CAV1) into Lt membranes was analogous to that of caveolin in native membranes. Electron tomography showed that caveolins generate domains of precise size and curvature. Cell-free caveolae were used in quantitative assays to test the interaction of membrane-inserted caveolin with signaling proteins and to determine the stoichiometry of interactions. Binding of membrane-inserted CAV1 to several proposed binding partners, including endothelial nitric-oxide synthase, was negligible, but a small number of proteins, including TRAF2, interacted with CAV1 in a phosphorylation-(CAV1 Y14 )-stimulated manner. In cells subjected to oxidative stress, phosphorylated CAV1 recruited TRAF2 to the early endosome forming a novel signaling platform. These findings lead to a novel model for cellular stress signaling by CAV1. © 2018 Jung et al.

The development of a cisgenic apple plant.

PubMed

Vanblaere, Thalia; Szankowski, Iris; Schaart, Jan; Schouten, Henk; Flachowsky, Henryk; Broggini, Giovanni A L; Gessler, Cesare

2011-07-20

Cisgenesis represents a step toward a new generation of GM crops. The lack of selectable genes (e.g. antibiotic or herbicide resistance) in the final product and the fact that the inserted gene(s) derive from organisms sexually compatible with the target crop should rise less environmental concerns and increase consumer's acceptance. Here we report the generation of a cisgenic apple plant by inserting the endogenous apple scab resistance gene HcrVf2 under the control of its own regulatory sequences into the scab susceptible apple cultivar Gala. A previously developed method based on Agrobacterium-mediated transformation combined with a positive and negative selection system and a chemically inducible recombination machinery allowed the generation of apple cv. Gala carrying the scab resistance gene HcrVf2 under its native regulatory sequences and no foreign genes. Three cisgenic lines were chosen for detailed investigation and were shown to carry a single T-DNA insertion and express the target gene HcrVf2. This is the first report of the generation of a true cisgenic plant. Copyright © 2011 Elsevier B.V. All rights reserved.

Thermal stability of G-rich anti-parallel DNA triplexes upon insertion of LNA and α-L-LNA.

PubMed

Kosbar, Tamer R; Sofan, Mamdouh A; Abou-Zeid, Laila; Pedersen, Erik B

2015-05-14

G-rich anti-parallel DNA triplexes were modified with LNA or α-L-LNA in their Watson-Crick and TFO strands. The triplexes were formed by targeting a pyrimidine strand to a putative hairpin formed by Hoogsteen base pairing in order to use the UV melting method to evaluate the stability of the triplexes. Their thermal stability was reduced when the TFO strand was modified with LNA or α-L-LNA. The same trend was observed when the TFO strand and the purine Watson-Crick strand both were modified with LNA. When all triad components were modified with α-L-LNA and LNA in the middle of the triplex, the thermal melting was increased. When the pyrimidine sequence was modified with a single insertion of LNA or α-L-LNA the ΔTm increased. Moreover, increasing the number of α-L-LNA in the pyrimidine target sequence to six insertions, leads to a high increase in the thermal stability. The conformational S-type structure of α-L-LNA in anti-parallel triplexes is preferable for triplex stability.

Deoxyhexanucleotide containing a vinyl chloride induced DNA lesion, 1,N/sup 6/-ethenoadenine: synthesis, physical characterization, and incorporation into a duplex bacteriophage M13 genome as part of an amber codon

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

Basu, A.K.; Niedernhofer, L.J.; Essigmann, J.M.

Organic synthesis and recombinant DNA techniques have been used to situate a single 1,N/sup 6/-ethenoadenine (epsilon Ade) DNA adduct at an amber codon in the genome of an M13mp19 phage derivative. The deoxyhexanucleotide d(GCT(epsilon A)GC) was chemically synthesized by the phosphotriester method. Physical studies involving fluorescence, circular dichroism , and /sup 1/H NMR indicated epsilon Ade to be very efficiently stacked in the hexamer, especially with the 5'-thymine. Melting profile and circular dichroism studies provided evidence of the loss of base-pairing capabilities attendant with formation of the etheno ring. The modified hexanucleotide was incorporated into a six-base gap formed inmore » the genome of an M13mp19 insertion mutant. Phage of the insertion mutant, M13mp19-NheI, produced light blue plaques on SupE strains because of the introduced amber codon. Formation of a hybrid between the single-strand DNA (plus strand) of M13mp19-NheI with SmaI-linearized M13mp19 replicative form produced a heteroduplex with a six-base gap in the minus strand. The modified hexamer (5'-/sup 32/P)d-(GCT(epsilon A)GC), after 5'-phosphorylation, was ligated into this gap by using bacteriophage T4 DNA ligase to generate a singly adducted genome with epsilon Ade at minus strand position 6274. Introduction of the radiolabel provided a useful marker for characterization of the singly adducted genome, and indeed the label appeared in the anticipated fragments when digested by several restriction endonucleases. Evidence that ligation occurred on both 5' and 3' sides of the oligonucleotide also was obtained. The M13mp19-NheI genome containing epsilon Ade will be used as a probe for studying mutagenesis and repair of this DNA adduct in Escherichia coli.« less

Flexible deep brain neural probes based on a parylene tube structure

NASA Astrophysics Data System (ADS)

Zhao, Zhiguo; Kim, Eric; Luo, Hao; Zhang, Jinsheng; Xu, Yong

2018-01-01

Most microfabricated neural probes have limited shank length, which prevents them from reaching many deep brain structures. This paper reports deep brain neural probes with ultra-long penetrating shanks based on a simple but novel parylene tube structure. The mechanical strength of the parylene tube shank is temporarily enhanced during implantation by inserting a metal wire. The metal wire can be removed after implantation, making the implanted probe very flexible and thus minimizing the stress caused by micromotions of brain tissues. Optogenetic stimulation and chemical delivery capabilities can be potentially integrated by taking advantage of the tube structure. Single-shank prototypes with a shank length of 18.2 mm have been developed. The microfabrication process comprises of deep reactive ion etching (DRIE) of silicon, parylene conformal coating/refilling, and XeF2 isotropic silicon etching. In addition to bench-top insertion characterization, the functionality of developed probes has been preliminarily demonstrated by implanting into the amygdala of a rat and recording neural signals.

Controlling the electronic and geometric structures of 2D insertions to realize high performance metal/insertion-MoS2 sandwich interfaces.

PubMed

Su, Jie; Feng, Liping; Zeng, Wei; Liu, Zhengtang

2017-06-08

Metal/insertion-MoS 2 sandwich interfaces are designed to reduce the Schottky barriers at metal-MoS 2 interfaces. The effects of geometric and electronic structures of two-dimensional (2D) insertion materials on the contact properties of metal/insertion-MoS 2 interfaces are comparatively studied by first-principles calculations. Regardless of the geometric and electronic structures of 2D insertion materials, Fermi level pinning effects and charge scattering at the metal/insertion-MoS 2 interface are weakened due to weak interactions between the insertion and MoS 2 layers, no gap states and negligible structural deformations for MoS 2 layers. The Schottky barriers at metal/insertion-MoS 2 interfaces are induced by three interface dipoles and four potential steps that are determined by the charge transfers and structural deformations of 2D insertion materials. The lower the electron affinities of 2D insertion materials, the more are the electrons lost from the Sc surface, resulting in lower n-type Schottky barriers at Sc/insertion-MoS 2 interfaces. The larger the ionization potentials and the thinner the thicknesses of 2D insertion materials, the fewer are the electrons that accumulate at the Pt surface, leading to lower p-type Schottky barriers at Pt/insertion-MoS 2 interfaces. All Sc/insertion-MoS 2 interfaces exhibited ohmic characters. The Pt/BN-MoS 2 interface exhibits the lowest p-type Schottky barrier of 0.52 eV due to the largest ionization potential (∼6.88 eV) and the thinnest thickness (single atomic layer thickness) of BN. These results in this work are beneficial to understand and design high performance metal/insertion-MoS 2 interfaces through 2D insertion materials.

Multi/demulti-plexer based on transverse mode conversion in photonic crystal waveguides.

PubMed

Zhou, Wen; Zhuang, Yuyang; Ji, Ke; Chen, He-ming

2015-09-21

A novel mode multiplexer and demultiplexer (MMUX/DEMMUX) based on 2-D photonic crystal (PC) at 1550 nm is proposed. The PC-based mode MMUX/DEMMUX including mode conversion function with a single-mode and multi-mode waveguides can be realized by quasi phase-matching TE(0) & TE(1) modes of two waveguides. 2DFinite-Difference-Time-Domain and beam propagation methods are used for simulation. The results show that PC-based mode MMUX/DEMMUX has the potential for high-capacity MDM optical communication systems with a low insertion loss (<0.36dB), low mode crosstalk (< -20.9 dB) and wide bandwidth (~100 nm).

Identifying transposon insertions and their effects from RNA-sequencing data.

PubMed

de Ruiter, Julian R; Kas, Sjors M; Schut, Eva; Adams, David J; Koudijs, Marco J; Wessels, Lodewyk F A; Jonkers, Jos

2017-07-07

Insertional mutagenesis using engineered transposons is a potent forward genetic screening technique used to identify cancer genes in mouse model systems. In the analysis of these screens, transposon insertion sites are typically identified by targeted DNA-sequencing and subsequently assigned to predicted target genes using heuristics. As such, these approaches provide no direct evidence that insertions actually affect their predicted targets or how transcripts of these genes are affected. To address this, we developed IM-Fusion, an approach that identifies insertion sites from gene-transposon fusions in standard single- and paired-end RNA-sequencing data. We demonstrate IM-Fusion on two separate transposon screens of 123 mammary tumors and 20 B-cell acute lymphoblastic leukemias, respectively. We show that IM-Fusion accurately identifies transposon insertions and their true target genes. Furthermore, by combining the identified insertion sites with expression quantification, we show that we can determine the effect of a transposon insertion on its target gene(s) and prioritize insertions that have a significant effect on expression. We expect that IM-Fusion will significantly enhance the accuracy of cancer gene discovery in forward genetic screens and provide initial insight into the biological effects of insertions on candidate cancer genes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrated Microbatteries for Implantable Medical Devices

NASA Technical Reports Server (NTRS)

Whitacre, Jay; West, William

2008-01-01

Integrated microbatteries have been proposed to satisfy an anticipated need for long-life, low-rate primary batteries, having volumes less than 1 mm3, to power electronic circuitry in implantable medical devices. In one contemplated application, such a battery would be incorporated into a tubular hearing-aid device to be installed against an eardrum. This device is based on existing tube structures that have already been approved by the FDA for use in human ears. As shown in the figure, the battery would comprise a single cell at one end of the implantable tube. A small volume of Li-based primary battery cathode material would be compacted and inserted in the tube near one end, followed by a thin porous separator, followed by a pressed powder of a Li-containing alloy. Current-collecting wires would be inserted, with suitably positioned insulators to prevent a short circuit. The battery would contain a liquid electrolyte consisting of a Li-based salt in an appropriate solvent. Hermetic seals would be created by plugging both ends with a waterproof polymer followed by deposition of parylene.

Single-row versus double-row repair of the distal Achilles tendon: a biomechanical comparison.

PubMed

Pilson, Holly; Brown, Philip; Stitzel, Joel; Scott, Aaron

2012-01-01

Surgery for recalcitrant insertional Achilles tendinopathy often consists of partial or total release of the insertion site, debridement of the diseased portion of the tendon, calcaneal ostectomy, and reattachment of the Achilles to the calcaneus. Although single-row and double-row techniques exist for repair of the detached Achilles tendon, biomechanical data are lacking to support one technique over the other. Based on data extrapolated from the study of rotator cuff repairs, we hypothesized that a double-row construct would provide superior fixation strength over a single-row repair. Eighteen human cadaveric Achilles tendons (9 matched pairs) with attached calcanei were repaired with single-row or double-row techniques. Specimens were mounted in a servohydraulic materials testing machine, subjected to a preconditioning cycle, and loaded to failure. Failure was defined as suture breakage or pullout, midsubstance tendon rupture, or anchor pullout. Among the failures were 12 suture failures, 5 proximal-row anchor failures, and 1 distal-row anchor failure. No midsubstance tendon ruptures or testing apparatus failures were observed. There were no statistically significant differences in the peak load to failure between the single-row and double-row repairs (p = .46). Similarly, no significant differences were observed with regards to mean energy expenditure to failure (p = .069). The present study demonstrated no biomechanical advantages of the double-row repair over a single-row repair. Despite the lack of a clear biomechanical advantage, there may exist clinical advantages of a double-row repair, such as reduction in knot prominence and restoration of the Achilles footprint. Copyright © 2012 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Gait Parameters and Functional Outcomes After Total Knee Arthroplasty Using Persona Knee System With Cruciate Retaining and Ultracongruent Knee Inserts.

PubMed

Rajgopal, Ashok; Aggarwal, Kalpana; Khurana, Anshika; Rao, Arun; Vasdev, Attique; Pandit, Hemant

2017-01-01

Total knee arthroplasty is a well-established treatment for managing end-stage symptomatic knee osteoarthritis. Currently, different designs of prostheses are available with majority ensuring similar clinical outcomes. Altered surface geometry is introduced to strive toward gaining superior outcomes. We aimed to investigate any differences in functional outcomes between 2 different polyethylene designs namely the Persona CR (cruciate retaining) and Persona UC (ultracongruent) tibial inserts (Zimmer-Biomet, Warsaw, IN). This prospective single blind, single-surgeon randomized controlled trial reports on 105 patients, (66 female and 39 male), who underwent simultaneous bilateral total knee arthroplasty using the Persona knee system (Zimmer-Biomet) UC inserts in one side and CR inserts in the contralateral side. By a blind assessor, at regular time intervals patients were assessed in terms of function and gait. The functional knee scoring scales used were the Western Ontario and McMaster Universities Osteoarthritis Index and Modified Knee Society Score. The gait parameters evaluated were foot pressure and step length. During the study period, no patient was lost to follow-up or underwent revision surgery for any cause. Western Ontario and McMaster Universities Osteoarthritis Index scores, Modified Knee Society Score, and knee range of motion of all 105 patients assessed preoperatively and postoperatively at 6 months, 1 year, and 2 years showed statistically better results (P < .05) for UC inserts. Gait analysis measuring foot pressures and step length, however, did not show any statistically significant differences at 2-year follow-up. Ultracongruent tibial inserts show significantly better functional outcomes as compared to CR inserts during a 2-year follow-up period. However, in this study these findings were not shown to be attributed to differences in gait parameters. Copyright © 2016 Elsevier Inc. All rights reserved.

Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond

PubMed Central

Le Bailly, Bryden A. F.; Byrne, Liam

2016-01-01

Abstract Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw‐sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22‐remote intermolecular asymmetric induction. PMID:26762559

Nanowire-based single-cell endoscopy

NASA Astrophysics Data System (ADS)

Yan, Ruoxue; Park, Ji-Ho; Choi, Yeonho; Heo, Chul-Joon; Yang, Seung-Man; Lee, Luke P.; Yang, Peidong

2012-03-01

One-dimensional smart probes based on nanowires and nanotubes that can safely penetrate the plasma membrane and enter biological cells are potentially useful in high-resolution and high-throughput gene and drug delivery, biosensing and single-cell electrophysiology. However, using such probes for optical communication across the cellular membrane at the subwavelength level remains limited. Here, we show that a nanowire waveguide attached to the tapered tip of an optical fibre can guide visible light into intracellular compartments of a living mammalian cell, and can also detect optical signals from subcellular regions with high spatial resolution. Furthermore, we show that through light-activated mechanisms the endoscope can deliver payloads into cells with spatial and temporal specificity. Moreover, insertion of the endoscope into cells and illumination of the guided laser did not induce any significant toxicity in the cells.

Seamless Insert-Plasmid Assembly at High Efficiency and Low Cost

PubMed Central

Benoit, Roger M.; Ostermeier, Christian; Geiser, Martin; Li, Julia Su Zhou; Widmer, Hans; Auer, Manfred

2016-01-01

Seamless cloning methods, such as co-transformation cloning, sequence- and ligation-independent cloning (SLIC) or the Gibson assembly, are essential tools for the precise construction of plasmids. The efficiency of co-transformation cloning is however low and the Gibson assembly reagents are expensive. With the aim to improve the robustness of seamless cloning experiments while keeping costs low, we examined the importance of complementary single-stranded DNA ends for co-transformation cloning and the influence of single-stranded gaps in circular plasmids on SLIC cloning efficiency. Most importantly, our data show that single-stranded gaps in double-stranded plasmids, which occur in typical SLIC protocols, can drastically decrease the efficiency at which the DNA transforms competent E. coli bacteria. Accordingly, filling-in of single-stranded gaps using DNA polymerase resulted in increased transformation efficiency. Ligation of the remaining nicks did not lead to a further increase in transformation efficiency. These findings demonstrate that highly efficient insert-plasmid assembly can be achieved by using only T5 exonuclease and Phusion DNA polymerase, without Taq DNA ligase from the original Gibson protocol, which significantly reduces the cost of the reactions. We successfully used this modified Gibson assembly protocol with two short insert-plasmid overlap regions, each counting only 15 nucleotides. PMID:27073895

A Forward Genetic Screening for Prostate Cancer Progression Genes

DTIC Science & Technology

2012-10-01

sequence  reads. For verifying  the  prevalence of insertions in tumors, PCR was  performed on  genomic  DNA corresponding to 15 insertional mutations using...and has been utilized with great effect in many organisms, from the bacterium to the fruit fly Drosophila melanogaster [1,2]. The Sleeping Beauty (SB...TX SL JC TN. References 1. Cooley L, Kelley R, Spradling A (1988) Insertional mutagenesis of the Drosophila genome with single P elements. Science

Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

PubMed

Hwang, Hanshin; Taylor, John-Stephen

2005-03-29

We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the Klenow fragment, and the lesser role of shape selection in insertion by pol eta due to its more open and less constrained active site.

Chromosome-based genetic complementation system for Xylella fastidiosa.

PubMed

Matsumoto, Ayumi; Young, Glenn M; Igo, Michele M

2009-03-01

Xylella fastidiosa is a xylem-limited, gram-negative bacterium that causes Pierce's disease of grapevine. Here, we describe the construction of four vectors that facilitate the insertion of genes into a neutral site (NS1) in the X. fastidiosa chromosome. These vectors carry a colE1-like (pMB1) replicon and DNA sequences from NS1 flanking a multiple-cloning site and a resistance marker for one of the following antibiotics: chloramphenicol, erythromycin, gentamicin, or kanamycin. In X. fastidiosa, vectors with colE1-like (pMB1) replicons have been found to result primarily in the recovery of double recombinants rather than single recombinants. Thus, the ease of obtaining double recombinants and the stability of the resulting insertions at NS1 in the absence of selective pressure are the major advantages of this system. Based on in vitro and in planta characterizations, strains carrying insertions within NS1 are indistinguishable from wild-type X. fastidiosa in terms of growth rate, biofilm formation, and pathogenicity. To illustrate the usefulness of this system for complementation analysis, we constructed a strain carrying a mutation in the X. fastidiosa cpeB gene, which is predicted to encode a catalase/peroxidase, and showed that the sensitivity of this mutant to hydrogen peroxide could be overcome by the introduction of a wild-type copy of cpeB at NS1. Thus, this chromosome-based complementation system provides a valuable genetic tool for investigating the role of specific genes in X. fastidiosa cell physiology and virulence.

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis.

PubMed

Waterfall, C M; Cobb, B D

2001-12-01

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a 'matrix-based' optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable.

The ATRX cDNA is prone to bacterial IS10 element insertions that alter its structure.

PubMed

Valle-García, David; Griffiths, Lyra M; Dyer, Michael A; Bernstein, Emily; Recillas-Targa, Félix

2014-01-01

The SWI/SNF-like chromatin-remodeling protein ATRX has emerged as a key factor in the regulation of α-globin gene expression, incorporation of histone variants into the chromatin template and, more recently, as a frequently mutated gene across a wide spectrum of cancers. Therefore, the availability of a functional ATRX cDNA for expression studies is a valuable tool for the scientific community. We have identified two independent transposon insertions of a bacterial IS10 element into exon 8 of ATRX isoform 2 coding sequence in two different plasmids derived from a single source. We demonstrate that these insertion events are common and there is an insertion hotspot within the ATRX cDNA. Such IS10 insertions produce a truncated form of ATRX, which significantly compromises its nuclear localization. In turn, we describe ways to prevent IS10 insertion during propagation and cloning of ATRX-containing vectors, including optimal growth conditions, bacterial strains, and suggested sequencing strategies. Finally, we have generated an insertion-free plasmid that is available to the community for expression studies of ATRX.

Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

NASA Astrophysics Data System (ADS)

Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

2016-04-01

Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel.

Zinc-finger Nuclease-induced Gene Repair With Oligodeoxynucleotides: Wanted and Unwanted Target Locus Modifications

PubMed Central

Radecke, Sarah; Radecke, Frank; Cathomen, Toni; Schwarz, Klaus

2010-01-01

Correcting a mutated gene directly at its endogenous locus represents an alternative to gene therapy protocols based on viral vectors with their risk of insertional mutagenesis. When solely a single-stranded oligodeoxynucleotide (ssODN) is used as a repair matrix, the efficiency of the targeted gene correction is low. However, as shown with the homing endonuclease I-SceI, ssODN-mediated gene correction can be enhanced by concomitantly inducing a DNA double-strand break (DSB) close to the mutation. Because I-SceI is hardly adjustable to cut at any desired position in the human genome, here, customizable zinc-finger nucleases (ZFNs) were used to stimulate ssODN-mediated repair of a mutated single-copy reporter locus stably integrated into human embryonic kidney-293 cells. The ZFNs induced faithful gene repair at a frequency of 0.16%. Six times more often, ZFN-induced DSBs were found to be modified by unfaithful addition of ssODN between the termini and about 60 times more often by nonhomologous end joining-related deletions and insertions. Additionally, ZFN off-target activity based on binding mismatch sites at the locus of interest was detected in in vitro cleavage assays and also in chromosomal DNA isolated from treated cells. Therefore, the specificity of ZFN-induced ssODN-mediated gene repair needs to be improved, especially regarding clinical applications. PMID:20068556

Optomechanical design of a buckling cavity in a low-cost high-performance ferruleless field-installable single-mode fiber connector

NASA Astrophysics Data System (ADS)

Ebraert, Evert; Van Erps, Jürgen; Beri, Stefano; Watté, Jan; Thienpont, Hugo

2014-10-01

To boost the deployment of fiber-to-the-home networks in order to meet the ever-increasing demand for bandwidth, there is a strong need for single-mode fiber (SMF) connectors which combine low insertion loss with field installability. Shifting from ferrule-based to ferruleless connectors can reduce average insertion losses appreciably and minimize modal noise interference. We propose a ferruleless connector and adaptor in which physical contact between two inline fibers is ensured by at least one fiber being in a buckled state. To this end, we design a buckling cavity in which the SMF can buckle in a controlled way to ensure good optical performance as well as mechanical stability. This design is based on both mechanical and optical considerations. Finite element analysis suggests that mechanically a minimal buckling cavity length of 17 mm is required, while the height of the cavity should be chosen such that the buckled SMF is not mechanically confined to ensure buckling in a first-order mode. The optical bending loss in the buckled SMF is calculated using a fully vectorial mode solver, showing that a minimal buckling cavity length of 20 mm is necessary to keep the excess optical loss from bending below 0.1 dB. Both our optical and mechanical simulation results are experimentally verified.

Urethral Foreign Bodies: Clinical Presentation and Management.

PubMed

Palmer, Cristina J; Houlihan, Matthew; Psutka, Sarah P; Ellis, K Alexandria; Vidal, Patricia; Hollowell, Courtney M P

2016-11-01

To review a single institution's 15-year experience with urethral foreign bodies, including evaluation, clinical findings, and treatment. In total, 27 patients comprising 35 episodes of inserted urethral foreign bodies were reviewed at Cook County Hospital between 2000 and 2015. Retrospective chart review was performed to describe the clinical presentation, rationale for insertion, management, recidivism, and sequelae. Median patient age was 26 (range 12-60). Twenty-six patients (97 %) were male, 1 was female (3%). Items inserted included pieces of plastic forks, spoons, metal screws and aluminum, pieces of cardboard or paper, staples, writing utensils such as pens and pencils, as well as coaxial cable and spray foam sealant. Reported reasons for insertion were self-stimulation, erectile enhancement, and attention seeking. Presenting symptoms included dysuria, gross hematuria, urinary retention, urinary tract infection, and penile discharge. The most common technique for removal was manual extraction with extrinsic pressure (n = 19, 54%). Other methods include endoscopic retrieval (n = 8, 23%), open cystotomy (n = 1, 3%), and voiding to expel the foreign body (n = 7, 20%). Postremoval complications included urinary tract infection (n = 7), sepsis (n = 4), urethral false passage (n = 5), laceration (n = 5), and stricture (n = 1). We present the largest single-institutional series of urethral foreign bodies to date. Urethral foreign body insertion is a relatively rare occurrence and, commonly, is a recurrent behavior. Urethral trauma related to foreign body insertion is associated with significant risk of infection and urethral injury with long-term sequelae. Copyright © 2016 Elsevier Inc. All rights reserved.

A single gene mutation that increases maize seed weight

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

Giroux, M.J.; Shaw, J.; Hannah, L.C.

1996-06-11

The maize endosperm-specific gene shrunken2 (Sh2) encodes the large subunit of the heterotetrameric starch synthetic enzyme adenosine diphosphoglucose pyrophosphorylase (AGP; EC 2.7.7.27). Here we exploit an in vivo, site-specific mutagenesis system to create short insertion mutations in a region of the gene known to be involved in the allosteric regulation of AGP. The site-specific mutagen is the transposable element dissociation (Ds). Approximately one-third (8 of 23) of the germinal revertants sequenced restored the wild-type sequence, whereas the remaining revertants contained insertions of 3 or 6 bp. All revertants retained the original reading frame 3 feet to the insertion site andmore » involved the addition of tyrosine and/or serine. Each insertion revertant reduced total AGP activity and the amount of the SH2 protein. The revertant containing additional tyrosine and serine residues increased seed weight 11-18% without increasing or decreasing the percentage of starch. Other insertion revertants lacking an additional serine reduced seed weight. Reduced sensitivity to phosphate, a long-known inhibitor of AGP, was found in the high seed-weight revertant. This alteration is likely universally important since insertion of tyrosine and serine in the potato large subunit of AGP at the comparable position and expression in Escherichia coli also led to a phosphate-insensitive enzyme. These results show that single gene mutations giving rise to increased seed weight, and therefore perhaps yield, are clearly possible in a plant with a long history of intensive and successful breeding efforts. 20 refs., 5 figs., 5 tabs.« less

A 3-year multicenter study of marginal bone level and soft tissue health of a 1-piece implant.

PubMed

Baer, Russell A; Shanaman, Richard; Clark, Paul K; Medley, Michael

2013-08-01

The study evaluated 1-piece implants in daily clinical situations. One-piece implants restoring both single teeth and partially edentulous sites were included. A single-stage procedure was used with immediate provisionalization within 24 hours after surgery. The definitive prosthesis was delivered within 6 months of implant insertion. One hundred fifteen implants have been placed in 84 patients at 4 centers. Two implants failed resulting in a cumulative survival rate of 98.3%. Normal periimplant mucosa and no visible plaque were observed in most of the implants. The soft tissue papilla scores improved considerably over time P < 0.001. Patient assessment improved significantly from implant insertion to the 3-year visit, P < 0.001. The mean bone level at implant insertion, 6-month, and 1-, 2-, and 3-year visits was 0.42, -0.58, -0.69, -0.80, and -0.66 mm, respectively. The mean change in bone level from implant insertion to 6 months and 1, 2, and 3 years was reported as -1.02, -1.12, -1.26, and -1.07 mm, respectively. The results indicate that this implant has the ability to preserve both hard and soft tissues' architecture.

Ten years single-centre experience with intra-aortic balloon pump.

PubMed

Vandenplas, Guy; Bové, Thierry; Caes, Frank; Van Belleghem, Yves; François, Katrien; De Somer, Filip; Taeymans, Yves; Van Nooten, Guido

2011-12-01

The objective of this study was to investigate the patient characteristics and outcomes in 1406 patients undergoing intra-aortic balloon pump (IABP) counterpulsation. Between 1998 and 2008, 1406 consecutive patients were recorded in a prospective database. Based on the main clinical indication for IABP use, we defined 3 groups: group A, 630 cases of coronary ischaemia or infarction without serious left ventricular (LV) dysfunction; group B, 466 patients with left ventricular failure or cardiogenic shock; group C, 310 patients where IABP was used for miscellaneous procedures such as weaning from cardiopulmonary bypass or during high-risk angioplasty or surgery. Global mortality was 28% (n = 390), with a significant difference between group A (15%, n = 95) and group B (41%, n = 191) (P < 0.001). Mortality in group C was 34% (n = 104). Most insertions were done in the catheterization laboratory (n = 943) with subsequent mortality of 23% whereas 199 balloons were inserted in the operation room with 34% mortality. 170 balloons inserted in the intensive care unit resulted in 46% mortality (P < 0.001). Major IABP-induced complications were 6.8% with no statistical differences between the three groups. Advanced age, left ventricular failure and low BMI were identified as prognostic risk factors for early mortality. IABP deployed at an early clinical stage yields the best results, especially for acute coronary patients with preserved LV function whereas LV failure and late insertion result in worse outcome.

Implanon NXT: Expert tips for best-practice insertion and removal.

PubMed

Pearson, Suzanne; Stewart, Mary; Bateson, Deborah

2017-03-01

The single rod etonogestrel contraceptive implant is available in Australia as Implanon NXT. It is a highly effective, long-acting reversible contraceptive method, which is suitable for most women across the reproductive lifespan. This article provides practical advice for clinicians who already insert and remove the contraceptive implant, as well as advice for those who have not yet acquired this procedural skill. Contraceptive implant procedures are usually performed in the general practice setting. Clinicians can support women in making an informed choice to have an implant by providing information about their benefits, side effects and risks, and timely access to insertion. Training in the procedures and compliance with procedural instructions are essential to minimise risks, including deep insertion and damage to neurovascular structures.

Changing genetic information through RNA editing

NASA Technical Reports Server (NTRS)

Maas, S.; Rich, A.

2000-01-01

RNA editing, the post-transcriptional alteration of a gene-encoded sequence, is a widespread phenomenon in eukaryotes. As a consequence of RNA editing, functionally distinct proteins can be produced from a single gene. The molecular mechanisms involved include single or multiple base insertions or deletions as well as base substitutions. In mammals, one type of substitutional RNA editing, characterized by site-specific base-modification, was shown to modulate important physiological processes. The underlying reaction mechanism of substitutional RNA editing involves hydrolytic deamination of cytosine or adenosine bases to uracil or inosine, respectively. Protein factors have been characterized that are able to induce RNA editing in vitro. A supergene family of RNA-dependent deaminases has emerged with the recent addition of adenosine deaminases specific for tRNA. Here we review the developments that have substantially increased our understanding of base-modification RNA editing over the past few years, with an emphasis on mechanistic differences, evolutionary aspects and the first insights into the regulation of editing activity.

Interchromosomal recombination in Zea mays.

PubMed Central

Hu, W; Timmermans, M C; Messing, J

1998-01-01

A new allele of the 27-kD zein locus in maize has been generated by interchromosomal recombination between chromosomes of two different inbred lines. A continuous patch of at least 11,817 bp of inbred W64A, containing the previously characterized Ra allele of the 27-kD zein gene, has been inserted into the genome of A188 by a single crossover. While both junction sequences are conserved, sequences of the two homologs between these junctions differ considerably. W64A contains the 7313-bp-long retrotransposon, Zeon-1. A188 contains a second copy of the 27-kD zein gene and a 2-kb repetitive element. Therefore, recombination results in a 7.3-kb insertion and a 14-kb deletion compared to the original S+A188 allele. If nonpairing sequences are looped out, 206 single base changes, frequently clustered, are present. The structure of this allele may explain how a recently discovered example of somatic recombination occurred in an A188/W64A hybrid. This would indicate that despite these sequence differences, pairing between these alleles could occur early during plant development. Therefore, such a somatically derived chimeric chromosome can also be heritable and give rise to new alleles. PMID:9799274

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

McDowell, G.A.; Blitzer, M.G.; Mules, E.H.

A study was undertaken to characterize the mutation(s) responsible for Tay-Sachs disease (TSD) in a Cajun population in southwest Louisiana and to identify the origins of these mutations. Eleven of 12 infantile TSD alleles examined in six families had the [beta]-hexosaminidase A (Hex A) [alpha]-subunit exon 11 insertion mutation that is present in approximately 70% of Ashkenazi Jewish TSD heterozygotes. The mutation in the remaining allele was a single-base transition in the donor splice site of the [alpha]-subunit intron 9. To determine the origins of these two mutations in the Cajun population, the TSD carrier status was enzymatically determined formore » 90 members of four of the six families, and extensive pedigrees were constructed for all carriers. A single ancestral couple from France was found to be common to most of the carriers of the exon 11 insertion. Pedigree data suggest that this mutation has been in the Cajun population since its founding over 2 centuries ago and that it may be widely distributed within the population. In contrast, the intron 9 mutation apparently was introduced within the last century and probably is limited to a few Louisiana families. 29 refs., 4 figs.« less

J-tube technique for double-j stent insertion during laparoscopic upper urinary tract surgical procedures.

PubMed

Kim, Hyung Suk; Lee, Byung Ki; Jung, Jin-Woo; Lee, Jung Keun; Byun, Seok-Soo; Lee, Sang Eun; Jeong, Chang Wook

2014-11-01

Double-J stent insertion has been generally performed during laparoscopic upper urinary tract (UUT) surgical procedures to prevent transient urinary tract obstruction and postoperative flank pain from ureteral edema and blood clots. Several restrictive conditions that make this procedure difficult and time consuming, however, include the coiled distal ends of the flexible Double-J stent and the limited bending angle of the laparoscopic instruments. To overcome these limitations, we devised a Double-J stent insertion method using the new J-tube technique. Between July 2011 and May 2013, Double-J stents were inserted using the J-tube technique in 33 patients who underwent a laparoscopic UUT surgical procedure by a single surgeon. The mean stent placement time was 4.8±2.7 minutes, and there were no intraoperative complications. In conclusion, the J-tube technique is a safe and time-saving method for Double-J stent insertion during laparoscopic surgical procedures.

High-quality Mach-Zehnder interferometer based on a microcavity in single-multi-single mode fiber structure for refractive index sensing.

PubMed

Liu, Yi; Wu, Guoqiang; Gao, Renxi; Qu, Shiliang

2017-02-01

A fiber inline Mach-Zehnder interferometer (MZI) based on a microcavity with two symmetric openings in single-multi-single mode fiber (SMSF) structure is proposed. By using the finite difference beam propagation method (FD-BPM), the interference spectrum simulation result shows that the MZI can still have high-quality interference even if the microcavity deviates along the radial direction for 3 μm. Therefore, it allows a larger fabrication tolerance and tremendously decreases the fabrication difficulty. Then a microcavity with two symmetric openings in SMSF was fabricated by using femtosecond laser-induced water breakdown. The insertion loss of the microcavity immerged in water is only -8  dB, and the MZ interference peak contrast in the transmission spectrum reaches more than 30 dB. The MZI based on the microcavity in SMSF can be used as a practical liquid refractive index sensor as its high-quality interference spectrum, ultrahigh sensitivity (9756.75 nm/RIU), high refractive index resolution (2×10^-5  RIU), good linearity (99.93%), and low-temperature crosstalk (0.04 nm/°C).

Spin dependent transport properties of Mn-Ga/MgO/Mn-Ga magnetic tunnel junctions with metal(Mg, Co, Cr) insertion layer

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

Liang, S. H.; Tao, L. L.; Liu, D. P., E-mail: dpliu@iphy.ac.cn

We report a first principles theoretical investigation of spin polarized quantum transport in Mn{sub 2}Ga/MgO/Mn{sub 2}Ga and Mn{sub 3}Ga/MgO/Mn{sub 3}Ga magnetic tunneling junctions (MTJs) with the consideration of metal(Mg, Co, Cr) insertion layer effect. By changing the concentration of Mn, our calculation shows a considerable disparity in transport properties: A tunneling magnetoresistance (TMR) ratio of 852% was obtained for Mn{sub 2}Ga-based MTJs, however, only a 5% TMR ratio for Mn{sub 3}Ga-based MTJs. In addition, the influence of insertion layer has been considered in our calculation. We found the Co insertion layer can increase the TMR of Mn{sub 2}Ga-based MTJ tomore » 904%; however, the Cr insertion layer can decrease the TMR by 668%; A negative TMR ratio can be obtained with Mg insertion layer. Our work gives a comprehensive understanding of the influence of different insertion layer in Mn-Ga based MTJs. It is proved that, due to the transmission can be modulated by the interfacial electronic structure of insertion, the magnetoresistance ratio of Mn{sub 2}Ga/MgO/Mn{sub 2}Ga MTJ can be improved by inserting Co layer.« less

The incidence of blood contamination of lead unit dose containers with and without single-use protective inserts used with commercially prepared radiopharmaceutical unit doses.

PubMed

Pickett, M W; Kosegi, J E; Thomas, K S; Waterstram-Rich, K M

1998-09-01

This investigation evaluated the effectiveness of disposable plastic inserts in radiopharmaceutical unit dose lead containers (pigs) in preventing the distribution of doses in blood-contaminated containers. Technologists commonly dispose of the syringes by placing them into the lead pigs, leaving the needles uncapped. This process raises the question of unsuspected blood contamination of these pigs. Consequently, the distribution of commercially prepared radiopharmaceutical doses in reusable lead pigs may result in radiopharmaceutical doses being distributed in containers that are contaminated with blood. Using a simple chemical wipe test designed to determine the presence or absence of blood contamination, 618 pigs from commercial radiopharmacies throughout the U.S. were tested for contamination. The inside of the pigs and inserts, if present, were wiped before and after dose administration. Of the pigs tested, 292 came from radiopharmacies that used a protective, disposable plastic insert inside the pig, and 326 came from radiopharmacies that did not use an insert. Of those pigs without the protective disposable inserts, 39.3% arrived in the nuclear medicine department in pigs contaminated with blood. Of those pigs with inserts, 1% arrived with blood-contaminated inserts. After dose administration, 46.3% of the pigs without inserts were contaminated with blood and 3% of the protective inserts were contaminated. The proper use of disposable plastic inserts reduces the possibility of distributing radiopharmaceutical unit doses in containers contaminated with blood.

Morphometric and molecular characterization of fungus Pestalotiopsis using nuclear ribosomal DNA analysis.

PubMed

Gehlot, Praveen; Singh, S K; Pathak, Rakesh

2012-09-01

Taxonomy of the fungus Pestalotiopsis based on morphological characters has been equivocal. Molecular characterization often Pestalotiopsis species was done based on nuclear ribosomal DNA internal transcribed spacer (ITS) amplifications. Results of the analyses showed that species of genus Pestalotiopsis are monophyletic. We report ITS length variations, single nucleotide polymorphisms (SNPs) and insertions/ deletions (INDELS) among ten species of Pestalotiopsis that did not cause any phylogenetic error at either genus or species designation levels. New gene sequences have been assigned (Gen Accession numbers from HM 190146 to HM 190155) by the National Centre for Biotechnology Information, USA.

Accuracy of pedicle screw insertion by AIRO® intraoperative CT in complex spinal deformity assessed by a new classification based on technical complexity of screw insertion.

PubMed

Rajasekaran, S; Bhushan, Manindra; Aiyer, Siddharth; Kanna, Rishi; Shetty, Ajoy Prasad

2018-01-09

To develop a classification based on the technical complexity encountered during pedicle screw insertion and to evaluate the performance of AIRO ® CT navigation system based on this classification, in the clinical scenario of complex spinal deformity. 31 complex spinal deformity correction surgeries were prospectively analyzed for performance of AIRO ® mobile CT-based navigation system. Pedicles were classified according to complexity of insertion into five types. Analysis was performed to estimate the accuracy of screw placement and time for screw insertion. Breach greater than 2 mm was considered for analysis. 452 pedicle screws were inserted (T1-T6: 116; T7-T12: 171; L1-S1: 165). The average Cobb angle was 68.3° (range 60°-104°). We had 242 grade 2 pedicles, 133 grade 3, and 77 grade 4, and 44 pedicles were unfit for pedicle screw insertion. We noted 27 pedicle screw breach (medial: 10; lateral: 16; anterior: 1). Among lateral breach (n = 16), ten screws were planned for in-out-in pedicle screw insertion. Among lateral breach (n = 16), ten screws were planned for in-out-in pedicle screw insertion. Average screw insertion time was 1.76 ± 0.89 min. After accounting for planned breach, the effective breach rate was 3.8% resulting in 96.2% accuracy for pedicle screw placement. This classification helps compare the accuracy of screw insertion in range of conditions by considering the complexity of screw insertion. Considering the clinical scenario of complex pedicle anatomy in spinal deformity AIRO ® navigation showed an excellent accuracy rate of 96.2%.

A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity

PubMed Central

Wahba, Alexander S.; Esmaeili, Abbasali; Damha, Masad J.; Hudson, Robert H. E.

2010-01-01

6-Phenylpyrrolocytidine (PhpC), a structurally conservative and highly fluorescent cytidine analog, was incorporated into oligoribonucleotides. The PhpC-containing RNA formed native-like duplex structures with complementary DNA or RNA. The PhpC-modification was found to act as a sensitive reporter group being non-disruptive to structure and the enzymatic activity of RNase H. A RNA/DNA hybrid possessing a single PhpC insert was an excellent substrate for HIV-1 RT Ribonuclease H and rapidly reported cleavage of the RNA strand with a 14-fold increase in fluorescence intensity. The PhpC-based assay for RNase H was superior to the traditional molecular beacon approach in terms of responsiveness, rapidity and ease (single label versus dual). Furthermore, the PhpC-based assay is amenable to high-throughput microplate assay format and may form the basis for a new screen for inhibitors of HIV-RT RNase H. PMID:19933258

Patient-specific surgical simulator for the pre-operative planning of single-incision laparoscopic surgery with bimanual robots.

PubMed

Turini, Giuseppe; Moglia, Andrea; Ferrari, Vincenzo; Ferrari, Mauro; Mosca, Franco

2012-01-01

The trend of surgical robotics is to follow the evolution of laparoscopy, which is now moving towards single-incision laparoscopic surgery. The main drawback of this approach is the limited maneuverability of the surgical tools. Promising solutions to improve the surgeon's dexterity are based on bimanual robots. However, since both robot arms are completely inserted into the patient's body, issues related to possible unwanted collisions with structures adjacent to the target organ may arise. This paper presents a simulator based on patient-specific data for the positioning and workspace evaluation of bimanual surgical robots in the pre-operative planning of single-incision laparoscopic surgery. The simulator, designed for the pre-operative planning of robotic laparoscopic interventions, was tested by five expert surgeons who evaluated its main functionalities and provided an overall rating for the system. The proposed system demonstrated good performance and usability, and was designed to integrate both present and future bimanual surgical robots.

Teleoperated master-slave needle insertion.

PubMed

Abolhassani, Niki; Patel, Rajni V

2009-12-01

Accuracy of needle tip placement and needle tracking in soft tissue are of particular importance in many medical procedures. In recent years, developing autonomous and teleoperated systems for needle insertion has become an active area of research. In this study, needle insertion was performed using a master-slave set-up with multi-degrees of freedom. The effect of force feedback on the accuracy of needle insertion was investigated. In addition, this study compared autonomous, teleoperated and semi-autonomous needle insertion. The results of this study show that incorporation of force feedback can improve teleoperated needle insertion. However, autonomous and semi-autonomous needle insertions, which use feedback from a deflection model, provide significantly better performance. Development of a haptic master-slave needle insertion system, which is capable of performing some autonomous tasks based on feedback from tissue deformation and needle deflection models, can improve the performance of autonomous robotics-based insertions as well as non-autonomous teleoperated manual insertions. Copyright (c) 2009 John Wiley & Sons, Ltd.

High efficiency and enhanced ESD properties of UV LEDs by inserting p-GaN/p-AlGaN superlattice

NASA Astrophysics Data System (ADS)

Huang, Yong; Li, PeiXian; Yang, Zhuo; Hao, Yue; Wang, XiaoBo

2014-05-01

Significantly improved electrostatic discharge (ESD) properties of InGaN/GaN-based UV light-emitting diode (LED) with inserting p-GaN/p-AlGaN superlattice (p-SLs) layers (instead of p-AlGaN single layer) between multiple quantum wells and Mg-doped GaN layer are reported. The pass yield of the LEDs increased from 73.53% to 93.81% under negative 2000 V ESD pulses. In addition, the light output power (LOP) and efficiency droop at high injection current were also improved. The mechanism of the enhanced ESD properties was then investigated. After excluding the effect of capacitance modulation, high-resolution X-ray diffraction (XRD) and atomic force microscope (AFM) measurements demonstrated that the dominant mechanism of the enhanced ESD properties is the material quality improved by p-SLs, which indicated less leakage paths, rather than the current spreading improved by p-SLs.

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis

PubMed Central

Waterfall, Christy M.; Cobb, Benjamin D.

2001-01-01

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a ‘matrix-based’ optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable. PMID:11726702

Fracture Resistance of Premolars Restored by Various Types and Placement Techniques of Resin Composites

PubMed Central

Moosavi, Horieh; Zeynali, Mahsa; Pour, Zahra Hosseini

2012-01-01

To verify the fracture resistance of premolars with mesioocclusodistal preparations restored by different resin composites and placement techniques. Sixty premolars were randomly divided into two groups based on type of composite resin: Filtek P60 or Nulite F, and then each group was separated into three subgroups: bulk, centripetal, and fiber insert according to the type of placement method (n = 10). Single-bond adhesive system was used as composite bonding according to the manufacturer's instructions. Specimens were restored in Groups 1, 2, and 3 with Filtek P60 and in Groups 4, 5, and 6 with Nulite F. After being stored 24 hours at 37°C, a 4 mm diameter steel sphere in a universal testing machine was applied on tooth buccal and lingual cusps at a cross-head speed of 5 mm/min until fracture occurred. Groups 3 and 6 showed higher fracture resistance than Groups 1, 2, 4, and 5. Among the placement techniques, the fiber insert method had a significant effect, but the type of composite was ineffective. The insertion technique in contrast to the type of material had a significant influence on the fracture resistance of premolar teeth. PMID:22666255

Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome.

PubMed

Tan, Ene-Choo; Li, Haixia

2006-07-19

Most of the studies on single nucleotide variations are on substitutions rather than insertions/deletions. In this study, we examined the distribution and characteristics of single nucleotide insertions/deletions (SNindels), using data available from dbSNP for all the human chromosomes. There are almost 300,000 SNindels in the database, of which only 0.8% are validated. They occur at the frequency of 0.887 per 10 kb on average for the whole genome, or approximately 1 for every 11,274 bp. More than half occur in regions with mononucleotide repeats the longest of which is 47 bases. Overall the mononucleotide repeats involving C and G are much shorter than those for A and T. About 12% are surrounded by palindromes. There is general correlation between chromosome size and total number for each chromosome. Inter-chromosomal variation in density ranges from 0.6 to 21.7 per kilobase. The overall spectrum shows very high proportion of SNindel of types -/A and -/T at over 81%. The proportion of -/A and -/T SNindels for each chromosome is correlated to its AT content. Less than half of the SNindels are within or near known genes and even fewer (<0.183%) in coding regions, and more than 1.4% of -/C and -/G are in coding compared to 0.2% for -/A and -/T types. SNindels of -/A and -/T types make up 80% of those found within untranslated regions but less than 40% of those within coding regions. A separate analysis using the subset of 2324 validated SNindels showed slightly less AT bias of 74%, SNindels not within mononucleotide repeats showed even less AT bias at 58%. Density of validated SNindels is 0.007/10 kb overall and 90% are found within or near genes. Among all chromosomes, Y has the lowest numbers and densities for all SNindels, validated SNindels, and SNindels not within repeats.

Linear motion device and method for inserting and withdrawing control rods

DOEpatents

Smith, Jay E.

1984-01-01

A linear motion device, more specifically a control rod drive mechanism (CRDM) for inserting and withdrawing control rods into a reactor core, is capable of independently and sequentially positioning two sets of control rods with a single motor stator and rotor. The CRDM disclosed can control more than one control rod lead screw without incurring a substantial increase in the size of the mechanism.

Facile insertion of a cyclic alkyl(amino) carbene carbon into the B-B bond of diboron(4) reagents.

PubMed

Eichhorn, Antonius F; Kuehn, Laura; Marder, Todd B; Radius, Udo

2017-10-24

We report herein the room temperature insertion of the carbene carbon atom of the cyclic (alkyl)(amino) carbene cAAC Me into the B-B single bonds of the diboron(4) compounds B 2 pin 2 , B 2 cat 2 , B 2 neop 2 , and B 2 eg 2 (pin = pinacolato, cat = catecholato, neop = neopentylglycolato, eg = ethyleneglycolato).

Biomechanical properties of double- and single-row suture anchor repair for surgical treatment of insertional Achilles tendinopathy.

PubMed

Beitzel, Knut; Mazzocca, Augustus D; Obopilwe, Elifho; Boyle, James W; McWilliam, James; Rincon, Lina; Dhar, Yasmin; Arciero, Robert A; Amendola, Annunziato

2013-07-01

Because of intratendinous ossifications, retrocalcaneal bursitis, or intratendinous necrosis commonly found in insertional tendinosis, it is often necessary to detach the tendon partially or entirely from its tendon-to-bone junction. Double-row repair for insertional Achilles tendinopathy will generate an increased contact area and demonstrate higher biomechanical stability. Controlled laboratory study. Eighteen cadaver Achilles tendons were split longitudinally and detached, exposing the calcaneus; an ostectomy was performed and the tendon was reattached to the calcaneus in 1 of 2 ways: 2 suture anchors (single row) or a 4-anchor (double row) construct. Footprint area measurements over time, displacement after cyclic loading (2000 cycles), and final load to failure were measured. The double-row refixation technique was statistically superior to the single-row technique in footprint area measurement initially and 5 minutes after repair (P = .009 and P = .01, respectively) but not after 24 hours (P = .713). The double-row construct demonstrated significantly improved measures for peak load (433.9 ± 84.3 N vs 212.0 ± 49.7 N; P = .042), load at yield (354.7 ± 106.2 N vs 198.7 ± 39.5 N; P = .01), and slope (51.8 ± 9.9 N/mm vs 66.7 ± 16.2 N/mm; P = .021). Cyclic loading did not demonstrate significant differences between the 2 constructs. Double-row construct for reinsertion of a completely detached Achilles tendon using proximal and distal rows resulted in significantly larger contact area initially and 5 minutes after repair and led to significantly higher peak load to failure on destructive testing. In treatment for insertional Achilles tendinosis, the tendon often has to be detached and anatomically reattached to its insertion at the calcaneus. To our knowledge there is a lack of biomechanical studies supporting either a number or a pattern of suture anchor fixation. Because the stresses going across the insertion site of the Achilles tendon are significant during rehabilitation and weightbearing activities, it is imperative to have a strong construct that allows satisfactory healing during the early postoperative process.

An in vitro biomechanical comparison of equine proximal interphalangeal joint arthrodesis techniques: an axial positioned dynamic compression plate and two abaxial transarticular cortical screws inserted in lag fashion versus three parallel transarticular cortical screws inserted in lag fashion.

PubMed

Sod, Gary A; Riggs, Laura M; Mitchell, Colin F; Hubert, Jeremy D; Martin, George S

2010-01-01

To compare in vitro monotonic biomechanical properties of an axial 3-hole, 4.5 mm narrow dynamic compression plate (DCP) using 5.5 mm cortical screws in conjunction with 2 abaxial transarticular 5.5 mm cortical screws inserted in lag fashion (DCP-TLS) with 3 parallel transarticular 5.5 mm cortical screws inserted in lag fashion (3-TLS) for the equine proximal interphalangeal (PIP) joint arthrodesis. Paired in vitro biomechanical testing of 2 methods of stabilizing cadaveric adult equine forelimb PIP joints. Cadaveric adult equine forelimbs (n=15 pairs). For each forelimb pair, 1 PIP joint was stabilized with an axial 3-hole narrow DCP (4.5 mm) using 5.5 mm cortical screws in conjunction with 2 abaxial transarticular 5.5 mm cortical screws inserted in lag fashion and 1 with 3 parallel transarticular 5.5 mm cortical screws inserted in lag fashion. Five matching pairs of constructs were tested in single cycle to failure under axial compression, 5 construct pairs were tested for cyclic fatigue under axial compression, and 5 construct pairs were tested in single cycle to failure under torsional loading. Mean values for each fixation method were compared using a paired t-test within each group with statistical significance set at P<.05. Mean yield load, yield stiffness, and failure load under axial compression and torsion, single cycle to failure, of the DCP-TLS fixation were significantly greater than those of the 3-TLS fixation. Mean cycles to failure in axial compression of the DCP-TLS fixation was significantly greater than that of the 3-TLS fixation. The DCP-TLS was superior to the 3-TLS in resisting the static overload forces and in resisting cyclic fatigue. The results of this in vitro study may provide information to aid in the selection of a treatment modality for arthrodesis of the equine PIP joint.

Strand Invasion Based Amplification (SIBA®): a novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.

PubMed

Hoser, Mark J; Mansukoski, Hannu K; Morrical, Scott W; Eboigbodin, Kevin E

2014-01-01

Isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (PCR) in that they do not require thermal cycling or sophisticated laboratory equipment. However, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. Here, we report a novel isothermal nucleic acid amplification technology, Strand Invasion Based Amplification (SIBA). SIBA technology is resistant to non-specific amplification, is able to detect a single molecule of target analyte, and does not require target-specific probes. The technology relies on the recombinase-dependent insertion of an invasion oligonucleotide (IO) into the double-stranded target nucleic acid. The duplex regions peripheral to the IO insertion site dissociate, thereby enabling target-specific primers to bind. A polymerase then extends the primers onto the target nucleic acid leading to exponential amplification of the target. The primers are not substrates for the recombinase and are, therefore unable to extend the target template in the absence of the IO. The inclusion of 2'-O-methyl RNA to the IO ensures that it is not extendible and that it does not take part in the extension of the target template. These characteristics ensure that the technology is resistant to non-specific amplification since primer dimers or mis-priming are unable to exponentially amplify. Consequently, SIBA is highly specific and able to distinguish closely-related species with single molecule sensitivity in the absence of complex probes or sophisticated laboratory equipment. Here, we describe this technology in detail and demonstrate its use for the detection of Salmonella.

Transoesophageal echocardiographic evaluation of central venous catheter positioning using Peres' formula or a radiological landmark-based approach: a prospective randomized single-centre study.

PubMed

Ahn, J H; Kim, I S; Yang, J H; Lee, I G; Seo, D H; Kim, S P

2017-02-01

The lower superior vena cava (SVC), near its junction with the right atrium (RA), is considered the ideal location for the central venous catheter tip to ensure proper function and prevent injuries. We determined catheter insertion depth with a new formula using the sternoclavicular joint and the carina as radiological landmarks, with a 1.5 cm safety margin. The accuracy of tip positioning with the radiological landmark-based technique (R) and Peres' formula (P) was compared using transoesophageal echocardiography. Real-time ultrasound-guided central venous catheter insertion was done through the right internal jugular or subclavian vein. Patients were randomly assigned to either the P group (n=93) or the R group (n=95). Optimal catheter tip position was considered to be within 2 cm above and 1 cm below the RA-SVC junction. Catheter tip position, abutment, angle to the vascular wall, and flow stream were evaluated on a bicaval view. The distance from the skin insertion point to the RA-SVC junction and determined depth of catheter insertion were more strongly correlated in the R group [17.4 (1.2) and 16.7 (1.5) cm; r=0.821, P<0.001] than in the P group [17.3 (1.2) and 16.4 (1.1) cm; r=0.517, P<0.001], with z=3.96 (P<0.001). More tips were correctly positioned in the R group than in the P group (74 vs 93%, P=0.001). Abutment, tip angle to the lateral wall >40°, and disrupted flow stream were comparable. Catheter tip position was more accurate with a radiological landmark-based technique than with Peres' formula. Clinical Trial Registry of Korea: https://cris.nih.go.kr/cris/index.jsp KCT0001937. © The Author 2017. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Improvement of single detector proton radiography by incorporating intensity of time-resolved dose rate functions

NASA Astrophysics Data System (ADS)

Zhang, Rongxiao; Jee, Kyung-Wook; Cascio, Ethan; Sharp, Gregory C.; Flanz, Jacob B.; Lu, Hsiao-Ming

2018-01-01

Proton radiography, which images patients with the same type of particles as those with which they are to be treated, is a promising approach to image guidance and water equivalent path length (WEPL) verification in proton radiation therapy. We have shown recently that proton radiographs could be obtained by measuring time-resolved dose rate functions (DRFs) using an x-ray amorphous silicon flat panel. The WEPL values were derived solely from the root-mean-square (RMS) of DRFs, while the intensity information in the DRFs was filtered out. In this work, we explored the use of such intensity information for potential improvement in WEPL accuracy and imaging quality. Three WEPL derivation methods based on, respectively, the RMS only, the intensity only, and the intensity-weighted RMS were tested and compared in terms of the quality of obtained radiograph images and the accuracy of WEPL values. A Gammex CT calibration phantom containing inserts made of various tissue substitute materials with independently measured relative stopping powers (RSP) was used to assess the imaging performances. Improved image quality with enhanced interfaces was achieved while preserving the accuracy by using intensity information in the calibration. Other objects, including an anthropomorphic head phantom, a proton therapy range compensator, a frozen lamb’s head and an ‘image quality phantom’ were also imaged. Both the RMS only and the intensity-weighted RMS methods derived RSPs within  ±  1% for most of the Gammex phantom inserts, with a mean absolute percentage error of 0.66% for all inserts. In the case of the insert with a titanium rod, the method based on RMS completely failed, whereas that based on the intensity-weighted RMS was qualitatively valid. The use of intensity greatly enhanced the interfaces between different materials in the obtained WEPL images, suggesting the potential for image guidance in areas such as patient positioning and tumor tracking by proton radiography.

Use of simulation-based education to reduce catheter-related bloodstream infections.

PubMed

Barsuk, Jeffrey H; Cohen, Elaine R; Feinglass, Joe; McGaghie, William C; Wayne, Diane B

2009-08-10

Simulation-based education improves procedural competence in central venous catheter (CVC) insertion. The effect of simulation-based education in CVC insertion on the incidence of catheter-related bloodstream infection (CRBSI) is unknown. The aim of this study was to determine if simulation-based training in CVC insertion reduces CRBSI. This was an observational education cohort study set in an adult intensive care unit (ICU) in an urban teaching hospital. Ninety-two internal medicine and emergency medicine residents completed a simulation-based mastery learning program in CVC insertion skills. Rates of CRBSI from CVCs inserted by residents in the ICU before and after the simulation-based educational intervention were compared over a 32-month period. There were fewer CRBSIs after the simulator-trained residents entered the intervention ICU (0.50 infections per 1000 catheter-days) compared with both the same unit prior to the intervention (3.20 per 1000 catheter-days) (P = .001) and with another ICU in the same hospital throughout the study period (5.03 per 1000 catheter-days) (P = .001). An educational intervention in CVC insertion significantly improved patient outcomes. Simulation-based education is a valuable adjunct in residency education.

Effect of single DNA lesions on in vitro replication with DNA polymerase III holoenzyme. Comparison with other polymerases.

PubMed

Belguise-Valladier, P; Maki, H; Sekiguchi, M; Fuchs, R P

1994-02-11

In the present work, we have studied in vitro replication of N-2-acetylaminofluorene (AAF) or cis-diamminedichloroplatinum II (cis-DDP) single modified DNA templates. We used the holoenzyme (pol III HE) or the alpha subunit of DNA polymerase III, which is involved in SOS mutagenesis, and other DNA polymerases in order to compare enzymes having different biological roles and properties. Single-stranded oligonucleotides (63-mer) bearing a single AAF adduct at one of the different guanine residues of the NarI sequence (-G1G2CG3CC-) have been used in primer extension assays. Site-specifically platinated 5'd(ApG) or 5'd(GpG) oligonucleotides were constructed and similarly used in primer extension assays. In all cases, irrespective of both the chemical nature of the lesion (i.e. AAF or cis-DDP) and its local sequence context (i.e. the 3 different sites for AAF adducts within the NarI site) replication by pol III HE and pol I Klenow fragment (pol I Kf) stops one base prior to the adduct site. Removal of the 3'-->5' proofreading activity alone was not sufficient to trigger bypass of DNA lesions. Indeed, when proofreading activity of pol I is inactivated by a point mutation (pol I Kf (exo-)), the major replication product corresponds to the position opposite the adduct site showing that incorporation across from the AAF adduct is possible. These results suggest that a polymerase with proofreading activity is actually found to stop one nucleotide before the adduct not because it is unable to insert a nucleotide opposite the adduct but most likely because elongation past the adduct is strongly impaired, giving thus an increased time frame for the proofreading exonuclease to remove the base inserted across from the adduct. These results are discussed in terms of their implications for error-free and error-prone bypass in vivo.

The Correlation between Insertion Depth of Prodisc-C Artificial Disc and Postoperative Kyphotic Deformity: Clinical Importance of Insertion Depth of Artificial Disc.

PubMed

Lee, Do-Youl; Kim, Se-Hoon; Suh, Jung-Keun; Cho, Tai-Hyoung; Chung, Yong-Gu

2012-09-01

This study was designed to investigate the correlation between insertion depth of artificial disc and postoperative kyphotic deformity after Prodisc-C total disc replacement surgery, and the range of artificial disc insertion depth which is effective in preventing postoperative whole cervical or segmental kyphotic deformity. A retrospective radiological analysis was performed in 50 patients who had undergone single level total disc replacement surgery. Records were reviewed to obtain demographic data. Preoperative and postoperative radiographs were assessed to determine C2-7 Cobb's angle and segmental angle and to investigate postoperative kyphotic deformity. A formula was introduced to calculate insertion depth of Prodisc-C artificial disc. Statistical analysis was performed to search the correlation between insertion depth of Prodisc-C artificial disc and postoperative kyphotic deformity, and to estimate insertion depth of Prodisc-C artificial disc to prevent postoperative kyphotic deformity. In this study no significant statistical correlation was observed between insertion depth of Prodisc-C artificial disc and postoperative kyphotic deformity regarding C2-7 Cobb's angle. Statistical correlation between insertion depth of Prodisc-C artificial disc and postoperative kyphotic deformity was observed regarding segmental angle (p<0.05). It failed to estimate proper insertion depth of Prodisc-C artificial disc effective in preventing postoperative kyphotic deformity. Postoperative segmental kyphotic deformity is associated with insertion depth of Prodisc-C artificial disc. Anterior located artificial disc leads to lordotic segmental angle and posterior located artificial disc leads to kyphotic segmental angle postoperatively. But C2-7 Cobb's angle is not affected by artificial disc location after the surgery.

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

Zhang, R; Jee, K; Sharp, G

Purpose: Proton radiography, which images the patients with the same type of particles that they are to be treated with, is a promising approach for image guidance and range uncertainties reduction. This study aimed to realize quality proton radiography by measuring dose rate functions (DRF) in time domain using a single flat panel and retrieve water equivalent path length (WEPL) from them. Methods: An amorphous silicon flat panel (PaxScan™ 4030CB, Varian Medical Systems, Inc., Palo Alto, CA) was placed behind phantoms to measure DRFs from a proton beam modulated by the modulator wheel. To retrieve WEPL and RSP, calibration modelsmore » based on the intensity of DRFs only, root mean square (RMS) of DRFs only and the intensity weighted RMS were tested. The quality of obtained WEPL images (in terms of spatial resolution and level of details) and the accuracy of WEPL were compared. Results: RSPs for most of the Gammex phantom inserts were retrieved within ± 1% errors by calibration models based on the RMS and intensity weighted RMS. The mean percentage error for all inserts was reduced from 1.08% to 0.75% by matching intensity in the calibration model. In specific cases such as the insert with a titanium rod, the calibration model based on RMS only fails while the that based on intensity weighted RMS is still valid. The quality of retrieved WEPL images were significantly improved for calibration models including intensity matching. Conclusion: For the first time, a flat panel, which is readily available in the beamline for image guidance, was tested to acquire quality proton radiography with WEPL accurately retrieved from it. This technique is promising to be applied for image-guided proton therapy as well as patient specific RSP determination to reduce uncertainties of beam ranges.« less

Correlation between model observers in uniform background and human observers in patient liver background for a low-contrast detection task in CT

NASA Astrophysics Data System (ADS)

Gong, Hao; Yu, Lifeng; Leng, Shuai; Dilger, Samantha; Zhou, Wei; Ren, Liqiang; McCollough, Cynthia H.

2018-03-01

Channelized Hotelling observer (CHO) has demonstrated strong correlation with human observer (HO) in both single-slice viewing mode and multi-slice viewing mode in low-contrast detection tasks with uniform background. However, it remains unknown if the simplest single-slice CHO in uniform background can be used to predict human observer performance in more realistic tasks that involve patient anatomical background and multi-slice viewing mode. In this study, we aim to investigate the correlation between CHO in a uniform water background and human observer performance at a multi-slice viewing mode on patient liver background for a low-contrast lesion detection task. The human observer study was performed on CT images from 7 abdominal CT exams. A noise insertion tool was employed to synthesize CT scans at two additional dose levels. A validated lesion insertion tool was used to numerically insert metastatic liver lesions of various sizes and contrasts into both phantom and patient images. We selected 12 conditions out of 72 possible experimental conditions to evaluate the correlation at various radiation doses, lesion sizes, lesion contrasts and reconstruction algorithms. CHO with both single and multi-slice viewing modes were strongly correlated with HO. The corresponding Pearson's correlation coefficient was 0.982 (with 95% confidence interval (CI) [0.936, 0.995]) and 0.989 (with 95% CI of [0.960, 0.997]) in multi-slice and single-slice viewing modes, respectively. Therefore, this study demonstrated the potential to use the simplest single-slice CHO to assess image quality for more realistic clinically relevant CT detection tasks.

Mandibular molar uprighting using mini-implants: different approaches for different clinical cases--two case reports.

PubMed

Derton, Nicola; Perini, Alessandro; Mutinelli, Sabrina; Gracco, Antonio

2012-01-01

To detail two different clinical protocols and case studies using mini-implant anchorage developed to respond to certain clinical conditions. Two clinical protocols are described to upright mesially tilted mandibular molars. In the first protocol, a single mini-implant is inserted distally to the molar to be uprighted, and an elastic traction chain is applied to the tooth. In the second clinical approach, two mini-implants are inserted mesially. A screw-suspended TMA sectional archwire is applied (Derton-Perini technique). Two cases, descriptive of the two different treatment protocols, are described. In the first case, the mandibular right second premolar was missing and the adjacent first molar needed to be uprighted. A single screw was inserted distally to the first molar, and an elastic chain was applied. In the second case, the mandibular left second molar was missing and the third molar needed to be uprighted. Two mini-implants were inserted mesially and a fully screw-supported sectional archwire was used to upright and bodily mesialize the third molar. Both uprighting approaches uprighted the molar axis without loss of anchorage. The two approaches to mandibular molar uprighting, developed as rational responses to different clinical cases, were both found to be effective.

Inserting pedicle screws in the upper thoracic spine without the use of fluoroscopy or image guidance. Is it safe?

PubMed

Schizas, Constantin; Theumann, Nicolas; Kosmopoulos, Victor

2007-05-01

Several studies have looked at accuracy of thoracic pedicle screw placement using fluoroscopy, image guidance, and anatomical landmarks. To our knowledge the upper thoracic spine (T1-T6) has not been specifically studied in the context of screw insertion and placement accuracy without the use of either image guidance or fluoroscopy. Our objective was to study the accuracy of upper thoracic screw placement without the use of fluoroscopy or image guidance, and report on implant related complications. A single surgeon inserted 60 screws in 13 consecutive non-scoliotic spine patients. These were the first 60 screws placed in the high thoracic spine in our institution. The most common diagnosis in our patient population was trauma. All screws were inserted using a modified Roy-Camille technique. Post-operative axial computed tomography (CT) images were obtained for each patient and analyzed by an independent senior radiologist for placement accuracy. Implant related complications were prospectively noted. No pedicle screw misplacement was found in 61.5% of the patients. In the remaining 38.5% of patients some misplacements were noted. Fifty-three screws out of the total 60 implanted were placed correctly within all the pedicle margins. The overall pedicle screw placement accuracy was 88.3% using our modified Roy-Camille technique. Five medial and two lateral violations were noted in the seven misplaced screws. One of the seven misplaced screws was considered to be questionable in terms of pedicle perforation. No implant related complications were noted. We found that inserting pedicle screws in the upper thoracic spine based solely on anatomical landmarks was safe with an accuracy comparable to that of published studies using image-guided navigation at the thoracic level.

Comparison of Insertional RNA Editing in Myxomycetes

PubMed Central

Chen, Cai; Frankhouser, David; Bundschuh, Ralf

2012-01-01

RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. PMID:22383871

Doping test results dependent on genotype of uridine diphospho-glucuronosyl transferase 2B17, the major enzyme for testosterone glucuronidation.

PubMed

Schulze, Jenny Jakobsson; Lundmark, Jonas; Garle, Mats; Skilving, Ilona; Ekström, Lena; Rane, Anders

2008-07-01

Testosterone abuse is conventionally assessed by the urinary testosterone/epitestosterone (T/E) ratio, levels above 4.0 being considered suspicious. The large variation in testosterone glucuronide (TG) excretion and its strong association with a deletion polymorphism in the uridine diphospho-glucuronosyl transferase (UGT) 2B17 gene challenge the accuracy of the T/E ratio test. Our objective was to investigate whether genotype-based cutoff values will improve the sensitivity and specificity of the test. This was an open three-armed comparative study. A total of 55 healthy male volunteers with either two, one, or no allele [insertion/insertion, insertion/deletion, or deletion/deletion (del/del)] of the UGT2B17 gene was included in the study. A single im dose of 500 mg testosterone enanthate was administered. Urinary excretion of TG after dose and the T/E ratio during 15 d were calculated. The degree and rate of increase in the TG excretion rate were highly dependent on the UGT2B17 genotype with a 20-fold higher average maximum increase in the insertion/insertion group compared with the del/del group. Of the del/del subjects, 40% never reached the T/E ratio of 4.0 on any of the 15 d after the dose. When differentiated cutoff levels for the del/del (1.0) and the other genotypes (6.0) were applied, the sensitivity increased substantially for the del/del group, and false positives in the other genotypes were eliminated. Consideration of the genetic variation in disposition of androgens will improve the sensitivity and specificity of the testosterone doping test. This is of interest not only for combating androgen doping in sports, but also for detecting and preventing androgen abuse in society.

Development and comparison of projection and image space 3D nodule insertion techniques

NASA Astrophysics Data System (ADS)

Robins, Marthony; Solomon, Justin; Sahbaee, Pooyan; Samei, Ehsan

2016-04-01

This study aimed to develop and compare two methods of inserting computerized virtual lesions into CT datasets. 24 physical (synthetic) nodules of three sizes and four morphologies were inserted into an anthropomorphic chest phantom (LUNGMAN, KYOTO KAGAKU). The phantom was scanned (Somatom Definition Flash, Siemens Healthcare) with and without nodules present, and images were reconstructed with filtered back projection and iterative reconstruction (SAFIRE) at 0.6 mm slice thickness using a standard thoracic CT protocol at multiple dose settings. Virtual 3D CAD models based on the physical nodules were virtually inserted (accounting for the system MTF) into the nodule-free CT data using two techniques. These techniques include projection-based and image-based insertion. Nodule volumes were estimated using a commercial segmentation tool (iNtuition, TeraRecon, Inc.). Differences were tested using paired t-tests and R2 goodness of fit between the virtually and physically inserted nodules. Both insertion techniques resulted in nodule volumes very similar to the real nodules (<3% difference) and in most cases the differences were not statistically significant. Also, R2 values were all <0.97 for both insertion techniques. These data imply that these techniques can confidently be used as a means of inserting virtual nodules in CT datasets. These techniques can be instrumental in building hybrid CT datasets composed of patient images with virtually inserted nodules.

Cryogenic expansion machine

DOEpatents

Pallaver, Carl B.; Morgan, Michael W.

1978-01-01

A cryogenic expansion engine includes intake and exhaust poppet valves each controlled by a cam having adjustable dwell, the valve seats for the valves being threaded inserts in the valve block. Each cam includes a cam base and a ring-shaped cam insert disposed at an exterior corner of the cam base, the cam base and cam insert being generally circular but including an enlarged cam dwell, the circumferential configuration of the cam base and cam dwell being identical, the cam insert being rotatable with respect to the cam base. GI CONTRACTUAL ORIGIN OF THE INVENTION The invention described herein was made in the course of, or under, a contract with the UNITED STATES ENERGY RESEARCH AND DEVELOPMENT ADMINISTRATION.

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

PubMed

Tajaddod, Mansoureh; Tanzer, Andrea; Licht, Konstantin; Wolfinger, Michael T; Badelt, Stefan; Huber, Florian; Pusch, Oliver; Schopoff, Sandy; Janisiw, Michael; Hofacker, Ivo; Jantsch, Michael F

2016-10-25

Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels. Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels. Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.

Indications, retrieval rate, and complications of inferior vena cava filters: Single-center experience in Saudi Arabia.

PubMed

Shabib, Abdullah Bin; Alsayed, Fahad; Aldughaythir, Saad; Habeeb, Hanan; Al Tamimi, Sumayyah; Masuadi, Emad; Alzahrani, Mohsen; Alaklabi, Ali; Alotaibi, Azzam; Rajendram, Rajkumar; Almegren, Mosaad

2018-01-01

Inferior vena cava (IVC) filter is indicated in patients with acute venous thromboembolism (VTE) in whom therapeutic anticoagulation is contraindicated. While prophylactic insertion of an IVC filter may be considered for patients at high risk of VTE, there are significant differences between clinical guidelines on the role of IVC filters. These discrepancies have arisen predominantly because of the paucity of data on the efficacy and safety of IVC filters. We, therefore, evaluated the indications for filter insertion, the rate of filter retrieval and complications in patients who received IVC filters at King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. A descriptive, retrospective review of electronic- and paper-based medical records was performed. Consecutive sampling was used to study all adult patients who received an IVC filter at KAMC between 2007 and 2016 and met the inclusion criteria. A total of 382 IVC filters were inserted. 113 patients (30%) had an acute VTE and a contraindication to anticoagulation while 53 patients (14%) received an IVC filter in the absence of VTE (i.e., prophylactic). Only 124 (32.5%) IVC filters were eventually retrieved. The most common reason for nonretrieval was the need for permanent filtration (155, 60%). Thrombotic complications developed in 72 (19%) patients; nine patients had fatal pulmonary embolism. The insertion of IVC filters in this cohort was associated with low retrieval rate and relatively high incidence of thrombotic complications. Follow-up of patients is required to detect IVC filter-related complications and to increase retrieval rate.

Method for producing labeled single-stranded nucleic acid probes

DOEpatents

Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

1999-10-19

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

Risk-based screening for Chlamydia trachomatis and Neisseria gonorrhoeae prior to intrauterine device insertion.

PubMed

Grentzer, Jaclyn M; Peipert, Jeffrey F; Zhao, Qiuhong; McNicholas, Colleen; Secura, Gina M; Madden, Tessa

2015-10-01

The objective was to compare three strategies for Chlamydia trachomatis and Neisseria gonorrhoeae screening prior to intrauterine device (IUD) insertion. This was a secondary analysis of the Contraceptive CHOICE Project. We measured the prevalence of C. trachomatis and/or N. gonorrhoeae at the time of IUD insertion. We then compared sensitivity, specificity, negative and positive predictive values, and likelihood ratios for three screening strategies for C. trachomatis and N. gonorrhoeae prior to IUD insertion: (a) "age-based" — age ≤25 years alone; (b) "age/partner-based" — age ≤25 and/or multiple sexual partners; and (c) "risk-based" — age ≤25, multiple sexual partners, inconsistent condom use and/or history of prior sexually transmitted infection (STI). Among 5087 IUD users, 140 (2.8%) tested positive for C. trachomatis, 16 (0.3%) tested positive for N. gonorrhoeae, and 6 (0.1%) were positive for both at the time of IUD insertion. The "risk-based" screening strategy had the highest sensitivity (99.3%) compared to "age-based" and "age/partner-based" screening (80.7% and 84.7%, respectively.) Only one (0.7%) woman with a chlamydia or gonorrhea infection would not have been screened using "risk-based" screening. A risk-based strategy to screen for C. trachomatis and N. gonorrhoeae prior to IUD insertion has higher sensitivity than screening based on age alone or age and multiple sexual partners. Using a risk-based screening strategy (age≤25, multiple sexual partners, inconsistent condom use and/or history of an STI) to determine who should be screened for C. trachomatis and N. gonorrhoeae prior to IUD insertion will miss very few cases of infection and obviates the need for universal screening. Copyright © 2015 Elsevier Inc. All rights reserved.

Low loss millimeter-wave switches based on the Vanadium Dioxide Metal - Insulator - Transition

NASA Astrophysics Data System (ADS)

Field, Mark; Hillman, Christopher; Stupar, Philip; Griffith, Zachary; Rodwell, Mark

2014-03-01

A new ultra-low-loss and broad band millimeter wave switch technology based on the reversible metal / insulator phase transition of vanadium dioxide has been developed. We report having fabricated series configured, single-pole single-throw (SPST) switches having measured S-parameters from DC to 110 GHz. The on-state insertion loss is 0.2 dB and off-state isolation is 21 dB at 50 GHz. The resulting impedance contrast ratio, ZOFF / ZON, is greater than 500:1 at 50 GHz (i.e. cut-off frequency fc ~ 40 THz). As a demonstration of the technology's utility, we also present the results of a 2-bit real time delay phase shifter incorporating a pair of VO2 SP4T switches. This switch technology's high impedance contrast ratio combined with its compactness, ease of integration, and low voltage operation make it an enabler of previously unachievable high-performance millimeter wave FPGAs.

Design Tools for Reconfigurable Hardware in Orbit (RHinO)

NASA Technical Reports Server (NTRS)

French, Mathew; Graham, Paul; Wirthlin, Michael; Larchev, Gregory; Bellows, Peter; Schott, Brian

2004-01-01

The Reconfigurable Hardware in Orbit (RHinO) project is focused on creating a set of design tools that facilitate and automate design techniques for reconfigurable computing in space, using SRAM-based field-programmable-gate-array (FPGA) technology. These tools leverage an established FPGA design environment and focus primarily on space effects mitigation and power optimization. The project is creating software to automatically test and evaluate the single-event-upsets (SEUs) sensitivities of an FPGA design and insert mitigation techniques. Extensions into the tool suite will also allow evolvable algorithm techniques to reconfigure around single-event-latchup (SEL) events. In the power domain, tools are being created for dynamic power visualiization and optimization. Thus, this technology seeks to enable the use of Reconfigurable Hardware in Orbit, via an integrated design tool-suite aiming to reduce risk, cost, and design time of multimission reconfigurable space processors using SRAM-based FPGAs.

Polycistronic lentiviral vector for "hit and run" reprogramming of adult skin fibroblasts to induced pluripotent stem cells.

PubMed

Chang, Chia-Wei; Lai, Yi-Shin; Pawlik, Kevin M; Liu, Kaimao; Sun, Chiao-Wang; Li, Chao; Schoeb, Trenton R; Townes, Tim M

2009-05-01

We report the derivation of induced pluripotent stem (iPS) cells from adult skin fibroblasts using a single, polycistronic lentiviral vector encoding the reprogramming factors Oct4, Sox2, and Klf4. Porcine teschovirus-1 2A sequences that trigger ribosome skipping were inserted between human cDNAs for these factors, and the polycistron was subcloned downstream of the elongation factor 1 alpha promoter in a self-inactivating (SIN) lentiviral vector containing a loxP site in the truncated 3' long terminal repeat (LTR). Adult skin fibroblasts from a humanized mouse model of sickle cell disease were transduced with this single lentiviral vector, and iPS cell colonies were picked within 30 days. These cells expressed endogenous Oct4, Sox2, Nanog, alkaline phosphatase, stage-specific embryonic antigen-1, and other markers of pluripotency. The iPS cells produced teratomas containing tissue derived from all three germ layers after injection into immunocompromised mice and formed high-level chimeras after injection into murine blastocysts. iPS cell lines with as few as three lentiviral insertions were obtained. Expression of Cre recombinase in these iPS cells resulted in deletion of the lentiviral vector, and sequencing of insertion sites demonstrated that remnant 291-bp SIN LTRs containing a single loxP site did not interrupt coding sequences, promoters, or known regulatory elements. These results suggest that a single, polycistronic "hit and run" vector can safely and effectively reprogram adult dermal fibroblasts into iPS cells.

Binding of insertion/deletion DNA mismatches by the heterodimer of yeast mismatch repair proteins MSH2 and MSH3.

PubMed

Habraken, Y; Sung, P; Prakash, L; Prakash, S

1996-09-01

DNA-mismatch repair removes mismatches from the newly replicated DNA strand. In humans, mutations in the mismatch repair genes hMSH2, hMLH1, hPMS1 and hPMS2 result in hereditary non-polyposis colorectal cancer (HNPCC) [1-8]. The hMSH2 (MSH for MutS homologue) protein forms a complex with a 160 kDa protein, and this heterodimer, hMutSalpha, has high affinity for a G/T mismatch [9,10]. Cell lines in which the 160 kDa subunit of hMutSalpha is mutated are specifically defective in the repair of base-base and single-nucleotide insertion/deletion mismatches [9,11]. Genetic studies in S. cerevisiae have suggested that MSH2 functions with either MSH3 or MSH6 in mismatch repair, and, in the absence of the latter two genes, MSH2 is inactive [12,13]. MSH6 encodes the yeast counterpart of the 160 kDa subunit of hMutSalpha [12,13]. As in humans, yeast MSH6 forms a complex with MSH2, and the MSH2-MSH6 heterodimer binds a G/T mismatch [14]. Here, we find that MSH2 and MSH3 form another stable heterodimer, and we purify this heterodimer to near homogeneity. We show that MSH2-MSH3 has low affinity for a G/T mismatch but binds to insertion/deletion mismatches with high specificity, unlike MSH2-MSH6.

The dynamics of long-term transgene expression in engrafted neural stem cells.

PubMed

Lee, Jean-Pyo; Tsai, David J; In Park, Kook; Harvey, Alan R; Snyder, Evan Y

2009-07-01

To assess the dynamics and confounding variables that influence transgene expression in neural stem cells (NSCs), we generated distinct NSC clones from the same pool of cells, carrying the same reporter gene transcribed from the same promoter, transduced by the same retroviral vector, and transplanted similarly at the same differentiation state, at the same time and location, into the brains of newborn mouse littermates, and monitored in parallel for over a year in vivo (without immunosuppression). Therefore, the sole variables were transgene chromosomal insertion site and copy number. We then adapted and optimized a technique that tests, at the single cell level, persistence of stem cell-mediated transgene expression in vivo based on correlating the presence of the transgene in a given NSC's nucleus (by fluorescence in situ hybridization [FISH]) with the frequency of that transgene's product within the same cell (by combined immunohistochemistry [IHC]). Under the above-stated conditions, insertion site is likely the most contributory variable dictating transgene downregulation in an NSC after 3 months in vivo. We also observed that this obstacle could be effectively and safely counteracted by simple serial infections (as few as three) inserting redundant copies of the transgene into the prospective donor NSC. (The preservation of normal growth control mechanisms and an absence of tumorigenic potential can be readily screened and ensured ex vivo prior to transplantation.) The combined FISH/IHC strategy employed here for monitoring the dynamics of transgene expression at the single cell level in vivo may be used for other types of therapeutic and housekeeping genes in endogenous and exogenous stem cells of many organs and lineages. Copyright 2009 Wiley-Liss, Inc.

Comparison of the analgesic effects of oral tramadol and naproxen sodium on pain relief during IUD insertion.

PubMed

Karabayirli, Safinaz; Ayrim, Aylin Aker; Muslu, Bunyamin

2012-01-01

To compare the analgesic efficacy of oral tramadol and naproxen sodium on pain during insertion of an intrauterine device (IUD). Randomized, double-blinded, clinical trial (Canadian Task Force classification I). University-affiliated hospital. Single-center. One hundred three patients scheduled for insertion of an IUD. Patients were randomly assigned to receive oral tramadol 50 mg capsules (n = 35) or naproxen sodium 550 mg tablets (n = 34) or placebo (n = 34) 1 hour before insertion of the IUD. After insertion of the IUD, pain intensity was evaluated using a visual analog scale (VAS, 0-10). Adverse effects, patient satisfaction with the medication, and preference for using it during future insertions were also recorded. The VAS scores were significantly different during IUD insertion among the 3 groups (p = .001). Pain scores in the tramadol group were significantly lower than in the naproxen group (p = .003), and the scores in the naproxen group was significantly lower than in the control group (p = .001). Patient satisfaction with the medication and preference for its future use were significantly lower in the control group than in the other 2 groups (p = .001). Prophylactic analgesia using 50 mg tramadol and 550 mg naproxen, delivered orally, can be used to relieve pain during IUD insertion. However, tramadol capsules were found to be more effective than naproxen tablets. Copyright © 2012 AAGL. Published by Elsevier Inc. All rights reserved.

Linear motion device and method for inserting and withdrawing control rods

DOEpatents

Smith, J.E.

Disclosed is a linear motion device and more specifically a control rod drive mechanism (CRDM) for inserting and withdrawing control rods into a reactor core. The CRDM and method disclosed is capable of independently and sequentially positioning two sets of control rods with a single motor stator and rotor. The CRDM disclosed can control more than one control rod lead screw without incurring a substantial increase in the size of the mechanism.

Evolution-based Virtual Content Insertion with Visually Virtual Interactions in Videos

NASA Astrophysics Data System (ADS)

Chang, Chia-Hu; Wu, Ja-Ling

With the development of content-based multimedia analysis, virtual content insertion has been widely used and studied for video enrichment and multimedia advertising. However, how to automatically insert a user-selected virtual content into personal videos in a less-intrusive manner, with an attractive representation, is a challenging problem. In this chapter, we present an evolution-based virtual content insertion system which can insert virtual contents into videos with evolved animations according to predefined behaviors emulating the characteristics of evolutionary biology. The videos are considered not only as carriers of message conveyed by the virtual content but also as the environment in which the lifelike virtual contents live. Thus, the inserted virtual content will be affected by the videos to trigger a series of artificial evolutions and evolve its appearances and behaviors while interacting with video contents. By inserting virtual contents into videos through the system, users can easily create entertaining storylines and turn their personal videos into visually appealing ones. In addition, it would bring a new opportunity to increase the advertising revenue for video assets of the media industry and online video-sharing websites.

Tibial tunnel aperture location during single-bundle posterior cruciate ligament reconstruction: comparison of tibial guide positions.

PubMed

Shin, Young-Soo; Han, Seung-Beom; Hwang, Yeok-Ku; Suh, Dong-Won; Lee, Dae-Hee

2015-05-01

We aimed to compare posterior cruciate ligament (PCL) tibial tunnel location after tibial guide insertion medial (between the PCL remnant and the medial femoral condyle) and lateral (between the PCL remnant and the anterior cruciate ligament) to the PCL stump as determined by in vivo 3-dimensional computed tomography (3D-CT). Tibial tunnel aperture location was analyzed by immediate postoperative in vivo CT in 66 patients who underwent single-bundle PCL reconstruction, 31 by over-the-PCL and 35 by under-the-PCL tibial guide insertion techniques. Tibial tunnel positions were measured in the medial to lateral and proximal to distal directions of the posterior proximal tibia. The center of the tibial tunnel aperture was located more laterally (by 2.7 mm) in the over-the-PCL group than in the under-the-PCL group (P = .040) and by a relative percentage (absolute value/tibial width) of 3.2% (P = .031). Tibial tunnel positions in the proximal to distal direction, determined by absolute value and relative percentage, were similar in the 2 groups. Tibial tunnel apertures were located more laterally after lateral-to-the-PCL tibial guide insertion than after medial-to-the-PCL tibial guide insertion. There was, however, no significant difference between these techniques in distance from the joint line to the tibial tunnel aperture. Insertion lateral to the PCL stump may result in better placement of the PCL in its anatomic footprint. Level III, retrospective comparative study. Copyright © 2015 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Method for introducing unidirectional nested deletions

DOEpatents

Dunn, J.J.; Quesada, M.A.; Randesi, M.

1999-07-27

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

Method for introducing unidirectional nested deletions

DOEpatents

Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

1999-07-27

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

Improved PMMA single-piece haptic materials

NASA Astrophysics Data System (ADS)

Healy, Donald D.; Wilcox, Christopher D.

1991-12-01

During the past fifteen years, Intraocular lens (IOL) haptic preferences have shifted from a variety of multi-piece haptic materials to single-piece PMMA. This is due in part to the research of David Apple, M.D., and other who have suggested that All-PMMA implants result in reduced cell flare and better centration. Consequently, single-piece IOLs now represent 45% of all IOL implants. However, many surgeons regard single-piece IOL designs as nonflexible and more difficult to implant than multipiece IOLs. These handling characteristics have slowed the shift from multi-piece to single-piece IOLs. As a result of these handling characteristics, single-piece lenses experience relatively high breakage rates because of handling before insertion and during insertion. To improve these characteristics, manufacturers have refined single-piece IOL haptic designs by pushing the limits of PMMA's physical properties. Furthermore, IOL manufacturers have begun to alter the material itself to change its physical properties. In particular, two new PMMA materials have emerged in the marketplace: Flexeon trademark, a crosslinked polymer and CM trademark, a material with molecularly realigned PMMA. This paper examines three specific measurements of a haptic's strength and flexibility: tensile strength, plastic memory and material plasticity/elasticity. The paper compares with Flexeon trademark and CM trademark lenses to noncrosslinked one-piece lenses and standard polypropylene multi-piece lenses.

Correlating Polymer Crystals via Self-Induced Nucleation

NASA Astrophysics Data System (ADS)

Reiter, Günter

Crystallizable polymers often form multiple stacks of uniquely oriented lamellae, which have good registry despite being separated by amorphous fold surfaces. These correlations require multiple synchronized, yet unidentified, nucleation events. Here, we demonstrate that in thin films of isotactic polystyrene, the probability of generating correlated lamellae is controlled by the branched morphology of a single primary lamella. The nucleation density ns of secondary lamellae is found to be dependent on the width of the branches of the primary lamella. This relation is independent of molecular weight, crystallization temperature, and film thickness. We propose a nucleation mechanism based on the insertion of polymers into a branched primary lamellar crystal. Even in single crystals, characterized by faceted structures with a well-defined envelope reflecting the underlying crystal unit cell, polymers are folded and thus in a meta-stable state. Annealing such meta-stable single crystals allowed to unveil the initial morphological framework of a dendritic single crystal, i.e. the initial stages of growth.

Does Navigation Improve Accuracy of Placement of Pedicle Screws in Single-level Lumbar Degenerative Spondylolisthesis?: A Comparison Between Free-hand and Three-dimensional O-Arm Navigation Techniques.

PubMed

Boon Tow, Benjamin Phak; Yue, Wai Mun; Srivastava, Abhishek; Lai, Jenn Ming; Guo, Chang Ming; Wearn Peng, Benedict Chan; Chen, John L T; Yew, Andy K S; Seng, Chusheng; Tan, Seang Beng

2015-10-01

This was a prospective, nonrandomized study. To assess the accuracy of O-arm navigation-based pedicle screw insertion in lumbar degenerative spondylolisthesis and to compare it with free-hand pedicle screw insertion technique in matched population. O-arm navigation is latest in navigation technology that can provide real-time intraoperative images in 3 dimensions while placing the pedicle screws to improve intraoperative pedicle screw accuracy. Degenerative lumbar spondylolisthesis is a locally unstable pathology and placement of pedicle screws can cause increased rotation and translation of the vertebral body. However, is this motion detected by the tracker placed across the unstable segment, is a matter of debate. Inability to detect these positional changes can lead to pedicle perforation while inserting screws using navigation. No study has evaluated the role of O-arm navigation in this patient population. The study population was divided into 2 groups with 19 patients each, one comprising patients who underwent O-arm navigation-based pedicle screw insertion (group 1) and the other comprising patients who underwent free-hand pedicle screw insertion technique (group 2). A total of 152 pedicle screws were implanted in 38 patients for 1-level instrumented fusion for degenerative lumbar spondylolisthesis. Intraoperative 3-dimensional computed tomography scans using the O-arm were obtained for all patients after insertion of pedicle screws. The images were reviewed intraoperatively and postoperatively for the analysis of pedicle breaches. Assessments in either of the group included (i) accuracy of placement of screws; (ii) the rate and direction of perforation; and (iii) the number of segments the perforated screw was away from the navigation tracker. Mean age of patients in group 1 (O-arm navigation-assisted) was 60 years (SD 11.25; range, 37-73 y), whereas in group 2 (free-hand pedicle screw) was 62 years (SD 18.07; range, 36-90 y). Overall anatomic perforation rate was 12.5% (19/152). Individually, group 1 had 14.47% (11/76) of perforations in comparison with 10.53% (8/76) observed in group 2. The difference was not statistically significant. The lateral margin was the most common site of perforation in both group 1 (64%, 7/11) and group 2 (62.5%, 5/8). Functional perforation rate for the series was 3.3% (5/152), with group 1 having 2.63% (2/76) and group 2 having 3.95% (3/76). The rate of perforation (PR) was significantly higher statistically when the tracker was placed 3 or more [PR 37.5% (6/16)] spinal segments away from instrumented segment compared with when it was placed 1 (0%) or 2 [PR 13.89% (5/36)] spinal segments away. Overall, 11 screws (11/152, 7.24%) had grade 2 perforations and had to be revised. No neurological complications were observed in the series. O-arm navigation does not provide any significant advantage over conventional free-hand pedicle screw insertion technique in patients with single-level degenerative spondylolisthesis. The accuracy is dependent on the distance of the tracker from the level of instrumentation. Lateral perforations are more common because of instability at the instrumented level leading to translation and rotation of the vertebral body while placing pedicle screws leading to preferential lateral trajectory. These lateral perforations could not be prevented by using navigation. However, no significant complications were noted in either technique.

Papaya (Carica papaya L.).

PubMed

Zhu, Yun J; Fitch, Maureen M M; Moore, Paul H

2006-01-01

Transgenic papaya plants were initially obtained using particle bombardment, a method having poor efficiency in producing intact, single-copy insertion of transgenes. Single-copy gene insertion was improved using Agrobacterium tumefaciens. With progress being made in genome sequencing and gene discovery, there is a need for more efficient methods of transformation in order to study the function of these genes. We describe a protocol for Agrobacterium-mediated transformation using carborundum-wounded papaya embryogenic calli. This method should lead to high-throughput transformation, which on average produced at least one plant that was positive in polymerase chain reaction (PCR), histochemical staining, or by Southern blot hybridization from 10 to 20% of the callus clusters that had been co-cultivated with Agrobacterium. Plants regenerated from the callus clusters in 9 to 13 mo.

Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase η.

PubMed

Patra, Amitraj; Zhang, Qianqian; Guengerich, F Peter; Egli, Martin

2016-11-11

O 6 -Methyl-2'-deoxyguanosine (O 6 -MeG) is a ubiquitous DNA lesion, formed not only by xenobiotic carcinogens but also by the endogenous methylating agent S-adenosylmethionine. It can introduce mutations during DNA replication, with different DNA polymerases displaying different ratios of correct or incorrect incorporation opposite this nucleoside. Of the "translesion" Y-family human DNA polymerases (hpols), hpol η is most efficient in incorporating equal numbers of correct and incorrect C and T bases. However, the mechanistic basis for this specific yet indiscriminate activity is not known. To explore this question, we report biochemical and structural analysis of the catalytic core of hpol η. Activity assays showed the truncated form displayed similar misincorporation properties as the full-length enzyme, incorporating C and T equally and extending from both. X-ray crystal structures of both dC and dT paired with O 6 -MeG were solved in both insertion and extension modes. The structures revealed a Watson-Crick-like pairing between O 6 -MeG and 2"-deoxythymidine-5"-[(α, β)-imido]triphosphate (approximating dT) at both the insertion and extension stages with formation of two H-bonds. Conversely, both the structures with O 6 - MeG opposite dCTP and dC display sheared configuration of base pairs but to different degrees, with formation of two bifurcated H-bonds and two single H-bonds in the structures trapped in the insertion and extension states, respectively. The structural data are consistent with the observed tendency of hpol η to insert both dC and dT opposite the O 6 -MeG lesion with similar efficiencies. Comparison of the hpol η active site configurations with either O 6 -MeG:dC or O 6 -MeG:dT bound compared with the corresponding situations in structures of complexes of Sulfolobus solfataricus Dpo4, a bypass pol that favors C relative to T by a factor of ∼4, helps rationalize the more error-prone synthesis opposite the lesion by hpol η. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2′-deoxyguanosine by Human DNA Polymerase η*

PubMed Central

Patra, Amitraj; Zhang, Qianqian; Guengerich, F. Peter; Egli, Martin

2016-01-01

O6-Methyl-2′-deoxyguanosine (O6-MeG) is a ubiquitous DNA lesion, formed not only by xenobiotic carcinogens but also by the endogenous methylating agent S-adenosylmethionine. It can introduce mutations during DNA replication, with different DNA polymerases displaying different ratios of correct or incorrect incorporation opposite this nucleoside. Of the “translesion” Y-family human DNA polymerases (hpols), hpol η is most efficient in incorporating equal numbers of correct and incorrect C and T bases. However, the mechanistic basis for this specific yet indiscriminate activity is not known. To explore this question, we report biochemical and structural analysis of the catalytic core of hpol η. Activity assays showed the truncated form displayed similar misincorporation properties as the full-length enzyme, incorporating C and T equally and extending from both. X-ray crystal structures of both dC and dT paired with O6-MeG were solved in both insertion and extension modes. The structures revealed a Watson-Crick-like pairing between O6-MeG and 2"-deoxythymidine-5"-[(α, β)-imido]triphosphate (approximating dT) at both the insertion and extension stages with formation of two H-bonds. Conversely, both the structures with O6- MeG opposite dCTP and dC display sheared configuration of base pairs but to different degrees, with formation of two bifurcated H-bonds and two single H-bonds in the structures trapped in the insertion and extension states, respectively. The structural data are consistent with the observed tendency of hpol η to insert both dC and dT opposite the O6-MeG lesion with similar efficiencies. Comparison of the hpol η active site configurations with either O6-MeG:dC or O6-MeG:dT bound compared with the corresponding situations in structures of complexes of Sulfolobus solfataricus Dpo4, a bypass pol that favors C relative to T by a factor of ∼4, helps rationalize the more error-prone synthesis opposite the lesion by hpol η. PMID:27694439

FIBER AND INTEGRATED OPTICS: Matching of fiber and strip optical waveguides by graded-index optical matching components

NASA Astrophysics Data System (ADS)

Shmal'ko, A. V.; Gordova, M. R.; Lamekin, V. F.; Nikolaev, I. V.; Sakharov, V. V.; Smirnov, V. L.; Polyantsev, A. S.

1990-01-01

A method for selection and calculation of the parameters of axisymmetric and anamorphic graded-index lenses for optical matching devices is developed and tested. These devices are intended for detachable connectors joining single-mode fibers to strip optical waveguides and are characterized by a greater tolerance to a mismatch between these waveguides. An experimental study is reported of a prototype of an optical matching device based on graded-index lenses characterized by insertion losses from 1-3 dB.

Spinal anaesthesia for caesarean section: comparison of 22-gauge and 25-gauge Whitacre needles with 26-gauge Quincke needles.

PubMed

Shutt, L E; Valentine, S J; Wee, M Y; Page, R J; Prosser, A; Thomas, T A

1992-12-01

We have studied 150 women undergoing elective Caesarean section under spinal anaesthesia. They were allocated randomly to have a 22-gauge Whitacre, a 25-gauge Whitacre or a 26-gauge Quincke needle inserted into the lumbar subarachnoid space. The groups were compared for ease of insertion, number of attempted needle insertions before identification of cerebrospinal fluid, quality of subsequent analgesia and incidence of postoperative complications. There were differences between groups, but they did not reach statistical significance. Postdural puncture headache (PDPH) was experienced by one mother in the 22-gauge Whitacre group, none in the 25-gauge Whitacre group and five in the 26-gauge Quincke group. Five of the six PDPH occurred after a single successful needle insertion. Seven of the 15 mothers in whom more than two needle insertions were made experienced backache, compared with 12 of the 129 receiving two or less (P < 0.001). We conclude that the use of 22- and 25-gauge Whitacre needles in elective Caesarean section patients is associated with a low incidence of PDPH and that postoperative backache is more likely when more than two attempts are made to insert a spinal needle.

Single-Incision Laparoscopic Anterior Resection Using a Curved Stapler.

PubMed

Watanabe, Jun; Ota, Mitsuyoshi; Suwa, Yusuke; Ishibe, Atsushi; Masui, Hidenobu; Nagahori, Kaoru

2016-11-01

Single-incision laparoscopic colectomy is technically limited because of such factors as instrument crowding, in-line viewing, and insufficient countertraction. In particular, it is technically difficult to cut the distal rectum from the umbilicus using an articulating linear stapler in single-incision laparoscopic anterior resection. After treating the mesorectum, the 5-mm trocar is replaced with a 12-mm trocar. The cartridge of the curved stapler is mounted while the shaft of the stapler is inserted into the 12-mm port extracorporeally. The curved stapler is inserted through the umbilical incision with the cartridge. A multichannel port is then mounted, and the abdominal cavity is reinsufflated. The curved stapler can then be operated intracorporeally. This procedure facilitates the vertical dissection of the rectum from the umbilicus. A total of 27 consecutive patients were analyzed in this study. All the procedures were safely performed without any complications. The median distance from the peritoneal reflection to the transection point of the distal bowel in single-incision laparoscopic anterior resection was 5.0 cm (range, -2.0 to 15.0). One stapler firing was required to achieve distal bowel division in 26 patients (96.3 %), whereas 2 firings were required in 1 patient (3.7 %). The median distal margin was 7.0 cm (range, 3.0-13.0). The time from the insertion of the stapler to transection was 180 seconds (range, 100-420). There were no cases of anastomotic leakage. In single-incision laparoscopic anterior resection, it is feasible to perform rectal transection from the umbilicus by using a curved stapler. This technique may allow for the omission of 1 trocar from the operation.

Method for introducing unidirectional nested deletions

DOEpatents

Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

2001-01-01

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment in the context of a cloning vector which contains an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment. Also disclosed is a method for producing single-stranded DNA probes utilizing the same cloning vector. An optimal vector, PZIP is described. Methods for introducing unidirectional deletions into a terminal location of a cloned DNA sequence which is inserted into the vector of the present invention are also disclosed. These methods are useful for introducing deletions into either or both ends of a cloned DNA insert, for high throughput sequencing of any DNA of interest.

Triple helix purification and sequencing

DOEpatents

Wang, Renfeng; Smith, Lloyd M.; Tong, Xinchun E.

1995-01-01

Disclosed herein are methods, kits, and equipment for purifying single stranded circular DNA and then using the DNA for DNA sequencing purposes. Templates are provided with an insert having a hybridization region. An elongated oligonucleotide has two regions that are complementary to the insert and the oligo is bound to a magnetic anchor. The oligo hybridizes to the insert on two sides to form a stable triple helix complex. The anchor can then be used to drag the template out of solution using a magnet. The system can purify sequencing templates, and if desired the triple helix complex can be opened up to a double helix so that the oligonucleotide will act as a primer for further DNA synthesis.

Triple helix purification and sequencing

DOEpatents

Wang, R.; Smith, L.M.; Tong, X.E.

1995-03-28

Disclosed herein are methods, kits, and equipment for purifying single stranded circular DNA and then using the DNA for DNA sequencing purposes. Templates are provided with an insert having a hybridization region. An elongated oligonucleotide has two regions that are complementary to the insert and the oligo is bound to a magnetic anchor. The oligo hybridizes to the insert on two sides to form a stable triple helix complex. The anchor can then be used to drag the template out of solution using a magnet. The system can purify sequencing templates, and if desired the triple helix complex can be opened up to a double helix so that the oligonucleotide will act as a primer for further DNA synthesis. 4 figures.

Improvement of the insertion axis for cochlear implantation with a robot-based system.

PubMed

Torres, Renato; Kazmitcheff, Guillaume; De Seta, Daniele; Ferrary, Evelyne; Sterkers, Olivier; Nguyen, Yann

2017-02-01

It has previously reported that alignment of the insertion axis along the basal turn of the cochlea was depending on surgeon' experience. In this experimental study, we assessed technological assistances, such as navigation or a robot-based system, to improve the insertion axis during cochlear implantation. A preoperative cone beam CT and a mastoidectomy with a posterior tympanotomy were performed on four temporal bones. The optimal insertion axis was defined as the closest axis to the scala tympani centerline avoiding the facial nerve. A neuronavigation system, a robot assistance prototype, and software allowing a semi-automated alignment of the robot were used to align an insertion tool with an optimal insertion axis. Four procedures were performed and repeated three times in each temporal bone: manual, manual navigation-assisted, robot-based navigation-assisted, and robot-based semi-automated. The angle between the optimal and the insertion tool axis was measured in the four procedures. The error was 8.3° ± 2.82° for the manual procedure (n = 24), 8.6° ± 2.83° for the manual navigation-assisted procedure (n = 24), 5.4° ± 3.91° for the robot-based navigation-assisted procedure (n = 24), and 3.4° ± 1.56° for the robot-based semi-automated procedure (n = 12). A higher accuracy was observed with the semi-automated robot-based technique than manual and manual navigation-assisted (p < 0.01). Combination of a navigation system and a manual insertion does not improve the alignment accuracy due to the lack of friendly user interface. On the contrary, a semi-automated robot-based system reduces both the error and the variability of the alignment with a defined optimal axis.

Canonical translation-modulating OFF-riboswitches with a single aptamer binding to a small molecule that function in a higher eukaryotic cell-free expression system.

PubMed

Ogawa, Atsushi; Murashige, Yuta; Takahashi, Hajime

2018-06-19

We have found that OFF-riboswitches that ligand-dependently downregulate the canonical translation in a higher eukaryotic expression system (wheat germ extract) can be easily created by inserting a single aptamer into the 5' untranslated region (UTR) of mRNA, even if its ligand is as small as theophylline. The key is the position of the inserted aptamer: the 5' end (+0 position) is much better than other positions for inhibiting canonical translation with the aptamer-ligand complex. The data showed that ribosome loading is suppressed by a rigid structure in the 5' end, and this suppression is dependent on the structure's stability but not on its size. Although this preference of aptamer insertion point contradicts the results in a lower eukaryote, it accords with the fact that the 5'-end structural hindrance is more effective for blocking the ribosome in higher eukaryotes. Therefore, the present type of OFF-riboswitch would function in various higher eukaryotic expression systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Experimental MRI-SPECT insert system with Hybrid Semiconductor detectors Timepix for MR animal scanner Bruker 47/20

NASA Astrophysics Data System (ADS)

Zajicek, J.; Burian, M.; Soukup, P.; Novak, V.; Macko, M.; Jakubek, J.

2017-01-01

Multimodal medical imaging based on Magnetic Resonance is mainly combinated with one of the scintigraphic method like PET or SPECT. These methods provide functional information whereas magnetic resonance imaging provides high spatial resolution of anatomical information or complementary functional information. Fusion of imaging modalities allows researchers to obtain complimentary information in a single measurement. The combination of MRI with SPECT is still relatively new and challenging in many ways. The main complication of using SPECT in MRI systems is the presence of a high magnetic field therefore (ferro)magnetic materials have to be eliminated. Furthermore the application of radiofrequency fields within the MR gantry does not allow for the use of conductive structures such as the common heavy metal collimators. This work presents design and construction of an experimental MRI-SPECT insert system and its initial tests. This unique insert system consists of an MR-compatible SPECT setup with CdTe pixelated sensors Timepix tungsten collimators and a radiofrequency coil. Measurements were performed on a gelatine and tissue phantom with an embedded radioisotopic source (57Co 122 keV γ ray) inside the RF coil by the Bruker BioSpec 47/20 (4.7 T) MR animal scanner. The project was performed in the framework of the Medipix Collaboration.

Random mutagenesis of the hyperthermophilic archaeon Pyrococcus furiosus using in vitro mariner transposition and natural transformation.

PubMed

Guschinskaya, Natalia; Brunel, Romain; Tourte, Maxime; Lipscomb, Gina L; Adams, Michael W W; Oger, Philippe; Charpentier, Xavier

2016-11-08

Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P. furiosus COM1 strain and of in vitro Mariner-based transposition. A transposon bearing a genetic marker is randomly transposed in vitro in genomic DNA that is then used for natural transformation of P. furiosus. A small-scale transposition reaction routinely generates several hundred and up to two thousands transformants. Southern analysis and sequencing showed that the obtained mutants contain a single and random genomic insertion. Polyploidy has been reported in Thermococcales and P. furiosus is suspected of being polyploid. Yet, about half of the mutants obtained on the first selection are homozygous for the transposon insertion. Two rounds of isolation on selective medium were sufficient to obtain gene conversion in initially heterozygous mutants. This transposition mutagenesis strategy will greatly facilitate functional exploration of the Thermococcales genomes.

A Diffusion-Based and Dynamic 3D-Printed Device That Enables Parallel in Vitro Pharmacokinetic Profiling of Molecules

PubMed Central

Lockwood, Sarah Y.; Meisel, Jayda E.; Monsma, Frederick J.; Spence, Dana M.

2016-01-01

The process of bringing a drug to market involves many steps, including the preclinical stage, where various properties of the drug candidate molecule are determined. These properties, which include drug absorption, distribution, metabolism, and excretion, are often displayed in a pharmacokinetic (PK) profile. While PK profiles are determined in animal models, in vitro systems that model in vivo processes are available, although each possesses shortcomings. Here, we present a 3D-printed, diffusion-based, and dynamic in vitro PK device. The device contains six flow channels, each with integrated porous membrane-based insert wells. The pores of these membranes enable drugs to freely diffuse back and forth between the flow channels and the inserts, thus enabling both loading and clearance portions of a standard PK curve to be generated. The device is designed to work with 96-well plate technology and consumes single-digit milliliter volumes to generate multiple PK profiles, simultaneously. Generation of PK profiles by use of the device was initially performed with fluorescein as a test molecule. Effects of such parameters as flow rate, loading time, volume in the insert well, and initial concentration of the test molecule were investigated. A prediction model was generated from this data, enabling the user to predict the concentration of the test molecule at any point along the PK profile within a coefficient of variation of ~5%. Depletion of the analyte from the well was characterized and was determined to follow first-order rate kinetics, indicated by statistically equivalent (p > 0.05) depletion half-lives that were independent of the starting concentration. A PK curve for an approved antibiotic, levofloxacin, was generated to show utility beyond the fluorescein test molecule. PMID:26727249

Switchable multi-wavelength fiber laser based on modal interference

NASA Astrophysics Data System (ADS)

Ma, Lin; Jiang, Sun; Qi, Yan-Hui; Kang, Ze-Xin; Jian, Shui-Sheng

2015-08-01

A comb fiber filter based on modal interference is proposed and demonstrated in this paper. Here two cascaded up-tapers are used to excite the cladding mode, and a core-offset jointing point is used to act as an interference component. Experimental results show that this kind of structure possesses a comb filter property in a range of the C-band. The measured extinction ratio is better than 12 dB with an insertion loss of about 11 dB. A switchable multi-wavelength erbium-doped fiber laser based on this novel comb filter is demonstrated. By adjusting the polarization controller, the output laser can be switched among single-, dual-, and three-wavelengths with a side mode suppression ratio of better than 45 dB.

Rectal suppository: commonsense and mode of insertion.

PubMed

Abd-el-Maeboud, K H; el-Naggar, T; el-Hawi, E M; Mahmoud, S A; Abd-el-Hay, S

1991-09-28

Rectal suppository is a well-known form of medication and its use is increasing. The commonest shape is one with an apex (pointed end) tapering to a base (blunt end). Because of a general lack of information about mode of insertion, we asked 360 lay subjects (Egyptians and non-Egyptians) and 260 medical personnel (physicians, pharmacists, and nurses) by questionnaire which end they inserted foremost. Apart from 2 individuals, all subjects suggested insertion with the apex foremost. Commonsense was the most frequent basis for this practice (86.9% of lay subjects and 84.6% of medical personnel) followed by information from a relative, a friend, or medical personnel, or from study at medical school. Suppository insertion with the base or apex foremost was compared in 100 subjects (60 adults, 40 infants and children). Retention with the former method was more easily achieved in 98% of the cases, with no need to introduce a finger in the anal canal (1% vs 83%), and lower expulsion rate (0% vs 3%). The designer of the "torpedo-shaped" suppository suggested its insertion with apex foremost. Our data suggest that a suppository is better inserted with the base foremost. Reversed vermicular contractions or pressure gradient of the anal canal might press it inwards.

L1-Associated Genomic Regions are Deleted in Somatic Cells of the Healthy Human Brain

PubMed Central

Erwin, Jennifer A.; Paquola, Apuã C.M.; Singer, Tatjana; Gallina, Iryna; Novotny, Mark; Quayle, Carolina; Bedrosian, Tracy; Ivanio, Francisco; Butcher, Cheyenne R.; Herdy, Joseph R.; Sarkar, Anindita; Lasken, Roger S.; Muotri, Alysson R.; Gage, Fred H.

2016-01-01

The healthy human brain is a mosaic of varied genomes. L1 retrotransposition is known to create mosaicism by inserting L1 sequences into new locations of somatic cell genomes. Using a machine learning-based, single-cell sequencing approach, we discovered that Somatic L1-Associated Variants (SLAVs) are actually composed of two classes: L1 retrotransposition insertions and retrotransposition-independent L1-associated variants. We demonstrate that a subset of SLAVs are, in fact, somatic deletions generated by L1 endonuclease cutting activity. Retrotransposition- independent rearrangements within inherited L1s resulted in the deletion of proximal genomic regions. These rearrangements were resolved by microhomology-mediated repair, which suggests that L1-associated genomic regions are hotspots for somatic copy number variants in the brain and therefore a heritable genetic contributor to somatic mosaicism. We demonstrate that SLAVs are present in crucial neural genes, such as DLG2/PSD93, and affect between 44–63% of cells of the cells in the healthy brain. PMID:27618310

Outcomes of single- vs double-cuff artificial urinary sphincter insertion in low- and high-risk profile male patients with severe stress urinary incontinence.

PubMed

Ahyai, Sascha A; Ludwig, Tim A; Dahlem, Roland; Soave, Armin; Rosenbaum, Clemens; Chun, Felix K-H; Fisch, Margit; Schmid, Marianne; Kluth, Luis A

2016-10-01

To evaluate continence and complication rates of bulbar single-cuff (SC) and distal bulbar double-cuff (DC) insertion in male patients with severe stress urinary incontinence (SUI) according to whether the men were considered low or high risk for unfavourable artificial urinary sphincter (AUS) outcomes. In all, 180 male patients who underwent AUS implantation between 2009 and 2013 were followed according to institutional standards. Patients with previous pelvic radiation therapy, open bulbar urethral or UI surgery ('high risk') underwent distal bulbar DC (123 patients) insertion, all others ('low risk') had proximal bulbar SC (57) insertion. Primary and secondary endpoints consisted of continence and complication rates. Kaplan-Meier analysis determined explantation-free survival, and Cox regression models assessed risk factors for persistent UI and explantation. The median follow-up was 24 months. Whereas there was no significant difference in pad usage/objective continence after SC vs DC insertion, superior rates of subjective/social continence and less persistent UI were reported by the patients with DC devices (all P ≤ 0.02). Overall, device explantation (erosion, infection or mechanical failure) occurred in 12.8% of patients. While early (<6 weeks) complication rates compared with SC patients were similar (P > 0.05), DC patients had a 5.7-fold higher risk of device explantation during late follow-up (P = 0.02) and significantly shorter explantation-free survival (log-rank, P = 0.003). Distal bulbar DC insertion in patients with a 'high-risk' profile (previous pelvic radiation, urethral surgery) leads to similar objective continence, but higher explantation rates when compared with patients considered 'low risk' with proximal bulbar SCs. Randomised controlled trials comparing both devices will be needed to determine whether the higher explanations rates are attributable to the DC device or to underlying risk factors. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

Genetic recombination pathways and their application for genome modification of human embryonic stem cells.

PubMed

Nieminen, Mikko; Tuuri, Timo; Savilahti, Harri

2010-10-01

Human embryonic stem cells are pluripotent cells derived from early human embryo and retain a potential to differentiate into all adult cell types. They provide vast opportunities in cell replacement therapies and are expected to become significant tools in drug discovery as well as in the studies of cellular and developmental functions of human genes. The progress in applying different types of DNA recombination reactions for genome modification in a variety of eukaryotic cell types has provided means to utilize recombination-based strategies also in human embryonic stem cells. Homologous recombination-based methods, particularly those utilizing extended homologous regions and those employing zinc finger nucleases to boost genomic integration, have shown their usefulness in efficient genome modification. Site-specific recombination systems are potent genome modifiers, and they can be used to integrate DNA into loci that contain an appropriate recombination signal sequence, either naturally occurring or suitably pre-engineered. Non-homologous recombination can be used to generate random integrations in genomes relatively effortlessly, albeit with a moderate efficiency and precision. DNA transposition-based strategies offer substantially more efficient random strategies and provide means to generate single-copy insertions, thus potentiating the generation of genome-wide insertion libraries applicable in genetic screens. 2010 Elsevier Inc. All rights reserved.

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

PubMed Central

Stranges, P. Benjamin; Palla, Mirkó; Kalachikov, Sergey; Nivala, Jeff; Dorwart, Michael; Trans, Andrew; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Tao, Chuanjuan; Morozova, Irina; Li, Zengmin; Shi, Shundi; Aberra, Aman; Arnold, Cleoma; Yang, Alexander; Aguirre, Anne; Harada, Eric T.; Korenblum, Daniel; Pollard, James; Bhat, Ashwini; Gremyachinskiy, Dmitriy; Bibillo, Arek; Chen, Roger; Davis, Randy; Russo, James J.; Fuller, Carl W.; Roever, Stefan; Ju, Jingyue; Church, George M.

2016-01-01

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin–polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform. PMID:27729524

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution.

PubMed

Nguyen, Thu H M; Carreira, Patricia E; Sanchez-Luque, Francisco J; Schauer, Stephanie N; Fagg, Allister C; Richardson, Sandra R; Davies, Claire M; Jesuadian, J Samuel; Kempen, Marie-Jeanne H C; Troskie, Robin-Lee; James, Cini; Beaven, Elizabeth A; Wallis, Tristan P; Coward, Jermaine I G; Chetty, Naven P; Crandon, Alexander J; Venter, Deon J; Armes, Jane E; Perrin, Lewis C; Hooper, John D; Ewing, Adam D; Upton, Kyle R; Faulkner, Geoffrey J

2018-06-26

LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Tandem Fusion of Hepatitis B Core Antigen Allows Assembly of Virus-Like Particles in Bacteria and Plants with Enhanced Capacity to Accommodate Foreign Proteins

PubMed Central

Peyret, Hadrien; Gehin, Annick; Thuenemann, Eva C.; Blond, Donatienne; El Turabi, Aadil; Beales, Lucy; Clarke, Dean; Gilbert, Robert J. C.; Fry, Elizabeth E.; Stuart, David I.; Holmes, Kris; Stonehouse, Nicola J.; Whelan, Mike; Rosenberg, William; Lomonossoff, George P.; Rowlands, David J.

2015-01-01

The core protein of the hepatitis B virus, HBcAg, assembles into highly immunogenic virus-like particles (HBc VLPs) when expressed in a variety of heterologous systems. Specifically, the major insertion region (MIR) on the HBcAg protein allows the insertion of foreign sequences, which are then exposed on the tips of surface spike structures on the outside of the assembled particle. Here, we present a novel strategy which aids the display of whole proteins on the surface of HBc particles. This strategy, named tandem core, is based on the production of the HBcAg dimer as a single polypeptide chain by tandem fusion of two HBcAg open reading frames. This allows the insertion of large heterologous sequences in only one of the two MIRs in each spike, without compromising VLP formation. We present the use of tandem core technology in both plant and bacterial expression systems. The results show that tandem core particles can be produced with unmodified MIRs, or with one MIR in each tandem dimer modified to contain the entire sequence of GFP or of a camelid nanobody. Both inserted proteins are correctly folded and the nanobody fused to the surface of the tandem core particle (which we name tandibody) retains the ability to bind to its cognate antigen. This technology paves the way for the display of natively folded proteins on the surface of HBc particles either through direct fusion or through non-covalent attachment via a nanobody. PMID:25830365

Detecting condylar contact loss using single-plane fluoroscopy: a comparison with in vivo force data and in vitro bi-plane data.

PubMed

Prins, A H; Kaptein, B L; Banks, S A; Stoel, B C; Nelissen, R G H H; Valstar, E R

2014-05-07

Knee contact mechanics play an important role in knee implant failure and wear mechanics. Femoral condylar contact loss in total knee arthroplasty has been reported in some studies and it is considered to potentially induce excessive wear of the polyethylene insert.Measuring in vivo forces applied to the tibial plateau with an instrumented prosthesis is a possible approach to assess contact loss in vivo, but this approach is not very practical. Alternatively, single-plane fluoroscopy and pose estimation can be used to derive the relative pose of the femoral component with respect to the tibial plateau and estimate the distance from the medial and lateral parts of the femoral component towards the insert. Two measures are reported in the literature: lift-off is commonly defined as the difference in distance between the medial and lateral condyles of the femoral component with respect to the tibial plateau; separation is determined by the closest distance of each condyle towards the polyethylene insert instead of the tibia plateau.In this validation study, lift-off and separation as measured with single-plane fluoroscopy are compared to in vivo contact forces measured with an instrumented knee implant. In a phantom study, lift-off and separation were compared to measurements with a high quality bi-plane measurement.The results of the in vivo contact-force experiment demonstrate a large discrepancy between single-plane fluoroscopy and the in vivo force data: single-plane fluoroscopy measured up to 5.1mm of lift-off or separation, whereas the force data never showed actual loss of contact. The phantom study demonstrated that the single-plane setup could introduce an overestimation of 0.22mm±±0.36mm. Correcting the out-of-plane position resulted in an underestimation of medial separation by -0.20mm±±0.29mm.In conclusion, there is a discrepancy between the in vivo force data and single-plane fluoroscopic measurements. Therefore contact loss may not always be determined reliably by single plane fluoroscopy analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of insertion speed and trocar stiffness on the accuracy of needle position for brachytherapy

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

McGill, Carl S.; Schwartz, Jonathon A.; Moore, Jason Z.

2012-04-15

Purpose: In prostate brachytherapy, accurate positioning of the needle tip to place radioactive seeds at its target site is critical for successful radiation treatment. During the procedure, needle deflection leads to seed misplacement and suboptimal radiation dose to cancerous cells. In practice, radiation oncologists commonly use high-speed hand needle insertion to minimize displacement of the prostate as well as the needle deflection. Effects of speed during needle insertion and stiffness of trocar (a solid rod inside the hollow cannula) on needle deflection are studied. Methods: Needle insertion experiments into phantom were performed using a 2{sup 2} factorial design (2 parametersmore » at 2 levels), with each condition having replicates. Analysis of the deflection data included calculating the average, standard deviation, and analysis of variance (ANOVA) to find significant single and two-way interaction factors. Results: The stiffer tungsten carbide trocar is effective in reducing the average and standard deviation of needle deflection. The fast insertion speed together with the stiffer trocar generated the smallest average and standard deviation for needle deflection for almost all cases. Conclusions: The combination of stiff tungsten carbide trocar and fast needle insertion speed are important to decreasing needle deflection. The knowledge gained from this study can be used to improve the accuracy of needle insertion during brachytherapy procedures.« less

Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers

PubMed Central

2012-01-01

Background Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. Results Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. Conclusions This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion. PMID:22541534

Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers.

PubMed

Walker, Jerilyn A; Konkel, Miriam K; Ullmer, Brygg; Monceaux, Christopher P; Ryder, Oliver A; Hubley, Robert; Smit, Arian Fa; Batzer, Mark A

2012-04-30

Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.

Design, Fabrication, and Packaging of Mach-Zehnder Interferometers for Biological Sensing Applications

NASA Astrophysics Data System (ADS)

Novak, Joseph

Optical biological sensors are widely used in the fields of medical testing, water treatment and safety, gene identification, and many others due to advances in nanofabrication technology. This work focuses on the design of fiber-coupled Mach-Zehnder Interferometer (MZI) based biosensors fabricated on silicon-on-insulator (SOI) wafer. Silicon waveguide sensors are designed with multimode and single-mode dimensions. Input coupling efficiency is investigated by design of various taper structures. Integration processing and packaging is performed for fiber attachment and enhancement of input coupling efficiency. Optical guided-wave sensors rely on single-mode operation to extract an induced phase-shift from the output signal. A silicon waveguide MZI sensor designed and fabricated for both multimode and single-mode dimensions. Sensitivity of the sensors is analyzed for waveguide dimensions and materials. An s-bend structure is designed for the multimode waveguide to eliminate higher-order mode power as an alternative to single-mode confinement. Single-mode confinement is experimentally demonstrated through near field imaging of waveguide output. Y-junctions are designed for 3dB power splitting to the MZI arms and for power recombination after sensing to utilize the interferometric function of the MZI. Ultra-short 10microm taper structures with curved geometries are designed to improve insertion loss from fiber-to-chip without significantly increasing device area and show potential for applications requiring misalignment tolerance. An novel v-groove process is developed for self-aligned integration of fiber grooves for attachment to sensor chips. Thermal oxidation at temperatures from 1050-1150°C during groove processing creates an SiO2 layer on the waveguide end facet to protect the waveguide facet during integration etch processing without additional e-beam lithography processing. Experimental results show improvement of insertion loss compared to dicing preparation and Focused Ion Beam methods using the thermal oxidation process.

Prediction, experimental results and analysis of the ITER TF insert coil quench propagation tests, using the 4C code

NASA Astrophysics Data System (ADS)

Zanino, R.; Bonifetto, R.; Brighenti, A.; Isono, T.; Ozeki, H.; Savoldi, L.

2018-07-01

The ITER toroidal field insert (TFI) coil is a single-layer Nb3Sn solenoid tested in 2016-2017 at the National Institutes for Quantum and Radiological Science and Technology (former JAEA) in Naka, Japan. The TFI, the last in a series of ITER insert coils, was tested in operating conditions relevant for the actual ITER TF coils, inserting it in the borehole of the central solenoid model coil, which provided the background magnetic field. In this paper, we consider the five quench propagation tests that were performed using one or two inductive heaters (IHs) as drivers; out of these, three used just one IH but with increasing delay times, up to 7.5 s, between the quench detection and the TFI current dump. The results of the 4C code prediction of the quench propagation up to the current dump are presented first, based on simulations performed before the tests. We then describe the experimental results, showing good reproducibility. Finally, we compare the 4C code predictions with the measurements, confirming the 4C code capability to accurately predict the quench propagation, and the evolution of total and local voltages, as well as of the hot spot temperature. To the best of our knowledge, such a predictive validation exercise is performed here for the first time for the quench of a Nb3Sn coil. Discrepancies between prediction and measurement are found in the evolution of the jacket temperatures, in the He pressurization and quench acceleration in the late phase of the transient before the dump, as well as in the early evolution of the inlet and outlet He mass flow rate. Based on the lessons learned in the predictive exercise, the model is then refined to try and improve a posteriori (i.e. in interpretive, as opposed to predictive mode) the agreement between simulation and experiment.

Single- and double-balloon enteroscopy-assisted endoscopic retrograde cholangiopancreatography in patients with Roux-en-Y plus hepaticojejunostomy anastomosis and Whipple resection.

PubMed

Itokawa, Fumihide; Itoi, Takao; Ishii, Kentaro; Sofuni, Atsushi; Moriyasu, Fuminori

2014-04-01

In patients with Roux-en-Y hepaticojejunostomy (HJ with R-Y) and Whipple resection, endoscopic retrograde cholangiopancreatography (ERCP) can be challenging. We report our experience with ERCP using balloon-assisted enteroscopy (BAE) (BAE-ERCP) in patients with HJ with R-Y, and Whipple resection. BAE-ERCP procedures were carried out in 62 patients (HJ with R-Y:Whipple resection=34:28). Overall, the rates of reaching the anastomosis were 85.3% (29/34) in HJ with R-Y and 96.4% (27/28) in Whipple resection. In terms of HJ with R-Y, insertion success rate by standard single-balloon enteroscopy (SBE) was 89.3% (25/28). Insertion success rate by short BAE, including SBE and double-balloon enteroscopy (DBE), was 50% (3/6). There was a statistically significant difference of insertion success rate between standard long BE and short BE (P=0.021). However, in the Whipple patients, insertion success rate by standard and short SBE was 93.8% (15/16) and 91.7% (11/12), respectively. Initial insertion success rate by short BAE in Whipple patients was significantly higher than in HJ with R-Y (91.7% vs 50%, P=0.045). Therapeutic interventions included dilation of anastomosis stricture, stone extraction, endoscopic mechanical lithotripsy, biliary stent placement, stent extraction, endoscopic nasobiliary drainage, direct cholangioscopy, and electrohydraulic lithotripsy. Our HJ with R-Y series and Whipple series treatment success rate was 90% (18/20) and 95.0% (19/20), respectively. BAE-ERCP enabled ERCP to be carried out in patients with HJ. It is considered safe and feasible. Further experience and device improvement are needed. © 2014 The Authors. Digestive Endoscopy © 2014 Japan Gastroenterological Endoscopy Society.

Therapeutic peroral direct cholangioscopy using a single balloon enteroscope in patients with Roux-en-Y anastomosis (with videos).

PubMed

Yamauchi, Hiroshi; Kida, Mitsuhiro; Okuwaki, Kosuke; Miyazawa, Shiro; Matsumoto, Takaaki; Uehara, Kazuho; Miyata, Eiji; Hasegawa, Rikiya; Kaneko, Toru; Laopeamthong, Issaree; Lei, Yang; Iwai, Tomohisa; Imaizumi, Hiroshi; Koizumi, Wasaburo

2018-01-01

Peroral cholangioscopic lithotripsy is a useful procedure in patients with a normal gastrointestinal anatomy who have difficult-to-treat stones. We evaluated the usefulness of peroral direct cholangioscopy (PDCS) using single-balloon enteroscope (SBE) in patients with difficult-to-treat stones who had undergone Roux-en-Y reconstruction. Among 118 patients (169 sessions) who underwent SBE-assisted endoscopic retrograde cholangiopancreatography to treat biliary stones after Roux-en-Y reconstruction, patients in whom it was difficult to remove biliary stones via a transpapillary or transanastomotic approach and difficult to switch to ultra-slim endoscope, were retrospectively enrolled. The biliary insertion success rate, procedure success rate, procedure time, and procedural complications were assessed. The SBE was inserted into the bile-duct, first using a free-hand technique, second using a guide wire, and third using the large balloon anchoring and deflation (LBAD) technique. A total of 11 patients (14 sessions) were enrolled in this study. The biliary insertion success rate was 100%. Bile-duct insertion was performed using a free-hand technique in 4 sessions, a guide wire in 3 sessions (rendezvous technique, 2 sessions), and the LBAD technique in 7 sessions. The procedure success rate was 86% in first session, and 100% in second session. The median procedure time was 81 min (range 49-137). The median procedure time in the bile-duct was 21.5 min (range 6-60). Mild pancreatitis occurred as a complication in one patient. The median follow-up was 528 days (range 282-764). No patient had stone recurrence. PDCS using SBE is a useful procedure in patients with Roux-en-Y reconstruction. The LBAD technique is an useful technique of inserting SBE into the bile-duct.

Three new insertion sequence elements ISLdl2, ISLdl3, and ISLdl4 in Lactobacillus delbrueckii: isolation, molecular characterization, and potential use for strain identification.

PubMed

Ravin, Victor; Alatossava, Tapani

2003-05-01

A group of new insertion sequence (IS) elements, ISLdl2, ISLdl3, and ISLdl4, from Lactobacillus delbrueckii subsp. lactis ATCC 15808 was isolated, characterized, and used for strain identification together with ISLdl1, recently characterized as an L. delbrueckii IS element belonging to the ISL3 family. ISLdl2 was 1367 bp in size and had a 24 bp IR and an 8 bp DR. The single ORF of ISLdl2 encoded a protein of 392 aa similar to transposases of the IS256 family. ISLdl3 had a single ORF encoding a protein of 343 aa similar to transposases of the IS30 family. Finally, ISLdl4 had a single ORF encoding a protein of 406 aa and displayed homology to the transposases of the IS110 family. ISLdl4 was only slight different from ISL4 (Accession No. AY040213). ISLdl1, ISLdl2, and ISLdl4 were present in all of the 10 L. delbrueckii subsp. lactis and subsp. delbrueckii strains tested, as well as in three of the 11 L. delbrueckii subsp. bulgaricus strains tested. ISLdl3 was present only in four closely related strains of L. delbrueckii subsp. lactis. These IS elements were not observed in Lactobacillus rhamnosus, Lactobacillus acidophilus, Lactobacillus helveticus, or Lactobacillus plantarum. A cluster of IS elements, ISLdl1, ISLdl2, ISLdl3, ISLdl4, and ISL6, was observed in L. delbrueckii subsp. lactis strain ATCC 15808. Within this cluster, ISLdl4 was inserted into ISLdl1 between the left IR and the start codon of ORF455, encoding a putative transposase. Most of the integration sites of the IS elements were strain-specific. We have observed that IS elements can migrate from one strain to another as integral parts of bacterial DNA by using phage LL-H as a vehicle. We demonstrate for the first time that inverse PCR and vectorette PCR methods with primers based on sequences of the IS elements could be used for identification of L. delbrueckii strains.

Ligand-accelerated enantioselective methylene C(sp3)-H bond activation.

PubMed

Chen, Gang; Gong, Wei; Zhuang, Zhe; Andrä, Michal S; Chen, Yan-Qiao; Hong, Xin; Yang, Yun-Fang; Liu, Tao; Houk, K N; Yu, Jin-Quan

2016-09-02

Effective differentiation of prochiral carbon-hydrogen (C-H) bonds on a single methylene carbon via asymmetric metal insertion remains a challenge. Here, we report the discovery of chiral acetyl-protected aminoethyl quinoline ligands that enable asymmetric palladium insertion into prochiral C-H bonds on a single methylene carbon center. We apply these palladium complexes to catalytic enantioselective functionalization of β-methylene C-H bonds in aliphatic amides. Using bidentate ligands to accelerate C-H activation of otherwise unreactive monodentate substrates is crucial for outcompeting the background reaction driven by substrate-directed cyclopalladation, thereby avoiding erosion of enantioselectivity. The potential of ligand acceleration in C-H activation is also demonstrated by enantioselective β-C-H arylation of simple carboxylic acids without installing directing groups. Copyright © 2016, American Association for the Advancement of Science.

Knee arthrodesis using a short locked intramedullary nail. A new technique.

PubMed

Cheng, S L; Gross, A E

1995-01-01

This article reports on the use of a new intramedullary nail designed specifically for fixation of knee fusions. The nail is a short locked stainless steel nail that is inserted through a single anterior knee incision and uses an outrigger targeting rod to guide the insertion of the locking screws. The successful use of this technique is illustrated in two cases. The advantages of this nail compared with previously reported techniques of fixation for knee fusions are that the short locked nail avoids the second incision required for the insertion of long knee fusion nails, the bulkiness of the double plating technique in the relatively subcutaneous anterior knee area, and the difficulties inherent with the prolonged use of pins for external fixation.

Development of the EpiOcular(TM) eye irritation test for hazard identification and labelling of eye irritating chemicals in response to the requirements of the EU cosmetics directive and REACH legislation.

PubMed

Kaluzhny, Yulia; Kandárová, Helena; Hayden, Patrick; Kubilus, Joseph; d'Argembeau-Thornton, Laurence; Klausner, Mitchell

2011-09-01

The recently implemented 7th Amendment to the EU Cosmetics Directive and the EU REACH legislation have heightened the need for in vitro ocular test methods. To address this need, the EpiOcular(TM) eye irritation test (EpiOcular-EIT), which utilises the normal (non-transformed) human cell-based EpiOcular tissue model, has been developed. The EpiOcular-EIT prediction model is based on an initial training set of 39 liquid and 21 solid test substances and uses a single exposure period and a single cut-off in tissue viability, as determined by the MTT assay. A chemical is classified as an irritant (GHS Category 1 or 2), if the tissue viability is ≤ 60%, and as a non-irritant (GHS unclassified), if the viability is > 60%. EpiOcular-EIT results for the training set, along with results for an additional 52 substances, which included a range of alcohols, hydrocarbons, amines, esters, and ketones, discriminated between ocular irritants and non-irritants with 98.1% sensitivity, 72.9% specificity, and 84.8% accuracy. To ensure the long-term commercial viability of the assay, EpiOcular tissues produced by using three alternative cell culture inserts were evaluated in the EpiOcular-EIT with 94 chemicals. The assay results obtained with the initial insert and the three alternative inserts were very similar, as judged by correlation coefficients (r²) that ranged from 0.82 to 0.96. The EpiOcular-EIT was pre-validated in 2007/2008, and is currently involved in a formal, multi-laboratory validation study sponsored by the European Cosmetics Association (COLIPA) under the auspices of the European Centre for the Validation of Alternative Methods (ECVAM). The EpiOcular-EIT, together with EpiOcular's long history of reproducibility and proven utility for ultra-mildness testing, make EpiOcular a useful model for addressing current legislation related to animal use in the testing of potential ocular irritants. 2011 FRAME.

Dynamic soft tissue deformation estimation based on energy analysis

NASA Astrophysics Data System (ADS)

Gao, Dedong; Lei, Yong; Yao, Bin

2016-10-01

The needle placement accuracy of millimeters is required in many needle-based surgeries. The tissue deformation, especially that occurring on the surface of organ tissue, affects the needle-targeting accuracy of both manual and robotic needle insertions. It is necessary to understand the mechanism of tissue deformation during needle insertion into soft tissue. In this paper, soft tissue surface deformation is investigated on the basis of continuum mechanics, where a geometry model is presented to quantitatively approximate the volume of tissue deformation. The energy-based method is presented to the dynamic process of needle insertion into soft tissue based on continuum mechanics, and the volume of the cone is exploited to quantitatively approximate the deformation on the surface of soft tissue. The external work is converted into potential, kinetic, dissipated, and strain energies during the dynamic rigid needle-tissue interactive process. The needle insertion experimental setup, consisting of a linear actuator, force sensor, needle, tissue container, and a light, is constructed while an image-based method for measuring the depth and radius of the soft tissue surface deformations is introduced to obtain the experimental data. The relationship between the changed volume of tissue deformation and the insertion parameters is created based on the law of conservation of energy, with the volume of tissue deformation having been obtained using image-based measurements. The experiments are performed on phantom specimens, and an energy-based analytical fitted model is presented to estimate the volume of tissue deformation. The experimental results show that the energy-based analytical fitted model can predict the volume of soft tissue deformation, and the root mean squared errors of the fitting model and experimental data are 0.61 and 0.25 at the velocities 2.50 mm/s and 5.00 mm/s. The estimating parameters of the soft tissue surface deformations are proven to be useful for compensating the needle-targeting error in the rigid needle insertion procedure, especially for percutaneous needle insertion into organs.

The Impact of Preoperative α-Adrenergic Antagonists on Ureteral Access Sheath Insertion Force and the Upper Limit of Force Required to Avoid Ureteral Mucosal Injury: A Randomized Controlled Study.

PubMed

Koo, Kyo Chul; Yoon, Jun-Ho; Park, No-Cheol; Lee, Hye Sun; Ahn, Hyun Kyu; Lee, Kwang Suk; Kim, Do Kyung; Cho, Kang Su; Chung, Byung Ha; Hong, Chang Hee

2018-06-01

Excessive bulking force during primary access of the ureteral access sheath may induce ureteral injury. We investigated the efficacy of preoperative α-blockade to reduce ureteral access sheath insertion force and determine the upper limit required to avoid ureteral injury. In this randomized controlled trial 135 patients from a single institution who had ureteropelvic junction or renal pelvis stones and were scheduled to undergo retrograde intrarenal surgery were prospectively enrolled from December 2015 to January 2017. Of the patients 41 and 42 were randomly assigned to the control and experimental groups, respectively. The experimental group received α-blockade preoperatively. The 21 patients who were pre-stented were assessed separately. We developed a homemade device to measure maximal ureteral access sheath insertion force. Our ureteral access sheath insertion force measurement device showed excellent reproducibility. Higher insertion velocity resulted in greater maximal sheath insertion force. Maximal insertion force in the α-blockade group was significantly lower than in the control group at the ureterovesical junction (p = 0.008) and the proximal ureter (p = 0.036). Maximal insertion force in the α-blockade group was comparable to that in pre-stented patients. Female patients and patients 70 years old or older showed a lower maximal ureteral access sheath insertion force than their counterparts. The rate of grade 2 or greater ureteral injury was lower in the α-blockade group than in controls (p = 0.038). No injury occurred in any case in which ureteral access sheath insertion force did not exceed 600 G. Preoperative α-blockade and slow sheath placement may reduce maximal ureteral access sheath insertion force. If the force exceeds 600 G, a smaller diameter sheath may be an alternative. Alternatively the procedure can be terminated and followed later by pre-stented retrograde intrarenal surgery. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

``Dressing'' lines and vertices in calculations of matrix elements with the coupled-cluster method and determination of Cs atomic properties

NASA Astrophysics Data System (ADS)

Derevianko, Andrei; Porsev, Sergey G.

2005-03-01

We consider evaluation of matrix elements with the coupled-cluster method. Such calculations formally involve infinite number of terms and we devise a method of partial summation (dressing) of the resulting series. Our formalism is built upon an expansion of the product C†C of cluster amplitudes C into a sum of n -body insertions. We consider two types of insertions: particle (hole) line insertion and two-particle (two-hole) random-phase-approximation-like insertion. We demonstrate how to “dress” these insertions and formulate iterative equations. We illustrate the dressing equations in the case when the cluster operator is truncated at single and double excitations. Using univalent systems as an example, we upgrade coupled-cluster diagrams for matrix elements with the dressed insertions and highlight a relation to pertinent fourth-order diagrams. We illustrate our formalism with relativistic calculations of the hyperfine constant A(6s) and the 6s1/2-6p1/2 electric-dipole transition amplitude for the Cs atom. Finally, we augment the truncated coupled-cluster calculations with otherwise omitted fourth order diagrams. The resulting analysis for Cs is complete through the fourth order of many-body perturbation theory and reveals an important role of triple and disconnected quadruple excitations.

GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database.

PubMed

Kleinboelting, Nils; Huep, Gunnar; Kloetgen, Andreas; Viehoever, Prisca; Weisshaar, Bernd

2012-01-01

T-DNA insertion mutants are very valuable for reverse genetics in Arabidopsis thaliana. Several projects have generated large sequence-indexed collections of T-DNA insertion lines, of which GABI-Kat is the second largest resource worldwide. User access to the collection and its Flanking Sequence Tags (FSTs) is provided by the front end SimpleSearch (http://www.GABI-Kat.de). Several significant improvements have been implemented recently. The database now relies on the TAIRv10 genome sequence and annotation dataset. All FSTs have been newly mapped using an optimized procedure that leads to improved accuracy of insertion site predictions. A fraction of the collection with weak FST yield was re-analysed by generating new FSTs. Along with newly found predictions for older sequences about 20,000 new FSTs were included in the database. Information about groups of FSTs pointing to the same insertion site that is found in several lines but is real only in a single line are included, and many problematic FST-to-line links have been corrected using new wet-lab data. SimpleSearch currently contains data from ~71,000 lines with predicted insertions covering 62.5% of the 27,206 nuclear protein coding genes, and offers insertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre.

Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9.

PubMed

Li, Jun; Meng, Xiangbing; Zong, Yuan; Chen, Kunling; Zhang, Huawei; Liu, Jinxing; Li, Jiayang; Gao, Caixia

2016-09-12

Sequence-specific nucleases have been exploited to create targeted gene knockouts in various plants(1), but replacing a fragment and even obtaining gene insertions at specific loci in plant genomes remain a serious challenge. Here, we report efficient intron-mediated site-specific gene replacement and insertion approaches that generate mutations using the non-homologous end joining (NHEJ) pathway using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system. Using a pair of single guide RNAs (sgRNAs) targeting adjacent introns and a donor DNA template including the same pair of sgRNA sites, we achieved gene replacements in the rice endogenous gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) at a frequency of 2.0%. We also obtained targeted gene insertions at a frequency of 2.2% using a sgRNA targeting one intron and a donor DNA template including the same sgRNA site. Rice plants harbouring the OsEPSPS gene with the intended substitutions were glyphosate-resistant. Furthermore, the site-specific gene replacements and insertions were faithfully transmitted to the next generation. These newly developed approaches can be generally used to replace targeted gene fragments and to insert exogenous DNA sequences into specific genomic sites in rice and other plants.

Prediction of the distance from skin to epidural space for low-thoracic epidural catheter insertion by computed tomography.

PubMed

Kao, M C; Tsai, S K; Chang, W K; Liu, H T; Hsieh, Y C; Hu, J S; Mok, M S

2004-02-01

It may be clinically useful to predict the depth of the epidural space. To investigate the accuracy of preoperative abdominal computed tomography (CT) in prediction of the distance for low-thoracic epidural insertion, a single group observational study was conducted in 30 male patients undergoing elective major abdominal surgery requiring epidural analgesia for postoperative pain relief. Using the paramedian approach, low-thoracic epidural insertion at T10-11 interspace was performed with a standardized procedure to obtain an actual insertion length (AIL). According to the principles of trigonometry, an estimated insertion length (EIL) was calculated as 1.26 times the distance from skin to epidural space measured from the preoperative abdominal CT. The mean (SD) EIL and AIL were 5.5 (0.7) and 5.1 (0.6) cm, respectively, with a significant correlation (r=0.899, P<0.01). The EIL tended to have a higher value than the AIL (0.4 (0.3) cm). There were significant correlations of both EIL and AIL with weight (P<0.01), BMI (P<0.01), and body fat percentage (P<0.01), but not with height (P>0.05). We conclude that the preoperative abdominal CT is helpful in prediction of the distance for low-thoracic epidural insertion using the paramedian approach.

Descemet's Stripping Automated Endothelial Keratoplasty Tissue Insertion Devices

PubMed Central

Khan, Salman Nasir; Shiakolas, Panos S.; Mootha, Venkateswara Vinod

2015-01-01

This review study provides information regarding the construction, design, and use of six commercially available endothelial allograft insertion devices applied for Descemet's stripping automated endothelial keratoplasty (DSAEK). We also highlight issues being faced in DSAEK and discuss the methods through which medical devices such as corneal inserters may alleviate these issues. Inserter selection is of high importance in the DSAEK procedure since overcoming the learning curve associated with the use of an insertion device is a time and energy consuming process. In the present review, allograft insertion devices were compared in terms of design, construction material, insertion technique, dimensions, incision requirements and endothelial cell loss to show their relative merits and capabilities based on available data in the literature. Moreover, the advantages/disadvantages of various insertion devices used for allograft insertion in DSAEK are reviewed and compared. The information presented in this review can be utilized for better selection of an insertion device for DSAEK. PMID:27051492

Flat midsubstance of the anterior cruciate ligament with tibial "C"-shaped insertion site.

PubMed

Siebold, Rainer; Schuhmacher, Peter; Fernandez, Francis; Śmigielski, Robert; Fink, Christian; Brehmer, Axel; Kirsch, Joachim

2015-11-01

This anatomical cadaver study was performed to investigate the flat appearance of the midsubstance shape of the anterior cruciate ligament (ACL) and its tibial "C"-shaped insertion site. The ACL midsubstance and the tibial ACL insertion were dissected in 20 cadaveric knees (n = 6 fresh frozen and n = 14 paraffined). Magnifying spectacles were used for all dissections. Morphometric measurements were performed using callipers and on digital photographs. In all specimens, the midsubstance of the ACL was flat with a mean width of 9.9 mm, thickness of 3.9 mm and cross-sectional area of 38.7 mm(2). The "direct" "C"-shaped tibial insertion runs from along the medial tibial spine to the anterior aspect of the lateral meniscus. The mean width (length) of the "C" was 12.6 mm, its thickness 3.3 mm and area 31.4 mm(2). The centre of the "C" was the bony insertion of the anterior root of the lateral meniscus overlayed by fat and crossed by the ACL. No posterolateral (PL) inserting ACL fibres were found. Together with the larger "indirect" part (area 79.6 mm(2)), the "direct" one formed a "duck-foot"-shaped footprint. The tibial ACL midsubstance and tibial "C"-shaped insertion are flat and are resembling a "ribbon". The centre of the "C" is the bony insertion of the anterior root of the lateral meniscus. There are no central or PL inserting ACL fibres. Anatomical ACL reconstruction may therefore require a flat graft and a "C"-shaped tibial footprint reconstruction with an anteromedial bone tunnel for single bundle and an additional posteromedial bone tunnel for double bundle.

Smooth muscle myosin isoform expression and LC20 phosphorylation in innate rat airway hyperresponsiveness.

PubMed

Gil, Fulvio R; Zitouni, Nedjma B; Azoulay, Eric; Maghni, Karim; Lauzon, Anne-Marie

2006-11-01

Four smooth muscle myosin heavy chain (SMMHC) isoforms are generated by alternative mRNA splicing of a single gene. Two of these isoforms differ by the presence [(+)insert] or absence [(-)insert] of a 7-amino acid insert in the motor domain. The rate of actin filament propulsion of the (+)insert SMMHC isoform, as measured in the in vitro motility assay, is twofold greater than that of the (-)insert isoform. We hypothesized that a greater expression of the (+)insert SMMHC isoform and greater regulatory light chain (LC(20)) phosphorylation contribute to airway hyperresponsiveness. We measured airway responsiveness to methacholine in Fischer hyperresponsive and Lewis normoresponsive rats and determined SMMHC isoform mRNA and protein expression, as well as essential light chain (LC(17)) isoforms, h-caldesmon, and alpha-actin protein expression in their tracheae. We also measured tracheal muscle strip contractility in response to methacholine and corresponding LC(20) phosphorylation. We found Fischer rats have more (+)insert mRNA (69.4 +/- 2.0%) (mean +/- SE) than Lewis rats (53.0 +/- 2.4%; P < 0.05) and a 44% greater content of (+)insert isoform relative to total myosin protein. No difference was found for LC(17) isoform, h-caldesmon, and alpha-actin expression. The contractility experiments revealed a greater isometric force for Fischer trachealis segments (4.2 +/- 0.8 mN) than Lewis (1.9 +/- 0.4 mN; P < 0.05) and greater LC(20) phosphorylation level in Fischer (55.1 +/- 6.4) than in Lewis (41.4 +/- 6.1; P < 0.05) rats. These results further support the contention that innate airway hyperresponsiveness is a multifactorial disorder in which increased expression of the fast (+)insert SMMHC isoform and greater activation of LC(20) lead to smooth muscle hypercontractility.

Evaluation of preferable insertion routes for esophagogastroduodenoscopy using ultrathin endoscopes

PubMed Central

Ono, Satoshi; Niimi, Keiko; Fujishiro, Mitsuhiro; Takahashi, Yu; Sakaguchi, Yoshiki; Nakayama, Chiemi; Minatsuki, Chihiro; Matsuda, Rie; Hirayama-Asada, Itsuko; Tsuji, Yosuke; Mochizuki, Satoshi; Kodashima, Shinya; Yamamichi, Nobutake; Ozeki, Atsuko; Matsumoto, Lumine; Ohike, Yumiko; Yamazaki, Tsutomu; Koike, Kazuhiko

2014-01-01

AIM: To evaluate the discomfort associated with esophagogastroduodenoscopy (EGD) using an ultrathin endoscope through different insertion routes. METHODS: This study (January 2012-March 2013) included 1971 consecutive patients [male/female (M/F), 1158/813, 57.5 ± 11.9 years] who visited a single institute for annual health checkups. Transnasal EGD was performed in 1394 patients and transoral EGD in 577. EGD-associated discomfort was assessed using a visual analog scale score (VAS score: 0-10). RESULTS: Multivariate analysis revealed gender (M vs F: 4.02 ± 2.15 vs 5.06 ± 2.43) as the only independent predictor of the VAS score in 180 patients who underwent EGD for the first time; whereas it revealed gender (M vs F 3.60 ± 2.20 vs 4.84 ± 2.37), operator, age group (A: < 39 years; B: 40-49 years; C: 50-59 years; D: 60-69 years; E: > 70 years; A/B/C/D/E: 4.99 ± 2.32/4.34 ± 2.49/4.19 ± 2.31/3.99 ± 2.27/3.63 ± 2.31), and type of insertion as independent predictors in the remaining patients. Subanalysis for gender, age group, and insertion route revealed that the VAS score decreased with age regardless of gender and insertion route, was high in female patients regardless of age and insertion route, and was low in males aged over 60 years who underwent transoral insertion. CONCLUSION: Although comprehensive analysis revealed that the insertion route may not be an independent predictor of the VAS score, transoral insertion may reduce EGD-associated discomfort in elderly patients. PMID:24803817

Associative list processing unit

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

Hemmert, Karl Scott; Underwood, Keith D

2014-04-01

An associative list processing unit and method comprising employing a plurality of prioritized cell blocks and permitting inserts to occur in a single clock cycle if all of the cell blocks are not full.

Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion.

PubMed

Ni, ZhouXian; Ye, YouJu; Bai, Tiandao; Xu, Meng; Xu, Li-An

2017-09-11

The chloroplast genome (CPG) of Pinus massoniana belonging to the genus Pinus (Pinaceae), which is a primary source of turpentine, was sequenced and analyzed in terms of gene rearrangements, ndh genes loss, and the contraction and expansion of short inverted repeats (IRs). P. massoniana CPG has a typical quadripartite structure that includes large single copy (LSC) (65,563 bp), small single copy (SSC) (53,230 bp) and two IRs (IRa and IRb, 485 bp). The 108 unique genes were identified, including 73 protein-coding genes, 31 tRNAs, and 4 rRNAs. Most of the 81 simple sequence repeats (SSRs) identified in CPG were mononucleotides motifs of A/T types and located in non-coding regions. Comparisons with related species revealed an inversion (21,556 bp) in the LSC region; P. massoniana CPG lacks all 11 intact ndh genes (four ndh genes lost completely; the five remained truncated as pseudogenes; and the other two ndh genes remain as pseudogenes because of short insertions or deletions). A pair of short IRs was found instead of large IRs, and size variations among pine species were observed, which resulted from short insertions or deletions and non-synchronized variations between "IRa" and "IRb". The results of phylogenetic analyses based on whole CPG sequences of 16 conifers indicated that the whole CPG sequences could be used as a powerful tool in phylogenetic analyses.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

PubMed Central

Gallus, Susanne; Janke, Axel

2017-01-01

Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

Immediate vs. delayed insertion of intrauterine contraception after second trimester abortion: study protocol for a randomized controlled trial.

PubMed

Norman, Wendy V; Kaczorowski, Janusz; Soon, Judith A; Brant, Rollin; Bryan, Stirling; Trouton, Konia J; Dicus, Lyda

2011-06-14

We describe the rationale and protocol for a randomized controlled trial (RCT) to assess whether intrauterine contraception placed immediately after a second trimester abortion will result in fewer pregnancies than current recommended practice of intended placement at 4 weeks post-abortion. Decision analysis suggests the novel strategy could substantially reduce subsequent unintended pregnancies and abortions. This paper highlights considerations of design, implementation and evaluation of a trial expected to provide rigorous evidence for appropriate insertion timing and health economics of intrauterine contraception after second trimester abortion. Consenting women choosing to use intrauterine contraception after abortion for a pregnancy of 12 to 24 weeks will be randomized to insertion timing groups either immediately (experimental intervention) or four weeks (recommended care) post abortion. Primary outcome measure is pregnancy rate at one year. Secondary outcomes include: cumulative pregnancy rates over five year follow-up period, comprehensive health economic analyses comparing immediate and delayed insertion groups, and device retention rates, complication rates (infection, expulsion) and, contraceptive method satisfaction. Web-based Contraception Satisfaction Questionnaires, clinical records and British Columbia linked health databases will be used to assess primary and secondary outcomes. Enrolment at all clinics in the province performing second trimester abortions began in May 2010 and is expected to complete in late 2011. Data on one year outcomes will be available for analysis in 2014. The RCT design combined with access to clinical records at all provincial abortion clinics, and to information in provincial single-payer linked administrative health databases, birth registry and hospital records, offers a unique opportunity to evaluate such an approach by determining pregnancy rate at one through five years among enrolled women. We highlight considerations of design, implementation and evaluation of a trial expected to provide rigorous evidence for appropriate insertion timing and health economics of intrauterine contraception after second trimester abortion.

Immediate vs. delayed insertion of intrauterine contraception after second trimester abortion: study protocol for a randomized controlled trial

PubMed Central

2011-01-01

Background We describe the rationale and protocol for a randomized controlled trial (RCT) to assess whether intrauterine contraception placed immediately after a second trimester abortion will result in fewer pregnancies than current recommended practice of intended placement at 4 weeks post-abortion. Decision analysis suggests the novel strategy could substantially reduce subsequent unintended pregnancies and abortions. This paper highlights considerations of design, implementation and evaluation of a trial expected to provide rigorous evidence for appropriate insertion timing and health economics of intrauterine contraception after second trimester abortion. Methods/Design Consenting women choosing to use intrauterine contraception after abortion for a pregnancy of 12 to 24 weeks will be randomized to insertion timing groups either immediately (experimental intervention) or four weeks (recommended care) post abortion. Primary outcome measure is pregnancy rate at one year. Secondary outcomes include: cumulative pregnancy rates over five year follow-up period, comprehensive health economic analyses comparing immediate and delayed insertion groups, and device retention rates, complication rates (infection, expulsion) and, contraceptive method satisfaction. Web-based Contraception Satisfaction Questionnaires, clinical records and British Columbia linked health databases will be used to assess primary and secondary outcomes. Enrolment at all clinics in the province performing second trimester abortions began in May 2010 and is expected to complete in late 2011. Data on one year outcomes will be available for analysis in 2014. Discussion The RCT design combined with access to clinical records at all provincial abortion clinics, and to information in provincial single-payer linked administrative health databases, birth registry and hospital records, offers a unique opportunity to evaluate such an approach by determining pregnancy rate at one through five years among enrolled women. We highlight considerations of design, implementation and evaluation of a trial expected to provide rigorous evidence for appropriate insertion timing and health economics of intrauterine contraception after second trimester abortion. Trial registration Current Controlled Trials ISRCTN19506752 PMID:21672213

Topology of the membrane protein LamB by epitope tagging and a comparison with the X-ray model.

PubMed

Newton, S M; Klebba, P E; Michel, V; Hofnung, M; Charbit, A

1996-06-01

We previously developed a genetic approach to study, with a single antibody, the topology of the outer membrane protein LamB, an Escherichia coli porin with specificity towards maltodextrins and a receptor for bacteriophage lambda. Our initial procedure consisted of inserting at random the same reporter epitope (the C3 neutralization epitope from poliovirus) into permissive sites of LamB (i.e., sites which tolerate insertions without deleterious effects on the protein activities or the cell). A specific monoclonal antibody was then used to examine the position of the inserted epitope with respect to the protein and the membrane. In the present work, we set up a site-directed procedure to insert the C3 epitope at new sites in order to distinguish between two-dimensional folding models. This allowed us to identify two new surface loops of LamB and to predict another periplasmic exposed region. The results obtained by random and directed epitope tagging are analyzed in light of the recently published X-ray structure of the LamB protein. Study of 23 hybrid LamB-C3 proteins led to the direct identification of five of the nine external loops (L4, L5, L6, L7, and L9) and led to the prediction of four periplasmic loops (I1, I4, I5, and I8) of LamB. Nine of the hybrid proteins did not lead to topological conclusions, and none led to the wrong predictions or conclusions. The comparison indicates that parts of models based on secondary structure predictions alone are not reliable and points to the importance of experimental data in the establishment of outer membrane protein topological models. The advantages and limitations of genetic foreign epitope insertion for the study of integral membrane proteins are discussed.

CE: Original Research: Does Certification in Vascular Access Matter? An Analysis of the PICC1 Survey.

PubMed

Chopra, Vineet; Kuhn, Latoya; Vaughn, Valerie; Ratz, David; Winter, Suzanne; Moureau, Nancy; Meyer, Britt; Krein, Sarah

2017-12-01

: Background: Although certification by an accredited agency is often a practice prerequisite in health care, it is not required of vascular access specialists who insert peripherally inserted central catheters (PICCs). Whether certification is associated with differences in practice among inserters is unknown. The purpose of this study was to gather information regarding whether certified and noncertified PICC inserters differ with respect to their practices and views about PICC use. We conducted a national survey of vascular access specialists, identifying certified PICC inserters as those who had received board certification from the Association for Vascular Access, the Infusion Nurses Society, or both. The 76-item survey asked about PICC policies and procedures at respondents' facilities, use of insertion technologies, device management, management of complications, perceptions about PICC use, and relationships with other health care providers. Additional data about respondents, including years in practice and primary practice settings, were also gathered. Bivariable comparisons were made using χ tests; two-sided α with P ≤ 0.05 was considered statistically significant. Of the 1,450 respondents in the final sample, 1,007 (69%) said they were certified inserters and 443 (31%) said they were not. Significantly higher percentages of certified than noncertified inserters reported having practiced for five or more years (78% versus 54%) and having placed 1,000 or more PICCs (58% versus 32%). Significantly more certified than noncertified inserters also reported being the vascular access lead for their facility (56% versus 44%). Reported practice patterns for insertion, care, and management of PICCs varied based on certification status. Some evidence-based practices (such as the use of ultrasound to measure catheter-to-vein ratios) were more often reported by certified inserters, while others (such as the use of maximal sterile barriers during PICC insertion) were not. Asked about their perceptions of PICC use at their institution, certified inserters reported higher percentages of inappropriate insertion and removal than noncertified inserters. Certified PICC inserters appear to be a distinct group of vascular access specialists. A better understanding of how and why practices differ between certified and noncertified inserters is necessary to ensuring safer, high-quality patient care.

Do dual-thread orthodontic mini-implants improve bone/tissue mechanical retention?

PubMed

Lin, Yang-Sung; Chang, Yau-Zen; Yu, Jian-Hong; Lin, Chun-Li

2014-12-01

The aim of this study was to understand whether the pitch relationship between micro and macro thread designs with a parametrical relationship in a dual-thread mini-implant can improve primary stability. Three types of mini-implants consisting of single-thread (ST) (0.75 mm pitch in whole length), dual-thread A (DTA) with double-start 0.375 mm pitch, and dual-thread B (DTB) with single-start 0.2 mm pitch in upper 2-mm micro thread region for performing insertion and pull-out testing. Histomorphometric analysis was performed in these specimens in evaluating peri-implant bone defects using a non-contact vision measuring system. The maximum inserted torque (Tmax) in type DTA was found to be the smallest significantly, but corresponding values found no significant difference between ST and DTB. The largest pull-out strength (Fmax) in the DTA mini-implant was found significantly greater than that for the ST mini-implant regardless of implant insertion orientation. Mini-implant engaged the cortical bone well as observed in ST and DTA types. Dual-thread mini-implant with correct micro thread pitch (parametrical relationship with macro thread pitch) in the cortical bone region can improve primary stability and enhanced mechanical retention.

Labeling viral envelope lipids with quantum dots by harnessing the biotinylated lipid-self-inserted cellular membrane.

PubMed

Lv, Cheng; Lin, Yi; Liu, An-An; Hong, Zheng-Yuan; Wen, Li; Zhang, Zhenfeng; Zhang, Zhi-Ling; Wang, Hanzhong; Pang, Dai-Wen

2016-11-01

Highly efficient labeling of viruses with quantum dots (QDs) is the prerequisite for the long-term tracking of virus invasion at the single virus level to reveal mechanisms of virus infection. As one of the structural components of viruses, viral envelope lipids are hard to be labeled with QDs due to the lack of efficient methods to modify viral envelope lipids. Moreover, it is still a challenge to maintain the intactness and infectivity of labeled viruses. Herein, a mild method has been developed to label viral envelope lipids with QDs by harnessing the biotinylated lipid-self-inserted cellular membrane. Biotinylated lipids can spontaneously insert in cellular membranes of host cells during culture and then be naturally assembled on progeny Pseudorabies virus (PrV) via propagation. The biotinylated PrV can be labeled with streptavidin-conjugated QDs, with a labeling efficiency of ∼90%. Such a strategy to label lipids with QDs can retain the intactness and infectivity of labeled viruses to the largest extent, facilitating the study of mechanisms of virus infection at the single virus level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Printed Antennas Made Reconfigurable by Use of MEMS Switches

NASA Technical Reports Server (NTRS)

Simons, Rainee N.

2005-01-01

A class of reconfigurable microwave antennas now undergoing development comprise fairly conventional printed-circuit feed elements and radiating patches integrated with novel switches containing actuators of the microelectromechanical systems (MEMS) type. In comparison with solid-state electronic control devices incorporated into some prior printed microwave antennas, the MEMS-based switches in these antennas impose lower insertion losses and consume less power. Because the radio-frequency responses of the MEMS switches are more nearly linear, they introduce less signal distortion. In addition, construction and operation are simplified because only a single DC bias line is needed to control each MEMS actuator.

Advanced RF Front End Technology

NASA Technical Reports Server (NTRS)

Herman, M. I.; Valas, S.; Katehi, L. P. B.

2001-01-01

The ability to achieve low-mass low-cost micro/nanospacecraft for Deep Space exploration requires extensive miniaturization of all subsystems. The front end of the Telecommunication subsystem is an area in which major mass (factor of 10) and volume (factor of 100) reduction can be achieved via the development of new silicon based micromachined technology and devices. Major components that make up the front end include single-pole and double-throw switches, diplexer, and solid state power amplifier. JPL's Center For Space Microsystems - System On A Chip (SOAC) Program has addressed the challenges of front end miniaturization (switches and diplexers). Our objectives were to develop the main components that comprise a communication front end and enable integration in a single module that we refer to as a 'cube'. In this paper we will provide the latest status of our Microelectromechanical System (MEMS) switches and surface micromachined filter development. Based on the significant progress achieved we can begin to provide guidelines of the proper system insertion for these emerging technologies. Additional information is contained in the original extended abstract.

DNA glycosylases search for and remove oxidized DNA bases.

PubMed

Wallace, Susan S

2013-12-01

This review article presents, an overview of the DNA glycosylases that recognize oxidized DNA bases using the Fpg/Nei family of DNA glycosylases as models for how structure can inform function. For example, even though human NEIL1 and the plant and fungal orthologs lack the zinc finger shown to be required for binding, DNA crystal structures revealed a "zincless finger" with the same properties. Moreover, the "lesion recognition loop" is not involved in lesion recognition, rather, it stabilizes 8-oxoG in the active site pocket. Unlike the other Fpg/Nei family members, Neil3 lacks two of the three void-filling residues that stabilize the DNA duplex and interact with the opposite strand to the damage which may account for its preference for lesions in single-stranded DNA. Also single-molecule approaches show that DNA glycosylases search for their substrates in a sea of undamaged DNA by using a wedge residue that is inserted into the DNA helix to probe for the presence of damage. Copyright © 2013 Wiley Periodicals, Inc.

Analysis and Design of a Novel W-band SPST Switch by Employing Full-Wave EM Simulator

NASA Astrophysics Data System (ADS)

Xu, Zhengbin; Guo, Jian; Qian, Cheng; Dou, Wenbin

2011-12-01

In this paper, a W-band single pole single throw (SPST) switch based on a novel PIN diode model is presented. The PIN diode is modeled using a full-wave electromagnetic (EM) simulator and its parasitic parameters under both forward and reverse bias states are described by a T-network. By this approach, the measurement-based model, which is usually a must for high performance switch design, is no longer necessary. A compensation structure is optimized to obtain a high isolation of the switch. Accordingly, a W-band SPST switch is designed using a full wave EM simulator. Measurement results agree very well with simulated ones. Our measurements show that the developed switch has less than 1.5 dB insertion loss under the `on' state from 88 GHz to 98 GHz. Isolation greater than 30 dB over 2 GHz bandwidth and greater than 20 dB over 5 GHz bandwidth can be achieved at the center frequency of 94 GHz under the `off' state.

30GHz Ge electro-absorption modulator integrated with 3 μm silicon-on-insulator waveguide.

PubMed

Feng, Ning-Ning; Feng, Dazeng; Liao, Shirong; Wang, Xin; Dong, Po; Liang, Hong; Kung, Cheng-Chih; Qian, Wei; Fong, Joan; Shafiiha, Roshanak; Luo, Ying; Cunningham, Jack; Krishnamoorthy, Ashok V; Asghari, Mehdi

2011-04-11

We demonstrate a compact waveguide-based high-speed Ge electro-absorption (EA) modulator integrated with a single mode 3 µm silicon-on-isolator (SOI) waveguide. The Ge EA modulator is based on a horizontally-oriented p-i-n structure butt-coupled with a deep-etched silicon waveguide, which transitions adiabatically to a shallow-etched single mode large core SOI waveguide. The demonstrated device has a compact active region of 1.0 × 45 µm(2), a total insertion loss of 2.5-5 dB and an extinction ratio of 4-7.5 dB over a wavelength range of 1610-1640 nm with -4V(pp) bias. The estimated Δα/α value is in the range of 2-3.3. The 3 dB bandwidth measurements show that the device is capable of operating at more than 30 GHz. Clear eye-diagram openings at 12.5 Gbps demonstrates large signal modulation at high transmission rate. © 2011 Optical Society of America

Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development

PubMed Central

Drögemüller, Cord; Tetens, Jens; Sigurdsson, Snaevar; Gentile, Arcangelo; Testoni, Stefania; Lindblad-Toh, Kerstin; Leeb, Tosso

2010-01-01

Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development. PMID:20865119

Development of large-aperture electro-optical switch for high power laser at CAEP

NASA Astrophysics Data System (ADS)

Zhang, Xiongjun; Wu, Dengsheng; Zhang, Jun; Lin, Donghui; Zheng, Jiangang; Zheng, Kuixing

2015-02-01

Large-aperture electro-optical switch based on plasma Pockels cell (PPC) is one of important components for inertial confinement fusion (ICF) laser facility. We have demonstrated a single-pulse driven 4×1 PPC with 400mm×400mm aperture for SGIII laser facility. And four 2×1 PPCs modules with 350mm×350mm aperture have been operated in SGII update laser facility. It is different to the PPC of NIF and LMJ for its simple operation to perform Pockels effect. With optimized operation parameters, the PPCs meet the SGII-U laser requirement of four-pass amplification control. Only driven by one high voltage pulser, the simplified PPC system would be provided with less associated diagnostics, and higher reliability. To farther reduce the insert loss of the PPC, research on the large-aperture PPC based on DKDP crystal driven by one pulse is developed. And several single-pulse driven PPCs with 80mm×80mm DKDP crystal have been manufactured and operated in laser facilities.

Acid-triggered membrane insertion of Pseudomonas exotoxin A involves an original mechanism based on pH-regulated tryptophan exposure.

PubMed

Méré, Jocelyn; Morlon-Guyot, Juliette; Bonhoure, Anne; Chiche, Laurent; Beaumelle, Bruno

2005-06-03

Exposure to low endosomal pH during internalization of Pseudomonas exotoxin A (PE) triggers membrane insertion of its translocation domain. This process is a prerequisite for PE translocation to the cytosol where it inactivates protein synthesis. Although hydrophobic helices enable membrane insertion of related bacterial toxins such as diphtheria toxin, the PE translocation domain is devoid of hydrophobic stretches and the structural features triggering acid-induced membrane insertion of PE are not known. Here we have identified a molecular device that enables PE membrane insertion. This process is promoted by exposure of a key tryptophan residue. At neutral pH, this Trp is buried in a hydrophobic pocket closed by the smallest alpha-helix of the translocation domain. Upon acidification, protonation of the Asp that is the N-cap residue of the helix leads to its destabilization, enabling Trp side chain insertion into the endosome membrane. This tryptophan-based membrane insertion system is surprisingly similar to the membrane-anchoring mechanism of human annexin-V and could be used by other proteins as well.

Arrays of Molecular Rotors with Triptycene Stoppers: Surface Inclusion in Hexagonal Tris(o-phenylenedioxy)cyclotriphosphazene.

PubMed

Kaleta, Jiří; Dron, Paul I; Zhao, Ke; Shen, Yongqiang; Císařová, Ivana; Rogers, Charles T; Michl, Josef

2015-06-19

A new generation of rod-shaped dipolar molecular rotors designed for controlled insertion into channel arrays in the surface of hexagonal tris(o-phenylenedioxy)cyclotriphosphazene (TPP) has been designed and synthesized. Triptycene is used as a stopper intended to prevent complete insertion, forcing the formation of a surface inclusion. Two widely separated (13)C NMR markers are present in the shaft for monitoring the degree of insertion. The structure of the two-dimensional rotor arrays contained in these surface inclusions was examined by solid-state NMR and X-ray powder diffraction. The NMR markers and the triptycene stopper functioned as designed, but half of the guest molecules were not inserted as deeply into the TPP channels as the other half. As a result, the dipolar rotators were distributed equally in two planes parallel to the crystal surface instead of being located in a single plane as would be required for ferroelectricity. Dielectric spectroscopy revealed rotational barriers of ∼4 kcal/mol but no ferroelectric behavior.

Cross sectional survey of ultrasound use for central venous catheter insertion among resident physicians.

PubMed

Nomura, Jason T; Sierzenski, Paul R; Nace, Jason E; Bollinger, Melissa

2008-07-01

Use of ultrasound guidance for Central Venous Catheter insertion has been associated with decreased complications and increased success rates. Previous reports show low rates of use among physicians. Evaluation of the frequency of Ultrasound Guidance use for Central Venous Catheter insertion among residents at a teaching institution. A cross sectional electronic survey of resident physicians at a tertiary care teaching hospital was conducted to evaluate use of Ultrasound Guidance for Central Venous Catheterization. Assessment included self reported frequency of ultrasound guidance use, and volume of central venous catheter placement. Attitudes toward the use of ultrasound were assessed using Likert scales. There is a high rate. over 90%, of ultrasound guidance use for Internal Jugular central venous catheters among residents. The majority of residents use sterile real-time imaging with a single operator with a reported success rate greater then 80%. Resident use of ultrasound guidance for Internal Jugular central venous catheter insertion can be much higher than previously reported in the literature.

Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion.

PubMed

Gladyshev, Eugene A; Arkhipova, Irina R

2009-12-15

Ribosomal DNA genes in many eukaryotes contain insertions of non-LTR retrotransposable elements belonging to the R2 clade. These elements persist in the host genomes by inserting site-specifically into multicopy target sites, thereby avoiding random disruption of single-copy host genes. Here we describe R9 retrotransposons from the R2 clade in the 28S RNA genes of bdelloid rotifers, small freshwater invertebrate animals best known for their long-term asexuality and for their ability to survive repeated cycles of desiccation and rehydration. While the structural organization of R9 elements is highly similar to that of other members of the R2 clade, they are characterized by two distinct features: site-specific insertion into a previously unreported target sequence within the 28S gene, and an unusually long target site duplication of 126 bp. We discuss the implications of these findings in the context of bdelloid genome organization and the mechanisms of target-primed reverse transcription.

Spin Hall driven domain wall motion in magnetic bilayers coupled by a magnetic oxide interlayer

NASA Astrophysics Data System (ADS)

Liu, Yang; Furuta, Masaki; Zhu, Jian-Gang Jimmy

2018-05-01

mCell, previously proposed by our group, is a four-terminal magnetoresistive device with isolated write- and read-paths for all-spin logic and memory applications. A mCell requires an electric-insulating magnetic layer to couple the spin Hall driven write-path to the magnetic free layer of the read-path. Both paths are magnetic layers with perpendicular anisotropy and their perpendicularly oriented magnetization needs to be maintained with this insertion layer. We have developed a magnetic oxide (FeOx) insertion layer to serve for these purposes. We show that the FeOx insertion layer provides sufficient magnetic coupling between adjacent perpendicular magnetic layers. Resistance measurement shows that this magnetic oxide layer can act as an electric-insulating layer. In addition, spin Hall driven domain wall motion in magnetic bi-layers coupled by the FeOx insertion layer is significantly enhanced compared to that in magnetic single layer; it also requires low voltage threshold that poses possibility for power-efficient device applications.

Highly Compact Circulators in Square-Lattice Photonic Crystal Waveguides

PubMed Central

Jin, Xin; Ouyang, Zhengbiao; Wang, Qiong; Lin, Mi; Wen, Guohua; Wang, Jingjing

2014-01-01

We propose, demonstrate and investigate highly compact circulators with ultra-low insertion loss in square-lattice- square-rod-photonic-crystal waveguides. Only a single magneto- optical square rod is required to be inserted into the cross center of waveguides, making the structure very compact and ultra efficient. The square rods around the center defect rod are replaced by several right-angled-triangle rods, reducing the insertion loss further and promoting the isolations as well. By choosing a linear-dispersion region and considering the mode patterns in the square magneto-optical rod, the operating mechanism of the circulator is analyzed. By applying the finite-element method together with the Nelder-Mead optimization method, an extremely low insertion loss of 0.02 dB for the transmitted wave and ultra high isolation of 46 dB∼48 dB for the isolated port are obtained. The idea presented can be applied to build circulators in different wavebands, e.g., microwave or Tera-Hertz. PMID:25415417

Highly compact circulators in square-lattice photonic crystal waveguides.

PubMed

Jin, Xin; Ouyang, Zhengbiao; Wang, Qiong; Lin, Mi; Wen, Guohua; Wang, Jingjing

2014-01-01

We propose, demonstrate and investigate highly compact circulators with ultra-low insertion loss in square-lattice- square-rod-photonic-crystal waveguides. Only a single magneto- optical square rod is required to be inserted into the cross center of waveguides, making the structure very compact and ultra efficient. The square rods around the center defect rod are replaced by several right-angled-triangle rods, reducing the insertion loss further and promoting the isolations as well. By choosing a linear-dispersion region and considering the mode patterns in the square magneto-optical rod, the operating mechanism of the circulator is analyzed. By applying the finite-element method together with the Nelder-Mead optimization method, an extremely low insertion loss of 0.02 dB for the transmitted wave and ultra high isolation of 46 dB∼48 dB for the isolated port are obtained. The idea presented can be applied to build circulators in different wavebands, e.g., microwave or Tera-Hertz.

Composition and structure of porcine digital flexor tendon-bone insertion tissues.

PubMed

Chandrasekaran, Sandhya; Pankow, Mark; Peters, Kara; Huang, Hsiao-Ying Shadow

2017-11-01

Tendon-bone insertion is a functionally graded tissue, transitioning from 200 MPa tensile modulus at the tendon end to 20 GPa tensile modulus at the bone, across just a few hundred micrometers. In this study, we examine the porcine digital flexor tendon insertion tissue to provide a quantitative description of its collagen orientation and mineral concentration by using Fast Fourier Transform (FFT) based image analysis and mass spectrometry, respectively. Histological results revealed uniformity in global collagen orientation at all depths, indicative of mechanical anisotropy, although at mid-depth, the highest fiber density, least amount of dispersion, and least cellular circularity were evident. Collagen orientation distribution obtained through 2D FFT of histological imaging data from fluorescent microscopy agreed with past measurements based on polarized light microscopy. Results revealed global fiber orientation across the tendon-bone insertion to be preserved along direction of physiologic tension. Gradation in the fiber distribution orientation index across the insertion was reflective of a decrease in anisotropy from the tendon to the bone. We provided elemental maps across the fibrocartilage for its organic and inorganic constituents through time-of-flight secondary ion mass spectrometry (TOF-SIMS). The apatite intensity distribution from the tendon to bone was shown to follow a linear trend, supporting past results based on Raman microprobe analysis. The merit of this study lies in the image-based simplified approach to fiber distribution quantification and in the high spatial resolution of the compositional analysis. In conjunction with the mechanical properties of the insertion tissue, fiber, and mineral distribution results for the insertion from this may potentially be incorporated into the development of a structural constitutive approach toward computational modeling. Characterizing the properties of the native insertion tissue would provide the microstructural basis for developing biomimetic scaffolds to recreate the graded morphology of a fibrocartilaginous insertion. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3050-3058, 2017. © 2017 Wiley Periodicals, Inc.

[Correlation analysis between single nucleotide polymorphism of FGF5 gene and wool yield in rabbits].

PubMed

Li, Chun-Xiao; Jiang, Mei-Shan; Chen, Shi-Yi; Lai, Song-Jia

2008-07-01

Single nucleotide polymorphism (SNP) in exon 1 and 3 of fibroblast growth factor (FGF5) gene was studied by DNA sequencing in Yingjing angora rabbit, Tianfu black rabbit and California rabbit. A frameshift mutation (TCT insert) at base position 217 (site A) of exon 1 and a T/C missense mutation at base position 59 (site B) of exon 3 were found in Yingjing angora rabbit with a high frequency; a T/C same-sense mutation at base position 3 (site C) of exon 3 was found with similar frequency in three rabbit breeds. Least square analysis showed that different genotypes had no significant association with wool yield in site A, and had high significant association with wool yield in site B (P<0.01) and significant association with wool yield in site C (P<0.05). It was concluded from the results that FGF5 gene could be the potential major gene affecting wool yield or link with the major gene, and polymorphic loci B and C may be used as molecular markers for im-proving wool yield in angora rabbits.

Insertion of targeting domains into the envelope glycoprotein of Moloney murine leukemia virus (MoMLV)-based vectors modulates the route of mCAT-1-mediated viral entry.

PubMed

Viejo-Borbolla, A; Pizzato, M; Blair, E D; Schulz, T F

2005-03-01

Several groups have inserted targeting domains into the envelope glycoprotein (Env) of Moloney murine leukemia virus (MoMLV) in an attempt to produce targeted retroviral vectors for human gene therapy. While binding of these modified Envs to the target molecule expressed on the surface of human cells was observed, specific high-titer infection of human cells expressing the target molecule was not achieved. Here we investigate the initial steps in the entry process of targeted MoMLV vectors both in murine and human cells expressing the MoMLV receptor, the mouse cationic amino acid transporter-1 (mCAT-1). We show that insertion of a small ligand targeted to E-selectin and of a single chain antibody (scFv) targeted to folate-binding protein (FBP) into the N-terminus of MoMLV Env results in the reduction of the infectivity and the kinetics of entry of the MoMLV vectors. The use of soluble receptor-binding domain (sRBD), bafilomycin A1 (BafA1) and methyl-beta-cyclodextrin (MbetaC) increase the infectivity of the MoMLV vectors targeted to FBP (MoMLV-FBP) suggesting that the scFv targeted to FBP increases the threshold for fusion and might re-route entry of the targeted MoMLV-FBP vector towards an endocytic, non-productive pathway.

Structural transformation during Li/Na insertion and theoretical cyclic voltammetry of the δ-NH4V4O10 electrode: a first-principles study.

PubMed

Sarkar, Tanmay; Kumar, Parveen; Bharadwaj, Mridula Dixit; Waghmare, Umesh

2016-04-14

A double layer δ-NH4V4O10, due to its high energy storage capacity and excellent rate capability, is a very promising cathode material for Li-ion and Na-ion batteries for large-scale renewable energy storage in transportation and smart grids. While it possesses better stability, and higher ionic and electronic conductivity than the most widely explored V2O5, the mechanisms of its cyclability are yet to be understood. Here, we present a theoretical cyclic voltammetry as a tool based on first-principles calculations, and uncover structural transformations that occur during Li(+)/Na(+) insertion (x) into (Lix/Nax)NH4V4O10. Structural distortions associated with single-phase and multi-phase structural changes during the insertion of Li(+)/Na(+), identified through the analysis of voltage profile and theoretical cyclic voltammetry are in agreement with the reported experimental electrochemical measurements on δ-NH4V4O10. We obtain an insight into its electronic structure with a lower band gap that is responsible for the high rate capability of (Lix/Nax) δ-NH4V4O10. The scheme of theoretical cyclic voltammetry presented here will be useful for addressing issues of cyclability and energy rate in other electrode materials.

Precision grid and hand motion for accurate needle insertion in brachytherapy

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

McGill, Carl S.; Schwartz, Jonathon A.; Moore, Jason Z.

2011-08-15

Purpose: In prostate brachytherapy, a grid is used to guide a needle tip toward a preplanned location within the tissue. During insertion, the needle deflects en route resulting in target misplacement. In this paper, 18-gauge needle insertion experiments into phantom were performed to test effects of three parameters, which include the clearance between the grid hole and needle, the thickness of the grid, and the needle insertion speed. Measurement apparatus that consisted of two datum surfaces and digital depth gauge was developed to quantify needle deflections. Methods: The gauge repeatability and reproducibility (GR and R) test was performed on themore » measurement apparatus, and it proved to be capable of measuring a 2 mm tolerance from the target. Replicated experiments were performed on a 2{sup 3} factorial design (three parameters at two levels) and analysis included averages and standard deviation along with an analysis of variance (ANOVA) to find significant single and two-way interaction factors. Results: Results showed that grid with tight clearance hole and slow needle speed increased precision and accuracy of needle insertion. The tight grid was vital to enhance precision and accuracy of needle insertion for both slow and fast insertion speed; additionally, at slow speed the tight, thick grid improved needle precision and accuracy. Conclusions: In summary, the tight grid is important, regardless of speed. The grid design, which shows the capability to reduce the needle deflection in brachytherapy procedures, can potentially be implemented in the brachytherapy procedure.« less

Reproductive performance of ewes after 5-day treatment with intravaginal inserts containing progesterone in combination with injection of prostaglandin f2alpha.

PubMed

Dixon, A B; Knights, M; Pate, J L; Lewis, P E; Inskeep, E K

2006-04-01

Three experiments were conducted with a total of 1579 ewes to examine reproductive performance in response to synchronization of oestrus during the breeding season, using controlled internal drug releasing (CIDR-G) inserts in regimens designed to provide high concentrations of circulating progesterone. In experiment 1, treatment with two CIDR-G inserts for 12 days produced conception rate (79%) and prolificacy (1.9) to first service equivalent to breeding at natural oestrus (56% and 2.0, respectively). Pregnancy rates to two service periods were 90 and 79%, respectively. In experiments 2 and 3, progesterone was delivered by a single CIDR-G insert for 5 days in combination with prostaglandin F2alpha (PGF2alpha; 5 mg i.m., twice, 3 h apart) the day before (experiment 2), or at insert removal (experiment 3). The combined treatments improved rates of synchronization of oestrus (p<0.01) by 23 and 20% points, respectively, and pregnancy rates to the first service period by 19 (p<0.05) and 13 (p<0.01) percentage points, respectively, compared to treatment with PGF2alpha alone. It is concluded that the combination of treatment for 5 days with a CIDR-G insert and two injections of 5 mg PGF2alpha, the day before, or the day of insert removal, were effective treatments to obtain high fertility at synchronized oestrus in ewes during the breeding season.

The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition

PubMed Central

Servant, Geraldine; Streva, Vincent A.; Derbes, Rebecca S.; Wijetunge, Madushani I.; Neeland, Marc; White, Travis B.; Belancio, Victoria P.; Roy-Engel, Astrid M.; Deininger, Prescott L.

2017-01-01

Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a “copy-and-paste” mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3′ DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway. To determine if the NER pathway prevents the insertion of retroelements in the genome, we monitored the retrotransposition efficiencies of engineered L1 elements in NER-deficient cells and in their complemented versions. Core proteins of the NER pathway, XPD and XPA, and the lesion binding protein, XPC, are involved in limiting L1 retrotransposition. In addition, sequence analysis of recovered de novo L1 inserts and their genomic locations in NER-deficient cells demonstrated the presence of abnormally large duplications at the site of insertion, suggesting that NER proteins may also play a role in the normal L1 insertion process. Here, we propose new functions for the NER pathway in the maintenance of genome integrity: limitation of insertional mutations caused by retrotransposons and the prevention of potentially mutagenic large genomic duplications at the site of retrotransposon insertion events. PMID:28049704

Effectiveness of the surgical torque limiter: a model comparing drill- and hand-based screw insertion into locking plates.

PubMed

Ioannou, Christopher; Knight, Matthew; Daniele, Luca; Flueckiger, Lee; Tan, Ezekiel S L

2016-10-17

The objective of this study is to analyse the effectiveness of the surgical torque limiter during operative use. The study also investigates the potential differences in torque between hand and drill-based screw insertion into locking plates using a standardised torque limiter. Torque for both hand and power screw insertion was measured through a load cell, registering 6.66 points per second. This was performed in a controlled environment using synthetic bone, a locking plate and locking screws to simulate plate fixation. Screws were inserted by hand and by drill with torque values measured. The surgical torque limiter (1.5 Nm) was effective as the highest recorded reading in the study was 1.409 Nm. Comparatively, there is a statistically significant difference between screw insertion methods. Torque produced for manually driven screw insertion into locking plates was 1.289 Nm (95 % CI 1.269-1.308) with drill-powered screw insertion at 0.740 Nm (95 % CI 0.723-0.757). The surgical torque limiter proved to be effective as per product specifications. Screws inserted under power produce significantly less torque when compared to manual insertion by hand. This is likely related to the mechanism of the torque limiter when being used at higher speeds for which it was designed. We conclude that screws may be inserted using power to the plate with the addition of a torque limiter. It is recommended that all screws inserted by drill be hand tightened to achieve adequate torque values.

Shoe inserts and orthotics for sport and physical activities.

PubMed

Nigg, B M; Nurse, M A; Stefanyshyn, D J

1999-07-01

The purposes of this paper were to discuss the perceived benefits of inserts and orthotics for sport activities and to propose a new concept for inserts and orthotics. There is evidence that inserts or orthotics reduce or prevent movement-related injuries. However, there is limited knowledge about the specific functioning an orthotic or insert provides. The same orthotic or insert is often proposed for different problems. Changes in skeletal movement due to inserts or orthotics seem to be small and not systematic. Based on the results of a study using bone pins, one may question the idea that a major function of orthotics or inserts consists in aligning the skeleton. Impact cushioning with shoe inserts or orthotics is typically below 10%. Such small reductions might not be important for injury reduction. It has been suggested that changes in material properties might produce adjustments in the muscular response of the locomotor system. The foot has various sensors to detect input signals with subject specific thresholds. Subjects with similar sensitivity threshold levels seem to respond in their movement pattern in a similar way. Comfort is an important variable. From a biomechanical point of view, comfort may be related to fit, additional stabilizing muscle work, fatigue, and damping of soft tissue vibrations. Based on the presented evidence, the concept of minimizing muscle work is proposed when using orthotics or inserts. A force signal acts as an input variable on the shoe. The shoe sole acts as a first filter, the insert or orthotic as a second filter, the plantar surface of the foot as a third filter for the force input signal. The filtered information is transferred to the central nervous system that provides a subject specific dynamic response. The subject performs the movement for the task at hand. For a given movement task, the skeleton has a preferred path. If an intervention supports/counteracts the preferred movement path, muscle activity can/must be reduced/increased. Based on this concept, an optimal insert or orthotic would reduce muscle activity, feel comfortable, and should increase performance.

SU-E-T-64: A Programmable Moving Insert for the ArcCHECK Phantom for Dose Verification of Respiratory-Gated VMAT

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

Gaede, S; Jordan, K; Western University, London, ON

Purpose: To present a customized programmable moving insert for the ArcCHECK™ phantom that can, in a single delivery, check both entrance dosimetry, while simultaneously verifying the delivery of respiratory-gated VMAT. Methods: The cylindrical motion phantom uses a computer-controlled stepping motor to move an insert inside a stationery sleeve. Insert motion is programmable and can include rotational motion in addition to linear motion along the axis of the cylinder. The sleeve fits securely in the bore of the ArcCHECK™. Interchangeable inserts, including an A1SL chamber, optically-stimulated luminescence dosimeters, radiochromic film, or 3D gels, allow this combination to be used for commissioning,more » routine quality assurance, and patient-specific dosimetric verification of respiratory-gated VMAT. Before clinical implementation, the effect of a moving insert on the ArcCHECK™ measurements was considered. First, the measured dose to the ArcCHECK™ containing multiple inserts in the static position was compared to the calculated dose during multiple VMAT treatment deliveries. Then, dose was measured under both sinusoidal and real-patient motion conditions to determine any effect of the moving inserts on the ArcCHECK™ measurements. Finally, dose was measured during gated VMAT delivery to the same inserts under the same motion conditions to examine any effect of various beam “on-and-off” and dose rate ramp “up-and-down”. Multiple comparisons between measured and calculated dose to different inserts were also considered. Results: The pass rate for the static delivery exceeded 98% for all measurements (3%/3mm), suggesting a valid setup for entrance dosimetry. The pass rate was not altered for any measurement delivered under motion conditions. A similar Result was observed under gated VMAT conditions, including agreement of measured and calculated dose to the various inserts. Conclusion: Incorporating a programmable moving insert within the ArcCHECK™ phantom provides an efficient verification of respiratory-gated VMAT delivery that is useful during commissioning, routine quality assurance, and patient-specific dose verification. Prototype phantom development and testing was performed in collaboration with Modus Medical Devices Inc. (London, ON). No financial support was granted.« less

Peripherally inserted central catheter - dressing change

MedlinePlus

... chlorhexidine) in a single-use small applicator Special sponges or wipes that contain a cleaning agent, such ... Clean your skin around the site with the sponge and cleaning solution for 30 seconds. Let the ...

Crispr-mediated Gene Targeting of Human Induced Pluripotent Stem Cells.

PubMed

Byrne, Susan M; Church, George M

2015-01-01

CRISPR/Cas9 nuclease systems can create double-stranded DNA breaks at specific sequences to efficiently and precisely disrupt, excise, mutate, insert, or replace genes. However, human embryonic stem or induced pluripotent stem cells (iPSCs) are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe an optimized protocol for genome engineering of human iPSCs using a simple transient transfection of plasmids and/or single-stranded oligonucleotides. With this protocol, we achieve transfection efficiencies greater than 60%, with gene disruption efficiencies from 1-25% and gene insertion/replacement efficiencies from 0.5-10% without any further selection or enrichment steps. We also describe how to design and assess optimal sgRNA target sites and donor targeting vectors; cloning individual iPSC by single cell FACS sorting, and genotyping successfully edited cells.

Button fixation technique for Achilles tendon reinsertion: a biomechanical study.

PubMed

Awogni, David; Chauvette, Guillaume; Lemieux, Marie-Line; Balg, Frédéric; Langelier, Ève; Allard, Jean-Pascal

2014-01-01

Chronic insertional tendinopathy of the Achilles tendon is a frequent and disabling pathologic entity. Operative treatment is indicated for patients for whom nonoperative management has failed. The treatment can consist of the complete detachment of the tendon insertion and extensive debridement. We biomechanically tested a new operative technique that uses buttons for fixation of the Achilles tendon insertion on the posterior calcaneal tuberosity and compared it with 2 standard bone anchor techniques. A total of 40 fresh-frozen cadaver specimens were used to compare 3 fixation techniques for reinserting the Achilles tendon: single row anchors, double row anchors, and buttons. The ultimate loads and failure mechanisms were recorded. The button assembly (median load 764 N, range 713 to 888) yielded a median fixation strength equal to 202% (range 137% to 251%) of that obtained with the double row anchors (median load 412 N, range 301 to 571) and 255% (range 213% to 317%) of that obtained with the single row anchors (median load 338 N, range 241 to 433N). The most common failure mechanisms were suture breakage with the buttons (55%) and pull out of the implant with the double row (70%) and single row (85%) anchors. The results of the present biomechanical cadaver study have shown that Achilles tendon reinsertion fixation using the button technique provides superior pull out strength than the bone anchors tested. Copyright © 2014 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Long-Term Outcomes of Single-Port Laparoscopic Placement of Peritoneal Dialysis Catheter.

PubMed

Pan, Alan; Poi, Mun J; Matos, Jesus; Jiang, Jenny S; Kfoury, Elias; Echeverria, Angela; Bechara, Carlos F; Lin, Peter H

2016-07-01

Laparoscopic insertion of peritoneal dialysis (PD) catheter has become a preferred method compared to the traditional open technique for PD catheter insertion. We retrospectively report the outcome of 1-port laparoscopic placement PD catheters in our institution. A total of 263 patients with end-stage renal disease who underwent single-trocar laparoscopic PD catheter insertion during a recent 6-year period were reviewed. Laparoscopic technique involves introducing a PD catheter over a stiff guidewire into the abdominal cavity through a 10-mm laparoscopic port. Pertinent clinical variables, procedural complications, and follow-up outcome were analyzed. There were 182 men and 81 women. The mean age was 56 years. Technical success was 95.8%. Catheter occlusion was the most common early complications (<6 months) that occurred in 4 (1.5%) patients. Late complications (> 6 months) including catheter occlusion, cuff extrusion, catheter leakage, catheter migration, infection, and hernia occurred in 5 patients (1.9%), 2 patients (0.8%), 3 patients (1.1%), 3 patients (1.1%), 6 patients (2.3%), and 4 patients (1.5), respectively. Mean follow-up time was 39 ± 18 months. Catheter survival rate at 1, 2, 3, 4, and 5 years was 96%, 94%, 90%, 85%, and 82%, respectively. Laparoscopic PD catheter implantation via a single-trocar utilizing a stiff guidewire technique is feasible and safe. This method can result in low complication and high catheter survival rate. © The Author(s) 2016.

Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design

PubMed Central

Singh, Sagar; Lo, Meng-Chen; Damodaran, Vinod B.; Kaplan, Hilton M.; Kohn, Joachim; Zahn, Jeffrey D.; Shreiber, David I.

2016-01-01

Single-unit recording neural probes have significant advantages towards improving signal-to-noise ratio and specificity for signal acquisition in brain-to-computer interface devices. Long-term effectiveness is unfortunately limited by the chronic injury response, which has been linked to the mechanical mismatch between rigid probes and compliant brain tissue. Small, flexible microelectrodes may overcome this limitation, but insertion of these probes without buckling requires supporting elements such as a stiff coating with a biodegradable polymer. For these coated probes, there is a design trade-off between the potential for successful insertion into brain tissue and the degree of trauma generated by the insertion. The objective of this study was to develop and validate a finite element model (FEM) to simulate insertion of coated neural probes of varying dimensions and material properties into brain tissue. Simulations were performed to predict the buckling and insertion forces during insertion of coated probes into a tissue phantom with material properties of brain. The simulations were validated with parallel experimental studies where probes were inserted into agarose tissue phantom, ex vivo chick embryonic brain tissue, and ex vivo rat brain tissue. Experiments were performed with uncoated copper wire and both uncoated and coated SU-8 photoresist and Parylene C probes. Model predictions were found to strongly agree with experimental results (<10% error). The ratio of the predicted buckling force-to-predicted insertion force, where a value greater than one would ideally be expected to result in successful insertion, was plotted against the actual success rate from experiments. A sigmoidal relationship was observed, with a ratio of 1.35 corresponding to equal probability of insertion and failure, and a ratio of 3.5 corresponding to a 100% success rate. This ratio was dubbed the “safety factor”, as it indicated the degree to which the coating should be over-designed to ensure successful insertion. Probability color maps were generated to visually compare the influence of design parameters. Statistical metrics derived from the color maps and multi-variable regression analysis confirmed that coating thickness and probe length were the most important features in influencing insertion potential. The model also revealed the effects of manufacturing flaws on insertion potential. PMID:26959021

Molecular transport through large-diameter DNA nanopores

NASA Astrophysics Data System (ADS)

Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.

2016-09-01

DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ~4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ~3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration.

Software-supported USER cloning strategies for site-directed mutagenesis and DNA assembly.

PubMed

Genee, Hans Jasper; Bonde, Mads Tvillinggaard; Bagger, Frederik Otzen; Jespersen, Jakob Berg; Sommer, Morten O A; Wernersson, Rasmus; Olsen, Lars Rønn

2015-03-20

USER cloning is a fast and versatile method for engineering of plasmid DNA. We have developed a user friendly Web server tool that automates the design of optimal PCR primers for several distinct USER cloning-based applications. Our Web server, named AMUSER (Automated DNA Modifications with USER cloning), facilitates DNA assembly and introduction of virtually any type of site-directed mutagenesis by designing optimal PCR primers for the desired genetic changes. To demonstrate the utility, we designed primers for a simultaneous two-position site-directed mutagenesis of green fluorescent protein (GFP) to yellow fluorescent protein (YFP), which in a single step reaction resulted in a 94% cloning efficiency. AMUSER also supports degenerate nucleotide primers, single insert combinatorial assembly, and flexible parameters for PCR amplification. AMUSER is freely available online at http://www.cbs.dtu.dk/services/AMUSER/.

Flexible microwave PIN diodes and switches employing transferrable single-crystal Si nanomembranes on plastic substrates

NASA Astrophysics Data System (ADS)

Qin, Guoxuan; Yuan, Hao-Chih; Celler, George K.; Zhou, Weidong; Ma, Zhenqiang

2009-12-01

This paper reports the realization of flexible RF/microwave PIN diodes and switches using transferrable single-crystal Si nanomembranes (SiNM) that are monolithically integrated on low-cost, flexible plastic substrates. High frequency response is obtained through the realization of low parasitic resistance achieved with heavy ion implantation before nanomembrane release and transfer. The flexible lateral SiNM PIN diodes exhibit typical rectifying characteristics with insertion loss and isolation better than 0.9 dB and 19.6 dB, respectively, from DC to 5 GHz, as well as power handling up to 22.5 dBm without gain compression. A single-pole single-throw (SPST) flexible RF switch employing shunt-series PIN diode configuration has achieved insertion loss and isolation better than 0.6 dB and 22.9 dB, respectively, from DC to 5 GHz. Furthermore, the SPST microwave switch shows performance improvement and robustness under mechanical deformation conditions. The study demonstrates the considerable potential of using properly processed transferrable SiNM for microwave passive components. Future investigations on transferrable SiNMs will lead to eventual realization of monolithic microwave integrated systems on low-cost flexible substrates.

Microdissection and molecular manipulation of single chromosomes in woody fruit trees with small chromosomes using pomelo (Citrus grandis) as a model. I. Construction of single chromosomal DNA libraries.

PubMed

Huang, D; Wu, W; Zhou, Y; Hu, Z; Lu, L

2004-05-01

Construction of single chromosomal DNA libraries by means of chromosome microdissection and microcloning will be useful for genomic research, especially for those species that have not been extensively studied genetically. Application of the technology of microdissection and microcloning to woody fruit plants has not been reported hitherto, largely due to the generally small sizes of metaphase chromosomes and the difficulty of chromosome preparation. The present study was performed to establish a method for single chromosome microdissection and microcloning in woody fruit species using pomelo as a model. The standard karyotype of a pomelo cultivar ( Citrus grandis cv. Guanxi) was established based on 20 prometaphase photomicrographs. According to the standard karyotype, chromosome 1 was identified and isolated with fine glass microneedles controlled by a micromanipulator. DNA fragments ranging from 0.3 kb to 2 kb were acquired from the isolated single chromosome 1 via two rounds of PCR mediated by Sau3A linker adaptors and then cloned into T-easy vectors to generate a DNA library of chromosome 1. Approximately 30,000 recombinant clones were obtained. Evaluation based on 108 randomly selected clones showed that the sizes of the cloned inserts varied from 0.5 kb to 1.5 kb with an average of 860 bp. Our research suggests that microdissection and microcloning of single small chromosomes in woody plants is feasible.

Efficiency and droop improvement in a blue InGaN-based light emitting diode with a p-InGaN layer inserted in the GaN barriers

NASA Astrophysics Data System (ADS)

Wang, Xing-Fu; Tong, Jin-Hui; Zhao, Bi-Jun; Chen, Xin; Ren, Zhi-Wei; Li, Dan-Wei; Zhuo, Xiang-Jing; Zhang, Jun; Yi, Han-Xiang; Li, Shu-Ti

2013-09-01

The advantages of a blue InGaN-based light-emitting diode with a p-InGaN layer inserted in the GaN barriers is studied. The carrier concentration in the quantum well, radiative recombination rate in the active region, output power, and internal quantum efficiency are investigated. The simulation results show that the InGaN-based light-emitting diode with a p-InGaN layer inserted in the barriers has better performance over its conventional counterpart and the light emitting diode with p-GaN inserted in the barriers. The improvement is due to enhanced Mg acceptor activation and enhanced hole injection into the quantum wells.

A novel (A)γδβ(0)-thalassemia caused by DNA deletion-inversion-insertion of the β-globin gene cluster and five olfactory receptor genes: Genetic interactions, hematological phenotypes and molecular characterization.

PubMed

Singha, Kritsada; Fucharoen, Goonnapa; Hama, Abdulloh; Fucharoen, Supan

2015-07-01

To report the phenotypes and genetic basis of a novel (A)γδβ(0)-thalassemia found in Thai individuals with several forms of thalassemia. An initial study was done in an adult Thai woman who had hypochromic microcytic red cells with unusually 100% Hb F. Extended study was carried out on her parents and another 17 unrelated individuals with elevated Hb F. Hb analysis was performed by capillary electrophoresis and DNA analysis was done using PCR. A novel diagnostic method based on multiplex PCR assays was developed. DNA analysis of the proband revealed the homozygosity for a novel deletion of 118.3 kb, removing the entire (A)γ, ψβ, δ-, β-globin and five olfactory receptor (OR) genes with an insertion of a 179 bp inverted DNA sequence located behind the OR52A5 gene located downstream and an insertion of 7 orphan nucleotides. Her parents were both carriers of this mutation. Further screening in suspected cases in our series unexpectedly led to identification of an additional 17 cases with this mutation in different genotypes including plain heterozygote, homozygote, compound heterozygote with Hb E, and double heterozygote with several forms of α-thalassemia. Hematological features associated with these genetic interactions are presented. Haplotype analysis indicated a single origin of this novel deletion-inversion-insertion (A)γδβ(0)-thalassemia in the Thai population. Differentiation of this mutation and other high Hb F determinants documented previously could be done by using a developed multiplex PCR assay. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Myofibroblasts Electrotonically Coupled to Cardiomyocytes Alter Conduction: Insights at the Cellular Level from a Detailed In silico Tissue Structure Model

PubMed Central

Jousset, Florian; Maguy, Ange; Rohr, Stephan; Kucera, Jan P.

2016-01-01

Fibrotic myocardial remodeling is typically accompanied by the appearance of myofibroblasts (MFBs). In vitro, MFBs were shown to slow conduction and precipitate ectopic activity following gap junctional coupling to cardiomyocytes (CMCs). To gain further mechanistic insights into this arrhythmogenic MFB-CMC crosstalk, we performed numerical simulations in cell-based high-resolution two-dimensional tissue models that replicated experimental conditions. Cell dimensions were determined using confocal microscopy of single and co-cultured neonatal rat ventricular CMCs and MFBs. Conduction was investigated as a function of MFB density in three distinct cellular tissue architectures: CMC strands with endogenous MFBs, CMC strands with coating MFBs of two different sizes, and CMC strands with MFB inserts. Simulations were performed to identify individual contributions of heterocellular gap junctional coupling and of the specific electrical phenotype of MFBs. With increasing MFB density, both endogenous and coating MFBs slowed conduction. At MFB densities of 5–30%, conduction slowing was most pronounced in strands with endogenous MFBs due to the MFB-dependent increase in axial resistance. At MFB densities >40%, very slow conduction and spontaneous activity was primarily due to MFB-induced CMC depolarization. Coating MFBs caused non-uniformities of resting membrane potential, which were more prominent with large than with small MFBs. In simulations of MFB inserts connecting two CMC strands, conduction delays increased with increasing insert lengths and block appeared for inserts >1.2 mm. Thus, electrophysiological properties of engineered CMC-MFB co-cultures depend on MFB density, MFB size and their specific positioning in respect to CMCs. These factors may influence conduction characteristics in the heterocellular myocardium. PMID:27833567

Selective Metal Cation Capture by Soft Anionic Metal-Organic Frameworks via Drastic Single-Crystal-to-Single-Crystal Transformations

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

Tian, Jian; Saraf, Laxmikant V.; Schwenzer, Birgit

2012-05-25

Flexible anionic metal-organic frameworks transform to neutral heterobimetallic systems via single-crystal-to-single-crystal processes invoked by cation insertion. These transformations are directed by cooperative bond breakage and formation, resulting in expansion or contraction of the 3D framework by up to 33% due to the flexible nature of the organic linker. These MOFs displays highly selective uptake of divalent transition metal cations (Co2+ and Ni2+ for example) over alkali metal cations (Li+ and Na+).

Erbium Distribution in Single Crystal YAG Fibers Grown by Laser-Heated Pedestal Growth Technique

DTIC Science & Technology

2015-08-28

single crystal YAG fibers grown by laser - heated pedestal growth technique Single crystal (SC) yttrium aluminum garnet (YAG, Y3Al5O12) as a host...inserted into a SC YAG tube. This rod-in-tube was used as a preform in our laser -heated pedestal growth (LHPG) apparatus to grow a fiber with a radial...fibers grown by laser -heated pedestal growth technique Report Title Single crystal (SC) yttrium aluminum garnet (YAG, Y3Al5O12) as a host material has

Folding Properties of Cytosine Monophosphate Kinase from E. coli Indicate Stabilization through an Additional Insert in the NMP Binding Domain

PubMed Central

Beitlich, Thorsten; Lorenz, Thorsten; Reinstein, Jochen

2013-01-01

The globular 25 kDa protein cytosine monophosphate kinase (CMPK, EC ID: 2.7.4.14) from E. coli belongs to the family of nucleoside monophosphate (NMP) kinases (NMPK). Many proteins of this family share medium to high sequence and high structure similarity including the frequently found α/β topology. A unique feature of CMPK in the family of NMPKs is the positioning of a single cis-proline residue in the CORE-domain (cis-Pro124) in conjunction with a large insert in the NMP binding domain. This insert is not found in other well studied NMPKs such as AMPK or UMP/CMPK. We have analyzed the folding pathway of CMPK using time resolved tryptophan and FRET fluorescence as well as CD. Our results indicate that unfolding at high urea concentrations is governed by a single process, whereas refolding in low urea concentrations follows at least a three step process which we interpret as follows: Pro124 in the CORE-domain is in cis in the native state (Nc) and equilibrates with its trans-isomer in the unfolded state (Uc - Ut). Under refolding conditions, at least the Ut species and possibly also the Uc species undergo a fast initial collapse to form intermediates with significant amount of secondary structure, from which the trans-Pro124 fraction folds to the native state with a 100-fold lower rate constant than the cis-Pro124 species. CMPK thus differs from homologous NMP kinases like UMP/CMP kinase or AMP kinase, where folding intermediates show much lower content of secondary structure. Importantly also unfolding is up to 100-fold faster compared to CMPK. We therefore propose that the stabilizing effect of the long NMP-domain insert in conjunction with a subtle twist in the positioning of a single cis-Pro residue allows for substantial stabilization compared to other NMP kinases with α/β topology. PMID:24205218

Torsional Dynamics of Steerable Needles: Modeling and Fluoroscopic Guidance

PubMed Central

Swensen, John P.; Lin, MingDe; Okamura, Allison M.; Cowan, Noah J.

2017-01-01

Needle insertions underlie a diversity of medical interventions. Steerable needles provide a means by which to enhance existing needle-based interventions and facilitate new ones. Tip-steerable needles follow a curved path and can be steered by twisting the needle base during insertion, but this twisting excites torsional dynamics that introduce a discrepancy between the base and tip twist angles. Here, we model the torsional dynamics of a flexible rod—such as a tip-steerable needle—during subsurface insertion and develop a new controller based on the model. The torsional model incorporates time-varying mode shapes to capture the changing boundary conditions inherent during insertion. Numerical simulations and physical experiments using two distinct setups—stereo camera feedback in semi-transparent artificial tissue and feedback control with real-time X-ray imaging in optically opaque artificial tissue— demonstrate the need to account for torsional dynamics in control of the needle tip. PMID:24860026

[The ISP (Safe Insertion of PICCs) protocol: a bundle of 8 recommendations to minimize the complications related to the peripherally inserted central venous catheters (PICC)].

PubMed

Emoli, Alessandro; Cappuccio, Serena; Marche, Bruno; Musarò, Andrea; Scoppettuolo, Giancarlo; Pittiruti, Mauro

2014-01-01

The ISP (Safe Insertion of PICCs) protocol: a bundle of 8 recommendations to minimize the complications related to the peripherally inserted central venous catheters (PICC). The insertion of a peripherally inserted central venous catheter (PICC) is not without risks. The Italian Group for the Study of Long-Term Central Venous Access Devices (GAVeCeLT) has developed a protocol (SIP: Safe Implantation of PICCs) with the aim of minimizing the risks which may be associated with the placement of PICCs. The protocol is based on recommendations available in the literature and on the main clinical practice guidelines. The SIP protocol, a bundle of evidence-based recommendations, it is is easy to use, inexpensive, and cost-effective. If routinely used and carefully inplemented, it greatly reduces complications such as failure of venipuncture, accidental arterial puncture, damage of median nerve, infection and catheter related venous thrombosis.

Characterization of GM events by insert knowledge adapted re-sequencing approaches

PubMed Central

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-01-01

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events. PMID:24088728

Characterization of GM events by insert knowledge adapted re-sequencing approaches.

PubMed

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-10-03

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

Increase in transmission loss of single panels by addition of mass inclusions to a poro-elastic layer: Experimental investigation

NASA Astrophysics Data System (ADS)

Kidner, M. R. F.; Fuller, C. R.; Gardner, B.

2006-06-01

The insertion loss of standard acoustic blankets can be significantly improved at low frequencies by the addition of randomly placed mass inclusions to the poro-elastic layers. The improvement is much greater than that due to the mass effect alone. The mass inclusions act as resonant systems and so increase the structure impedance. This paper reports the results of experimental investigations into this phenomenon. Increases in insertion loss of 15 dB in the 100 Hz third octave band are reported.

A low-loss, single-pole, four-throw RF MEMS switch driven by a double stop comb drive

NASA Astrophysics Data System (ADS)

Kang, S.; Kim, H. C.; Chun, K.

2009-03-01

Our goal was to develop a single-pole four-throw (SP4T) radio frequency microelectromechanical system (RF MEMS) switch for band selection in a multi-band, multi-mode, front-end module of a wireless transceiver system. The SP4T RF MEMS switch was based on an arrangement of four single-pole single-throw (SPST) RF MEMS switches. The SP4T RF MEMS switch was driven by a double stop (DS) comb drive, with a lateral resistive contact, and composed of single crystalline silicon (SCS) on glass. A large contact force at a low-drive voltage was achieved by electrostatic actuation of the DS comb drive. Good RF characteristics were achieved by the large contact force and the lateral resistive Au-to-Au contact. Mechanical reliability was achieved by using SCS which has no residual stress as a structure material. The developed SP4T RF MEMS switch has a drive voltage of 15 V, an insertion loss below 0.31 dB at 6 GHz after more than one million cycles under a 10 mW signal, a return loss above 20 dB and an isolation value above 36 dB.

Lensless, ultra-wideband fiber optic rotary joint for biomedical applications.

PubMed

Kim, Wihan; Chen, Xi; Jo, Javier A; Applegate, Brian E

2016-05-01

The demands of optical fiber-based biomedical applications can, in many cases, outstrip the capabilities of lens-based commercially available fiber optic rotary joints. In some circumstances, it is necessary to use very broad spectral bandwidths (near UV to short-wave IR) and specialized optical fibers, such as double-clad fiber, and have the capacity to accommodate high rotational velocities. The broad spectrum, stretching down into the UV, presents two problems: (1) adequate chromatic correction in the lenses across the entire bandwidth and (2) strong UV absorption by the fluids used to lubricate the rotary joint. To accommodate these types of applications, we have developed an ultra-wideband lensless fiber optic rotary joint based on the principle that when two optical fibers are coaligned and placed in contact (or very close), the optical losses at the junction are very low. The advances demonstrated here enable excellent performance (<0.2  dB insertion loss), even down into the UV and spanning a wavelength range of at least 355-1360 nm with single-mode, multimode, and double-clad fibers. We also demonstrate excellent performance, ∼0.38  dB insertion loss, at rotational velocities up to 8800 rpm (146 Hz). To the best of our knowledge, this is the first demonstration of this type of rotary joint capable of such a wide bandwidth and high rotational velocities.

DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels

PubMed Central

Knechtel, Johann

2017-01-01

Abstract We have developed a novel approach for creating membrane-spanning protein-based pores. The construction principle is based on using well-defined, circular DNA nanostructures to arrange a precise number of pore-forming protein toxin monomers. We can thereby obtain, for the first time, protein pores with specifically set diameters. We demonstrate this principle by constructing artificial alpha-hemolysin (αHL) pores. The DNA/αHL hybrid nanopores composed of twelve, twenty or twenty-six monomers show stable insertions into lipid bilayers during electrical recordings, along with steady, pore size-dependent current levels. Our approach successfully advances the applicability of nanopores, in particular towards label-free studies of single molecules in large nanoscaled biological structures. PMID:29088457

A passively mode locked thulium doped fiber laser using bismuth telluride deposited multimode interference

NASA Astrophysics Data System (ADS)

Jung, M.; Lee, J.; Song, W.; Lee, Y. L.; Lee, J. H.; Shin, W.

2016-05-01

We proposed a multimode interference (MMI) fiber based saturable absorber using bismuth telluride at  ∼2 μm region. Our MMI based saturable absorber was fabricated by fusion splicing with single mode fiber and null core fiber. The MMI functioned as both wavelength fixed filter and saturable absorber. The 3 dB bandwidth and insertion loss of MMI were 42 nm and 3.4 dB at wavelength of 1958 nm, respectively. We have also reported a passively mode locked thulium doped fiber laser operating at a wavelength of 1958 nm using a multimode interference. A temporal bandwidth of  ∼46 ps was experimentally obtained at a repetition rate of 8.58 MHz.

CaFe2O4 as a self-sufficient solar energy converter

NASA Astrophysics Data System (ADS)

Tablero, C.

2017-10-01

An ideal solar energy to electricity or fuel converter should work without the use of any external bias potential. An analysis of self-sufficiency when CaFe2O4 is used to absorb the sunlight is carried out based on the CaFe2O4 absorption coefficient. We started to obtain this coefficient theoretically within the experimental bandgap range in order to fix the interval of possible values of photocurrents, maximum absorption efficiencies, and photovoltages and thus that of self-sufficiency considering only the radiative processes. Also for single-gap CaFe2O4, we evaluate an alternative for increasing the photocurrent and maximum absorption efficiency based on inserting an intermediate band using high doping or alloying.

Analysis of the 227 bp short interspersed nuclear element (SINE) insertion of the promoter of the myostatin (MSTN) gene in different horse breeds.

PubMed

Dall'Olio, Stefania; Scotti, Emilio; Fontanesi, Luca; Tassinari, Marco

2014-01-01

The myostatin (MSTN) gene encodes a protein known to be a negative regulator of muscle mass in mammalian species. Different polymorphisms of the horse (Equus caballus) MSTN gene have been identified, including single nucleotide polymorphisms and a short interspersed nuclear element (SINE) insertion of 227 bp within the promoter of the gene. The SINE insertion has been associated with performance traits in Thoroughbred racehorses and it was proposed as a predictor of optimum racing distance. The aims of this study were to perform in silico analysis to identify putative gains or abrogation of transcription-factor binding sites (TFBSs) generated by the SINE allele of the promoter and to analyse the frequency of the SINE insertion in horses used for racing (gallop and trot) and other purposes. The SINE insertion was genotyped in 227 horses from 10 breeds belonging to different morphological types (brachimorphic, mesomorphic, meso-dolichomorphic and dolichomorphic). The presence of the insertion was confirmed in the Quarter Horse (SINE allele frequency of 0.81) and in the Thoroughbred (0.51), whereas the SINE allele did not segregate in any of the other analysed breeds. As the SINE MSTN gene polymorphism may be population or breed specific, it is not a useful marker for association studies in all breeds.

Experimental Investigation of Oscillatory Flow Pressure and Pressure Drop Through Complex Geometries

NASA Technical Reports Server (NTRS)

Ibrahim, Mounir B.; Wang, Meng; Gedeon, David

2005-01-01

A series of experiments have been performed to investigate the oscillatory flow pressure and pressure drop through complex geometries. These experiments were conducted at the CSU-SLRE facility which is a horizontally opposed, two-piston, single-acting engine with a split crankshaft driving mechanism. Flow through a rectangular duct, with no insert (obstruction), was studied first. Then four different inserts were examined: Abrupt, Manifold, Diverging Short and Diverging Long. The inserts were mounted in the center of the rectangular duct to represent different type of geometries that could be encountered in Stirling machines. The pressure and pressure drop of the oscillating flow was studied for: 1) different inserts, 2) different phase angle between the two pistons of the engine (zero, 90 lead, 180, and 90 lag), and 3) for different piston frequencies (5, 10, 15, and 20 Hz). It was found that the pressure drop of the oscillatory flow increases with increasing Reynolds number. The pressure drop was shown to be mainly due to the gas inertia for the case of oscillatory flow through a rectangular duct with no insert. On the other hand, for the cases with different inserts into the rectangular duct, the pressure drop has three sources: inertia, friction, and local losses. The friction pressure drop is only a small fraction of the total pressure drop. It was also shown that the dimensionless pressure drop decreases with increasing kinetic Reynolds number.

Recent developments in turning hardened steels - A review

NASA Astrophysics Data System (ADS)

Sivaraman, V.; Prakash, S.

2017-05-01

Hard materials ranging from HRC 45 - 68 such as hardened AISI H13, AISI 4340, AISI 52100, D2 STL, D3 STEEL Steel etc., need super hard tool materials to machine. Turning of these hard materials is termed as hard turning. Hard turning makes possible direct machining of the hard materials and also eliminates the lubricant requirement and thus favoring dry machining. Hard turning is a finish turning process and hence conventional grinding is not required. Development of the new advanced super hard tool materials such as ceramic inserts, Cubic Boron Nitride, Polycrystalline Cubic Boron Nitride etc. enabled the turning of these materials. PVD and CVD methods of coating have made easier the production of single and multi layered coated tool inserts. Coatings of TiN, TiAlN, TiC, Al2O3, AlCrN over cemented carbide inserts has lead to the machining of difficult to machine materials. Advancement in the process of hard machining paved way for better surface finish, long tool life, reduced tool wear, cutting force and cutting temperatures. Micro and Nano coated carbide inserts, nanocomposite coated PCBN inserts, micro and nano CBN coated carbide inserts and similar developments have made machining of hardened steels much easier and economical. In this paper, broad literature review on turning of hardened steels including optimizing process parameters, cooling requirements, different tool materials etc., are done.

Visualization of air and metal inhomogeneities in phantoms irradiated by carbon ion beams using prompt secondary ions.

PubMed

Gaa, T; Reinhart, M; Hartmann, B; Jakubek, J; Soukup, P; Jäkel, O; Martišíková, M

2017-06-01

Non-invasive methods for monitoring of the therapeutic ion beam extension in the patient are desired in order to handle deteriorations of the dose distribution related to changes of the patient geometry. In carbon ion radiotherapy, secondary light ions represent one of potential sources of information about the dose distribution in the irradiated target. The capability to detect range-changing inhomogeneities inside of an otherwise homogeneous phantom, based on single track measurements, is addressed in this paper. Air and stainless steel inhomogeneities, with PMMA equivalent thickness of 10mm and 4.8mm respectively, were inserted into a PMMA-phantom at different positions in depth. Irradiations of the phantom with therapeutic carbon ion pencil beams were performed at the Heidelberg Ion Beam Therapy Center. Tracks of single secondary ions escaping the phantom under irradiation were detected with a pixelized semiconductor detector Timepix. The statistical relevance of the found differences between the track distributions with and without inhomogeneities was evaluated. Measured shifts of the distal edge and changes in the fragmentation probability make the presence of inhomogeneities inserted into the traversed medium detectable for both, 10mm air cavities and 1mm thick stainless steel. Moreover, the method was shown to be sensitive also on their position in the observed body, even when localized behind the Bragg-peak. The presented results demonstrate experimentally, that the method using distributions of single secondary ion tracks is sensitive to the changes of homogeneity of the traversed material for the studied geometries of the target. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Ku to V-band 4-bit MEMS phase shifter bank using high isolation SP4T switches and DMTL structures

NASA Astrophysics Data System (ADS)

Dey, Sukomal; Koul, Shiban K.; Poddar, Ajay K.; Rohde, Ulrich L.

2017-10-01

This work presents a micro-electro-mechanical system (MEMS) based on a wide-band 4-bit phase shifter using two back-to-back single-pole-four-throw (SP4T) switches and four different distributed MEMS transmission line (DMTL) structures that are implemented on 635 µm alumina substrate using surface micromachining process. An SP4T switch is designed with a series-shunt configuration and it demonstrates an average return loss of  >17 dB, an insertion loss of  <1.97 dB and maximum isolation of  >28 dB up to 60 GHz. A maximum area of the SP4T switch is ~0.76 mm2. Single-pole-single-throw and SP4T switches are capable of handling 1 W of radio frequency (RF) power up to  >100 million cycles at 25° C; they can even sustained up to  >70 million cycles with 1 W at 85 °C. The proposed wide-band phase shifter works at 17 GHz (Ku-band), 25 GHz (K-band), 35 GHz (Ka-band) and 60 GHz (V-band) frequencies. Finally,a 4-bit phase shifter demonstrates an average insertion loss of  <6 dB, return loss of  >10 dB and maximum phase error of ~3.8° at 60 GHz frequency over 500 MHz bandwidth. Total area of the fabricated device is ~11 mm2. In addition, the proposed device works well up to  >107 cycles with 1 W of RF power. To the best of the author’s knowledge, this is the best reported wide-band MEMS 4-bit phase shifter in the literature that works with a constant resolution.

[Multidimensional Strategy Regarding the Reduction of Central-Line Associated Infection in Pediatric Intensive Care].

PubMed

Rodrigues, Jorge; Dias, Andrea; Oliveira, Guiomar; Farela Neves, José

2016-06-01

To determine the central-line associated bloodstream infection rate after implementation of central venous catheter-care practice bundles and guidelines and to compare it with the previous central-line associated bloodstream infection rate. A prospective, longitudinal, observational descriptive study with an exploratory component was performed in a Pediatric Intensive Care Unit during five months. The universe was composed of every child admitted to Pediatric Intensive Care Unit who inserted a central venous catheter. A comparative study with historical controls was performed to evaluate the result of the intervention (group 1 versus group 2). Seventy five children were included, with a median age of 23 months: 22 (29.3%) newborns; 28 (37.3%) with recent surgery and 32 (43.8%) with underlying illness. A total of 105 central venous catheter were inserted, the majority a single central venous catheter (69.3%), with a mean duration of 6.8 ± 6.7 days. The most common type of central venous catheter was the short-term, non-tunneled central venous catheter (45.7%), while the subclavian and brachial flexure veins were the most frequent insertion sites (both 25.7%). There were no cases of central-line associated bloodstream infection reported during this study. Comparing with historical controls (group 1), both groups were similar regarding age, gender, department of origin and place of central venous catheter insertion. In the current study (group 2), the median length of stay was higher, while the mean duration of central venous catheter (excluding peripherally inserted central line) was similar in both groups. There were no statistical differences regarding central venous catheter caliber and number of lumens. Fewer children admitted to Pediatric Intensive Care Unit had central venous catheter inserted in group 2, with no significant difference between single or multiple central venous catheter. After multidimensional strategy implementation there was no reported central-line associated bloodstream infection Conclusions: Efforts must be made to preserve the same degree of multidimensional prevention, in order to confirm the effective reduction of the central-line associated bloodstream infection rate and to allow its maintenance.

Lysenin Toxin Membrane Insertion Is pH-Dependent but Independent of Neighboring Lysenins.

PubMed

Munguira, Ignacio L B; Takahashi, Hirohide; Casuso, Ignacio; Scheuring, Simon

2017-11-07

Pore-forming toxins form a family of proteins that act as virulence factors of pathogenic bacteria, but similar proteins are found in all kingdoms of life, including the vertebrate immune system. They are secreted as soluble monomers that oligomerize on target membranes in the so-called prepore state; after activation, they insert into the membrane and adopt the pore state. Lysenin is a pore-forming toxin from the earthworm Eisenida foetida, of which both the soluble and membrane-inserted structures are solved. However, the activation and membrane-insertion mechanisms have remained elusive. Here, we used high-speed atomic force microscopy to directly visualize the membrane-insertion mechanism. Changing the environmental pH from pH 7.5 to below pH 6.0 favored membrane insertion. We detected a short α-helix in the soluble structure that comprised three glutamic acids (Glu92, Glu94, and Glu97) that we hypothesized may represent a pH-sensor (as in similar toxins, e.g., Listeriolysin). Mutant lysenin still can form pores, but mutating these glutamic acids to glutamines rendered the toxin pH-insensitive. On the other hand, toxins in the pore state did not favor insertion of neighboring prepores; indeed, pore insertion breaks the hexagonal ordered domains of prepores and separates from neighboring molecules in the membrane. pH-dependent activation of toxins may represent a common feature of pore-forming toxins. High-speed atomic force microscopy with single-molecule resolution at high temporal resolution and the possibility of exchanging buffers during the experiments presents itself as a unique tool for the study of toxin-state conversion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Percutaneous insertion of peritoneal dialysis catheters using ultrasound and fluoroscopic guidance: A single centre experience and review of literature.

PubMed

De Boo, Diederick W; Mott, Nigel; Tregaskis, Peter; Quach, Trung; Menahem, Solomon; Walker, Rowan G; Koukounaras, Jim

2015-12-01

Various methods of peritoneal dialysis (PD) catheter insertion are available. The purpose of this study was to evaluate a percutaneous insertion technique using ultrasound (US) and fluoroscopy performed under conscious sedation and as day case procedure. Data of 87 percutaneous inserted dialysis catheters were prospectively collected, including patients' age, gender, body mass index, history of previous abdominal surgery and cause of end stage renal failure. Length of hospital stay, early complications and time to first use were also recorded. Institutional review board approval was obtained. A 100% technical success rate was observed. Early complications included bleeding (n = 3), catheter dysfunction (n = 6), exit site infection (n = 1) and exit site leakage (n = 1). All cases of catheter dysfunction and one case of bleeding required surgical revision. Median time of follow-up was 18 months (range 3-35), and median time from insertion to first use was days 14 (1-47). Of the 82 patients who started dialysis, 20 (23%) ceased PD at some stage during follow-up. Most frequently encountered reasons include deteriorating patient cognitive or functional status (n = 5), successful transplant kidney (n = 4) and pleuro-peritoneal fistula (n = 4). Sixty-two (71%) PD catheter insertions were performed as day case. The remaining insertions were performed on patients already admitted to the hospital. Percutaneous insertion of dialysis catheter using US and fluoroscopy is not only safe but can be performed as day case procedure in most patients, even with a medical history of abdominal surgery and/or obesity. © 2015 The Royal Australian and New Zealand College of Radiologists.

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

PubMed

Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

2017-10-01

Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Rest Intervals Reduce the Number of Loading Bouts Required to Enhance Bone Formation

PubMed Central

Srinivasan, Sundar; Ausk, Brandon J.; Bain, Steven D.; Gardiner, Edith M.; Kwon, Ronald Y.; Gross, Ted S.

2015-01-01

Purpose As our society becomes increasingly sedentary, compliance with exercise regimens that require numerous high-energy activities each week become less likely. Alternatively, given an osteogenic exercise intervention that required minimal effort, it is reasonable to presume that participation would be enhanced. Insertion of brief rest-intervals between each cycle of mechanical loading holds potential to achieve this result as substantial osteoblast function is activated by many fewer loading repetitions within each loading bout. Here, we examined the complementary hypothesis that the number of bouts/wk of rest-inserted loading could be reduced from 3/wk without loss of osteogenic efficacy. Methods We conducted a series of 3 wk in vivo experiments that non-invasively exposed the right tibiae of mice to either cyclic (1 Hz) or rest-inserted loading interventions and quantified osteoblast function via dynamic histomorphometry. Results While reducing loading bouts from 3/wk (i.e., 9 total bouts) to 1/wk (3 total bouts) effectively mitigated the osteogenic benefit of cyclic loading, the same reduction did not significantly reduce periosteal bone formation parameters induced by rest-inserted loading. The osteogenic response was robust to the timing of the rest-inserted loading bouts (3 bouts in the first week vs 1 bout/wk for three weeks). However, elimination of any single bout of the three 1/wk bouts mitigated the osteogenic response to rest-inserted loading. Finally, periosteal osteoblast function assessed after the 3 wk intervention was not sensitive to the timing or number of rest-inserted loading bouts. Conclusions We conclude that rest-inserted loading holds potential to retain the osteogenic benefits of mechanical loading with significantly reduced frequency of bouts of activity while also enabling greater flexibility in the timing of the activity. PMID:25207932

Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe.

PubMed

Chen, Bo-Ruei; Hale, Devin C; Ciolek, Peter J; Runge, Kurt W

2012-05-03

Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches.

Basecalling with LifeTrace

PubMed Central

Walther, Dirk; Bartha, Gábor; Morris, Macdonald

2001-01-01

A pivotal step in electrophoresis sequencing is the conversion of the raw, continuous chromatogram data into the actual sequence of discrete nucleotides, a process referred to as basecalling. We describe a novel algorithm for basecalling implemented in the program LifeTrace. Like Phred, currently the most widely used basecalling software program, LifeTrace takes processed trace data as input. It was designed to be tolerant to variable peak spacing by means of an improved peak-detection algorithm that emphasizes local chromatogram information over global properties. LifeTrace is shown to generate high-quality basecalls and reliable quality scores. It proved particularly effective when applied to MegaBACE capillary sequencing machines. In a benchmark test of 8372 dye-primer MegaBACE chromatograms, LifeTrace generated 17% fewer substitution errors, 16% fewer insertion/deletion errors, and 2.4% more aligned bases to the finished sequence than did Phred. For two sets totaling 6624 dye-terminator chromatograms, the performance improvement was 15% fewer substitution errors, 10% fewer insertion/deletion errors, and 2.1% more aligned bases. The processing time required by LifeTrace is comparable to that of Phred. The predicted quality scores were in line with observed quality scores, permitting direct use for quality clipping and in silico single nucleotide polymorphism (SNP) detection. Furthermore, we introduce a new type of quality score associated with every basecall: the gap-quality. It estimates the probability of a deletion error between the current and the following basecall. This additional quality score improves detection of single basepair deletions when used for locating potential basecalling errors during the alignment. We also describe a new protocol for benchmarking that we believe better discerns basecaller performance differences than methods previously published. PMID:11337481

Molecular cloning of cDNAs for the nerve-cell specific phosphoprotein, synapsin I.

PubMed Central

Kilimann, M W; DeGennaro, L J

1985-01-01

To provide access to synapsin I-specific DNA sequences, we have constructed cDNA clones complementary to synapsin I mRNA isolated from rat brain. Synapsin I mRNA was specifically enriched by immunoadsorption of polysomes prepared from the brains of 10-14 day old rats. Employing this enriched mRNA, a cDNA library was constructed in pBR322 and screened by differential colony hybridization with single-stranded cDNA probes made from synapsin I mRNA and total polysomal poly(A)+ RNA. This screening procedure proved to be highly selective. Five independent recombinant plasmids which exhibited distinctly stronger hybridization with the synapsin I probe were characterized further by restriction mapping. All of the cDNA inserts gave restriction enzyme digestion patterns which could be aligned. In addition, some of the cDNA inserts were shown to contain poly(dA) sequences. Final identification of synapsin I cDNA clones relied on the ability of the cDNA inserts to hybridize specifically to synapsin I mRNA. Several plasmids were tested by positive hybridization selection. They specifically selected synapsin I mRNA which was identified by in vitro translation and immunoprecipitation of the translation products. The established cDNA clones were used for a blot-hybridization analysis of synapsin I mRNA. A fragment (1600 bases) from the longest cDNA clone hybridized with two discrete RNA species 5800 and 4500 bases long, in polyadenylated RNA from rat brain and PC12 cells. No hybridization was detected to RNA from rat liver, skeletal muscle or cardiac muscle. Images Fig. 1. Fig. 2. Fig. 4. Fig. 5. PMID:3933975

Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

NASA Astrophysics Data System (ADS)

Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

2016-08-01

This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

Inter-algorithm lesion volumetry comparison of real and 3D simulated lung lesions in CT

NASA Astrophysics Data System (ADS)

Robins, Marthony; Solomon, Justin; Hoye, Jocelyn; Smith, Taylor; Ebner, Lukas; Samei, Ehsan

2017-03-01

The purpose of this study was to establish volumetric exchangeability between real and computational lung lesions in CT. We compared the overall relative volume estimation performance of segmentation tools when used to measure real lesions in actual patient CT images and computational lesions virtually inserted into the same patient images (i.e., hybrid datasets). Pathologically confirmed malignancies from 30 thoracic patient cases from Reference Image Database to Evaluate Therapy Response (RIDER) were modeled and used as the basis for the comparison. Lesions included isolated nodules as well as those attached to the pleura or other lung structures. Patient images were acquired using a 16 detector row or 64 detector row CT scanner (Lightspeed 16 or VCT; GE Healthcare). Scans were acquired using standard chest protocols during a single breath-hold. Virtual 3D lesion models based on real lesions were developed in Duke Lesion Tool (Duke University), and inserted using a validated image-domain insertion program. Nodule volumes were estimated using multiple commercial segmentation tools (iNtuition, TeraRecon, Inc., Syngo.via, Siemens Healthcare, and IntelliSpace, Philips Healthcare). Consensus based volume comparison showed consistent trends in volume measurement between real and virtual lesions across all software. The average percent bias (+/- standard error) shows -9.2+/-3.2% for real lesions versus -6.7+/-1.2% for virtual lesions with tool A, 3.9+/-2.5% and 5.0+/-0.9% for tool B, and 5.3+/-2.3% and 1.8+/-0.8% for tool C, respectively. Virtual lesion volumes were statistically similar to those of real lesions (< 4% difference) with p >.05 in most cases. Results suggest that hybrid datasets had similar inter-algorithm variability compared to real datasets.

Mass-spring matching layers for high-frequency ultrasound transducers: a new technique using vacuum deposition.

PubMed

Brown, Jeremy; Sharma, Srikanta; Leadbetter, Jeff; Cochran, Sandy; Adamson, Rob

2014-11-01

We have developed a technique of applying multiple matching layers to high-frequency (>30 MHz) imaging transducers, by using carefully controlled vacuum deposition alone. This technique uses a thin mass-spring matching layer approach that was previously described in a low-frequency (1 to 10 MHz) transducer design with epoxied layers. This mass- spring approach is more suitable to vacuum deposition in highfrequency transducers over the conventional quarter-wavelength resonant cavity approach, because thinner layers and more versatile material selection can be used, the difficulty in precisely lapping quarter-wavelength matching layers is avoided, the layers are less attenuating, and the layers can be applied to a curved surface. Two different 3-mm-diameter 45-MHz planar lithium niobate transducers and one geometrically curved 3-mm lithium niobate transducer were designed and fabricated using this matching layer approach with copper as the mass layer and parylene as the spring layer. The first planar lithium niobate transducer used a single mass-spring matching network, and the second planar lithium niobate transducer used a single mass-spring network to approximate the first layer in a dual quarter-wavelength matching layer system in addition to a conventional quarter-wavelength layer as the second matching layer. The curved lithium niobate transducer was press focused and used a similar mass-spring plus quarter-wavelength matching layer network. These transducers were then compared with identical transducers with no matching layers and the performance improvement was quantified. The bandwidth of the lithium niobate transducer with the single mass-spring layer was measured to be 46% and the insertion loss was measured to be -21.9 dB. The bandwidth and insertion loss of the lithium niobate transducer with the mass-spring network plus quarter-wavelength matching were measured to be 59% and -18.2 dB, respectively. These values were compared with the unmatched transducer, which had a bandwidth of 28% and insertion loss of -34.1 dB. The bandwidth and insertion loss of the curved lithium niobate transducer with the mass-spring plus quarter-wavelength matching layer combination were measured to be 68% and -26 dB, respectively; this compared with the measured unmatched bandwidth and insertion loss of 35% and -37 dB. All experimentally measured values were in excellent agreement with theoretical Krimholtz-Leedom-Matthaei (KLM) model predictions.

Efficient mouse genome engineering by CRISPR-EZ technology.

PubMed

Modzelewski, Andrew J; Chen, Sean; Willis, Brandon J; Lloyd, K C Kent; Wood, Joshua A; He, Lin

2018-06-01

CRISPR/Cas9 technology has transformed mouse genome editing with unprecedented precision, efficiency, and ease; however, the current practice of microinjecting CRISPR reagents into pronuclear-stage embryos remains rate-limiting. We thus developed CRISPR ribonucleoprotein (RNP) electroporation of zygotes (CRISPR-EZ), an electroporation-based technology that outperforms pronuclear and cytoplasmic microinjection in efficiency, simplicity, cost, and throughput. In C57BL/6J and C57BL/6N mouse strains, CRISPR-EZ achieves 100% delivery of Cas9/single-guide RNA (sgRNA) RNPs, facilitating indel mutations (insertions or deletions), exon deletions, point mutations, and small insertions. In a side-by-side comparison in the high-throughput KnockOut Mouse Project (KOMP) pipeline, CRISPR-EZ consistently outperformed microinjection. Here, we provide an optimized protocol covering sgRNA synthesis, embryo collection, RNP electroporation, mouse generation, and genotyping strategies. Using CRISPR-EZ, a graduate-level researcher with basic embryo-manipulation skills can obtain genetically modified mice in 6 weeks. Altogether, CRISPR-EZ is a simple, economic, efficient, and high-throughput technology that is potentially applicable to other mammalian species.

L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

PubMed

Erwin, Jennifer A; Paquola, Apuã C M; Singer, Tatjana; Gallina, Iryna; Novotny, Mark; Quayle, Carolina; Bedrosian, Tracy A; Alves, Francisco I A; Butcher, Cheyenne R; Herdy, Joseph R; Sarkar, Anindita; Lasken, Roger S; Muotri, Alysson R; Gage, Fred H

2016-12-01

The healthy human brain is a mosaic of varied genomes. Long interspersed element-1 (LINE-1 or L1) retrotransposition is known to create mosaicism by inserting L1 sequences into new locations of somatic cell genomes. Using a machine learning-based, single-cell sequencing approach, we discovered that somatic L1-associated variants (SLAVs) are composed of two classes: L1 retrotransposition insertions and retrotransposition-independent L1-associated variants. We demonstrate that a subset of SLAVs comprises somatic deletions generated by L1 endonuclease cutting activity. Retrotransposition-independent rearrangements in inherited L1s resulted in the deletion of proximal genomic regions. These rearrangements were resolved by microhomology-mediated repair, which suggests that L1-associated genomic regions are hotspots for somatic copy number variants in the brain and therefore a heritable genetic contributor to somatic mosaicism. We demonstrate that SLAVs are present in crucial neural genes, such as DLG2 (also called PSD93), and affect 44-63% of cells of the cells in the healthy brain.

New t-gap insertion-deletion-like metrics for DNA hybridization thermodynamic modeling.

PubMed

D'yachkov, Arkadii G; Macula, Anthony J; Pogozelski, Wendy K; Renz, Thomas E; Rykov, Vyacheslav V; Torney, David C

2006-05-01

We discuss the concept of t-gap block isomorphic subsequences and use it to describe new abstract string metrics that are similar to the Levenshtein insertion-deletion metric. Some of the metrics that we define can be used to model a thermodynamic distance function on single-stranded DNA sequences. Our model captures a key aspect of the nearest neighbor thermodynamic model for hybridized DNA duplexes. One version of our metric gives the maximum number of stacked pairs of hydrogen bonded nucleotide base pairs that can be present in any secondary structure in a hybridized DNA duplex without pseudoknots. Thermodynamic distance functions are important components in the construction of DNA codes, and DNA codes are important components in biomolecular computing, nanotechnology, and other biotechnical applications that employ DNA hybridization assays. We show how our new distances can be calculated by using a dynamic programming method, and we derive a Varshamov-Gilbert-like lower bound on the size of some of codes using these distance functions as constraints. We also discuss software implementation of our DNA code design methods.

Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003.

PubMed

Ruiz, Lorena; Motherway, Mary O'Connell; Lanigan, Noreen; van Sinderen, Douwe

2013-01-01

Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.

Effect of the Molecular Nature of Mutation on the Efficiency of Intrachromosomal Gene Conversion in Mouse Cells

PubMed Central

Letsou, Anthea; Liskay, R. Michael

1987-01-01

With the intent of further exploring the nature of gene conversion in mammalian cells, we systematically addressed the effects of the molecular nature of mutation on the efficiency of intrachromosomal gene conversion in cultured mouse cells. Comparison of conversion rates revealed that all mutations studied were suitable substrates for gene conversion; however, we observed that the rates at which different mutations converted to wild-type could differ by two orders of magnitude. Differences in conversion rates were correlated with the molecular nature of the mutations. In general, rates of conversion decreased with increasing size of the molecular lesions. In comparisons of conversion rates for single base pair insertions and deletions we detected a genotype-directed path for conversion, by which an insertion was converted to wild-type three to four times more efficiently than was a deletion which maps to the same site. The data are discussed in relation to current theories of gene conversion, and are consistent with the idea that gene conversion in mammalian cells can result from repair of heteroduplex DNA (hDNA) intermediates. PMID:2828159

Inherited Creutzfeldt-Jakob disease in a British family associated with a novel 144 base pair insertion of the prion protein gene.

PubMed Central

Nicholl, D; Windl, O; de Silva, R; Sawcer, S; Dempster, M; Ironside, J W; Estibeiro, J P; Yuill, G M; Lathe, R; Will, R G

1995-01-01

A case of familial Creutzfeldt-Jakob disease associated with a 144 base pair insertion in the open reading frame of the prion protein gene is described. Sequencing of the mutated allele showed an arrangement of six octapeptide repeats, distinct from that of a recently described British family with an insertion of similar size. Thirteen years previously the brother of the proband had died from "Huntington's disease", but re-examination of his neuropathology revealed spongiform encephalopathy and anti-prion protein immunocytochemistry gave a positive result. The independent evolution of at least two distinct pathological 144 base pair insertions in Britain is proposed. The importance of maintaining a high index of suspicion of inherited Creutzfeldt-Jakob disease in cases of familial neurodegenerative disease is stressed. Images PMID:7823070

Pressure redistribution by molded inserts in diabetic footwear: a pilot study.

PubMed

Lord, M; Hosein, R

1994-08-01

A small-scale trial is described to demonstrate and evaluate the redistribution of plantar pressure resulting from the use of custom-molded inserts in the orthopedic shoes of diabetic patients at risk of plantar ulceration. A pressure-measuring insole based on force-sensitive resistor technology enabled the load distribution to be compared using molded inserts and flat inserts fitted into the same shoes. An analysis of the 12 peaks of pressure that could be identified under a discrete metatarsal head of six subjects in the trial showed that the pressure was significantly reduced with the use of molded inserts (flat inserts: 305 +/- 79 kPa; molded inserts: 216 +/- 70 kPa; n = 6 p < 0.005). Technical limitations of the equipment and the difficult choice of match of flat insert to molded for comparison suggest that further studies are required for a definitive result.

A small indel mutation in an anthocyanin transporter causes variegated colouration of peach flowers.

PubMed

Cheng, Jun; Liao, Liao; Zhou, Hui; Gu, Chao; Wang, Lu; Han, Yuepeng

2015-12-01

The ornamental peach cultivar 'Hongbaihuatao (HBH)' can simultaneously bear pink, red, and variegated flowers on a single tree. Anthocyanin content in pink flowers is extremely low, being only 10% that of a red flower. Surprisingly, the expression of anthocyanin structural and potential regulatory genes in white flowers was not significantly lower than that in both pink and red flowers. However, proteomic analysis revealed a GST encoded by a gene-regulator involved in anthocyanin transport (Riant)-which is expressed in the red flower, but almost undetectable in the variegated flower. The Riant gene contains an insertion-deletion (indel) polymorphism in exon 3. In white flowers, the Riant gene is interrupted by a 2-bp insertion in the last exon, which causes a frameshift and a premature stop codon. In contrast, both pink and red flowers that arise from bud sports are heterozygous for the Riant locus, with one functional allele due to the 2-bp deletion or a novel 1-bp insertion. Southern blot analysis indicated that the Riant gene occurs in a single copy in the peach genome and it is not interrupted by a transposon. The function of the Riant gene was confirmed by its ectopic expression in the Arabidopsis tt19 mutant, where it complements the anthocyanin phenotype, but not the proanthocyanidin pigmentation in seed coat. Collectively,these results indicate that a small indel mutation in the Riant gene, which is not the result of a transposon insertion or excision, causes variegated colouration of peach flowers. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens.

PubMed

Huff, Chad D; Xing, Jinchuan; Rogers, Alan R; Witherspoon, David; Jorde, Lynn B

2010-02-02

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10(-30)), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

A small indel mutation in an anthocyanin transporter causes variegated colouration of peach flowers

PubMed Central

Cheng, Jun; Liao, Liao; Zhou, Hui; Gu, Chao; Wang, Lu; Han, Yuepeng

2015-01-01

The ornamental peach cultivar ‘Hongbaihuatao (HBH)’ can simultaneously bear pink, red, and variegated flowers on a single tree. Anthocyanin content in pink flowers is extremely low, being only 10% that of a red flower. Surprisingly, the expression of anthocyanin structural and potential regulatory genes in white flowers was not significantly lower than that in both pink and red flowers. However, proteomic analysis revealed a GST encoded by a gene—regulator involved in anthocyanin transport (Riant)—which is expressed in the red flower, but almost undetectable in the variegated flower. The Riant gene contains an insertion-deletion (indel) polymorphism in exon 3. In white flowers, the Riant gene is interrupted by a 2-bp insertion in the last exon, which causes a frameshift and a premature stop codon. In contrast, both pink and red flowers that arise from bud sports are heterozygous for the Riant locus, with one functional allele due to the 2-bp deletion or a novel 1-bp insertion. Southern blot analysis indicated that the Riant gene occurs in a single copy in the peach genome and it is not interrupted by a transposon. The function of the Riant gene was confirmed by its ectopic expression in the Arabidopsis tt19 mutant, where it complements the anthocyanin phenotype, but not the proanthocyanidin pigmentation in seed coat. Collectively,these results indicate that a small indel mutation in the Riant gene, which is not the result of a transposon insertion or excision, causes variegated colouration of peach flowers. PMID:26357885

Polarization preserving single mode fiber optic coupler

NASA Technical Reports Server (NTRS)

Nelson, M. D.; Goss, W. C.

1982-01-01

A technique is described for fabrication of etched single mode fiber optical waveguide couplers which preserve the polarization state to within 0.0001. The coupling ratio is tunable over a broad range (0-9 percent) during fabrication. Back-coupling is less than 0.001, insertion loss is less than 1.5 dB, and coupling ratio thermal coefficient is about 1 percent per degree C.

Low cost anaerobic system for Indonesia: single baffled septic tank.

PubMed

Wibisono, G; Mathew, K; Ho, Goen

2003-01-01

The insertion of a single baffle into a laboratory septic tank to mix incoming feed with sludge has been shown to improve anaerobic degradation of the feed. This is particularly true of soluble organic matter such as glucose. Oil or cellulose fed separately does not undergo degradation. It is expected however that a balanced feed such as sewage will be better degraded.

Updates to Simulation of a Single-Element Lean-Direct Injection Combustor Using a Polyhedral Mesh Derived From Hanging-Node Elements

NASA Technical Reports Server (NTRS)

Wey, Changju Thomas; Liu, Nan-Suey

2014-01-01

This paper summarizes the procedures of inserting a thin-layer mesh to existing inviscid polyhedral mesh either with or without hanging-node elements as well as presents sample results from its applications to the numerical solution of a single-element LDI combustor using a releasable edition of the National Combustion Code (NCC).

Updates to Simulation of a Single-Element Lean-Direct Injection Combustor Using a Polyhedral Mesh Derived from Hanging-Node Elements

NASA Technical Reports Server (NTRS)

Wey, Thomas; Liu, Nan-Suey

2014-01-01

This paper summarizes the procedures of inserting a thin-layer mesh to existing inviscid polyhedral mesh either with or without hanging-node elements as well as presents sample results from its applications to the numerical solution of a single-element LDI combustor using a releasable edition of the National Combustion Code (NCC).

Arthroscopic repair of a type II SLAP lesion using a single corkscrew anchor.

PubMed

Kartus, Jüri; Perko, Mark

2002-03-01

The use of a double-looped 5-mm Corkscrew anchor (Arthrex, Naples, FL) enables the surgeon to use a single anchor to perform a secure fixation of both the anterior labrum as well as the biceps insertion in a type II SLAP lesion. The technique involves tying 1 knot through the anterior portal and a second knot through the posterior portal.

Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos

PubMed Central

Ochiai, Hiroshi; Sakamoto, Naoaki; Fujita, Kazumasa; Nishikawa, Masatoshi; Suzuki, Ken-ichi; Matsuura, Shinya; Miyamoto, Tatsuo; Sakuma, Tetsushi; Shibata, Tatsuo; Yamamoto, Takashi

2012-01-01

To understand complex biological systems, such as the development of multicellular organisms, it is important to characterize the gene expression dynamics. However, there is currently no universal technique for targeted insertion of reporter genes and quantitative imaging in multicellular model systems. Recently, genome editing using zinc-finger nucleases (ZFNs) has been reported in several models. ZFNs consist of a zinc-finger DNA-binding array with the nuclease domain of the restriction enzyme FokI and facilitate targeted transgene insertion. In this study, we successfully inserted a GFP reporter cassette into the HpEts1 gene locus of the sea urchin, Hemicentrotus pulcherrimus. We achieved this insertion by injecting eggs with a pair of ZFNs for HpEts1 with a targeting donor construct that contained ∼1-kb homology arms and a 2A-histone H2B–GFP cassette. We increased the efficiency of the ZFN-mediated targeted transgene insertion by in situ linearization of the targeting donor construct and cointroduction of an mRNA for a dominant-negative form of HpLig4, which encodes the H. pulcherrimus homolog of DNA ligase IV required for error-prone nonhomologous end joining. We measured the fluorescence intensity of GFP at the single-cell level in living embryos during development and found that there was variation in HpEts1 expression among the primary mesenchyme cells. These findings demonstrate the feasibility of ZFN-mediated targeted transgene insertion to enable quantification of the expression levels of endogenous genes during development in living sea urchin embryos. PMID:22711830

Anterior transarticular C1-C2 fixation with contralateral screw insertion: a report of two cases and technical note.

PubMed

Lvov, Ivan; Grin, Andrey; Kaykov, Aleksandr; Smirnov, Vladimir; Krylov, Vladimir

2017-08-08

Anterior transarticular fixation of the C1-C2 vertebrae is a well-known technique that involves screw insertion through the body of the C2 vertebra into the lateral masses of the atlas through an anterior transcervical approach. Meanwhile, contralateral screw insertion has been previously described only in anatomical studies. We describe two case reports of the clinical application of this new technique. In Case 1, the patient was diagnosed with an unstable C1 fracture. The clinical features of the case did not allow for any type of posterior atlantoaxial fusion, Halo immobilization, or routine anterior fixation using the Reindl and Koller techniques. The possible manner of screw insertion into the anterior third of the right lateral mass was via a contralateral trajectory, which was performed in this case. Case 2 involved a patient with neglected posteriorly dislocated dens fracture who could not lie in the prone position due to concomitant cardiac pathology. Reduction of atlantoaxial dislocation was insufficient, even after scar tissue resection at the fracture, while transdental fusion was not possible. Considering the success of the previous case, atlantoaxial fixation was performed through the small approach, using the Reindl technique and contralateral screw insertion. These two cases demonstrate the potential of anterior transarticular fixation of C1-C2 vertebrae in cases where posterior atlantoaxial fusion is not achievable. This type of fixation can be performed through a single approach if one screw is inserted using the Reindl technique and another is inserted via a contralateral trajectory.

The Hairless Stem Phenotype of Cotton (Gossypium barbadense) Is Linked to a Copia-Like Retrotransposon Insertion in a Homeodomain-Leucine Zipper Gene (HD1)

PubMed Central

Ding, Mingquan; Ye, Wuwei; Lin, Lifeng; He, Shae; Du, Xiongming; Chen, Aiqun; Cao, Yuefen; Qin, Yuan; Yang, Fen; Jiang, Yurong; Zhang, Hua; Wang, Xiyin; Paterson, Andrew H.; Rong, Junkang

2015-01-01

Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. In this study, a homeodomain-leucine zipper gene (HD1) was found to cosegregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern Gossypium barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in the At subgenome HD1 gene (At-GbHD1). In both the At and Dt subgenomes, reduced transcription of GbHD1 genes is caused by this insertion. The disruption of At-HD1 further affects the expression of downstream GbMYB25 and GbHOX3 genes. Analyses of primitive cultivated accessions identified another retrotransposon insertion event in the sixth exon of At-GbHD1 that might predate the previously identified retrotransposon in modern varieties. Although both retrotransposon insertions results in similar phenotypic changes, the timing of these two retrotransposon insertion events fits well with our current understanding of the history of cotton speciation and dispersal. Taken together, the results of genetics mapping, gene expression and association analyses suggest that GbHD1 is an important component that controls stem trichome development and is a promising candidate gene for the T1 locus. The interspecific phenotypic difference in stem trichome traits also may be attributable to HD1 inactivation associated with retrotransposon insertion. PMID:26133897

Lateral Intercondylar Ridge: Is it a reliable landmark for femoral ACL insertion?: An anatomical study.

PubMed

Bhattacharyya, Rahul; Ker, Andrew; Fogg, Quentin; Spencer, Simon J; Joseph, Jibu

2018-02-01

Incorrect femoral tunnel placement is the most common cause of graft failure during Anterior Cruciate Ligament (ACL) Reconstruction. A reliable landmark can minimize errors. To identify whether the Lateral Intercondylar Ridge (LIR) is a consistent anatomical structure and define its relationship with the femoral ACL insertion. Phase 1: we studied 23 femoral dry bone specimens macroscopically. Using a digital microscribe, the medial surface of the lateral femoral condyle was reconstructed (3D) to evaluate whether there was an identifiable bony ridge. Phase 2: 7 cadaveric specimens with intact soft tissues were dissected to identify the femoral ACL insertion. A 3D reconstruction of the femoral ACL insertion and the surface allowed us to define the relationship between the LIR and the ACL insertion. All specimens had a defined LIR on the medial surface of the lateral femoral condyle. The ridge was consistently located just anterior to the femoral ACL insertion. The ACL footprint was present in the depression between the ridge and the Inferior Articular Cartilage Margin (IACM). The mean distance from the midpoint of the IACM to the LIR was 10.1 mm. This is the first study to use the microscribe to digitally reconstruct the medial surface of the lateral femoral condyle. It shows that the LIR is a consistent anatomical structure that defines the anterior margin of the femoral ACL insertion, which guides femoral tunnel placement. Our findings support the ruler technique, which is a commonly used method for anatomic single bundle ACL reconstruction. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

PubMed Central

Chao, Michael C.; Pritchard, Justin R.; Zhang, Yanjia J.; Rubin, Eric J.; Livny, Jonathan; Davis, Brigid M.; Waldor, Matthew K.

2013-01-01

The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data. PMID:23901011

Olodaterol Oral Inhalation

MedlinePlus

... not be all the way in the inhaler. Push the cartridge against a firm surface to ensure that it is correctly inserted. Do not remove the cartridge once it has been inserted into the inhaler. Put the clear base back into place. Do not remove the clear base ...

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

PubMed Central

Fuller, Carl W.; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Bibillo, Arek; Stranges, P. Benjamin; Dorwart, Michael; Tao, Chuanjuan; Li, Zengmin; Guo, Wenjing; Shi, Shundi; Korenblum, Daniel; Trans, Andrew; Aguirre, Anne; Liu, Edward; Harada, Eric T.; Pollard, James; Bhat, Ashwini; Cech, Cynthia; Yang, Alexander; Arnold, Cleoma; Palla, Mirkó; Hovis, Jennifer; Chen, Roger; Morozova, Irina; Kalachikov, Sergey; Russo, James J.; Kasianowicz, John J.; Davis, Randy; Roever, Stefan; Church, George M.; Ju, Jingyue

2016-01-01

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods. PMID:27091962

Heat Shock Protein 70 Enhances Mucosal Immunity against Human Norovirus When Coexpressed from a Vesicular Stomatitis Virus Vector

PubMed Central

Ma, Yuanmei; Duan, Yue; Wei, Yongwei; Liang, Xueya; Niewiesk, Stefan; Oglesbee, Michael

2014-01-01

ABSTRACT Human norovirus (NoV) accounts for 95% of nonbacterial gastroenteritis worldwide. Currently, there is no vaccine available to combat human NoV as it is not cultivable and lacks a small-animal model. Recently, we demonstrated that recombinant vesicular stomatitis virus (rVSV) expressing human NoV capsid protein (rVSV-VP1) induced strong immunities in mice (Y. Ma and J. Li, J. Virol. 85:2942–2952, 2011). To further improve the safety and efficacy of the vaccine candidate, heat shock protein 70 (HSP70) was inserted into the rVSV-VP1 backbone vector. A second construct was generated in which the firefly luciferase (Luc) gene was inserted in place of HSP70 as a control for the double insertion. The resultant recombinant viruses (rVSV-HSP70-VP1 and rVSV-Luc-VP1) were significantly more attenuated in cell culture and viral spread in mice than rVSV-VP1. At the inoculation dose of 1.0 × 106 PFU, rVSV-HSP70-VP1 triggered significantly higher vaginal IgA than rVSV-VP1 and significantly higher fecal and vaginal IgA responses than rVSV-Luc-VP1, although serum IgG and T cell responses were similar. At the inoculation dose of 5.0 × 106 PFU, rVSV-HSP70-VP1 stimulated significantly higher T cell, fecal, and vaginal IgA responses than rVSV-VP1. Fecal and vaginal IgA responses were also significantly increased when combined vaccination of rVSV-VP1 and rVSV-HSP70 was used. Collectively, these data indicate that (i) insertion of an additional gene (HSP70 or Luc) into the rVSV-VP1 backbone further attenuates the VSV-based vaccine in vitro and in vivo, thus improving the safety of the vaccine candidate, and (ii) HSP70 enhances the human NoV-specific mucosal and T cell immunities triggered by a VSV-based human NoV vaccine. IMPORTANCE Human norovirus (NoV) is responsible for more than 95% of acute nonbacterial gastroenteritis worldwide. Currently, there is no vaccine for this virus. Development of a live attenuated vaccine for human NoV has not been possible because it is uncultivable. Thus, a live vector-based vaccine may provide an alternative vaccine strategy. In this study, we developed a vesicular stomatitis virus (VSV)-based human NoV vaccine candidate. We constructed rVSV-HSP70-VP1, coexpressing heat shock protein (HSP70) and capsid (VP1) genes of human NoV, and rVSV-Luc-VP1, coexpressing firefly luciferase (Luc) and VP1 genes. We found that VSVs with a double gene insertion were significantly more attenuated than VSV with a single VP1 insertion (rVSV-VP1). Furthermore, we found that coexpression or coadministration of HSP70 from VSV vector significantly enhanced human NoV-specific mucosal immunity. Collectively, we developed an improved live vectored vaccine candidate for human NoV which will be useful for future clinical studies. PMID:24574391

Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae

PubMed Central

Mesarich, Carl H.; Rees-George, Jonathan; Gardner, Paul P.; Ghomi, Fatemeh Ashari; Gerth, Monica L.; Andersen, Mark T.; Rikkerink, Erik H. A.; Fineran, Peter C.

2017-01-01

Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker, is one of the most devastating plant diseases of recent times. We have generated two mini-Tn5-based random insertion libraries of Psa ICMP 18884. The first, a ‘phenotype of interest’ (POI) library, consists of 10,368 independent mutants gridded into 96-well plates. By replica plating onto selective media, the POI library was successfully screened for auxotrophic and motility mutants. Lipopolysaccharide (LPS) biosynthesis mutants with ‘Fuzzy-Spreader’-like morphologies were also identified through a visual screen. The second, a ‘mutant of interest’ (MOI) library, comprises around 96,000 independent mutants, also stored in 96-well plates, with approximately 200 individuals per well. The MOI library was sequenced on the Illumina MiSeq platform using Transposon-Directed Insertion site Sequencing (TraDIS) to map insertion sites onto the Psa genome. A grid-based PCR method was developed to recover individual mutants, and using this strategy, the MOI library was successfully screened for a putative LPS mutant not identified in the visual screen. The Psa chromosome and plasmid had 24,031 and 1,236 independent insertion events respectively, giving insertion frequencies of 3.65 and 16.6 per kb respectively. These data suggest that the MOI library is near saturation, with the theoretical probability of finding an insert in any one chromosomal gene estimated to be 97.5%. However, only 47% of chromosomal genes had insertions. This surprisingly low rate cannot be solely explained by the lack of insertions in essential genes, which would be expected to be around 5%. Strikingly, many accessory genes, including most of those encoding type III effectors, lacked insertions. In contrast, 94% of genes on the Psa plasmid had insertions, including for example, the type III effector HopAU1. These results suggest that some chromosomal sites are rendered inaccessible to transposon insertion, either by DNA-binding proteins or by the architecture of the nucleoid. PMID:28249011

Anatomical Footprint of the Tibialis Anterior Tendon: Surgical Implications for Foot and Ankle Reconstructions.

PubMed

Willegger, Madeleine; Seyidova, Nargiz; Schuh, Reinhard; Windhager, Reinhard; Hirtler, Lena

2017-01-01

This study aimed to analyze precisely the dimensions, shapes, and variations of the insertional footprints of the tibialis anterior tendon (TAT) at the medial cuneiform (MC) and first metatarsal (MT1) base. Forty-one formalin-fixed human cadaveric specimens were dissected. After preparation of the TAT footprint, standardized photographs were made and the following parameters were evaluated: the footprint length, width, area of insertion, dorsoplantar location, shape, and additional tendon slips. Twenty feet (48.8%) showed an equal insertion at the MC and MT1, another 20 feet (48.8%) had a wide insertion at the MC and a narrow insertion at the MT1, and 1 foot (2.4%) demonstrated a narrow insertion at the MC and a wide insertion at the MT1. Additional tendon slips inserting at the metatarsal shaft were found in two feet (4.8%). Regarding the dorsoplantar orientation, the footprints were located medial in 29 feet (70.7%) and medioplantar in 12 feet (29.3%). The most common shape at the MT1 base was the crescent type (75.6%) and the oval type at the MC (58.5%). The present study provided more detailed data on the dimensions and morphologic types of the tibialis anterior tendon footprint. The established anatomical data may allow for a safer surgical preparation and a more anatomical reconstruction.

Alu Insertions and Genetic Diversity: A Preliminary Investigation by an Undergraduate Bioinformatics Class

ERIC Educational Resources Information Center

Elwess, Nancy L.; Duprey, Stephen L.; Harney, Lindesay A.; Langman, Jessie E.; Marino, Tara C.; Martinez, Carolina; McKeon, Lauren L.; Moss, Chantel I. E.; Myrie, Sasha S.; Taylor, Luke Ryan

2008-01-01

"Alu"-insertion polymorphisms were used by an undergraduate Bioinformatics class to study how these insertion sites could be the basis for an investigation in human population genetics. Based on the students' investigation, both allele and genotype "Alu" frequencies were determined for African-American and Japanese populations as well as a…

Effectiveness of electrocardiographic guidance in CVAD tip placement.

PubMed

Walker, Graham; Chan, Raymond J; Alexandrou, Evan; Webster, Joan; Rickard, Claire

International standard practice for the correct confirmation of the central venous access device is the chest X-ray. The intracavitary electrocardiogram-based insertion method is radiation-free, and allows real-time placement verification, providing immediate treatment and reduced requirement for post-procedural repositioning. Relevant databases were searched for prospective randomised controlled trials (RCTs) or quasi RCTs that compared the effectiveness of electrocardiogram-guided catheter tip positioning with placement using surface-anatomy-guided insertion plus chest X-ray confirmation. The primary outcome was accurate catheter tip placement. Secondary outcomes included complications, patient satisfaction and costs. Five studies involving 729 participants were included. Electrocardiogram-guided insertion was more accurate than surface anatomy guided insertion (odds ratio: 8.3; 95% confidence interval (CI) 1.38; 50.07; p=0.02). There was a lack of reporting on complications, patient satisfaction and costs. The evidence suggests that intracavitary electrocardiogram-based positioning is superior to surface-anatomy-guided positioning of central venous access devices, leading to significantly more successful placements. This technique could potentially remove the requirement for post-procedural chest X-ray, especially during peripherally inserted central catheter (PICC) line insertion.

Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions.

PubMed

Bakker, Theo C M; Giger, Thomas; Frommen, Joachim G; Largiadèr, Carlo R

2017-08-01

There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences. Three molecular PCR-based sex tests were developed, in which the first, the second or both insertions were covered. In five European populations (from DE, CH, NL, GB) of three-spined sticklebacks, tests with both insertions combined showed two clearly separated bands on agarose minigels in males and one band in females. The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods.

Comparison of outcomes after single or DOUBLE-CUFF artificial urinary sphincter insertion.

PubMed

O'Connor, R Corey; Gerber, Glenn S; Avila, Desiderio; Chen, Andrew A; Bales, Gregory T

2003-10-01

To assess the effectiveness and complications associated with single and double-cuff artificial urinary sphincter (AUS) implantation for postprostatectomy stress urinary incontinence. A retrospective study of 56 men with postprostatectomy stress urinary incontinence who underwent either single (28 patients) or double (28 patients) cuff AUS placement was performed. Patients in each cohort were matched on the basis of preoperative pad use, risk factors for complications, and age. Patient selection was blinded relative to outcome. Continence, quality of life, and complications were assessed using the Incontinence Impact Questionnaire Short Form (IIQ-7), postoperative pad use, and chart review. The mean age was 67 years for each group. Daily pad use decreased from 7.7 to 1.1 in patients treated with a single-cuff AUS and from 7.8 to 0.7 in patients with a double-cuff AUS (P = 0.25). Complete continence (0 pads daily) was reported in 3 (11%) of 28 men with single-cuff and 12 (43%) of 28 men with double-cuff sphincters (P = 0.008). The IIQ-7 scores improved from 14.8 to 3.1 after single-cuff placement and from 16.3 to 2.5 after double-cuff placement (P = 0.03). With an average follow-up of 41.3 and 21.2 months for the single and double-cuff cohorts, respectively, five complications were reported in the single-cuff recipients and four in the double-cuff patients. A significantly greater rate of complete continence and improvement in the IIQ-7 were seen in men with double-cuff AUS compared with single-cuff devices. Additional study is needed to confirm the relative advantages of double-cuff insertion.

Increased drop formation frequency via reduction of surfactant interactions in flow-focusing microfluidic devices.

PubMed

Josephides, Dimitris N; Sajjadi, Shahriar

2015-01-27

Glass capillary based microfluidic devices are able to create extremely uniform droplets, when formed under the dripping regime, at low setup costs due to their ease of manufacture. However, as they are rarely parallelized, simple methods to increase droplet production from a single device are sought. Surfactants used to stabilize drops in such systems often limit the maximum flow rate that highly uniform drops can be produced due to the lowering interfacial tension causing jetting. In this paper we show that by simple design changes we can limit the interactions of surfactants and maximize uniform droplet production. Three flow-focused configurations are explored: a standard glass capillary device (consisting of a single round capillary inserted into a square capillary), a nozzle fed device, and a surfactant shielding device (both consisting of two round capillaries inserted into either end of a square capillary). In principle, the maximum productivity of uniform droplets is achieved if surfactants are not present. It was found that surfactants in the standard device greatly inhibit droplet production by means of interfacial tension lowering and tip-streaming phenomena. In the nozzle fed configuration, surfactant interactions were greatly limited, yielding flow rates comparable to, but lower than, a surfactant-free system. In the surfactant shielding configuration, flow rates were equal to that of a surfactant-free system and could make uniform droplets at rates an order of magnitude above the standard surfactant system.

Evaluation of single port access gastropexy and ovariectomy using articulating instruments and angled telescopes in dogs.

PubMed

Runge, Jeffrey J; Mayhew, Philipp D

2013-10-01

To describe in dogs, a technique for single port access gastropexy and ovariectomy (SPAGO) using a commercially available multitrocar port and to evaluate short-term outcome. Retrospective case series. Dogs (n = 18). A commercially available multitrocar port was inserted into the abdomen lateral to the rectus abdominis muscle and 2-5 cm caudal to the right rib. Dogs were tilted 45° in both left and right recumbency and bilateral ovariectomy performed using articulating graspers, a bipolar vessel sealing device and a 30° telescope. The laparoscopic assisted incisional gastropexy was performed after ovariectomy at the multitrocar port insertion site by grasping the antral portion of the stomach with a 10 mm DuVall forceps and suturing the seromuscular layer of the antral region of the stomach to the transversus abdominis muscle. Eighteen dogs (median weight, 34.5 kg; range, 14.7-59.2 kg) met the inclusion criteria. Median surgical time for SPAGO was 65 minutes (range, 50-225 minutes). Intra-operative complications included, incorrect multitrocar port placement location (n = 3) and mild hemorrhage from a splenic laceration (1) All dogs recovered from surgery and were discharged from the hospital. Single port access gastropexy and ovariectomy is a feasible procedure to provide prophylaxis against gastric dilation-volvulus and a simultaneous means of sterilization in female dogs. Careful and accurate initial multitrocar port insertion is necessary to have optimal operative viewing as well as to reduce the chances of inadvertent splenic laceration. © Copyright 2013 by The American College of Veterinary Surgeons.

Inactivation of SAM-Methyltransferase is the Mechanism of Attenuation of a Historic Louse Borne Typhus Vaccine Strain

PubMed Central

Liu, Yan; Wu, Bin; Weinstock, George; Walker, David H.; Yu, Xue-jie

2014-01-01

Louse borne typhus (also called epidemic typhus) was one of man's major scourges, and epidemics of the disease can be reignited when social, economic, or political systems are disrupted. The fear of a bioterrorist attack using the etiologic agent of typhus, Rickettsia prowazekii, was a reality. An attenuated typhus vaccine, R. prowazekii Madrid E strain, was observed to revert to virulence as demonstrated by isolation of the virulent revertant Evir strain from animals which were inoculated with Madrid E strain. The mechanism of the mutation in R. prowazekii that affects the virulence of the vaccine was not known. We sequenced the genome of the virulent revertant Evir strain and compared its genome sequence with the genome sequences of its parental strain, Madrid E. We found that only a single nucleotide in the entire genome was different between the vaccine strain Madrid E and its virulent revertant strain Evir. The mutation is a single nucleotide insertion in the methyltransferase gene (also known as PR028) in the vaccine strain that inactivated the gene. We also confirmed that the vaccine strain E did not cause fever in guinea pigs and the virulent revertant strain Evir caused fever in guinea pigs. We concluded that a single nucleotide insertion in the methyltransferase gene of R. prowazekii attenuated the R. prowazekii vaccine strain E. This suggested that an irreversible insertion or deletion mutation in the methyl transferase gene of R. prowazekii is required for Madrid E to be considered a safe vaccine. PMID:25412248

Inactivation of SAM-methyltransferase is the mechanism of attenuation of a historic louse borne typhus vaccine strain.

PubMed

Liu, Yan; Wu, Bin; Weinstock, George; Walker, David H; Yu, Xue-Jie

2014-01-01

Louse borne typhus (also called epidemic typhus) was one of man's major scourges, and epidemics of the disease can be reignited when social, economic, or political systems are disrupted. The fear of a bioterrorist attack using the etiologic agent of typhus, Rickettsia prowazekii, was a reality. An attenuated typhus vaccine, R. prowazekii Madrid E strain, was observed to revert to virulence as demonstrated by isolation of the virulent revertant Evir strain from animals which were inoculated with Madrid E strain. The mechanism of the mutation in R. prowazekii that affects the virulence of the vaccine was not known. We sequenced the genome of the virulent revertant Evir strain and compared its genome sequence with the genome sequences of its parental strain, Madrid E. We found that only a single nucleotide in the entire genome was different between the vaccine strain Madrid E and its virulent revertant strain Evir. The mutation is a single nucleotide insertion in the methyltransferase gene (also known as PR028) in the vaccine strain that inactivated the gene. We also confirmed that the vaccine strain E did not cause fever in guinea pigs and the virulent revertant strain Evir caused fever in guinea pigs. We concluded that a single nucleotide insertion in the methyltransferase gene of R. prowazekii attenuated the R. prowazekii vaccine strain E. This suggested that an irreversible insertion or deletion mutation in the methyl transferase gene of R. prowazekii is required for Madrid E to be considered a safe vaccine.

Tissue-like phantoms

DOEpatents

Frangioni, John V.; De Grand, Alec M.

2007-10-30

The invention is based, in part, on the discovery that by combining certain components one can generate a tissue-like phantom that mimics any desired tissue, is simple and inexpensive to prepare, and is stable over many weeks or months. In addition, new multi-modal imaging objects (e.g., beads) can be inserted into the phantoms to mimic tissue pathologies, such as cancer, or merely to serve as calibration standards. These objects can be imaged using one, two, or more (e.g., four) different imaging modalities (e.g., x-ray computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), and near-infrared (NIR) fluorescence) simultaneously.

Simultaneous bending-curvature and temperature measurements based on a fiber Bragg grating and a Mach-Zehnder interferometer

NASA Astrophysics Data System (ADS)

Huang, Jun; Huang, Shenneng; Shen, Changyu; Jin, Yongxing

2018-02-01

A design for simultaneous bending-curvature and temperature measurement using a fiber Bragg grating (FBG) inserted between two peanut-shaped structures is presented. The peanut-shaped structure is fabricated in the single-mode fiber by a fusion splicer and then connected with another peanut-shaped structure to form a Mach-Zehnder interferometer (MZI). By measuring the wavelength variation of the MZI and FBG in the spectral response of this configuration, simultaneous bending-curvature and temperature measurement is obtained. The experiment results show that curvature sensitivity is -27.58 nm / m ? 1 and FBG is 0.03869 and 0.01217 nm / ° C.

Functional Reconstitution of a Fungal Natural Product Gene Cluster by Advanced Genome Editing.

PubMed

Weber, Jakob; Valiante, Vito; Nødvig, Christina S; Mattern, Derek J; Slotkowski, Rebecca A; Mortensen, Uffe H; Brakhage, Axel A

2017-01-20

Filamentous fungi produce varieties of natural products even in a strain dependent manner. However, the genetic basis of chemical speciation between strains is still widely unknown. One example is trypacidin, a natural product of the opportunistic human pathogen Aspergillus fumigatus, which is not produced among different isolates. Combining computational analysis with targeted gene editing, we could link a single nucleotide insertion in the polyketide synthase of the trypacidin biosynthetic pathway and reconstitute its production in a nonproducing strain. Thus, we present a CRISPR/Cas9-based tool for advanced molecular genetic studies in filamentous fungi, exploiting selectable markers separated from the edited locus.

Plasma synthesis of lithium based intercalation powders for solid polymer electrolyte batteries

DOEpatents

Kong, Peter C [Idaho Falls, ID; Pink, Robert J [Pocatello, ID; Nelson, Lee O [Idaho Falls, ID

2005-01-04

The invention relates to a process for preparing lithium intercalation compounds by plasma reaction comprising the steps of: forming a feed solution by mixing lithium nitrate or lithium hydroxide or lithium oxide and the required metal nitrate or metal hydroxide or metal oxide and between 10-50% alcohol by weight; mixing the feed solution with O.sub.2 gas wherein the O.sub.2 gas atomizes the feed solution into fine reactant droplets, inserting the atomized feed solution into a plasma reactor to form an intercalation powder; and if desired, heating the resulting powder to from a very pure single phase product.

Facial asymmetry and clinical manifestations in patients with novel insertion of the TCOF1 gene.

PubMed

Su, P-H; Liu, Y-F; Yu, J-S; Chen, J-Y; Chen, S-J; Lai, Y-J

2012-11-01

This study explored the role of TCOF1 insertion mutations in Taiwanese patients with craniofacial anomalies. Twelve patients with single or multiple, asymmetrical congenital craniofacial anomalies were enrolled. Genomic DNA was prepared from leukocytes; the coding regions of TCOF1 were analyzed by polymerase chain reaction and direct sequencing. Clinical manifestations were correlated to the TCOF1 mutation. Six of 12 patients diagnosed with hemifacial microsomia exhibited a novel insertion mutation 4127 ins G (frameshift) in exon 24 in the TCOF1 gene. All six patients were diagnosed with anomalies on the left side. In addition, four of these six patients had hearing impairment; three had other major anomalies; and two had developmental delay. The insertion caused a frameshift, an early truncation, the loss of two putative nuclear localization signals (residues 1404-1420 and 1424-1440), and the loss of coiled coil domain (1406-1426) in treacle protein. These findings support the existence of two regulators of growth of the mandibular condyles. © 2011 John Wiley & Sons A/S.

Instrumented socket inserts for sensing interaction at the limb-socket interface.

PubMed

Swanson, Eric C; McLean, Jake B; Allyn, Katheryn J; Redd, Christian B; Sanders, Joan E

2018-01-01

The objective of this research was to investigate a strategy for designing and fabricating computer-manufactured socket inserts that were embedded with sensors for field monitoring of limb-socket interactions of prosthetic users. An instrumented insert was fabricated for a single trans-tibial prosthesis user that contained three sensor types (proximity sensor, force sensing resistor, and inductive sensor), and the system was evaluated through a sequence of laboratory clinical tests and two days of field use. During in-lab tests 3 proximity sensors accurately distinguish between don and doff states; 3 of 4 force sensing resistors measured gradual pressure increases as weight-bearing increased; and the inductive sensor indicated that as prosthetic socks were added the limb moved farther out of the socket and pistoning amplitude decreased. Multiple sensor types were necessary in analysis of field collected data to interpret how sock changes affected limb-socket interactions. Instrumented socket inserts, with sensors selected to match clinical questions of interest, have the potential to provide important insights to improve patient care. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Study of low insertion loss and miniaturization wavelet transform and inverse transform processor using SAW devices.

PubMed

Jiang, Hua; Lu, Wenke; Zhang, Guoan

2013-07-01

In this paper, we propose a low insertion loss and miniaturization wavelet transform and inverse transform processor using surface acoustic wave (SAW) devices. The new SAW wavelet transform devices (WTDs) use the structure with two electrode-widths-controlled (EWC) single phase unidirectional transducers (SPUDT-SPUDT). This structure consists of the input withdrawal weighting interdigital transducer (IDT) and the output overlap weighting IDT. Three experimental devices for different scales 2(-1), 2(-2), and 2(-3) are designed and measured. The minimum insertion loss of the three devices reaches 5.49dB, 4.81dB, and 5.38dB respectively which are lower than the early results. Both the electrode width and the number of electrode pairs are reduced, thus making the three devices much smaller than the early devices. Therefore, the method described in this paper is suitable for implementing an arbitrary multi-scale low insertion loss and miniaturization wavelet transform and inverse transform processor using SAW devices. Copyright © 2013 Elsevier B.V. All rights reserved.

Conformational Dynamics inside Amino-Terminal Disease Hotspot of Ryanodine Receptor

PubMed Central

Zhong, Xiaowei; Liu, Ying; Zhu, Li; Meng, Xing; Wang, Ruiwu; Van Petegem, Filip; Wagenknecht, Terence; Wayne Chen, S. R.; Liu, Zheng

2013-01-01

Summary The N-terminal region of both skeletal and cardiac ryanodine receptor is a disease mutation hotspot. Recently, a crystal structure of the RyR1 fragment (residues 1-559) was solved. This N-terminal structure contains three separate domains, A, B, and C, and was docked into a central vestibule in a full-length RyR1 cryo-EM map. Here we reconstructed 3D cryo-EM structures of two GFP-tagged RyR2s with GFP inserted after residue Glu-310 and Ser-437, respectively. The structures of RyR2E310-GFP and RyR2S437-GFP displayed an extra mass on domain B and C, directly validating the predicted docking model. Next, we revealed domain movements in molecular dynamics flexible fitting models in both the closed and open state cryo-EM maps. To further probe the conformational changes, we generated FRET pairs by inserting CFP or YFP in two selected domains, FRET studies of three dual-insertion pairs and three co-expressed single-insertion pairs showed the dynamic structural changes within the N-terminal domains. PMID:24139989

Non-destructive Faraday imaging of dynamically controlled ultracold atoms

NASA Astrophysics Data System (ADS)

Gajdacz, Miroslav; Pedersen, Poul; Mørch, Troels; Hilliard, Andrew; Arlt, Jan; Sherson, Jacob

2013-05-01

We investigate non-destructive measurements of ultra-cold atomic clouds based on dark field imaging of spatially resolved Faraday rotation. In particular, we pursue applications to dynamically controlled ultracold atoms. The dependence of the Faraday signal on laser detuning, atomic density and temperature is characterized in a detailed comparison with theory. In particular the destructivity per measurement is extremely low and we illustrate this by imaging the same cloud up to 2000 times. The technique is applied to avoid the effect of shot-to-shot fluctuations in atom number calibration. Adding dynamic changes to system parameters, we demonstrate single-run vector magnetic field imaging and single-run spatial imaging of the system's dynamic behavior. The method can be implemented particularly easily in standard imaging systems by the insertion of an extra polarizing beam splitter. These results are steps towards quantum state engineering using feedback control of ultracold atoms.

The role of the substrate surface morphology and water in growth of vertically aligned single-walled carbon nanotubes.

PubMed

Pint, Cary; Pheasant, Sean; Nicholas, Nolan; Horton, Charles; Hauge, Robert

2008-11-01

Growth of high quality, vertically aligned single-walled carbon nanotubes (carpets) is achieved using a rapid insertion hot filament chemical vapor deposition (HF-CVD) technique. The effect of the substrate morphology on growth is explored by comparing carpets grown on epitaxially polished MgO substrates to those grown on "as-cut", macroscopically rough MgO substrates. Depending on the substrate morphology, we observe differences in both the overall carpet morphology as well as the diameter distribution of nanotubes grown in the carpet based on optical measurements. In addition, we explore the role of water in the growth of carpets on MgO and the conventional Al2O3 coated Si substrates. We find that the addition of a small amount of water is beneficial to the growth rates of the SWNT carpets, enhancing the growth rates by up to eight times.

Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping

NASA Astrophysics Data System (ADS)

Bongiovanni, Marie N.; Godet, Julien; Horrocks, Mathew H.; Tosatto, Laura; Carr, Alexander R.; Wirthensohn, David C.; Ranasinghe, Rohan T.; Lee, Ji-Eun; Ponjavic, Aleks; Fritz, Joelle V.; Dobson, Christopher M.; Klenerman, David; Lee, Steven F.

2016-12-01

Super-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures. We validated this by studying synthetic lipid vesicles of known composition. We then applied both to super-resolve the hydrophobicity of amyloid aggregates implicated in neurodegenerative diseases, and the hydrophobic changes in mammalian cell membranes. Our technique is easily implemented by inserting a transmission diffraction grating into the optical path of a localization-based super-resolution microscope, enabling all the information to be extracted simultaneously from a single image plane.

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible (3)He/10 T cryostat.

PubMed

von Allwörden, H; Ruschmeier, K; Köhler, A; Eelbo, T; Schwarz, A; Wiesendanger, R

2016-07-01

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped (3)He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping

PubMed Central

Bongiovanni, Marie N.; Godet, Julien; Horrocks, Mathew H.; Tosatto, Laura; Carr, Alexander R.; Wirthensohn, David C.; Ranasinghe, Rohan T.; Lee, Ji-Eun; Ponjavic, Aleks; Fritz, Joelle V.; Dobson, Christopher M.; Klenerman, David; Lee, Steven F.

2016-01-01

Super-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures. We validated this by studying synthetic lipid vesicles of known composition. We then applied both to super-resolve the hydrophobicity of amyloid aggregates implicated in neurodegenerative diseases, and the hydrophobic changes in mammalian cell membranes. Our technique is easily implemented by inserting a transmission diffraction grating into the optical path of a localization-based super-resolution microscope, enabling all the information to be extracted simultaneously from a single image plane. PMID:27929085

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

PubMed

Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas

2013-06-01

We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.

Multi-party Semi-quantum Key Agreement with Delegating Quantum Computation

NASA Astrophysics Data System (ADS)

Liu, Wen-Jie; Chen, Zhen-Yu; Ji, Sai; Wang, Hai-Bin; Zhang, Jun

2017-10-01

A multi-party semi-quantum key agreement (SQKA) protocol based on delegating quantum computation (DQC) model is proposed by taking Bell states as quantum resources. In the proposed protocol, the participants only need the ability of accessing quantum channel and preparing single photons {|0〉, |1〉, |+〉, |-〉}, while the complicated quantum operations, such as the unitary operations and Bell measurement, will be delegated to the remote quantum center. Compared with previous quantum key agreement protocols, this client-server model is more feasible in the early days of the emergence of quantum computers. In order to prevent the attacks from outside eavesdroppers, inner participants and quantum center, two single photon sequences are randomly inserted into Bell states: the first sequence is used to perform the quantum channel detection, while the second is applied to disorder the positions of message qubits, which guarantees the security of the protocol.

The incidence and causative organisms of infection in elective shoulder surgery.

PubMed

Mayne, Alistair I W; Bidwai, Amit S; Clifford, Rachael; Smith, Matthew G; Guisasola, Inigo; Brownson, Peter

2018-07-01

Deep infection remains a serious complication of orthopaedic surgery. Knowledge of infection rates and causative organisms is important to guide infection control measures. The aim of the present study was to determine infection rates and causative organisms in elective shoulder surgery. Cases complicated by infection were identified and prospectively recorded over a 2-year period. All patients undergoing elective shoulder surgery in the concurrent period at a single Specialist Upper Limb Unit in the UK were identified from the hospital electronic database. In total, 1574 elective shoulder cases were performed: 1359 arthroscopic (540 with implant insertion) and 215 open (197 with implant insertion). The overall infection rate in open surgery of 2.5% was significantly higher than arthroscopic implant cases at 0.7% ( p  < 0.005). The overall infection rate in implant arthroscopic surgery was significantly higher at 0.7% compared to 0% in non-implant related surgery. ( p  < 0.05). Patients undergoing open shoulder surgery have a significantly higher risk of infection compared to arthroscopic shoulder surgery. Arthroscopic surgery with implant insertion has a statistically significantly higher risk of developing deep infection compared to procedures with no implant insertion. We recommend prophylactic antibiotics in open shoulder surgery and arthroscopic shoulder surgery with implant insertion.

Complicated vascular access port removals: incidence, antecedents and avoidance.

PubMed

Teague, Warwick J; Fouad, Dina; Munro, Fraser D; McCabe, Amanda J

2015-09-01

Port removal is usually a straightforward procedure delegated to trainees. However, some port removals are complicated by central venous catheter (CVC) fragmentation, a challenge for even experienced surgeons. This study aimed to determine the incidence of, and risk factors for, complicated port removal in children. A single-centre study assessed the outcome of removal for all paediatric ports inserted from 1996 to 2012. Data were recorded detailing patient, insertion, device and removal characteristics. Risk factors for complicated removals were scrutinised using Chi-square tests; p < 0.05 significant. Of 628 ports inserted from 1996 to 2012, 443 were subsequently removed at the same centre. 8/443 (1.8%) removals were complicated by CVC fragmentation, a median of 3.3 (2.4-3.9) years after insertion. Of complicated cases, 8/8 underwent formal neck dissection, 3/8 intravascular dissection, and 1/8 endovascular retrieval. 2/8 cases have retained intravascular CVC fragments. Risk factors for complication were CVC caliber <6Fr (p < 0.001) and use duration >2 years (p < 0.001). Greatest care and senior supervision should be ensured when removing ports with CVC caliber <6Fr and/or >2 years since insertion. However, complications also occur with larger CVCs or after shorter durations. Therefore, the key to avoiding complicated port removal may simply be: preparation, preparation, neck preparation.

Lentiviral vector-based insertional mutagenesis identifies genes associated with liver cancer

PubMed Central

Ranzani, Marco; Cesana, Daniela; Bartholomae, Cynthia C.; Sanvito, Francesca; Pala, Mauro; Benedicenti, Fabrizio; Gallina, Pierangela; Sergi, Lucia Sergi; Merella, Stefania; Bulfone, Alessandro; Doglioni, Claudio; von Kalle, Christof; Kim, Yoon Jun; Schmidt, Manfred; Tonon, Giovanni; Naldini, Luigi; Montini, Eugenio

2013-01-01

Transposons and γ-retroviruses have been efficiently used as insertional mutagens in different tissues to identify molecular culprits of cancer. However, these systems are characterized by recurring integrations that accumulate in tumor cells, hampering the identification of early cancer-driving events amongst bystander and progression-related events. We developed an insertional mutagenesis platform based on lentiviral vectors (LVV) by which we could efficiently induce hepatocellular carcinoma (HCC) in 3 different mouse models. By virtue of LVV’s replication-deficient nature and broad genome-wide integration pattern, LVV-based insertional mutagenesis allowed identification of 4 new liver cancer genes from a limited number of integrations. We validated the oncogenic potential of all the identified genes in vivo, with different levels of penetrance. Our newly identified cancer genes are likely to play a role in human disease, since they are upregulated and/or amplified/deleted in human HCCs and can predict clinical outcome of patients. PMID:23314173

Comparative Assessment of Cutting Inserts and Optimization during Hard Turning: Taguchi-Based Grey Relational Analysis

NASA Astrophysics Data System (ADS)

Venkata Subbaiah, K.; Raju, Ch.; Suresh, Ch.

2017-08-01

The present study aims to compare the conventional cutting inserts with wiper cutting inserts during the hard turning of AISI 4340 steel at different workpiece hardness. Type of insert, hardness, cutting speed, feed, and depth of cut are taken as process parameters. Taguchi’s L18 orthogonal array was used to conduct the experimental tests. Parametric analysis carried in order to know the influence of each process parameter on the three important Surface Roughness Characteristics (Ra, Rz, and Rt) and Material Removal Rate. Taguchi based Grey Relational Analysis (GRA) used to optimize the process parameters for individual response and multi-response outputs. Additionally, the analysis of variance (ANOVA) is also applied to identify the most significant factor.

Development of a universal medical X-ray imaging phantom prototype.

PubMed

Groenewald, Annemari; Groenewald, Willem A

2016-11-08

Diagnostic X-ray imaging depends on the maintenance of image quality that allows for proper diagnosis of medical conditions. Maintenance of image quality requires quality assurance programs on the various X-ray modalities, which consist of pro-jection radiography (including mobile X-ray units), fluoroscopy, mammography, and computed tomography (CT) scanning. Currently a variety of modality-specific phantoms are used to perform quality assurance (QA) tests. These phantoms are not only expensive, but suitably trained personnel are needed to successfully use them and interpret the results. The question arose as to whether a single universal phantom could be designed and applied to all of the X-ray imaging modalities. A universal phantom would reduce initial procurement cost, possibly reduce the time spent on QA procedures and simplify training of staff on the single device. The aim of the study was to design and manufacture a prototype of a universal phantom, suitable for image quality assurance in general X-rays, fluoroscopy, mammography, and CT scanning. The universal phantom should be easy to use and would enable automatic data analysis, pass/fail reporting, and corrective action recommendation. In addition, a universal phantom would especially be of value in low-income countries where finances and human resources are limited. The design process included a thorough investigation of commercially available phantoms. Image quality parameters necessary for image quality assurance in the different X-ray imaging modalities were determined. Based on information obtained from the above-mentioned investigations, a prototype of a universal phantom was developed, keeping ease of use and reduced cost in mind. A variety of possible phantom housing and insert materials were investigated, considering physical properties, machinability, and cost. A three-dimensional computer model of the first phantom prototype was used to manufacture the prototype housing and inserts. Some of the inserts were 3D-printed, others were machined from different materials. The different components were assembled to form the first prototype of the universal X-ray imaging phantom. The resulting prototype of the universal phantom conformed to the aims of a single phantom for multiple imag-ing modalities, which would be easy to use and manufacture at a reduced cost. A PCT International Patent Application No. PCT/IB2016/051165 has been filed for this technology. © 2016 The Authors.

Anatomic Double Bundle single tunnel Foreign Material Free ACL-Reconstruction – a technical note

PubMed Central

Felmet, Gernot

2011-01-01

Summary The anterior cruciate ligament (ACL) consists of two bundles, the anteromedial (AM) and posterolateral bundle (PM). Double bundle reconstructions appear to give better rotational stability. The usual technique is to make two tunnels in the femur and two in the tibia. This is difficult and in small knees may not even be possible. We have developed a foreign material free press fit fixation for double bundle ACL reconstruction using a single femoral tunnel (R). This is based on the ALL PRESS FIT ACL reconstruction. It is suitable for the most common medium and, otherwise difficult, small sizes of knees. Method: Using diamond edged wet grinding hollow reamers, bone cylinders in different diameters are harvested from the implantation tunnels of the tibia and femur and used for the press fit fixation. Using the press fit technique the graft is first fixed in tibia. It is then similarly fixed under tension in the femoral side with the knee in 120 degree flexion. This is called Bottom To Top Fixation (BTT). On extending the knee the graft tension is self adapting. Depending on the size of the individual knee, the diameter of the femoral bone plug is varied from 8 to 13 mm to achieve an anatomic spread with a double bundle-like insertion. The tibia tunnel can be applied with two 7 or 8 mm diameter tunnels overlapping to a semi oval tunnel between 10 to 13 mm. Results: Since May 2003 we have carried out ACL-reconstructions with Hamstring grafts without foreign material using the ALL PRESS FIT technique. Initially, an 8 mm press fit fixation was used proximally with good results. Since April 2008, the range of diameters was increased up to 13 mm. The results of the Lachman tests have been good to excellent. Results of the Pivot shift test suggested more stability with femoral broader diameters of 9,5 to 13 mm. Conclusions: The foreign material free fixation of ham-string in the ALL PRESS FIT Bottom To Top Fixation is a successful method for ACL Reconstruction. The Diamond Instruments and tubed guiding devices are precise, reliable and easy to manage. On this basis a double bundle reconstruction is achieved using a single tunnel. A broad anatomic femoral insertion with autogenous bone plugs inserted near the cortex seems to improve rotational stability. PMID:23738263

The loss-of-allele assay for ES cell screening and mouse genotyping.

PubMed

Frendewey, David; Chernomorsky, Rostislav; Esau, Lakeisha; Om, Jinsop; Xue, Yingzi; Murphy, Andrew J; Yancopoulos, George D; Valenzuela, David M

2010-01-01

Targeting vectors used to create directed mutations in mouse embryonic stem (ES) cells consist, in their simplest form, of a gene for drug selection flanked by mouse genomic sequences, the so-called homology arms that promote site-directed homologous recombination between the vector and the target gene. The VelociGene method for the creation of targeted mutations in ES cells employs targeting vectors, called BACVecs, that are based on bacterial artificial chromosomes. Compared with conventional short targeting vectors, BacVecs provide two major advantages: (1) their much larger homology arms promote high targeting efficiencies without the need for isogenicity or negative selection strategies; and (2) they enable deletions and insertions of up to 100kb in a single targeting event, making possible gene-ablating definitive null alleles and other large-scale genomic modifications. Because of their large arm sizes, however, BACVecs do not permit screening by conventional assays, such as long-range PCR or Southern blotting, that link the inserted targeting vector to the targeted locus. To exploit the advantages of BACVecs for gene targeting, we inverted the conventional screening logic in developing the loss-of-allele (LOA) assay, which quantifies the number of copies of the native locus to which the mutation was directed. In a correctly targeted ES cell clone, the LOA assay detects one of the two native alleles (for genes not on the X or Y chromosome), the other allele being disrupted by the targeted modification. We apply the same principle in reverse as a gain-of-allele assay to quantify the copy number of the inserted targeting vector. The LOA assay reveals a correctly targeted clone as having lost one copy of the native target gene and gained one copy of the drug resistance gene or other inserted marker. The combination of these quantitative assays makes LOA genotyping unequivocal and amenable to automated scoring. We use the quantitative polymerase chain reaction (qPCR) as our method of allele quantification, but any method that can reliably distinguish the difference between one and two copies of the target gene can be used to develop an LOA assay. We have designed qPCR LOA assays for deletions, insertions, point mutations, domain swaps, conditional, and humanized alleles and have used the insert assays to quantify the copy number of random insertion BAC transgenics. Because of its quantitative precision, specificity, and compatibility with high throughput robotic operations, the LOA assay eliminates bottlenecks in ES cell screening and mouse genotyping and facilitates maximal speed and throughput for knockout mouse production. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Clostridium perfringens type A–E toxin plasmids

PubMed Central

Freedman, John C.; Theoret, James R.; Wisniewski, Jessica A.; Uzal, Francisco A.; Rood, Julian I.; McClane, Bruce A.

2014-01-01

Clostridium perfringens relies upon plasmid-encoded toxin genes to cause intestinal infections. These toxin genes are associated with insertion sequences that may facilitate their mobilization and transfer, giving rise to new toxin plasmids with common backbones. Most toxin plasmids carry a transfer of clostridial plasmids locus mediating conjugation, which likely explains the presence of similar toxin plasmids in otherwise unrelated C. perfringens strains. The association of many toxin genes with insertion sequences and conjugative plasmids provides virulence flexibility when causing intestinal infections. However, incompatibility issues apparently limit the number of toxin plasmids maintained by a single cell. PMID:25283728

Fabrication of an infrared Shack-Hartmann sensor by combining high-speed single-point diamond milling and precision compression molding processes.

PubMed

Zhang, Lin; Zhou, Wenchen; Naples, Neil J; Yi, Allen Y

2018-05-01

A novel fabrication method by combining high-speed single-point diamond milling and precision compression molding processes for fabrication of discontinuous freeform microlens arrays was proposed. Compared with slow tool servo diamond broaching, high-speed single-point diamond milling was selected for its flexibility in the fabrication of true 3D optical surfaces with discontinuous features. The advantage of single-point diamond milling is that the surface features can be constructed sequentially by spacing the axes of a virtual spindle at arbitrary positions based on the combination of rotational and translational motions of both the high-speed spindle and linear slides. By employing this method, each micro-lenslet was regarded as a microstructure cell by passing the axis of the virtual spindle through the vertex of each cell. An optimization arithmetic based on minimum-area fabrication was introduced to the machining process to further increase the machining efficiency. After the mold insert was machined, it was employed to replicate the microlens array onto chalcogenide glass. In the ensuing optical measurement, the self-built Shack-Hartmann wavefront sensor was proven to be accurate in detecting an infrared wavefront by both experiments and numerical simulation. The combined results showed that precision compression molding of chalcogenide glasses could be an economic and precision optical fabrication technology for high-volume production of infrared optics.

Laparoscopic insertion of the Moss feeding tube.

PubMed

Albrink, M H; Hagan, K; Rosemurgy, A S

1993-12-01

Placement of enteral feeding tubes is an important part of a surgeon's skill base. Surgical insertion of feeding tubes has been performed safely for many years with very few modifications. With the recent surge in interest and applicability of other laparoscopic procedures, it is well within the skills of the average laparoscopic surgeon to insert feeding tubes. We describe herein a simple technique for the insertion of the Moss feeding tube. The procedure described has a minimum of invasion, along with simplicity, safety, and accuracy.

Improvement of electron mobility in La:BaSnO{sub 3} thin films by insertion of an atomically flat insulating (Sr,Ba)SnO{sub 3} buffer layer

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

Shiogai, Junichi, E-mail: junichi.shiogai@imr.tohoku.ac.jp; Nishihara, Kazuki; Sato, Kazuhisa

One perovskite oxide, ASnO{sub 3} (A = Sr, Ba), is a candidate for use as a transparent conductive oxide with high electron mobility in single crystalline form. However, the electron mobility of films grown on SrTiO{sub 3} substrates does not reach the bulk value, probably because of dislocation scattering that originates from the large lattice mismatch. This study investigates the effect of insertion of bilayer BaSnO{sub 3} / (Sr,Ba)SnO{sub 3} for buffering this large lattice mismatch between La:BaSnO{sub 3} and SrTiO{sub 3} substrate. The insertion of 200-nm-thick BaSnO{sub 3} on (Sr,Ba)SnO{sub 3} bilayer buffer structures reduces the number of dislocationsmore » and improves surface smoothness of the films after annealing as proved respectively by scanning transmission electron microscopy and atomic force microscopy. A systematic investigation of BaSnO{sub 3} buffer layer thickness dependence on Hall mobility of the electron transport in La:BaSnO{sub 3} shows that the highest obtained value of mobility is 78 cm{sup 2}V{sup −1}s{sup −1} because of its fewer dislocations. High electron mobility films based on perovskite BaSnO{sub 3} can provide a good platform for transparent-conducting-oxide electronic devices and for creation of fascinating perovskite heterostructures.« less

Visible light-sensitive APTES-bound ZnO nanowire toward a potent nanoinjector sensing biomolecules in a living cell

NASA Astrophysics Data System (ADS)

Lee, Jooran; Choi, Sunyoung; Bae, Seon Joo; Yoon, Seok Min; Choi, Joon Sig; Yoon, Minjoong

2013-10-01

Nanoscale cell injection techniques combined with nanoscopic photoluminescence (PL) spectroscopy have been important issues in high-resolution optical biosensing, gene and drug delivery and single-cell endoscopy for medical diagnostics and therapeutics. However, the current nanoinjectors remain limited for optical biosensing and communication at the subwavelength level, requiring an optical probe such as semiconductor quantum dots, separately. Here, we show that waveguided red emission is observed at the tip of a single visible light-sensitive APTES-modified ZnO nanowire (APTES-ZnO NW) and it exhibits great enhancement upon interaction with a complementary sequence-based double stranded (ds) DNA, whereas it is not significantly affected by non-complementary ds DNA. Further, the tip of a single APTES-ZnO NW can be inserted into the subcellular region of living HEK 293 cells without significant toxicity, and it can also detect the enhancement of the tip emission from subcellular regions with high spatial resolution. These results indicate that the single APTES-ZnO NW would be useful as a potent nanoinjector which can guide visible light into intracellular compartments of mammalian cells, and can also detect nanoscopic optical signal changes induced by interaction with the subcellular specific target biomolecules without separate optical probes.Nanoscale cell injection techniques combined with nanoscopic photoluminescence (PL) spectroscopy have been important issues in high-resolution optical biosensing, gene and drug delivery and single-cell endoscopy for medical diagnostics and therapeutics. However, the current nanoinjectors remain limited for optical biosensing and communication at the subwavelength level, requiring an optical probe such as semiconductor quantum dots, separately. Here, we show that waveguided red emission is observed at the tip of a single visible light-sensitive APTES-modified ZnO nanowire (APTES-ZnO NW) and it exhibits great enhancement upon interaction with a complementary sequence-based double stranded (ds) DNA, whereas it is not significantly affected by non-complementary ds DNA. Further, the tip of a single APTES-ZnO NW can be inserted into the subcellular region of living HEK 293 cells without significant toxicity, and it can also detect the enhancement of the tip emission from subcellular regions with high spatial resolution. These results indicate that the single APTES-ZnO NW would be useful as a potent nanoinjector which can guide visible light into intracellular compartments of mammalian cells, and can also detect nanoscopic optical signal changes induced by interaction with the subcellular specific target biomolecules without separate optical probes. Electronic supplementary information (ESI) available: Synthesis of APTES-modified ZnO nanowires, DNA functionalization and spectroscopic measurements with additional fluorescence image ad fluorescence decay times, cell culture, injection of a single nanowire into living cells, subcellular imaging and determination of cytotoxicity. See DOI: 10.1039/c3nr03042c

Designing robust watermark barcodes for multiplex long-read sequencing.

PubMed

Ezpeleta, Joaquín; Krsticevic, Flavia J; Bulacio, Pilar; Tapia, Elizabeth

2017-03-15

To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed. We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process. Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark . ezpeleta@cifasis-conicet.gov.ar. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Predictors for cecal insertion time: the impact of abdominal visceral fat measured by computed tomography.

PubMed

Nagata, Naoyoshi; Sakamoto, Kayo; Arai, Tomohiro; Niikura, Ryota; Shimbo, Takuro; Shinozaki, Masafumi; Noda, Mitsuhiko; Uemura, Naomi

2014-10-01

Several factors affect the risk for longer cecal insertion time. The aim of this study was to identify the predictors of longer insertion time and to evaluate the effect of visceral fat measured by CT. This is a retrospective observational study. Outpatients for colorectal cancer screening who underwent colonoscopies and CT were enrolled. Computed tomography was performed in individuals who requested cancer screening and in those with GI bleeding. Information on obesity indices (BMI, visceral adipose tissue, and subcutaneous adipose tissue area), constipation score, history of abdominal surgery, poor preparation, fellow involvement, diverticulosis, patient discomfort, and the amount of sedation used was collected. The cecal insertion rate was 95.2% (899/944), and 899 patients were analyzed. Multiple regression analysis showed that female sex, lower BMI, lower visceral adipose tissue area, lower subcutaneous adipose tissue area, higher constipation score, history of surgery, poor bowel preparation, and fellow involvement were independently associated with longer insertion time. When obesity indices were considered simultaneously, smaller subcutaneous adipose tissue area (p = 0.038), but not lower BMI (p = 0.802) or smaller visceral adipose tissue area (p = 0.856), was associated with longer insertion time; the other aforementioned factors remained associated with longer insertion time. In the subanalysis of normal-weight patients (BMI <25 kg/m), a smaller subcutaneous adipose tissue area (p = 0.002), but not a lower BMI (p = 0.782), was independently associated with a longer insertion time. Longer insertion time had a positive correlation with a higher patient discomfort score (ρ = 0.51, p < 0.001) and a greater amount of midazolam use (ρ = 0.32, p < 0.001). This single-center retrospective study includes a potential selection bias. In addition to BMI and intra-abdominal fat, female sex, constipation, history of abdominal surgery, poor preparation, and fellow involvement were predictors of longer cecal insertion time. Among the obesity indices, high subcutaneous fat accumulation was the best predictive factor for easier passage of the colonoscope, even when body weight was normal.

Jet Injection of 1% buffered lidocaine versus topical ELA-Max for anesthesia before peripheral intravenous catheterization in children: a randomized controlled trial.

PubMed

Spanos, Stephanie; Booth, Rebekah; Koenig, Heidi; Sikes, Kendra; Gracely, Edward; Kim, In K

2008-08-01

Peripheral intravenous (PIV) catheter insertion is a frequent, painful procedure that is often performed with little or no anesthesia. Current approaches that minimize pain for PIV catheter insertion have several limitations: significant delay for onset of anesthesia, inadequate anesthesia, infectious disease exposure risk from needlestick injuries, and patients' needle phobia. Comparison of the anesthetic effectiveness of J-Tip needle-free jet injection of 1% buffered lidocaine to the anesthetic effectiveness of topical 4% ELA-Max for PIV catheter insertion. A prospective, block-randomized, controlled trial comparing J-Tip jet injection of 1% buffered lidocaine to a 30-minute application of 4% ELA-Max for topical anesthesia in children 8 to 15 years old presenting to a tertiary care pediatric emergency department for PIV catheter insertion. All subjects recorded self-reported visual analog scale (VAS) scores for pain at time of enrollment and pain felt following PIV catheter insertion. Jet injection subjects also recorded pain of jet injection. Subjects were videotaped during jet injection and PIV catheter insertion. Videotapes were reviewed by a single blinded reviewer for observer-reported VAS pain scores for jet injection and PIV catheter insertion. Of the 70 children enrolled, 35 were randomized to the J-Tip jet injection group and 35 to the ELA-Max group. Patient-recorded enrollment VAS scores for pain were similar between groups (P = 0.74). Patient-recorded VAS scores were significantly different between groups immediately after PIV catheter insertion (17.3 for J-Tip jet injection vs 44.6 for ELA-Max, P < 0.001). Blinded reviewer assessed VAS scores for pain after PIV catheter insertion demonstrated a similar trend, but the comparison was not statistically significant (21.7 for J-Tip jet injection vs 31.9 ELA-Max, P = 0.23). J-Tip jet injection of 1% buffered lidocaine provided greater anesthesia than a 30-minute application of ELA-Max according to patient self-assessment of pain for children aged 8 to 15 years undergoing PIV catheter insertion.

The Effect of Insertion Torque on the Clinical Outcome of Single Implants: A Randomized Clinical Trial.

PubMed

Barone, Antonio; Alfonsi, Fortunato; Derchi, Giacomo; Tonelli, Paolo; Toti, Paolo; Marchionni, Saverio; Covani, Ugo

2016-06-01

The insertion torque value has been extensively used as an indicator for implant primary stability, which is considered a determining parameter for the implants success. The primary goal of the present randomized clinical trial was to evaluate and compare the clinical outcome for implants placed with high insertion torque (between 50 Ncm and 100 Ncm) and regular insertion torque (within 50 Ncm) in healed ridges. Partially edentulous patients, missing one or more mandibular or maxillary teeth, having an adequate amount of bone, requiring implant placement, were randomized to receive Blossom CT implants with regular insertion torque (<50 Ncm) or CT implants with high insertion torque (≥50 Ncm). Implants were left to heal submerged for 3 months. Implants were restored with individualized abutments and cemented metal-ceramic crowns. Acquired measurements were: insertion torque values (IT), thickness of buccal bone plate after implant osteotomy preparation (BBT), marginal bone level (MBL), and facial soft tissue level (FST). All patients were followed 12 months after implant placement. One hundred sixteen implants were placed in one hundred sixteen patients and enrolled for the study. Fifty-eight implants were randomly allocated in regular-IT and high-IT groups with a mean insertion torque ranging from 20 Ncm to 50 Ncm and from 50 Ncm to 100 Ncm, respectively. Three implants failed, and another five implants showed at the 12-month evaluation a marginal bone loss (ΔMBL) greater than 1.5 mm, being considered unsuccessful. The findings suggested that implants inserted with high-IT (≥50 Ncm) in healed bone ridges showed more peri-implant bone remodeling and buccal soft tissue recession than implants inserted with a regular-IT (<50 Ncm). Moreover, sites with a thick buccal bone wall (≥1 mm) - after implant osteotomy site preparation - seemed to be less prone to buccal soft tissue recession after 12 months than sites with a thin buccal bone wall (<1 mm). © 2015 Wiley Periodicals, Inc.

Design and characterisation of a polyethylene oxide matrix with the potential use as a teat insert for prevention/treatment of bovine mastitis.

PubMed

Bhattarai, Sushila; Alany, Raid G; Bunt, Craig R; Abdelkader, Hamdy; Rathbone, Michael J

2015-01-01

This manuscript reports (for the first time) on antibiotic-free polymeric inserts for the prevention and/or treatment of bovine mastitis. Polyethylene oxide (PEO)-based inserts were prepared using different concentrations of various hydrophilic polymers and water-soluble and water-insoluble drug-release-modifying excipients. A simple and scalable melt-extrusion method was employed to prepare the inserts. The prepared inserts were characterised for their dimension, rheological and mechanical properties. The in vitro release of a model bacteriostatic drug (salicylic acid) from the prepared inserts was studied to demonstrate the effectiveness and reproducibility of the melt-extrusion manufacturing method. Further, the in vitro stability of the inserts was evaluated using gel permeation chromatography (GPC) to monitor any change in molecular weight under real-time and accelerated storage conditions. The investigated inserts were stable at accelerated storage conditions over a period of 6 months. PEO inserts have the potential to serve a dual purpose, act as a physical barrier against pathogens invading the teat canal of cows and possibly control the release of a drug.

Noncontact speckle-based optical sensor for detection of glucose concentration using magneto-optic effect

NASA Astrophysics Data System (ADS)

Ozana, Nisan; Beiderman, Yevgeny; Anand, Arun; Javidi, Baharam; Polani, Sagi; Schwarz, Ariel; Shemer, Amir; Garcia, Javier; Zalevsky, Zeev

2016-06-01

We experimentally verify a speckle-based technique for noncontact measurement of glucose concentration in the bloodstream. The final device is intended to be a single wristwatch-style device containing a laser, a camera, and an alternating current (ac) electromagnet generated by a solenoid. The experiments presented are performed in vitro as proof of the concept. When a glucose substance is inserted into a solenoid generating an ac magnetic field, it exhibits Faraday rotation, which affects the temporal changes of the secondary speckle pattern distributions. The temporal frequency resulting from the ac magnetic field was found to have a lock-in amplification role, which increased the observability of the relatively small magneto-optic effect. Experimental results to support the proposed concept are presented.

Metal-polymer nanocomposites for stretchable optics and plasmonics

NASA Astrophysics Data System (ADS)

Potenza, Marco A. C.; Minnai, Chloé; Milani, Paolo

2016-12-01

Stretchable and conformable optical devices open very exciting perspectives for the fabrication of systems incorporating diffracting and optical power in a single element and of tunable plasmonic filters and absorbers. The use of nanocomposites obtained by inserting metallic nanoparticles produced in the gas phase into polymeric matrices allows to effectively fabricate cheap and simple stretchable optical elements able to withstand thousands of deformations and stretching cycles without any degradation of their optical properties. The nanocomposite-based reflective optical devices show excellent performances and stability compared to similar devices fabricated with standard techniques. The nanocomposite-based devices can be therefore applied to arbitrary curved non-optical grade surfaces in order to achieve optical power and to minimize aberrations like astigmatism. Examples discussed here include stretchable reflecting gratings, plasmonic filters tunable by mechanical stretching and light absorbers.

Fracture of Reduced-Diameter Zirconia Dental Implants Following Repeated Insertion.

PubMed

Karl, Matthias; Scherg, Stefan; Grobecker-Karl, Tanja

Achievement of high insertion torque values indicating good primary stability is a goal during dental implant placement. The objective of this study was to evaluate whether or not two-piece implants made from zirconia ceramic may be damaged as a result of torque application. A total of 10 two-piece zirconia implants were repeatedly inserted into polyurethane foam material with increasing density and decreasing osteotomy size. The insertion torque applied was measured, and implants were checked for fractures by applying the fluorescent penetrant method. Weibull probability of failure was calculated based on the recorded insertion torque values. Catastrophic failures could be seen in five of the implants from two different batches at insertion torques ranging from 46.0 to 70.5 Ncm, while the remaining implants (all belonging to one batch) survived. Weibull probability of failure seems to be low at the manufacturer-recommended maximum insertion torque of 35 Ncm. Chipping fractures at the thread tips as well as tool marks were the only otherwise observed irregularities. While high insertion torques may be desirable for immediate loading protocols, zirconia implants may fracture when manufacturer-recommended insertion torques are exceeded. Evaluating bone quality prior to implant insertion may be useful.

The carnegie protein trap library: a versatile tool for Drosophila developmental studies.

PubMed

Buszczak, Michael; Paterno, Shelley; Lighthouse, Daniel; Bachman, Julia; Planck, Jamie; Owen, Stephenie; Skora, Andrew D; Nystul, Todd G; Ohlstein, Benjamin; Allen, Anna; Wilhelm, James E; Murphy, Terence D; Levis, Robert W; Matunis, Erika; Srivali, Nahathai; Hoskins, Roger A; Spradling, Allan C

2007-03-01

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions.

Scattering by a groove in an impedance plane

NASA Technical Reports Server (NTRS)

Bindiganavale, Sunil; Volakis, John L.

1993-01-01

An analysis of two-dimensional scattering from a narrow groove in an impedance plane is presented. The groove is represented by a impedance surface and the problem reduces to that of scattering from an impedance strip in an otherwise uniform impedance plane. On the basis of this model, appropriate integral equations are constructed using a form of the impedance plane Green's functions involving rapidly convergent integrals. The integral equations are solved by introducing a single basis representation of the equivalent current on the narrow impedance insert. Both transverse electric (TE) and transverse magnetic (TM) polarizations are treated. The resulting solution is validated by comparison with results from the standard boundary integral method (BIM) and a high frequency solution. It is found that the presented solution for narrow impedance inserts can be used in conjunction with the high frequency solution for the characterization of impedance inserts of any given width.

Semiconductor radiation detector

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

Patt, Bradley E.; Iwanczyk, Jan S.; Tull, Carolyn R.

A semiconductor radiation detector is provided to detect x-ray and light photons. The entrance electrode is segmented by using variable doping concentrations. Further, the entrance electrode is physically segmented by inserting n+ regions between p+ regions. The p+ regions and the n+ regions are individually biased. The detector elements can be used in an array, and the p+ regions and the n+ regions can be biased by applying potential at a single point. The back side of the semiconductor radiation detector has an n+ anode for collecting created charges and a number of p+ cathodes. Biased n+ inserts can bemore » placed between the p+ cathodes, and an internal resistor divider can be used to bias the n+ inserts as well as the p+ cathodes. A polysilicon spiral guard can be implemented surrounding the active area of the entrance electrode or surrounding an array of entrance electrodes.« less

Coexistence of optically active radial and axial CdTe insertions in single ZnTe nanowire.

PubMed

Wojnar, P; Płachta, J; Zaleszczyk, W; Kret, S; Sanchez, Ana M; Rudniewski, R; Raczkowska, K; Szymura, M; Karczewski, G; Baczewski, L T; Pietruczik, A; Wojtowicz, T; Kossut, J

2016-03-14

We report on the growth, cathodoluminescence and micro-photoluminescence of individual radial and axial CdTe insertions in ZnTe nanowires. In particular, the cathodoluminescence technique is used to determine the position of each emitting object inside the nanowire. It is demonstrated that depending on the CdTe deposition temperature, one can obtain an emission either from axial CdTe insertions only, or from both, radial and axial heterostructures, simultaneously. At 350 °C CdTe grows only axially, whereas at 310 °C and 290 °C, there is also significant deposition on the nanowire sidewalls resulting in radial core/shell heterostructures. The presence of Cd atoms on the sidewalls is confirmed by energy dispersive X-ray spectroscopy. Micro-photoluminescence study reveals a strong linear polarization of the emission from both types of heterostructures in the direction along the nanowire axis.

Efficacy of a Clinic-Based Safer Sex Program for Human Immunodeficiency Virus-Uninfected and Human Immunodeficiency Virus-Infected Young Black Men Who Have Sex With Men: A Randomized Controlled Trial.

PubMed

Crosby, Richard A; Mena, Leandro; Salazar, Laura F; Hardin, James W; Brown, Tim; Vickers Smith, Rachel

2018-03-01

To test the efficacy of a single-session, clinic-based intervention designed to promote condom use among young black men who have sex with men (YBMSM). Six hundred YBMSM were enrolled in a randomized controlled trial, using a 12-month observation period. An intent-to-treat analysis was performed, with multiple imputation for missing data. Compared with the reference group, human immunodeficiency virus (HIV)-infected men in the intervention group had 64% greater odds of reporting consistent condom use for anal receptive sex over 12 months (estimated odds ratio, 1.64; 95% confidence interval, 1.23-2.17, P = 0.001). Also, compared with the reference group, HIV-uninfected men in the intervention group had more than twice the odds of reporting consistent condom use for anal receptive sex over 12 months (estimated odds ratio, 2.14; 95% confidence interval, 1.74-2.63, P < 0.001). Significant intervention effects relative to incident sexually transmitted diseases were not observed. A single-session, clinic-based, intervention may help protect HIV-uninfected YBMSM against HIV acquisition and HIV-infected YBMSM from transmitting the virus to insertive partners.

An Assessment of Radiologically Inserted Transoral and Transgastric Gastroduodenal Stents to Treat Malignant Gastric Outlet Obstruction

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

Miller, Bethany H. T., E-mail: bmiller@doctors.org.uk; Griffiths, Ewen A., E-mail: Eagriffiths@doctors.org.uk; Pursnani, Kishore G., E-mail: Kish.Pursnani@lthtr.nhs.uk

2013-12-15

IntroductionSelf-expanding metallic stents (SEMS) are used to palliate malignant gastric outlet obstruction (GOO) and are useful in patients with limited life expectancy or severe medical comorbidity, which would preclude surgery. Stenting can be performed transorally or by a percutaneous transgastric technique. Our goal was to review the outcome of patients who underwent radiological SEMS insertion performed by a single consultant interventional radiologist. Methods: Patients were identified from a prospectively collected database held by one consultant radiologist. Data were retrieved from radiological reports, multidisciplinary team meetings, and the patients' case notes. Univariate survival analysis was performed. Results: Between December 2000 andmore » January 2011, 100 patients (63 males, 37 females) had 110 gastroduodenal stenting procedures. Median age was 73 (range 39-89) years. SEMS were inserted transorally (n = 66) or transgastrically (n = 44). Site of obstruction was the stomach (n = 37), duodenum (n = 50), gastric pull-up (n = 10), or gastroenterostomy (n = 13). Seven patients required biliary stents. Technical success was 86.4 %: 83.3 % for transoral insertion, 90.9 % for transgastric insertion. Eleven patients developed complications. Median GOO severity score: 1 pre-stenting, 2 post-stenting (p = 0.0001). Median survival was 54 (range 1-624) days. Post-stenting GOO severity score was predictive of survival (p = 0.0001). Conclusions: The technical success rate for insertion of palliative SEMS is high. Insertional technique can be tailored to the individual depending on the location of the tumor and whether it is possible to access the stomach percutaneously. Patients who have successful stenting and return to eating a soft/normal diet have a statistically significant increase in survival.« less

Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma

PubMed Central

Weiser, Keith C.; Liu, Bin; Hansen, Gwenn M.; Skapura, Darlene; Hentges, Kathryn E.; Yarlagadda, Sujatha; Morse III, Herbert C.

2007-01-01

AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFκB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at http://www.mouse-genome.bcm.tmc.edu/vision. PMID:17926094

Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma.

PubMed

Weiser, Keith C; Liu, Bin; Hansen, Gwenn M; Skapura, Darlene; Hentges, Kathryn E; Yarlagadda, Sujatha; Morse Iii, Herbert C; Justice, Monica J

2007-10-01

AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFkappaB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at http://www.mouse-genome.bcm.tmc.edu/vision .

Ureteric stent dwelling time: a risk factor for post-ureteroscopy sepsis.

PubMed

Nevo, Amihay; Mano, Roy; Baniel, Jack; Lifshitz, David A

2017-07-01

To evaluate the association between stent dwelling time and sepsis after ureteroscopy, and identify risk factors for sepsis in this setting. The prospectively collected database of a single institution was queried for all patients who underwent ureteroscopy for stone extraction between 2010 and 2016. Demographic, clinical, preoperative and operative data were collected. The primary study endpoint was sepsis within 48 h of ureteroscopy. Logistic regressions were performed to identify predictors of post-ureteroscopy sepsis in the ureteroscopy cohort and specifically in patients with prior stent insertion. Between October 2010 and April 2016, 1 256 patients underwent ureteroscopy for stone extraction. Risk factors for sepsis included prior stent placement, female gender and Charlson comorbidity index. A total of 601 patients had a ureteric stent inserted before the operation and were included in the study cohort, in which the median age was 56 years, 90 patients were women (30%), and 97 patients were treated for positive preoperative urine cultures (16.1%). Postoperative sepsis, <48 h after surgery, occurred in eight (1.2%) non-stented patients and in 28 patients (4.7%) with prior stent insertion. Sepsis rates after stent dwelling times of 1, 2, 3 and >3 months were 1, 4.9, 5.5 and 9.2%, respectively. On multivariate analysis, stent dwelling time, stent insertion because of sepsis, and female gender were significantly associated with post-ureteroscopy sepsis in patients with prior stent placement. Patients who undergo ureteroscopy after ureteric stent insertion have a higher risk of postoperative sepsis. Prolonged stent dwelling time, sepsis as an indication for stent insertion, and female gender are independent risk factors. Stent placement should be considered cautiously, and if inserted, ureteroscopy should be performed within 1 month. © 2017 The Authors BJU International © 2017 BJU International Published by John Wiley & Sons Ltd.

Comparison of 2 cuff inflation methods of laryngeal mask airway Classic for safe use without cuff manometer in adults.

PubMed

Kim, Min-Soo; Lee, Jeong-Rim; Shin, Yang-Sik; Chung, Ji-Won; Lee, Kyu-Ho; Ahn, Ki Ryang

2014-03-01

This single-center, prospective, randomized, double-blind, 2-arm, parallel group comparison trial was performed to establish whether the adult-sized laryngeal mask airway (LMA) Classic (The Laryngeal Mask Company Ltd, Henley-on-Thames, UK) could be used safely without any consideration of cuff hyperinflation when a cuff of the LMA Classic was inflated using half the maximum inflation volume or the resting volume before insertion of device. Eighty patients aged 20 to 70 years scheduled for general anesthesia using the LMA Classic were included. Before insertion, the cuff was partially filled with half the maximum inflation volume in the half volume group or the resting volume created by opening the pilot balloon valve to equalize with atmospheric pressure in the resting volume group. Several parameters regarding insertion, intracuff pressure, airway leak pressure, and leakage volume/fraction were collected after LMA insertion. The LMA Classic with a partially inflated cuff was successfully inserted in all enrolled patients. Both groups had the same success rate of 95% at the first insertion attempt. The half volume group had a lower mean intracuff pressure compared with the resting volume group (54.5 ± 16.1 cm H2O vs 61.8 ± 16.1 cm H2O; P = .047). There was no difference in airway leak pressure or leakage volume/fraction between the 2 groups under mechanical ventilation. The partially inflated cuff method using half the maximum recommended inflation volume or the resting volume is feasible with the adult-sized LMA Classic, resulting in a high success rate of insertion and adequate range of intracuff pressures. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing.

PubMed

Miyao, Akio; Nakagome, Mariko; Ohnuma, Takako; Yamagata, Harumi; Kanamori, Hiroyuki; Katayose, Yuichi; Takahashi, Akira; Matsumoto, Takashi; Hirochika, Hirohiko

2012-01-01

Somaclonal variation is a phenomenon that results in the phenotypic variation of plants regenerated from cell culture. One of the causes of somaclonal variation in rice is the transposition of retrotransposons. However, many aspects of the mechanisms that result in somaclonal variation remain undefined. To detect genome-wide changes in regenerated rice, we analyzed the whole-genome sequences of three plants independently regenerated from cultured cells originating from a single seed stock. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were detected in the genomes of the regenerated plants. The transposition of only Tos17 among 43 transposons examined was detected in the regenerated plants. Therefore, the SNPs and indels contribute to the somaclonal variation in regenerated rice in addition to the transposition of Tos17. The observed molecular spectrum was similar to that of the spontaneous mutations in Arabidopsis thaliana. However, the base change ratio was estimated to be 1.74 × 10(-6) base substitutions per site per regeneration, which is 248-fold greater than the spontaneous mutation rate of A. thaliana.

DNA Glycosylases Search for and Remove Oxidized DNA Bases

PubMed Central

Wallace, Susan S.

2014-01-01

The following mini review summarizes recent research from the Author’s laboratory as presented to the Environmental Mutagen Society in October 2012. It provides an overview of the DNA glycosylases that recognize oxidized DNA bases using the Fpg/Nei family of DNA glycosylases as models for how structure can inform function. For example, even though human NEIL1 and the plant and fungal orthologs lack the zinc finger shown to be required for binding, DNA crystal structures revealed a “zincless finger” with the same properties. Also the “lesion recognition loop” is not involved in lesion recognition rather stabilization of 8-oxoG in the active site pocket. Unlike the other Fpg/Nei family members, Neil3 lacks two of the three void-filling residues that stabilize the duplex and interact with the opposite strand which may account for its preference for lesions in single stranded DNA. We also showed, using single molecule approaches, that DNA glycosylases search for their substrates in a sea of undamaged DNA by using a wedge residue that is inserted into the DNA helix to probe for the presence of damage. PMID:24123395

Reference genotype and exome data from an Australian Aboriginal population for health-based research

PubMed Central

Tang, Dave; Anderson, Denise; Francis, Richard W.; Syn, Genevieve; Jamieson, Sarra E.; Lassmann, Timo; Blackwell, Jenefer M.

2016-01-01

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians. PMID:27070114

Reference genotype and exome data from an Australian Aboriginal population for health-based research.

PubMed

Tang, Dave; Anderson, Denise; Francis, Richard W; Syn, Genevieve; Jamieson, Sarra E; Lassmann, Timo; Blackwell, Jenefer M

2016-04-12

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

The impact of low-Z and high-Z metal implants in IMRT: A Monte Carlo study of dose inaccuracies in commercial dose algorithms

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

Spadea, Maria Francesca, E-mail: mfspadea@unicz.it; Verburg, Joost Mathias; Seco, Joao

2014-01-15

Purpose: The aim of the study was to evaluate the dosimetric impact of low-Z and high-Z metallic implants on IMRT plans. Methods: Computed tomography (CT) scans of three patients were analyzed to study effects due to the presence of Titanium (low-Z), Platinum and Gold (high-Z) inserts. To eliminate artifacts in CT images, a sinogram-based metal artifact reduction algorithm was applied. IMRT dose calculations were performed on both the uncorrected and corrected images using a commercial planning system (convolution/superposition algorithm) and an in-house Monte Carlo platform. Dose differences between uncorrected and corrected datasets were computed and analyzed using gamma index (Pγ{submore » <1}) and setting 2 mm and 2% as distance to agreement and dose difference criteria, respectively. Beam specific depth dose profiles across the metal were also examined. Results: Dose discrepancies between corrected and uncorrected datasets were not significant for low-Z material. High-Z materials caused under-dosage of 20%–25% in the region surrounding the metal and over dosage of 10%–15% downstream of the hardware. Gamma index test yielded Pγ{sub <1}>99% for all low-Z cases; while for high-Z cases it returned 91% < Pγ{sub <1}< 99%. Analysis of the depth dose curve of a single beam for low-Z cases revealed that, although the dose attenuation is altered inside the metal, it does not differ downstream of the insert. However, for high-Z metal implants the dose is increased up to 10%–12% around the insert. In addition, Monte Carlo method was more sensitive to the presence of metal inserts than superposition/convolution algorithm. Conclusions: The reduction in terms of dose of metal artifacts in CT images is relevant for high-Z implants. In this case, dose distribution should be calculated using Monte Carlo algorithms, given their superior accuracy in dose modeling in and around the metal. In addition, the knowledge of the composition of metal inserts improves the accuracy of the Monte Carlo dose calculation significantly.« less

Non-interventional 1-year follow-up study of peri-implant soft tissues following previous soft tissue augmentation and crown insertion in single-tooth gaps.

PubMed

Huber, Samuel; Zeltner, Marco; Hämmerle, Christoph H F; Jung, Ronald E; Thoma, Daniel S

2018-04-01

To assess peri-implant soft tissue dimensions at implant sites, previously augmented with a collagen matrix (VCMX) or an autogenous subepithelial connective tissue graft (SCTG), between crown insertion and 1 year. Twenty patients with single-tooth implants received soft tissue augmentation prior to abutment connection randomly using VCMX or SCTG. Following abutment connection 3 months later, final reconstructions were fabricated and inserted (baseline). Patients were recalled at 6 months (6M) and at 1 year (FU-1). Measurements included clinical data, soft tissue thickness, volumetric outcomes and patient-reported outcome measures (PROMs). The buccal soft tissue thickness showed a median decrease of -0.5 mm (-1.0;0.3) (VCMX) and 0.0 mm (-0.5;1.0) (SCTG) (p = .243) up to FU-1. The soft tissue volume demonstrated a median decrease between BL and FU-1 of -0.1 mm (-0.2;0.0) (p = .301) for VCMX and a significant decrease of -0.2 mm (-0.4; -0.1) (p = .002) for SCTG, respectively. Intergroup comparisons did not reveal any significant differences between the groups for peri-implant soft tissue dimensions and changes up to FU-1 (p > .05). PROMs did not show any significant changes over time nor differences between the groups. Between crown insertion and 1 year, the buccal peri-implant soft tissue dimensions remained stable without relevant differences between sites that had previously been grafted with VCMX or SCTG. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif

PubMed Central

Shchedrina, Valentina A.; Novoselov, Sergey V.; Malinouski, Mikalai Yu.; Gladyshev, Vadim N.

2007-01-01

Selenocysteine (Sec, U) insertion into proteins is directed by translational recoding of specific UGA codons located upstream of a stem-loop structure known as Sec insertion sequence (SECIS) element. Selenoproteins with known functions are oxidoreductases containing a single redox-active Sec in their active sites. In this work, we identified a family of selenoproteins, designated SelL, containing two Sec separated by two other residues to form a UxxU motif. SelL proteins show an unusual occurrence, being present in diverse aquatic organisms, including fish, invertebrates, and marine bacteria. Both eukaryotic and bacterial SelL genes use single SECIS elements for insertion of two Sec. In eukaryotes, the SECIS is located in the 3′ UTR, whereas the bacterial SelL SECIS is within a coding region and positioned at a distance that supports the insertion of either of the two Sec or both of these residues. SelL proteins possess a thioredoxin-like fold wherein the UxxU motif corresponds to the catalytic CxxC motif in thioredoxins, suggesting a redox function of SelL proteins. Distantly related SelL-like proteins were also identified in a variety of organisms that had either one or both Sec replaced with Cys. Danio rerio SelL, transiently expressed in mammalian cells, incorporated two Sec and localized to the cytosol. In these cells, it occurred in an oxidized form and was not reducible by DTT. In a bacterial expression system, we directly demonstrated the formation of a diselenide bond between the two Sec, establishing it as the first diselenide bond found in a natural protein. PMID:17715293

Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids

PubMed Central

2015-01-01

Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies. PMID:26505212

Axial load-bearing capacity of an osteochondral autograft stabilized with a resorbable osteoconductive bone cement compared with a press-fit graft in a bovine model.

PubMed

Kiss, Marc-Olivier; Levasseur, Annie; Petit, Yvan; Lavigne, Patrick

2012-05-01

Osteochondral autografts in mosaicplasty are inserted in a press-fit fashion, and hence, patients are kept nonweightbearing for up to 2 months after surgery to allow bone healing and prevent complications. Very little has been published regarding alternative fixation techniques of those grafts. Osteochondral autografts stabilized with a resorbable osteoconductive bone cement would have a greater load-bearing capacity than standard press-fit grafts. Controlled laboratory study. Biomechanical testing was conducted on 8 pairs of cadaveric bovine distal femurs. For the first 4 pairs, 6 single osteochondral autografts were inserted in a press-fit fashion on one femur. On the contralateral femur, 6 grafts were stabilized with a calcium triglyceride osteoconductive bone cement. For the 4 remaining pairs of femurs, 4 groups of 3 adjacent press-fit grafts were inserted on one femur, whereas on the contralateral femur, grafts were cemented. After a maturation period of 48 hours, axial loading was applied on all single grafts and on the middle graft of each 3-in-a-row series. For the single-graft configuration, median loads required to sink the press-fit and cemented grafts by 2 and 3 mm were 281.87 N versus 345.56 N (P = .015) and 336.29 N versus 454.08 N (P = .018), respectively. For the 3-in-a-row configuration, median loads required to sink the press-fit and cemented grafts by 2 and 3 mm were 260.31 N versus 353.47 N (P = .035) and 384.83 N versus 455.68 N (P = .029), respectively. Fixation of osteochondral grafts using bone cement appears to improve immediate stability over the original mosaicplasty technique for both single- and multiple-graft configurations. Achieving greater primary stability of osteochondral grafts could potentially accelerate postoperative recovery, allowing early weightbearing and physical therapy.

Pyrosequencing for Microbial Identification and Characterization

PubMed Central

Cummings, Patrick J.; Ahmed, Ray; Durocher, Jeffrey A.; Jessen, Adam; Vardi, Tamar; Obom, Kristina M.

2013-01-01

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns. PMID:23995536

Pyrosequencing for microbial identification and characterization.

PubMed

Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

2013-08-22

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

PubMed Central

Pham, Nikki T.; Wei, Tong; Schackwitz, Wendy S.; Lipzen, Anna M.; Duong, Phat Q.; Jones, Kyle C.; Ruan, Deling; Bauer, Diane; Peng, Yi; Schmutz, Jeremy

2017-01-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. PMID:28576844

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

Li, Guotian; Jain, Rashmi; Chern, Mawsheng

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

Influence of Screw Length and Bone Thickness on the Stability of Temporary Implants

PubMed Central

Fernandes, Daniel Jogaib; Elias, Carlos Nelson; Ruellas, Antônio Carlos de Oliveira

2015-01-01

The purpose of this work was to study the influence of screw length and bone thickness on the stability of temporary implants. A total of 96 self-drilling temporary screws with two different lengths were inserted into polyurethane blocks (n = 66), bovine femurs (n = 18) and rabbit tibia (n = 12) with different cortical thicknesses (1 to 8 mm). Screws insertion in polyurethane blocks was assisted by a universal testing machine, torque peaks were collected by a digital torquemeter and bone thickness was monitored by micro-CT. The results showed that the insertion torque was significantly increased with the thickness of cortical bone from polyurethane (p < 0.0001), bovine (p = 0.0035) and rabbit (p < 0.05) sources. Cancellous bone improved significantly the mechanical implant stability. Insertion torque and insertion strength was successfully moduled by equations, based on the cortical/cancellous bone behavior. Based on the results, insertion torque and bone strength can be estimate in order to prevent failure of the cortical layer during temporary screw placement. The stability provided by a cortical thickness of 2 or 1 mm coupled to cancellous bone was deemed sufficient for temporary implants stability. PMID:28793582

Single-snapshot 2D color measurement by plenoptic imaging system

NASA Astrophysics Data System (ADS)

Masuda, Kensuke; Yamanaka, Yuji; Maruyama, Go; Nagai, Sho; Hirai, Hideaki; Meng, Lingfei; Tosic, Ivana

2014-03-01

Plenoptic cameras enable capture of directional light ray information, thus allowing applications such as digital refocusing, depth estimation, or multiband imaging. One of the most common plenoptic camera architectures contains a microlens array at the conventional image plane and a sensor at the back focal plane of the microlens array. We leverage the multiband imaging (MBI) function of this camera and develop a single-snapshot, single-sensor high color fidelity camera. Our camera is based on a plenoptic system with XYZ filters inserted in the pupil plane of the main lens. To achieve high color measurement precision of this system, we perform an end-to-end optimization of the system model that includes light source information, object information, optical system information, plenoptic image processing and color estimation processing. Optimized system characteristics are exploited to build an XYZ plenoptic colorimetric camera prototype that achieves high color measurement precision. We describe an application of our colorimetric camera to color shading evaluation of display and show that it achieves color accuracy of ΔE<0.01.

Conventional sample enrichment strategies combined with high-performance liquid chromatography-solid phase extraction-nuclear magnetic resonance analysis allows analyte identification from a single minuscule Corydalis solida plant tuber.

PubMed

Sturm, Sonja; Seger, Christoph; Godejohann, Markus; Spraul, Manfred; Stuppner, Hermann

2007-09-07

Identification of putative biomarker molecules within the genus Corydalis (Papaveraceae) was pursued by combining conventional off-line sample enrichment with high-performance liquid chromatography-solid phase extraction-nuclear magnetic resonance (HPLC-SPE-NMR) based structure elucidation. Off-line reversed phase solid phase extraction (SPE) was used to enrich the desired analytes from a methanolic extract (93 mg dry weight) of a miniscule single tuber (233 mg dry weight) of C. solida. An aliquot of the SPE fraction (2.1 mg) was subjected to separation in the HPLC-SPE-NMR hyphenation. Chromatographic peaks bearing the metabolites under investigation were trapped in the SPE device in a single experiment and transferred to a 600 MHz NMR spectrometer equipped with a 30 microl cryofit insert fed into a 3 mm cryoprobe. Recorded homo- and heteronuclear 1D and 2D NMR data allowed the identification of the three analytes under investigation as protopine, allocryptopine, and N-methyl-laudanidinium acetate. The latter is a rare alkaloid, which has been isolated only once before.

Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe

PubMed Central

2012-01-01

Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches. PMID:22554201

Microleakage of Posterior Composite Restorations with Fiber Inserts Using two Adhesives after ging

PubMed Central

Sharafeddin, F; Yousefi, H; Modiri, Sh; Tondari, A; Safaee Jahromi, SR

2013-01-01

Statement of Problem: Microleakage is one of the most frequent problems associated with resin composites, especially at the gingival margin of posterior restorations. Insertion of fibers in composite restorations can reduce the total amount of composite and help to decrease the shrinkage. Purpose: The aim of this study was to evaluate the effect of polyethylene fiber inserts on gingival microleakage of class II composite restorations using two different adhesive systems. Materials and Method: In this experimental study, class II cavities were prepared on 60 premolars. The gingival floor was located 1.0 mm below the CEJ. Dimension of each cavity were 3 mm buccolingually and 1.5 mm in axial depth. The specimens were divided into 4 groups according to the adhesive type and fiber insert (n=4). Single bond and Clearfill SE bond and Filtek p60 were used to restore the cavities. In groups without fiber inserts composite was adapted onto cavities using layering technique. For cavities with fiber inserts, 3 mm piece of fiber insert was placed onto the composite increment and cured. The specimens were stored in distilled water at 37oC for 6 months. All specimens were subjected to 3000 thermo-cycling. The tooth surfaces except for 1 mm around the restoration margins covered with two layers of nail varnish .The teeth were immersed in 2% Basic Fuchsin for 24 hours, then rinsed and sectioned mesiodistally. The microleakage was determined under a stereomicroscope (40X). Data were statistically analyzed by Kruskal-wallis and Mann-Whitney U tests (p< 0.05). Results: The Kruskal-Wallis test revealed no significant differences in mean microleakage scores among all groups (p= 0.281). Conclusion: Use of polyethylene fiber inserts and etch-and-rinse and self-etch adhesives had no effect on microleakage in class II resin composite restorations with gingival margins below the CEJ after 6- month water storage. PMID:24724129

Unexpected formal insertion of CO 2 into the C-Si bonds of a zinc compound

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

Kemp, Richard A.; McGrew, Genette I.; Khatri, Pathik A.

Reaction of [κ 2-PR 2C(SiMe 3)Py] 2Zn (R = Ph, 2a; iPr, 2b) with CO 2 affords the products of formal insertion at the C–Si bond, [κ 2-PR 2CC(O)O(SiMe 3)Py] 2Zn (R = Ph, 3a; iPr, 3b). Insertion product 3b was structurally characterized. As a result, the reaction appears to be a stepwise insertion and rearrangement of CO 2 based on kinetic data.

Unexpected formal insertion of CO 2 into the C-Si bonds of a zinc compound

DOE PAGES

Kemp, Richard A.; McGrew, Genette I.; Khatri, Pathik A.; ...

2015-09-08

Reaction of [κ 2-PR 2C(SiMe 3)Py] 2Zn (R = Ph, 2a; iPr, 2b) with CO 2 affords the products of formal insertion at the C–Si bond, [κ 2-PR 2CC(O)O(SiMe 3)Py] 2Zn (R = Ph, 3a; iPr, 3b). Insertion product 3b was structurally characterized. As a result, the reaction appears to be a stepwise insertion and rearrangement of CO 2 based on kinetic data.

End Restraints for Impact-Energy-Absorbing Tube Specimens

NASA Technical Reports Server (NTRS)

Farley, G. L.; Modlin, J. T.

1985-01-01

Inexpensive device developed that eliminates tipping problem without affecting crushing process. Device consists of soft sponge-rubber insert approximately 0.5 inches (1.3 centimeters) thick, cut to same diameter as internal diameter of tube specimen. Metal washer, slightly smaller than internal diameter of tube, placed on top of rubber insert. Screw passed through washer and rubber insert and threaded into base of test machine. As screw tightened against washer, rubber insert compressed and expands radially. Radial expansion applies pressure against internal wall of tube specimen, which provides sufficient support to tube to prevent tipping.

The Insertion and Management of External Ventricular Drains: An Evidence-Based Consensus Statement : A Statement for Healthcare Professionals from the Neurocritical Care Society.

PubMed

Fried, Herbert I; Nathan, Barnett R; Rowe, A Shaun; Zabramski, Joseph M; Andaluz, Norberto; Bhimraj, Adarsh; Guanci, Mary McKenna; Seder, David B; Singh, Jeffrey M

2016-02-01

External ventricular drains (EVDs) are commonly placed to monitor intracranial pressure and manage acute hydrocephalus in patients with a variety of intracranial pathologies. The indications for EVD insertion and their efficacy in the management of these various conditions have been previously addressed in guidelines published by the Brain Trauma Foundation, American Heart Association and combined committees of the American Association of Neurological Surgeons and the Congress of Neurological Surgeons. While it is well recognized that placement of an EVD may be a lifesaving intervention, the benefits can be offset by procedural and catheter-related complications, such as hemorrhage along the catheter tract, catheter malposition, and CSF infection. Despite their widespread use, there are a lack of high-quality data regarding the best methods for placement and management of EVDs to minimize these risks. Existing recommendations are frequently based on observational data from a single center and may be biased to the authors' view. To address the need for a comprehensive set of evidence-based guidelines for EVD management, the Neurocritical Care Society organized a committee of experts in the fields of neurosurgery, neurology, neuroinfectious disease, critical care, pharmacotherapy, and nursing. The Committee generated clinical questions relevant to EVD placement and management. They developed recommendations based on a thorough literature review using the Grading of Recommendations Assessment, Development, and Evaluation system, with emphasis placed not only on the quality of the evidence, but also on the balance of benefits versus risks, patient values and preferences, and resource considerations.

Thoracic pedicle classification determined by inner cortical width of pedicles on computed tomography images: its clinical significance for posterior vertebral column resection to treat rigid and severe spinal deformities-a retrospective review of cases.

PubMed

Zhang, Ying; Xie, Jingming; Wang, Yingsong; Bi, Ni; Zhao, Zhi; Li, Tao

2014-08-13

Posterior vertebral column resection (PVCR) is an effective alternative for treating rigid and severe spinal deformities. Accurate placement of pedicle screws, especially apically, is crucial. As morphologic evaluations of thoracic pedicles have not provided objective criteria, we propose a thoracic pedicle classification for treating rigid and severe spinal deformities. A consecutive series of 56 patients with severe and rigid spinal deformities who underwent PVCR at a single institution were reviewed retrospectively. Altogether, 1098 screws were inserted into thoracic pedicles at T2-T12. Based on the inner cortical width of the thoracic pedicles, the patients were divided into four groups: group 1 (0-1.0 mm), group 2 (1.1-2.0 mm), group 3 (2.1-3.0 mm), group 4 (≥3.1 mm). The proportion of screws accurately inserted in thoracic pedicles for each group was calculated. Statistical analysis was also performed regarding types of thoracic pedicles classified by Lenke et al. (SPINE 35:1836-1842, 2010) using a morphological method. There were statistically significant differences in the rates of screws inserted in thoracic pedicles between the groups (P < 0.008) except groups 3 and 4 (P > 0.008), which were then combined. The accuracies for the three new groups were 35.05%, 65.34%, and 88.32%, respectively, with statistically significant differences between the groups (P < 0.017). Rates of screws inserted in thoracic pedicles classified by Lenke et al. (SPINE 35:1836-1842, 2010) were 82.31%, 83.40%, 80.00%, and 30.28% for types A, B, C, and D, respectively. There was no statistically significant difference (P > 0.008) between these types except between type D and the other three types (P < 0.008). The inner cortical width of thoracic pedicles is the sole factor crucial for accurate placement of thoracic pedicle screws. We propose a computed tomography-based classification of the pedicle's inner cortical width: type I thoracic pedicle: absent channel, inner cortical width of 0-1 mm; type II: presence of a channel of which type IIa has an inner cortical width of 1.1-2.0 mm and type IIb a width of ≥2.1 mm. The proposed classification can help surgeons predict whether screws can be inserted into the thoracic pedicle, thus guiding instrumentation when PVCR is performed.

Homogenizing microwave illumination in thermoacoustic tomography by a linear-to-circular polarizer based on frequency selective surfaces

NASA Astrophysics Data System (ADS)

He, Yu; Shen, Yuecheng; Feng, Xiaohua; Liu, Changjun; Wang, Lihong V.

2017-08-01

A circularly polarized antenna, providing more homogeneous illumination compared to a linearly polarized antenna, is more suitable for microwave induced thermoacoustic tomography (TAT). The conventional realization of a circular polarization is by using a helical antenna, but it suffers from low efficiency, low power capacity, and limited aperture in TAT systems. Here, we report an implementation of a circularly polarized illumination method in TAT by inserting a single-layer linear-to-circular polarizer based on frequency selective surfaces between a pyramidal horn antenna and an imaging object. The performance of the proposed method was validated by both simulations and experimental imaging of a breast tumor phantom. The results showed that a circular polarization was achieved, and the resultant thermoacoustic signal-to-noise was twice greater than that in the helical antenna case. The proposed method is more desirable in a waveguide-based TAT system than the conventional method.

Strength of inserts in titanium alloy machining

NASA Astrophysics Data System (ADS)

Kozlov, V.; Huang, Z.; Zhang, J.

2016-04-01

In this paper, a stressed state of a non-worn cutting wedge in a machined titanium alloy (Ti6Al2Mo2Cr) is analyzed. The distribution of contact loads on the face of a cutting tool was obtained experimentally with the use of a ‘split cutting tool’. Calculation of internal stresses in the indexable insert made from cemented carbide (WC8Co) was carried out with the help of ANSYS 14.0 software. Investigations showed that a small thickness of the cutting insert leads to extremely high compressive stresses near the cutting edge, stresses that exceed the ultimate compressive strength of cemented carbide. The face and the base of the insert experience high tensile stresses, which approach the ultimate tensile strength of cemented carbide and increase a probability of cutting insert destruction. If the thickness of the cutting insert is bigger than 5 mm, compressive stresses near the cutting edge decrease, and tensile stresses on the face and base decrease to zero. The dependences of the greatest normal and tangential stresses on thickness of the cutting insert were found. Abbreviation and symbols: m/s - meter per second (cutting speed v); mm/r - millimeter per revolution (feed rate f); MPa - mega Pascal (dimension of specific contact loads and stresses); γ - rake angle of the cutting tool [°] α - clearance angle of the sharp cutting tool [°].

Single-cell optoporation and transfection using femtosecond laser and optical tweezers.

PubMed

Waleed, Muhammad; Hwang, Sun-Uk; Kim, Jung-Dae; Shabbir, Irfan; Shin, Sang-Mo; Lee, Yong-Gu

2013-01-01

In this paper, we demonstrate a new single-cell optoporation and transfection technique using a femtosecond Gaussian laser beam and optical tweezers. Tightly focused near-infrared (NIR) femtosecond laser pulse was employed to transiently perforate the cellular membrane at a single point in MCF-7 cancer cells. A distinct technique was developed by trapping the microparticle using optical tweezers to focus the femtosecond laser precisely on the cell membrane to puncture it. Subsequently, an external gene was introduced in the cell by trapping and inserting the same plasmid-coated microparticle into the optoporated cell using optical tweezers. Various experimental parameters such as femtosecond laser exposure power, exposure time, puncture hole size, exact focusing of the femtosecond laser on the cell membrane, and cell healing time were closely analyzed to create the optimal conditions for cell viability. Following the insertion of plasmid-coated microparticles in the cell, the targeted cells exhibited green fluorescent protein (GFP) under the fluorescent microscope, hence confirming successful transfection into the cell. This new optoporation and transfection technique maximizes the level of selectivity and control over the targeted cell, and this may be a breakthrough method through which to induce controllable genetic changes in the cell.

Iodine insertion and dispersion of refractive index in organic single crystal semiconductor.

PubMed

Kwon, Seonho; Bae, Junwan; Lee, I J

2018-02-20

Insertion of halogens such as bromine or iodine affects the electronic polarizability of ions and the local field inside the medium, and thus modifies the refractive index. Acquiring precise knowledge of the dispersion of refractive index and ultimately tailoring conventional semiconductors for wide-range refractive index control have been a vital issue to resolve before realizing advanced organic optoelectronic devices. In this report, dispersions of the refractive index of a single crystal tetramethyltetraselenafulvalene [C 10 H 12 Se 4 ] (TMTSF) are thoroughly studied from broadband interference modulations of photoluminescence (PL) spectra at various temperatures and doping levels. A large enhancement of the refractive index, more than 20% of the intrinsic value, is achieved with inclusion of a small composition of iodide ions, while the structural and optical properties remain mostly intact. Nearly temperature independent dispersion of the refractive index suggests that, unlike most polymers in which the thermal expansion coefficient dominates over the change of polarizability with temperature, the latter enhances significantly and may become more or less comparable to the thermal expansion coefficient given by 1.71 × 10 -4 /K, when single crystal TMTSF is doped by iodine.

Microstructure evolution of the Ir-inserted Ni silicides with additional annealing

NASA Astrophysics Data System (ADS)

Yoon, Kijeong; Song, Ohsung

2009-02-01

Thermally-evaporated 10 nm-Ni/1 nm-Ir/(poly)Si structures were fabricated in order to investigate the thermal stability of Ir-inserted nickel silicide after additional annealing. The silicide samples underwent rapid thermal annealing at 300 ° C to 1200 ° C for 40 s, followed by 30 min annealing at the given RTA temperatures. Silicides suitable for the salicide process were formed on the top of the single crystal and polycrystalline silicon substrates, mimicking actives and gates. The sheet resistance was measured using a four-point probe. High resolution x-ray diffraction and Auger depth profiling were used for phase and chemical composition analysis, respectively. Transmission electron microscope and scanning probe microscope were used to determine the cross-section structure and surface roughness. The silicide, which formed on single crystal silicon substrate with surface agglomeration after additional annealing, could defer the transformation of Ni(Ir)Si to Ni(Ir)Si2 and was stable at temperatures up to 1200 °C. Moreover, the silicide thickness doubled. There were no outstanding changes in the silicide thickness on polycrystalline silicon. However, after additional annealing, the silicon-silicide mixing became serious and showed high resistance at temperatures >700 °C. Auger depth profiling confirmed the increased thickness of the silicide layers after additional annealing without a change in composition. For a single crystal silicon substrate, the sheet resistance increased slightly due to the significant increases in surface roughness caused by surface agglomeration after additional annealing. Otherwise, there were almost no changes in surface roughness on the polycrystalline silicon substrate. The Ir-inserted nickel monosilicide was able to maintain a low resistance in a wide temperature range and is considered suitable for the nano-thick silicide process.

Double- vs. single-balloon enteroscopy: single center experience with emphasis on procedural performance.

PubMed

Lenz, Philipp; Roggel, Moritz; Domagk, Dirk

2013-09-01

This study aims to compare double- (DBE) and single-balloon enteroscopy (SBE) in small bowel disorders with respect to procedural performance and clinical impact. This retrospective analysis at a tertial referral center included 1,052 DBEs and 515 SBEs performed in 904 patients over 7 years. Procedural and patients' characteristics were precisely analyzed. Significantly more patients with anemia and gastrointestinal bleeding were investigated by DBE (P < 0.01). Oral insertion depth and length of investigated small bowel in the combined approach were significantly higher in the DBE compared to the SBE group (245 ± 65.3 vs. 218 ± 62.6 and 355 ± 101.9 vs. 319 ± 91.2, respectively; P < 0.001, each). By analyzing only recent years of enteroscopy (2008-2011), no difference in small bowel visualization could be observed. The anal insertion depths and complete enteroscopy rates (CER) were comparable. Procedure times were significantly shorter within the SBE procedure (oral: 50 vs. 40 min; anal: 55 vs. 46 min, P < 0.001) and the usage of sedation was significantly less (propofol: P < 0.001; pethidine: P < 0.05). Diagnostic yield was significantly higher in the SBE, compared to the DBE group (61.7 vs. 48.2 %; P < 0.001). The rate of severe adverse events was close to zero. Both enteroscopy techniques are safe diagnostic tools and proved to be indispensable in the daily gastroenterological practice. The lower insertion depths, but higher diagnostic yield, of SBE may reflect the more focused selection of patients scheduled for small bowel diagnostics in recent years.

Nontraumatic tibial polyethylene insert cone fracture in mobile-bearing posterior-stabilized total knee arthroplasty.

PubMed

Tanikake, Yohei; Hayashi, Koji; Ogawa, Munehiro; Inagaki, Yusuke; Kawate, Kenji; Tomita, Tetsuya; Tanaka, Yasuhito

2016-12-01

A 72-year-old male patient underwent mobile-bearing posterior-stabilized total knee arthroplasty for osteoarthritis. He experienced a nontraumatic polyethylene tibial insert cone fracture 27 months after surgery. Scanning electron microscopy of the fracture surface of the tibial insert cone suggested progress of ductile breaking from the posterior toward the anterior of the cone due to repeated longitudinal bending stress, leading to fatigue breaking at the anterior side of the cone, followed by the tibial insert cone fracture at the anterior side of the cone, resulting in fracture at the base of the cone. This analysis shows the risk of tibial insert cone fracture due to longitudinal stress in mobile-bearing posterior-stabilized total knee arthroplasty in which an insert is designed to highly conform to the femoral component.

Folding and insertion thermodynamics of the transmembrane WALP peptide

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

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Bennett, W. F. Drew; Pfaendtner, Jim

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of meanmore » force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.« less

Mutational analysis of a predicted double β-propeller domain of the DspA/E effector of Erwinia amylovora.

PubMed

Siamer, Sabrina; Gaubert, Stéphane; Boureau, Tristan; Brisset, Marie-Noëlle; Barny, Marie-Anne

2013-05-01

The bacterium Erwinia amylovora causes fire blight, an invasive disease that threatens apple trees, pear trees and other plants of the Rosaceae family. Erwinia amylovora pathogenicity relies on a type III secretion system and on a single effector DspA/E. This effector belongs to the widespread AvrE family of effectors whose biological function is unknown. In this manuscript, we performed a bioinformatic analysis of DspA/E- and AvrE-related effectors. Motif search identified nuclear localization signals, peroxisome targeting signals, endoplasmic reticulum membrane retention signals and leucine zipper motifs, but none of these motifs were present in all the AvrE-related effectors analysed. Protein threading analysis, however, predicted a conserved double β-propeller domain in the N-terminal part of all the analysed effector sequences. We then performed a random pentapeptide mutagenesis of DspA/E, which led to the characterization of 13 new altered proteins with a five amino acids insertion. Eight harboured the insertion inside the predicted β-propeller domain and six of these eight insertions impaired DspA/E stability or function. Conversely, the two remaining insertions generated proteins that were functional and abundantly secreted in the supernatant suggesting that these two insertions stabilized the protein. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Folding and insertion thermodynamics of the transmembrane WALP peptide

NASA Astrophysics Data System (ADS)

Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

2015-12-01

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

Method and device for supporting blood vessels during anastomosis

DOEpatents

Doss, J.D.

1985-05-20

A device and method for preventing first and second severed blood vessels from collapsing during attachment to each other. The device comprises a dissolvable non-toxic stent that is sufficiently rigid to prevent the blood vessels from collapsing during anastomosis. The stent can be hollow or have passages to permit blood flow before it dissolves. A single stent can be inserted with an end in each of the two blood vessels or separate stents can be inserted into each blood vessel. The stent may include a therapeutically effective amount of a drug which is slowly released into the blood stream as the stent dissolves. 12 figs.

A linear 180 nm SOI CMOS antenna switch module using integrated passive device filters for cellular applications

NASA Astrophysics Data System (ADS)

Jie, Cui; Lei, Chen; Peng, Zhao; Xu, Niu; Yi, Liu

2014-06-01

A broadband monolithic linear single pole, eight throw (SP8T) switch has been fabricated in 180 nm thin film silicon-on-insulator (SOI) CMOS technology with a quad-band GSM harmonic filter in integrated passive devices (IPD) technology, which is developed for cellular applications. The antenna switch module (ASM) features 1.2 dB insertion loss with filter on 2G bands and 0.4 dB insertion loss in 3G bands, less than -45 dB isolation and maximum -103 dB intermodulation distortion for mobile front ends by applying distributed architecture and adaptive supply voltage generator.

[The development and operation of a package inserts service system for electronic medical records].

PubMed

Yamada, Hidetoshi; Nishimura, Sachiho; Shimamori, Yoshimitsu; Sato, Seiji; Hayase, Yukitoshi

2003-03-01

To promote the appropriate use of pharmaceuticals and to prevent side effects, physicians need package inserts on medicinal drugs as soon as possible. A medicinal drug information service system was established for electronic medical records to speed up and increase the efficiency of package insert communications within a medical institution. Development of this system facilitates access to package inserts by, for example, physicians. The time required to maintain files of package inserts was shortened, and the efficiency of the drug information service increased. As a source of package inserts for this system, package inserts using a standard generalized markup language (SGML) form were used, which are accessible to the public on the homepage of the Organization for Pharmaceutical Safety and Research (OPSR). This study found that a delay occurred in communicating revised package inserts from pharmaceutical companies to the OPSR. Therefore a pharmaceutical department page was set up as part of the homepage of the medical institution for electronic medical records to shorten the delay in the revision of package inserts posted on the medicinal drug information service homepage of the OPSR. The usefulness of this package insert service system for electronic medical records is clear. For more effective use of this system based on the OPSR homepage pharmaceutical companies have been requested to provide quicker updating of package inserts.

Cryo-EM near-atomic structure of a dsRNA fungal virus shows ancient structural motifs preserved in the dsRNA viral lineage

PubMed Central

Luque, Daniel; Gómez-Blanco, Josué; Garriga, Damiá; Brilot, Axel F.; González, José M.; Havens, Wendy M.; Carrascosa, José L.; Trus, Benes L.; Verdaguer, Nuria; Ghabrial, Said A.; Castón, José R.

2014-01-01

Viruses evolve so rapidly that sequence-based comparison is not suitable for detecting relatedness among distant viruses. Structure-based comparisons suggest that evolution led to a small number of viral classes or lineages that can be grouped by capsid protein (CP) folds. Here, we report that the CP structure of the fungal dsRNA Penicillium chrysogenum virus (PcV) shows the progenitor fold of the dsRNA virus lineage and suggests a relationship between lineages. Cryo-EM structure at near-atomic resolution showed that the 982-aa PcV CP is formed by a repeated α-helical core, indicative of gene duplication despite lack of sequence similarity between the two halves. Superimposition of secondary structure elements identified a single “hotspot” at which variation is introduced by insertion of peptide segments. Structural comparison of PcV and other distantly related dsRNA viruses detected preferential insertion sites at which the complexity of the conserved α-helical core, made up of ancestral structural motifs that have acted as a skeleton, might have increased, leading to evolution of the highly varied current structures. Analyses of structural motifs only apparent after systematic structural comparisons indicated that the hallmark fold preserved in the dsRNA virus lineage shares a long (spinal) α-helix tangential to the capsid surface with the head-tailed phage and herpesvirus viral lineage. PMID:24821769

Design methodology and performance analysis of a wideband 90° phase switch for radiometer applications

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

Villa, Enrique, E-mail: villae@unican.es; Aja, Beatriz; Cagigas, Jaime

2013-12-15

This paper presents the analysis, design, and characterization of a wideband 90° phase switch in Ka-band. The phase switch is based on two microstrip bandpass filters in which the commutation is performed by a novel single-pole double-throw (SPDT) switch. The analysis of π-network bandpass filters is provided, obtaining the phase difference and amplitude imbalance between filters and their scattering parameters; tested results show an average phase difference of 88.9° ± 5° and an amplitude imbalance of 0.15 dB from 24 to 37 GHz. The new broadband SPDT switch is based on a coplanar waveguide-to-slotline-to-microstrip structure, which enables a full planarmore » integration with shifting branches. PIN diodes are used to perform the switching between outputs. The SPDT shows isolation better than 19 dB, insertion loss of around 1.8 dB, and return loss better than 15 dB. The full integration of the phase switch achieves a return loss better than 11 dB and insertion loss of around 4 dB over the band 26–36 GHz, with an average phase difference of 87.1° ± 4° and an average amplitude imbalance of 0.3 dB. It provides an excellent performance for this frequency range, suitable for radio-astronomy receivers.« less

Performance study of a PET scanner based on monolithic scintillators for different DoI-dependent methods

NASA Astrophysics Data System (ADS)

Preziosi, E.; Sánchez, S.; González, A. J.; Pani, R.; Borrazzo, C.; Bettiol, M.; Rodriguez-Alvarez, M. J.; González-Montoro, A.; Moliner, L.; Benlloch, J. M.

2016-12-01

One of the technical objectives of the MindView project is developing a brain-dedicated PET insert based on monolithic scintillation crystals. It will be inserted in MRI systems with the purpose to obtain simultaneous PET and MRI brain images. High sensitivity, high image quality performance and accurate detection of the Depth-of-Interaction (DoI) of the 511keV photons are required. We have developed a DoI estimation method, dedicated to monolithic scintillators, allowing continuous DoI estimation and a DoI-dependent algorithm for the estimation of the photon planar impact position, able to improve the single module imaging capabilities. In this work, through experimental measurements, the proposed methods have been used for the estimation of the impact positions within the monolithic crystal block. We have evaluated the PET system performance following the NEMA NU 4-2008 protocol by reconstructing the images using the STIR 3D platform. The results obtained with two different methods, providing discrete and continuous DoI information, are compared with those obtained from an algorithm without DoI capabilities and with the ideal response of the detector. The proposed DoI-dependent imaging methods show clear improvements in the spatial resolution (FWHM) of reconstructed images, allowing to obtain values from 2mm (at the center FoV) to 3mm (at the FoV edges).

Spy: a new group of eukaryotic DNA transposons without target site duplications.

PubMed

Han, Min-Jin; Xu, Hong-En; Zhang, Hua-Hao; Feschotte, Cédric; Zhang, Ze

2014-06-24

Class 2 or DNA transposons populate the genomes of most eukaryotes and like other mobile genetic elements have a profound impact on genome evolution. Most DNA transposons belong to the cut-and-paste types, which are relatively simple elements characterized by terminal-inverted repeats (TIRs) flanking a single gene encoding a transposase. All eukaryotic cut-and-paste transposons so far described are also characterized by target site duplications (TSDs) of host DNA generated upon chromosomal insertion. Here, we report a new group of evolutionarily related DNA transposons called Spy, which also include TIRs and DDE motif-containing transposase but surprisingly do not create TSDs upon insertion. Instead, Spy transposons appear to transpose precisely between 5'-AAA and TTT-3' host nucleotides, without duplication or modification of the AAATTT target sites. Spy transposons were identified in the genomes of diverse invertebrate species based on transposase homology searches and structure-based approaches. Phylogenetic analyses indicate that Spy transposases are distantly related to IS5, ISL2EU, and PIF/Harbinger transposases. However, Spy transposons are distinct from these and other DNA transposon superfamilies by their lack of TSD and their target site preference. Our findings expand the known diversity of DNA transposons and reveal a new group of eukaryotic DDE transposases with unusual catalytic properties. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

An experimental investigation on heat transfer enhancement in the laminar flow of water/TiO2 nanofluid through a tube heat exchanger fitted with modified butterfly inserts

NASA Astrophysics Data System (ADS)

Venkitaraj, K. P.; Suresh, S.; Alwin Mathew, T.; Bibin, B. S.; Abraham, Jisa

2018-03-01

Nanofluids are advanced heat transfer fluids that exhibit thermal properties superior than that of the conventional fluids such as water, oil etc. This paper reports the experimental study on convective heat transfer characteristics of water based titanium dioxide nanofluids in fully developed flow through a uniformly heated pipe heat exchanger fitted with modified butterfly inserts. Nanofluids are prepared by dispersing TiO2 nanoparticles of average particle size 29 nm in deionized water. The heat transfer experiments are performed in laminar regime using nanofluids prepared with 0.1% and 0.3% volume fractions of TiO2 nanoparticles. The thermal performance characteristics of conventional butterfly inserts and modified butterfly inserts are also compared using TiO2 nanofluid. The inserts with different pitches 6 cm, 9 cm and 12 cm are tested to determine the effect of pitch distance of inserts in the heat transfer and friction. The experimental results showed that the modification made in the butterfly inserts were able to produce higher heat transfer than conventional butterfly inserts.

Protein Interactions and Localization of the Escherichia coli Accessory Protein HypA during Nickel Insertion to [NiFe] Hydrogenase*

PubMed Central

Chan Chung, Kim C.; Zamble, Deborah B.

2011-01-01

Nickel delivery during maturation of Escherichia coli [NiFe] hydrogenase 3 includes the accessory proteins HypA, HypB, and SlyD. Although the isolated proteins have been characterized, little is known about how they interact with each other and the hydrogenase 3 large subunit, HycE. In this study the complexes of HypA and HycE were investigated after modification with the Strep-tag II. Multiprotein complexes containing HypA, HypB, SlyD, and HycE were observed, consistent with the assembly of a single nickel insertion cluster. An interaction between HypA and HycE did not require the other nickel insertion proteins, but HypB was not found with the large subunit in the absence of HypA. The HypA-HycE complex was not detected in the absence of the HypC or HypD proteins, involved in the preceding iron insertion step, and this interaction is enhanced by nickel brought into the cell by the NikABCDE membrane transporter. Furthermore, without the hydrogenase 1, 2, and 3 large subunits, complexes between HypA, HypB, and SlyD were observed. These results support the hypothesis that HypA acts as a scaffold for assembly of the nickel insertion proteins with the hydrogenase precursor protein after delivery of the iron center. At different stages of the hydrogenase maturation process, HypA was observed at or near the cell membrane by using fluorescence confocal microscopy, as was HycE, suggesting membrane localization of the nickel insertion event. PMID:22016389

Cercosporin-deficient mutants by plasmid tagging in the asexual fungus Cercospora nicotianae.

PubMed

Chung, K-R; Ehrenshaft, M; Wetzel, D K; Daub, M E

2003-11-01

We have successfully adapted plasmid insertion and restriction enzyme-mediated integration (REMI) to produce cercosporin toxin-deficient mutants in the asexual phytopathogenic fungus Cercospora nicotianae. The use of pre-linearized plasmid or restriction enzymes in the transformation procedure significantly decreased the transformation frequency, but promoted a complicated and undefined mode of plasmid integration that leads to mutations in the C. nicotianae genome. Vector DNA generally integrated in multiple copies, and no increase in single-copy insertion was observed when enzymes were added to the transformation mixture. Out of 1873 transformants tested, 39 putative cercosporin toxin biosynthesis ( ctb) mutants were recovered that showed altered levels of cercosporin production. Seven ctb mutants were recovered using pre-linearized plasmids without the addition of enzymes, and these were considered to be non-REMI mutants. The correlation between a specific insertion and a mutant phenotype was confirmed using rescued plasmids as gene disruption vectors in the wild-type strain. Six out of fifteen rescued plasmids tested yielded cercosporin-deficient transformants when re-introduced into the wild-type strain, suggesting a link between the insertion site and the cercosporin-deficient phenotype. Sequence analysis of a fragment flanking the insert site recovered from one insertion mutant showed it to be disrupted in sequences with high homology to the acyl transferase domain of polyketide synthases from other fungi. Disruption of this polyketide synthase gene ( CTB1) using a rescued plasmid resulted in mutants that were defective in cercosporin production. Thus, we provide the first molecular evidence that cercosporin is synthesized via a polyketide pathway as previously hypothesized.

Combination therapy for male erectile dysfunction and urinary incontinence.

PubMed

Zafirakis, Helen; Wang, Run; Westney, O Lenaine

2008-01-01

Urinary incontinence (UI) and erectile dysfunction (ED) are both very prevalent conditions. Insertion of an artificial urinary sphincter (AUS) and penile prosthesis (PP) is an effective and proven method of treatment for both conditions. With advancing age, as well as with increasing populations of patients radically treated for prostate cancer, the occurrence of both conditions found in the same patient is increasing. The purpose of this article was to analyze the available evidence for simultaneous surgical management of male ED and UI using prosthetic devices. The existing literature pertaining to dual implantation of AUS and PP was reviewed. The concomitant insertion of the PP with the male perineal sling was also considered. Concurrent ED and UI are increasingly seen in the post radical prostatectomy population, who are often younger and less willing to suffer with these conditions. Insertion of an AUS and PP, either simultaneously or as a two-stage procedure, appears to be a safe, efficacious and long-lasting method of treatment. The improvements in design of both the AUS and PP as well as the development of the single transverse scrotal incision have made simultaneous insertion of these prostheses possible. Dual implantation of the PP and male sling looks promising in a selected population. In conclusion, the insertion of the AUS and PP for the treatment of concurrent UI and ED is safe and effective. Simultaneous insertion of these prostheses in the same patient offers potential advantages in operative and recovery time and is associated with high patient satisfaction. Combination therapy should therefore be included in the arsenal of treatment of these conditions.

Medical-grade honey does not reduce skin colonization at central venous catheter-insertion sites of critically ill patients: a randomized controlled trial

PubMed Central

2012-01-01

Introduction Catheter-related bloodstream infections (CRBSIs) associated with short-term central venous catheters (CVCs) in intensive care unit (ICU) patients are a major clinical problem. Bacterial colonization of the skin at the CVC insertion site is an important etiologic factor for CRBSI. The aim of this study was to assess the efficacy of medical-grade honey in reducing bacterial skin colonization at insertion sites. Methods A prospective, single-center, open-label randomized controlled trial was performed at the ICU of a university hospital in The Netherlands to assess the efficacy of medical-grade honey to reduce skin colonization of insertion sites. Medical-grade honey was applied in addition to standard CVC-site dressing and disinfection with 0.5% chlorhexidine in 70% alcohol. Skin colonization was assessed on a daily basis before CVC-site disinfection. The primary end point was colonization of insertion sites with >100 colony-forming units at the last sampling before removal of the CVC or transfer of the patient from the ICU. Secondary end points were quantitative levels of colonization of the insertion sites and colonization of insertion sites stratified for CVC location. Results Colonization of insertion sites was not affected by the use of medical-grade honey, as 44 (34%) of 129 and 36 (34%) of 106 patients in the honey and standard care groups, respectively, had a positive skin culture (P = 0.98). Median levels of skin colonization at the last sampling were 1 (0 to 2.84) and 1 (0 to 2.70) log colony-forming units (CFUs)/swab for the honey and control groups, respectively (P = 0.94). Gender, days of CVC placement, CVC location, and CVC type were predictive for a positive skin culture. Correction for these variables did not change the effect of honey on skin-culture positivity. Conclusions Medical-grade honey does not affect colonization of the skin at CVC insertion sites in ICU patients when applied in addition to standard disinfection with 0.5% chlorhexidine in 70% alcohol. Trial registration Netherlands Trial Registry, NTR1652. PMID:23111148

Medical-grade honey does not reduce skin colonization at central venous catheter-insertion sites of critically ill patients: a randomized controlled trial.

PubMed

Kwakman, Paulus H; Müller, Marcella C; Binnekade, Jan M; van den Akker, Johannes P; de Borgie, Corianne A; Schultz, Marcus J; Zaat, Sebastian A

2012-10-30

Catheter-related bloodstream infections (CRBSIs) associated with short-term central venous catheters (CVCs) in intensive care unit (ICU) patients are a major clinical problem. Bacterial colonization of the skin at the CVC insertion site is an important etiologic factor for CRBSI. The aim of this study was to assess the efficacy of medical-grade honey in reducing bacterial skin colonization at insertion sites. A prospective, single-center, open-label randomized controlled trial was performed at the ICU of a university hospital in The Netherlands to assess the efficacy of medical-grade honey to reduce skin colonization of insertion sites. Medical-grade honey was applied in addition to standard CVC-site dressing and disinfection with 0.5% chlorhexidine in 70% alcohol. Skin colonization was assessed on a daily basis before CVC-site disinfection. The primary end point was colonization of insertion sites with >100 colony-forming units at the last sampling before removal of the CVC or transfer of the patient from the ICU. Secondary end points were quantitative levels of colonization of the insertion sites and colonization of insertion sites stratified for CVC location. Colonization of insertion sites was not affected by the use of medical-grade honey, as 44 (34%) of 129 and 36 (34%) of 106 patients in the honey and standard care groups, respectively, had a positive skin culture (P = 0.98). Median levels of skin colonization at the last sampling were 1 (0 to 2.84) and 1 (0 to 2.70) log colony-forming units (CFUs)/swab for the honey and control groups, respectively (P = 0.94). Gender, days of CVC placement, CVC location, and CVC type were predictive for a positive skin culture. Correction for these variables did not change the effect of honey on skin-culture positivity. Medical-grade honey does not affect colonization of the skin at CVC insertion sites in ICU patients when applied in addition to standard disinfection with 0.5% chlorhexidine in 70% alcohol. Netherlands Trial Registry, NTR1652.

Simulator trials to determine the wear of the combination aluminium oxide ceramic-carbon fibre reinforced plastic (CFRP) used as an insert in a hip socket.

PubMed

Scheller, G; Schwarz, M; Früh, H J; Jani, L

1999-01-01

Hip simulator trials were conducted to determine the initial wear between alumina femoral heads and carbon fibre reinforced plastic (CFRP, CAPROMAN) insert in a titanium socket. A force of 2500 N and a frequency of 0.857 H were applied. Using surface and sphericity measurement techniques, the amount of wear was determined. After 500,000 cycles, the centre of the head had moved by 10 microm into the insert, and the average radius increased by 2 microm. After 1 million cycles, the additional changes were less than 1 microm. Based on an examination of retrieved implants (wear rate: 6.1 microm/year) and based on the simulator results, the combination alumina-CFRP inserts could be approved for total hip replacement.

Management of computed tomography-detected pneumothorax in patients with blunt trauma: experience from a community-based hospital

PubMed Central

Hefny, Ashraf F; Kunhivalappil, Fathima T; Matev, Nikolay; Avila, Norman A; Bashir, Masoud O; Abu-Zidan, Fikri M

2018-01-01

INTRODUCTION Diagnoses of pneumothorax, especially occult pneumothorax, have increased as the use of computed tomography (CT) for imaging trauma patients becomes near-routine. However, the need for chest tube insertion remains controversial. We aimed to study the management of pneumothorax detected on CT among patients with blunt trauma, including the decision for tube thoracostomy, in a community-based hospital. METHODS Chest CT scans of patients with blunt trauma treated at Al Rahba Hospital, Abu Dhabi, United Arab Emirates, from October 2010 to October 2014 were retrospectively studied. Variables studied included demography, mechanism of injury, endotracheal intubation, pneumothorax volume, chest tube insertion, Injury Severity Score, hospital length of stay and mortality. RESULTS CT was performed in 703 patients with blunt trauma. Overall, pneumothorax was detected on CT for 74 (10.5%) patients. Among the 65 patients for whom pneumothorax was detected before chest tube insertion, 25 (38.5%) needed chest tube insertion, while 40 (61.5%) did not. Backward stepwise likelihood regression showed that independent factors that significantly predicted chest tube insertion were endotracheal intubation (p = 0.01), non-United Arab Emirates nationality (p = 0.01) and pneumothorax volume (p = 0.03). The receiver operating characteristic curve showed that the best pneumothorax volume that predicted chest tube insertion was 30 mL. CONCLUSION Chest tube was inserted in less than half of the patients with blunt trauma for whom pneumothorax was detected on CT. Pneumothorax volume should be considered in decision-making regarding chest tube insertion. Conservative treatment may be sufficient for pneumothorax of volume < 30 mL. PMID:28741012

Management of computed tomography-detected pneumothorax in patients with blunt trauma: experience from a community-based hospital.

PubMed

Hefny, Ashraf F; Kunhivalappil, Fathima T; Matev, Nikolay; Avila, Norman A; Bashir, Masoud O; Abu-Zidan, Fikri M

2018-03-01

Diagnoses of pneumothorax, especially occult pneumothorax, have increased as the use of computed tomography (CT) for imaging trauma patients becomes near-routine. However, the need for chest tube insertion remains controversial. We aimed to study the management of pneumothorax detected on CT among patients with blunt trauma, including the decision for tube thoracostomy, in a community-based hospital. Chest CT scans of patients with blunt trauma treated at Al Rahba Hospital, Abu Dhabi, United Arab Emirates, from October 2010 to October 2014 were retrospectively studied. Variables studied included demography, mechanism of injury, endotracheal intubation, pneumothorax volume, chest tube insertion, Injury Severity Score, hospital length of stay and mortality. CT was performed in 703 patients with blunt trauma. Overall, pneumothorax was detected on CT for 74 (10.5%) patients. Among the 65 patients for whom pneumothorax was detected before chest tube insertion, 25 (38.5%) needed chest tube insertion, while 40 (61.5%) did not. Backward stepwise likelihood regression showed that independent factors that significantly predicted chest tube insertion were endotracheal intubation (p = 0.01), non-United Arab Emirates nationality (p = 0.01) and pneumothorax volume (p = 0.03). The receiver operating characteristic curve showed that the best pneumothorax volume that predicted chest tube insertion was 30 mL. Chest tube was inserted in less than half of the patients with blunt trauma for whom pneumothorax was detected on CT. Pneumothorax volume should be considered in decision-making regarding chest tube insertion. Conservative treatment may be sufficient for pneumothorax of volume < 30 mL. Copyright: © Singapore Medical Association.

Demonstration of Compact and Low-Loss Athermal Arrayed-Waveguide Grating Module Based on 2.5%-Δ Silica-Based Waveguides

NASA Astrophysics Data System (ADS)

Maru, Koichi; Abe, Yukio; Uetsuka, Hisato

2008-10-01

We demonstrated a compact and low-loss athermal arrayed-waveguide grating (AWG) module utilizing silica-based planar lightwave circuit (PLC) technology. Spot-size converters based on a vertical ridge-waveguide taper were integrated with a 2.5%-Δ athermal AWG to reduce the loss at chip-to-fiber interface. Spot-size converters based on a segmented core were formed around resin-filled trenches for athermalization formed in the slab to reduce the diffraction loss at the trenches. A 16-channel athermal AWG module with 100-GHz channel spacing was fabricated. The use of a 2.5%-Δ athermal chip with a single-side fiber array enabled a compact package of the size of 41.6×16.6×4.5 mm3. Athermal characteristics and a small insertion loss of 3.5-3.8 dB were obtained by virtue of low fiber-to-chip coupling loss and athermalization with low excess loss.

Sequencing cDNAs: An Introduction to DNA Sequence Analysis in the Undergraduate Molecular Genetics Course.

ERIC Educational Resources Information Center

Galewsky, Samuel

2000-01-01

Introduces a series of molecular genetics laboratories where students pick a single colony from a Drosophila melanogester embryo cDNA library and purify the plasmid, then analyze the insert through restriction digests and gel electrophoresis. (Author/YDS)

2 CFR 176.200 - Procedure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Single Audit Information for Recipients of Recovery Act Funds § 176.200 Procedure. The award official shall insert the standard award term in this subpart in all awards funded in whole or in part with... AND BUDGET GOVERNMENTWIDE GUIDANCE FOR GRANTS AND AGREEMENTS Reserved AWARD TERMS FOR ASSISTANCE...

In vivo white light and contrast-enhanced vital-dye fluorescence imaging of Barrett's-related neoplasia in a single-endoscopic insertion

NASA Astrophysics Data System (ADS)

Tang, Yubo; Carns, Jennifer; Polydorides, Alexandros D.; Anandasabapathy, Sharmila; Richards-Kortum, Rebecca R.

2016-08-01

A modular video endoscope is developed to enable both white light imaging (WLI) and vital-dye fluorescence imaging (VFI) in a single-endoscopic insertion for the early detection of cancer in Barrett's esophagus (BE). We demonstrate that VFI can be achieved in conjunction with white light endoscopy, where appropriate white balance is used to correct for the presence of the emission filter. In VFI mode, a contrast enhancement feature is implemented in real time to further highlight glandular patterns in BE and related malignancies without introducing artifacts. In a pilot study, we demonstrate accurate correlation of images in two widefield modalities, with representative images showing the disruption and effacement of glandular architecture associated with cancer development in BE. VFI images of these alterations exhibit enhanced contrast when compared to WLI. Results suggest that the usefulness of VFI in the detection of BE-related neoplasia should be further evaluated in future in vivo studies.

Development of a challenge-protective vaccine concept by modification of the viral RNA-dependent RNA polymerase of canine distemper virus.

PubMed

Silin, D; Lyubomska, O; Ludlow, M; Duprex, W P; Rima, B K

2007-12-01

We demonstrate that insertion of the open reading frame of enhanced green fluorescent protein (EGFP) into the coding sequence for the second hinge region of the viral L (large) protein (RNA-dependent RNA polymerase) attenuates a wild-type canine distemper virus. Moreover, we show that single intranasal immunization with this recombinant virus provides significant protection against challenge with the virulent parental virus. Protection against wild-type challenge was gained either after recovery of cellular immunity postimmunization or after development of neutralizing antibodies. Insertion of EGFP seems to result in overattenuation of the virus, while our previous experiments demonstrated that the insertion of an epitope tag into a similar position did not affect L protein function. Thus, a desirable level of attenuation could be reached by manipulating the length of the insert (in the second hinge region of the L protein), providing additional tools for optimization of controlled attenuation. This strategy for controlled attenuation may be useful for a "quick response" in vaccine development against well-known and "new" viral infections and could be combined efficiently with other strategies of vaccine development and delivery systems.

Modeling crack growth during Li insertion in storage particles using a fracture phase field approach

NASA Astrophysics Data System (ADS)

Klinsmann, Markus; Rosato, Daniele; Kamlah, Marc; McMeeking, Robert M.

2016-07-01

Fracture of storage particles is considered to be one of the major reasons for capacity fade and increasing power loss in many commercial lithium ion batteries. The appearance of fracture and cracks in the particles is commonly ascribed to mechanical stress, which evolves from inhomogeneous swelling and shrinkage of the material when lithium is inserted or extracted. Here, a coupled model of lithium diffusion, mechanical stress and crack growth using a phase field method is applied to investigate how the formation of cracks depends on the size of the particle and the presence or absence of an initial crack, as well as the applied flux at the boundary. The model shows great versatility in that it is free of constraints with respect to particle geometry, dimension or crack path and allows simultaneous observation of the evolution of lithium diffusion and crack growth. In this work, we focus on the insertion process. In particular, we demonstrate the presence of intricate fracture phenomena, such as, crack branching or complete breakage of storage particles within just a single half cycle of lithium insertion, a phenomenon that was only speculated about before.

Essential role of the unordered VP2 n-terminal domain of the parvovirus MVM capsid in nuclear assembly and endosomal enlargement of the virion fivefold channel for cell entry

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

Sanchez-Martinez, Cristina; Grueso, Esther; Carroll, Miles

The unordered N-termini of parvovirus capsid proteins (Nt) are translocated through a channel at the icosahedral five-fold axis to serve for virus traffick. Heterologous peptides were genetically inserted at the Nt of MVM to study their functional tolerance to manipulations. Insertion of a 5T4-single-chain antibody at VP2-Nt (2Nt) yielded chimeric capsid subunits failing to enter the nucleus. The VEGFR2-binding peptide (V1) inserted at both 2Nt and VP1-Nt efficiently assembled in virions, but V1 disrupted VP1 and VP2 entry functions. The VP2 defect correlated with restricted externalization of V1-2Nt out of the coat. The specific infectivity of MVM and wtVP-pseudotyped mosaicmore » MVM-V1 virions, upon heating and/or partial 2Nt cleavage, demonstrated that some 2Nt domains become intracellularly translocated out of the virus shell and cleaved to initiate entry. The V1 insertion defines a VP2-driven endosomal enlargement of the channel as an essential structural rearrangement performed by the MVM virion to infect.« less

Heat Transport Enhancement of Turbulent Thermal Convection by Inserted Channels

NASA Astrophysics Data System (ADS)

Xia, Ke-Qing; Zhang, Lu

2017-11-01

We report an experimental study on the heat transport properties of turbulent Rayleigh Benard Convection (RBC) in a rectangular cell with two types of 3D-printed structures inserted inside. The first one splits the original rectangular cell into 60 identical sub cells whose aspect ratio is 1:1:10 (length, width, height). The second one splits the cell into 30 sub cells, each with a 1:2:10 aspect ratio and a baffle in the center. We find that for large Rayleigh numbers (Ra), the Nusselt numbers (Nu) of both structures increase compared with that of the empty rectangular cell. An enhancement in Nu as much as 20% is found for the second type of insertion at Rayleigh number 2 ×109 . Moreover, the Nu-Ra scaling shows a transition with both geometries. The particle image velocimetry (PIV) measurement within a single sub unit indicates that the transition may be related to the laminar to turbulent transition in flow field. Direct numerical simulations (DNS) confirm the experimental results. Our results demonstrate the potential in using insertions to enhance passive heat transfer. This work was supported by the Research Grants Council (RGC) of HKSAR (Nos. CUHK404513 and CUHK14301115).

Development of a Challenge-Protective Vaccine Concept by Modification of the Viral RNA-Dependent RNA Polymerase of Canine Distemper Virus▿

PubMed Central

Silin, D.; Lyubomska, O.; Ludlow, M.; Duprex, W. P.; Rima, B. K.

2007-01-01

We demonstrate that insertion of the open reading frame of enhanced green fluorescent protein (EGFP) into the coding sequence for the second hinge region of the viral L (large) protein (RNA-dependent RNA polymerase) attenuates a wild-type canine distemper virus. Moreover, we show that single intranasal immunization with this recombinant virus provides significant protection against challenge with the virulent parental virus. Protection against wild-type challenge was gained either after recovery of cellular immunity postimmunization or after development of neutralizing antibodies. Insertion of EGFP seems to result in overattenuation of the virus, while our previous experiments demonstrated that the insertion of an epitope tag into a similar position did not affect L protein function. Thus, a desirable level of attenuation could be reached by manipulating the length of the insert (in the second hinge region of the L protein), providing additional tools for optimization of controlled attenuation. This strategy for controlled attenuation may be useful for a “quick response” in vaccine development against well-known and “new” viral infections and could be combined efficiently with other strategies of vaccine development and delivery systems. PMID:17898047

Switchable dual-wavelength erbium-doped fiber laser based on the photonic crystal fiber loop mirror and chirped fiber Bragg grating

NASA Astrophysics Data System (ADS)

Chen, Wei-Guo; Lou, Shu-Qin; Wang, Li-Wen; Li, Hong-Lei; Guo, Tieying; Jian, Shui-Sheng

2010-03-01

The switchable dual-wavelength erbium-doped fiber laser (EDFL) with a two-mode photonic crystal fiber (PCF) loop mirror and a chirped fiber Bragg grating (CFBG) at room temperature is proposed and experimentally demonstrated. The two-mode PCF loop mirror is formed by inserting a piece of two-mode PCF into a Sagnac loop mirror, with the air-holes of the PCF intentionally collapsing at the splices. By adjusting the state of the polarization controller (PC) appropriately, the laser can be switched between the stable single- and dual-wavelength operations by means of the polarization hole burning (PHB) and spectral hole burning (SHB) effects.

Guanidinoacetate methyltransferase deficiency: the first inborn error of creatine metabolism in man.

PubMed Central

Stöckler, S.; Isbrandt, D.; Hanefeld, F.; Schmidt, B.; von Figura, K.

1996-01-01

In two children with an accumulation of guanidinoacetate in brain and a deficiency of creatine in blood, a severe deficiency of guanidinoacetate methyltransferase (GAMT) activity was detected in the liver. Two mutant GAMT alleles were identified that carried a single base substitution within a 5' splice site or a 13-nt insertion and gave rise to four mutant transcripts. Three of the transcripts encode truncated polypeptides that lack a residue known to be critical for catalytic activity of GAMT. Deficiency of GAMT is the first inborn error of creatine metabolism. It causes a severe developmental delay and extrapyramidal symptoms in early infancy and is treatable by oral substitution with creatine. Images Figure 2 PMID:8651275

Three-Dimensional Large Screen Display Using Polymer-Dispersed Liquid-Crystal Light Valves and a Schlieren Optical System: Proposal and Basic Experiments

NASA Astrophysics Data System (ADS)

Takizawa, Kuniharu

A novel three-dimensional (3-D) projection display used with polarized eyeglasses is proposed. It consists of polymer-dispersed liquid crystal-light valves that modulate the illuminated light based on light scattering, a polarization beam splitter, and a Schlieren projection system. The features of the proposed display include a 3-D image display with a single projector, half size and half power consumption compared with a conventional 3-D projector with polarized glasses. Measured electro-optic characteristics of a polymer-dispersed liquid-crystal cell inserted between crossed polarizers suggests that the proposed display achieves small cross talk and high-extinction ratio.

Design and analysis of a low-loss linear analog phase modulator for deep space spacecraft X-band transponder applications

NASA Technical Reports Server (NTRS)

Mysoor, N. R.; Mueller, R. O.

1991-01-01

This article summarizes the design concepts, analyses, and development of an X-band (8145 MHz) transponder low-loss linear phase modulator for deep space spacecraft applications. A single-section breadboard circulator-coupled reflection phase modulator has been analyzed, fabricated, and evaluated. A linear phase deviation of 92 deg with a linearity tolerance of +/- 8 percent was measured for this modulator from 8257 MHz to 8634 MHz over the temperature range -20 to 75 C. The measured insertion loss and the static delay variation with temperature were 2 +/- 0.3 dB and 0.16 psec/ C, respectively. Based on this design, cascaded sections have been modeled, and simulations were performed to provide an X-band deep space transponder (DST) phase modulator with +/- 2.5 radians (+/- 143 deg) of peak phase deviation to accommodate downlink signal modulation with composite telemetry data and ranging, with a deviation linearity tolerance of +/- 8 percent and insertion loss of less than 10 +/- 0.5 dB. A two-section phase modulator using constant gamma hyperabrupt varactors and an efficient modulator driver circuit was breadboarded. The measured results satisfy the DST phase-modulator requirements and show excellent agreement with the predicted results.

The Identification and Differentiation between Burkholderia mallei and Burkholderia pseudomallei Using One Gene Pyrosequencing.

PubMed

Gilling, Damian H; Luna, Vicki Ann; Pflugradt, Cori

2014-01-01

The etiologic agents for melioidosis and glanders, Burkholderia mallei and Burkholderia pseudomallei respectively, are genetically similar making identification and differentiation from other Burkholderia species and each other challenging. We used pyrosequencing to determine the presence or absence of an insertion sequence IS407A within the flagellin P (fliP) gene and to exploit the difference in orientation of this gene in the two species. Oligonucleotide primers were designed to selectively target the IS407A-fliP interface in B. mallei and the fliP gene specifically at the insertion point in B. pseudomallei. We then examined DNA from ten B. mallei, ten B. pseudomallei, 14 B. cepacia, eight other Burkholderia spp., and 17 other bacteria. Resultant pyrograms encompassed the target sequence that contained either the fliP gene with the IS407A interruption or the fully intact fliP gene with 100% sensitivity and 100% specificity. These pyrosequencing assays based upon a single gene enable investigators to reliably identify the two species. The information obtained by these assays provides more knowledge of the genomic reduction that created the new species B. mallei from B. pseudomallei and may point to new targets that can be exploited in the future.

Bacterial Artificial Chromosome Libraries for Mouse Sequencing and Functional Analysis

PubMed Central

Osoegawa, Kazutoyo; Tateno, Minako; Woon, Peng Yeong; Frengen, Eirik; Mammoser, Aaron G.; Catanese, Joseph J.; Hayashizaki, Yoshihide; de Jong, Pieter J.

2000-01-01

Bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) libraries providing a combined 33-fold representation of the murine genome have been constructed using two different restriction enzymes for genomic digestion. A large-insert PAC library was prepared from the 129S6/SvEvTac strain in a bacterial/mammalian shuttle vector to facilitate functional gene studies. For genome mapping and sequencing, we prepared BAC libraries from the 129S6/SvEvTac and the C57BL/6J strains. The average insert sizes for the three libraries range between 130 kb and 200 kb. Based on the numbers of clones and the observed average insert sizes, we estimate each library to have slightly in excess of 10-fold genome representation. The average number of clones found after hybridization screening with 28 probes was in the range of 9–14 clones per marker. To explore the fidelity of the genomic representation in the three libraries, we analyzed three contigs, each established after screening with a single unique marker. New markers were established from the end sequences and screened against all the contig members to determine if any of the BACs and PACs are chimeric or rearranged. Only one chimeric clone and six potential deletions have been observed after extensive analysis of 113 PAC and BAC clones. Seventy-one of the 113 clones were conclusively nonchimeric because both end markers or sequences were mapped to the other confirmed contig members. We could not exclude chimerism for the remaining 41 clones because one or both of the insert termini did not contain unique sequence to design markers. The low rate of chimerism, ∼1%, and the low level of detected rearrangements support the anticipated usefulness of the BAC libraries for genome research. [The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AQ797173–AQ797398.] PMID:10645956

Recombinant Parainfluenza Virus 5 Expressing Hemagglutinin of Influenza A Virus H5N1 Protected Mice against Lethal Highly Pathogenic Avian Influenza Virus H5N1 Challenge

PubMed Central

Li, Zhuo; Mooney, Alaina J.; Gabbard, Jon D.; Gao, Xiudan; Xu, Pei; Place, Ryan J.; Hogan, Robert J.; Tompkins, S. Mark

2013-01-01

A safe and effective vaccine is the best way to prevent large-scale highly pathogenic avian influenza virus (HPAI) H5N1 outbreaks in the human population. The current FDA-approved H5N1 vaccine has serious limitations. A more efficacious H5N1 vaccine is urgently needed. Parainfluenza virus 5 (PIV5), a paramyxovirus, is not known to cause any illness in humans. PIV5 is an attractive vaccine vector. In our studies, a single dose of a live recombinant PIV5 expressing a hemagglutinin (HA) gene of H5N1 (rPIV5-H5) from the H5N1 subtype provided sterilizing immunity against lethal doses of HPAI H5N1 infection in mice. Furthermore, we have examined the effect of insertion of H5N1 HA at different locations within the PIV5 genome on the efficacy of a PIV5-based vaccine. Interestingly, insertion of H5N1 HA between the leader sequence, the de facto promoter of PIV5, and the first viral gene, nucleoprotein (NP), did not lead to a viable virus. Insertion of H5N1 HA between NP and the next gene, V/phosphorprotein (V/P), led to a virus that was defective in growth. We have found that insertion of H5N1 HA at the junction between the small hydrophobic (SH) gene and the hemagglutinin-neuraminidase (HN) gene gave the best immunity against HPAI H5N1 challenge: a dose as low as 1,000 PFU was sufficient to protect against lethal HPAI H5N1 challenge in mice. The work suggests that recombinant PIV5 expressing H5N1 HA has great potential as an HPAI H5N1 vaccine. PMID:23077314

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla

PubMed Central

Macé, Matthias; Crouau-Roy, Brigitte

2008-01-01

Background The early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia). There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields. Results and discussion We report a large interstitial insertion in the Y amelogenin locus in most of the Cetartiodactyla lineages (cetaceans and ruminants). This sex-linked size polymorphism is the result of a 460–465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species. When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in Cetartiodactyla whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion. The 1 kbp Amel-Y amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region. Conclusion The gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the Cetartiodactyla but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science. PMID:18925953

Development of mitral stenosis after single MitraClip insertion for severe mitral regurgitation.

PubMed

Cockburn, James; Fragkou, Paraskevi; Hildick-Smith, David

2014-02-01

We report the first case of mitral stenosis following Mitra-Clip insertion in a patient with symptomatic NYHA IV heart failure, secondary to severe mitral regurgitation (MR). A 79-year-old female with a history of prior aortic valve replacement underwent percutaneous mitral valve (MV) repair. A single clip was advanced coaxially down onto the MV under TOE guidance, with the anterior and posterior leaflets clipped together between A2 and P2. TOE confirmed a significant reduction in MR (grade 4 to grade 1). Despite initial symptomatic relief, she represented 3 months later with similar symptoms. Repeat TOE confirmed a well positioned Mitra-Clip with mild residual MR. However, the possibility of significant mitral stenosis was raised due to the presence of significant turbulence through the bi-orifice valve, with a peak gradient of 25 mm Hg. In addition there was evidence of severe functional tricuspid valve (TV) regurgitation with elevated pulmonary artery pressures (PAP 90 mm Hg), confirmed on subsequent right heart catheterization. After repeated heart team discussions and a failure of optimal medical therapy, and despite a logistic EuroScore of 35.5, minimally invasive surgical replacement of the MV and simultaneous TV repair was undertaken via a right thoracotomy. Despite procedural success and initial good postoperative response, the patient died subsequently from a combination of hospital-acquired pneumonia and significant gastrointestinal bleeding (post operative day 35). Mitra-Clip is a promising novel approach to MV repair. The establishment of further clinical and echocardiographic based selection criteria will help identify the correct patients for this treatment. Copyright © 2013 Wiley Periodicals, Inc.

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato.

PubMed

Shirasawa, Kenta; Hirakawa, Hideki; Nunome, Tsukasa; Tabata, Satoshi; Isobe, Sachiko

2016-01-01

Genome-wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro-Tom genome were identified by a whole-genome shotgun sequencing analysis to estimate the spectrum and distribution of whole-genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired-end reads for four EMS-induced mutants and three gamma-ray-irradiated lines as well as a wild-type line were obtained by next-generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma-ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1,140,687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild-type Micro-Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild-type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse-genetic approaches. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Single-Vector, Single-Injection Recombinant Vesicular Stomatitis Virus Vaccines Against High-Containment Viruses.

PubMed

Whitt, Michael A; Geisbert, Thomas W; Mire, Chad E

2016-01-01

There are many avenues for making an effective vaccine against viruses. Depending on the virus these can include one of the following: inactivation of whole virions; attenuation of viruses; recombinant viral proteins; non-replication-competent virus particles; or surrogate virus vector systems such as vesicular stomatitis virus (VSV). VSV is a prototypic enveloped animal virus that has been used for over four decades to study virus replication, entry, and assembly due to its ability to replicate to high titers in a wide variety of mammalian and insect cells. The use of reverse genetics to recover infectious and single-cycle replicating VSV from plasmid DNA transfected in cell culture began a revolution in the study of recombinant VSV (rVSV). This platform can be manipulated to study the viral genetic sequences and proteins important in the virus life cycle. Additionally, foreign genes can be inserted between naturally occurring or generated start/stop signals and polyadenylation sites within the VSV genome. VSV has a tolerance for foreign gene expression which has led to numerous rVSVs reported in the literature. Of particular interest are the very effective single-dose rVSV vaccine vectors against high-containment viruses such as filoviruses, henipaviruses, and arenaviruses. Herein we describe the methods for selecting foreign antigenic genes, selecting the location within the VSV genome for insertion, generation of rVSV using reverse genetics, and proper vaccine study designs.

Kinetic measurement of 2-aminopurine X cytosine and 2-aminopurine X thymine base pairs as a test of DNA polymerase fidelity mechanisms.

PubMed Central

Watanabe, S M; Goodman, M F

1982-01-01

Enzyme kinetic measurements are presented showing that Km rather than maximum velocity (Vmax) discrimination governs the frequency of forming 2-aminopurine X cytosine base mispairs by DNA polymerase alpha. An in vitro system is used in which incorporation of dTMP or dCMP occurs opposite a template 2-aminopurine, and values for Km and Vmax are obtained. Results from a previous study in which dTTP and dCTP were competing simultaneously for insertion opposite 2-aminopurine indicated that dTMP is inserted 22 times more frequently than dCMP. We now report that the ratio of Km values KCm/KTm = 25 +/- 6, which agrees quantitatively with the dTMP/dCMP incorporation ratio obtained previously. We also report that VCmax is indistinguishable from VTmax. These Km and Vmax data are consistent with predictions from a model, the Km discrimination model, in which replication fidelity is determined by free energy differences between matched and mismatched base pairs. Central to this model is the prediction that the ratio of Km values for insertion of correct and incorrect nucleotides specifies the insertion fidelity, and the maximum velocities of insertion are the same for both nucleotides. PMID:6959128

Factors affecting the electrofusion of mouse and ferret oocytes with ferret somatic cells.

PubMed

Li, Ziyi; Sun, Xingshen; Chen, Juan; Leno, Gregory H; Engelhardt, John F

2005-09-01

The domestic ferret, Mustela putorius furos, holds great promise as a genetic model for human lung disease, provided that key technologies for somatic cell nuclear transfer (SCNT) are developed. In this report, we extend our understanding of SCNT in this species by defining conditions for efficient cell fusion by electrical pulse. Two experimental systems were employed in this study. First, in vivo-matured mouse oocytes and ferret somatic cells were used to establish general parameters for fusion. One fibroblast, or cumulus cell, was agglutinated to nucleate, zona pellucida-free, mouse oocytes, and subjected to an electrical pulse. Similar electrical pulse conditions were also tested with 1 or 2 somatic cells inserted into the perivitelline space (PVS) of intact mouse oocytes. The fusion rate for a single fibroblast with a zona-free oocyte was 80.2%, significantly higher (P < 0.05) than that observed for 1, or 2, fibroblasts placed in the PVS (52.0% and 63.8%, respectively). The fusion rate (44.1%) following insertion of two cumulus cells was significantly higher (P < 0.05) than that following insertion of one cumulus cell (25.1%). Second, in vitro-matured ferret oocytes were enucleated, and one to three fibroblasts or cumulus cells were inserted into the PVS. Zona pellucida-free ferret oocytes were fragile and excluded from the study. The fusion rates with two or three fibroblasts were 71.4% and 76.8%, respectively; significantly higher (P < 0.05) than that for one fibroblast (48.6%). This cell number-dependent difference in fusion efficiency was also observed with cumulus cells. Fusion-derived (ferret-ferret) NT embryos cleaved, formed blastocysts in vitro, and underwent early-stage fetal development following embryo transfer. The rate of development was cell type-independent, in contrast to the cell type-dependent differences observed in fusion efficiency. In conclusion, fibroblasts fused more efficiently than cumulus cells and the efficiency of single cell fusions was improved when two or more cells were inserted into the PVS. These studies define conditions for efficient cell fusion with ferret oocytes and should facilitate SCNT and the development of genetically defined animal models in this species.

Office-based insertion of pressure equalization tubes: the role of laser-assisted tympanic membrane fenestration.

PubMed

Brodsky, L; Brookhauser, P; Chait, D; Reilly, J; Deutsch, E; Cook, S; Waner, M; Shaha, S; Nauenberg, E

1999-12-01

To describe the role of the hand-held otoscope combined with a flashscanner CO2 laser, OtoLAM (ESC/Sharplan, Yokneam, Israel), for pressure equalization tube (PET) insertion in an office setting. Prospective, multisite, clinical cohort trial (Institutional Review Board approved; informed consent) in the setting of pediatric otolaryngology outpatient departments at four tertiary care children's hospitals. Selected for the study were 54 patients (96 ears), ages 6 months to 23 years, who met standard indications for PET insertion using cold-knife myringotomy and tube insertion under general anesthesia. PETs were indicated for recurrent otitis media, chronic otitis media with effusion, and eustachian tube dysfunction-all unresponsive to medical therapy. Topical anesthesia was achieved with iontophoresis (n = 1) or topical anesthesia: 8% tetracaine on an Otowick (Xomed Surgical Products, Jacksonville, FL, catalogue No. 400141) against the tympanic membrane for 45 to 180 minutes (n = 53). Laser-assisted tympanic membrane fenestration was performed with the OtoLAM set at single pulse, 2.0- to 2.6-mm spot size, and between 3 and 18 W. Insertion of grommets was accomplished using the otomicroscope and an "alligator" microforceps. Restraints with papoose were used in 79% of children with a mean age of 34.4 months (SD = 60.9 mo). Clinical, parent/patient, and physician satisfaction and comparative cost impact outcomes are described. All ears but three (3%) underwent successful placement of a PET. Pain was described as "absent" in 39%, "present but tolerable" in 30%, and "severe" in 30% of children at the time of procedure; 5 minutes after the procedure pain was described as "absent" in 75%, "present but tolerable" in 22%, and "severe" in 3%. Tube plugging (3 of 74 available ears; 4%) or persistent otorrhea (1 of 74 ears; 1.4%) occurred infrequently at the 1-month follow-up. Before PET insertion, hearing loss was noted in 66% of cases (mild, 38%; moderate, 22%; and severe, 6%). Mild hearing loss was noted in only 8% and moderate hearing loss in 2% of 47 (50%) of the ears at the 3-month follow-up. Ninety-two percent of parents were highly satisfied with the procedure in preference to PETs in the operating room under general anesthesia, and 97% preferred OtoLAM with PET insertion, rather than further courses of antibiotics; only one parent would rather have had the PET insertion under general anesthesia. Cost savings to health care organizations, particularly payers, and to parents are substantial (32%-48%) and warrant attention. Cost to the physician is manageable only if an appropriate approach to the third party payers results in a substantial increase in reimbursements. The data indicate excellent clinical effectiveness, reduced risk, and high parent and physician satisfaction. Strong incentives for physicians to use this technique are in all stakeholders' best interests. These incentives need to evolve as soon as possible for the more widespread acceptance of OtoLAM with PET insertion in an office setting for appropriately selected patients.

Chronic behavior evaluation of a micro-machined neural implant with optimized design based on an experimentally derived model.

PubMed

Andrei, Alexandru; Welkenhuysen, Marleen; Ameye, Lieveke; Nuttin, Bart; Eberle, Wolfgang

2011-01-01

Understanding the mechanical interactions between implants and the surrounding tissue is known to have an important role for improving the bio-compatibility of such devices. Using a recently developed model, a particular micro-machined neural implant design aiming the reduction of insertion forces dependence on the insertion speed was optimized. Implantations with 10 and 100 μm/s insertion speeds showed excellent agreement with the predicted behavior. Lesion size, gliosis (GFAP), inflammation (ED1) and neuronal cells density (NeuN) was evaluated after 6 week of chronic implantation showing no insertion speed dependence.

Insertion of a single-molecule magnet inside a ferromagnetic lattice based on a 3D bimetallic oxalate network: towards molecular analogues of permanent magnets.

PubMed

Clemente-León, Miguel; Coronado, Eugenio; Gómez-García, Carlos J; López-Jordà, Maurici; Camón, Agustín; Repollés, Ana; Luis, Fernando

2014-02-03

The insertion of the single-molecule magnet (SMM) [Mn(III)(salen)(H2O)]2(2+) (salen(2-) = N,N'-ethylenebis-(salicylideneiminate)) into a ferromagnetic bimetallic oxalate network affords the hybrid compound [Mn(III)(salen)(H2O)]2[Mn(II)Cr(III)(ox)3]2⋅(CH3OH)⋅(CH3CN)2 (1). This cationic Mn2 cluster templates the growth of crystals formed by an unusual achiral 3D oxalate network. The magnetic properties of this hybrid magnet are compared with those of the analogous compounds [Mn(III)(salen)(H2O)]2[Zn(II)Cr(III)(ox)3]2⋅(CH3OH)⋅(CH3CN)2 (2) and [In(III)(sal2-trien)][Mn(II)Cr(III)(ox)3]⋅(H2O)0.25⋅(CH3OH)0.25⋅(CH3CN)0.25 (3), which are used as reference compounds. In 2 it has been shown that the magnetic isolation of the Mn2 clusters provided by their insertion into a paramagnetic oxalate network of Cr(III) affords a SMM behavior, albeit with blocking temperatures well below 500 mK even for frequencies as high as 160 kHz. In 3 the onset of ferromagnetism in the bimetallic Mn(II) Cr(III) network is observed at Tc = 5 K. Finally, in the hybrid compound 1 the interaction between the two magnetic networks leads to the antiparallel arrangement of their respective magnetizations, that is, to a ferrimagnetic phase. This coupling induces also important changes on the magnetic properties of 1 with respect to those of the reference compounds 2 and 3. In particular, compound 1 shows a large magnetization hysteresis below 1 K, which is in sharp contrast with the near-reversible magnetizations that the SMMs and the oxalate ferromagnetic lattice show under the same conditions. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrated optical refractometer based on bend waveguide with air trench structure

NASA Astrophysics Data System (ADS)

Ryu, Jin Hwa; Park, Jaehoon; Kang, Chan-mo; Son, Youngdal; Do, Lee-Mi; Baek, Kyu-Ha

2015-07-01

This study proposed a novel optical sensor based on a refractometer integrating a bend waveguide and a trench structure. The optical sensor is a planar lightwave circuit (PLC) device involving a bend waveguide with maximum optical loss. A trench structure was aligned with the partially exposed core layer's sidewall of the bend waveguide, providing a quantitative measurement condition. The insertion losses of the proposed 1 x 2 single-mode optical splitter-type sensor were 4.38 dB and 8.67 dB for the reference waveguide and sensing waveguide, respectively, at a wavelength of 1,550 nm. The optical loss of the sensing waveguide depends on the change in the refractive index of the material in contact with the trench, but the reference waveguide had stable optical propagating characteristic regardless of the variations of the refractive index.

Interface thermal conductance characterization by infrared thermography: A tool for the study of insertions in bronze ancient Statuary

NASA Astrophysics Data System (ADS)

Mercuri, F.; Caruso, G.; Orazi, N.; Zammit, U.; Cicero, C.; Colacicchi Alessandri, O.; Ferretti, M.; Paoloni, S.

2018-05-01

In this paper, a new method based on the use of infrared thermography is proposed for the characterization of repairs and inserted parts on ancient bronzes. In particular, the quality of the contact between different kind of insertions and the main body of bronze statues is investigated by analysing the heat conduction process occurring across the interface between them. The thermographic results have been used to establish the nature of these inserted elements and the way they have been coupled to the main body of the statue during and after the manufacturing process. A model for the heat conduction based on the numerical finite elements method has been applied to compare the obtained results to the theoretical predictions. Measurements have been first carried out on test samples and then in the field on the Boxer at Rest (Museo Nazionale Romano in Rome), a masterpiece of the Greek Statuary, which contains a large variety of inserted items and repairs which are typical of the manufacturing process of bronze artefacts in general.

A Risk Based Approach to Node Insertion Within Social Networks

DTIC Science & Technology

2015-03-26

changes to enemy networks, tactical involvement must evolve, beginning with the intelligent use of network infiltration through the application of the...counterterrorism begins with the intelligent use of network infiltration, or the covert insertion of assets into a network, otherwise known as node insertion. The...Federal Bureau of Intelligence (FBI) defines an undercover operation as “an investigation involving a series of related undercover activities over a

Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

DTIC Science & Technology

2008-07-17

Membrane insertion profiles of peptides probed by molecular dynamics simulations In-Chul Yeh,* Mark A. Olson,# Michael S. Lee,*#§ and Anders...a methodology based on molecular dynamics simulation techniques to probe the insertion profiles of small peptides across the membrane interface. The...profiles of peptides probed by molecular dynamics simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

App-based serious gaming for training of chest tube insertion: study protocol for a randomized controlled trial.

PubMed

Friedrich, Mirco; Bergdolt, Christian; Haubruck, Patrick; Bruckner, Thomas; Kowalewski, Karl-Friedrich; Müller-Stich, Beat Peter; Tanner, Michael C; Nickel, Felix

2017-02-06

Chest tube insertion is a standard intervention for management of various injuries of the thorax. Quick and accurate execution facilitates efficient therapy without further complications. Here, we propose a new training concept comprised of e-learning elements as well as continuous rating using an objective structured assessment of technical skills (OSATS) tool. The study protocol is presented for a randomized trial to evaluate e-learning with app-based serious gaming for chest drain insertion. The proposed randomized trial will be carried out at the Department of Orthopedics and Traumatology at Heidelberg University in the context of regular curricular teaching for medical students (n = 90, 3rd to 6th year). The intervention group will use e-learning with the serious gaming app Touch Surgery (TM) for chest drain insertion, whereas the control group uses serious gaming for an unrelated procedure. Primary endpoint is operative performance of chest drain insertion in a porcine cadaveric model according to OSATS. The randomized trial will help determine the value of e-learning with the serious gaming app Touch Surgery (TM) for chest drain insertion by using the OSATS score. The study will improve surgical training for trauma situations. Trial Registration Number, DRKS00009994 . Registered on 27 May 2016.

Response of Escherichia coli growth rate to osmotic shock.

PubMed

Rojas, Enrique; Theriot, Julie A; Huang, Kerwyn Casey

2014-05-27

It has long been proposed that turgor pressure plays an essential role during bacterial growth by driving mechanical expansion of the cell wall. This hypothesis is based on analogy to plant cells, for which this mechanism has been established, and on experiments in which the growth rate of bacterial cultures was observed to decrease as the osmolarity of the growth medium was increased. To distinguish the effect of turgor pressure from pressure-independent effects that osmolarity might have on cell growth, we monitored the elongation of single Escherichia coli cells while rapidly changing the osmolarity of their media. By plasmolyzing cells, we found that cell-wall elastic strain did not scale with growth rate, suggesting that pressure does not drive cell-wall expansion. Furthermore, in response to hyper- and hypoosmotic shock, E. coli cells resumed their preshock growth rate and relaxed to their steady-state rate after several minutes, demonstrating that osmolarity modulates growth rate slowly, independently of pressure. Oscillatory hyperosmotic shock revealed that although plasmolysis slowed cell elongation, the cells nevertheless "stored" growth such that once turgor was reestablished the cells elongated to the length that they would have attained had they never been plasmolyzed. Finally, MreB dynamics were unaffected by osmotic shock. These results reveal the simple nature of E. coli cell-wall expansion: that the rate of expansion is determined by the rate of peptidoglycan insertion and insertion is not directly dependent on turgor pressure, but that pressure does play a basic role whereby it enables full extension of recently inserted peptidoglycan.

Response of Escherichia coli growth rate to osmotic shock

PubMed Central

Rojas, Enrique; Theriot, Julie A.; Huang, Kerwyn Casey

2014-01-01

It has long been proposed that turgor pressure plays an essential role during bacterial growth by driving mechanical expansion of the cell wall. This hypothesis is based on analogy to plant cells, for which this mechanism has been established, and on experiments in which the growth rate of bacterial cultures was observed to decrease as the osmolarity of the growth medium was increased. To distinguish the effect of turgor pressure from pressure-independent effects that osmolarity might have on cell growth, we monitored the elongation of single Escherichia coli cells while rapidly changing the osmolarity of their media. By plasmolyzing cells, we found that cell-wall elastic strain did not scale with growth rate, suggesting that pressure does not drive cell-wall expansion. Furthermore, in response to hyper- and hypoosmotic shock, E. coli cells resumed their preshock growth rate and relaxed to their steady-state rate after several minutes, demonstrating that osmolarity modulates growth rate slowly, independently of pressure. Oscillatory hyperosmotic shock revealed that although plasmolysis slowed cell elongation, the cells nevertheless “stored” growth such that once turgor was reestablished the cells elongated to the length that they would have attained had they never been plasmolyzed. Finally, MreB dynamics were unaffected by osmotic shock. These results reveal the simple nature of E. coli cell-wall expansion: that the rate of expansion is determined by the rate of peptidoglycan insertion and insertion is not directly dependent on turgor pressure, but that pressure does play a basic role whereby it enables full extension of recently inserted peptidoglycan. PMID:24821776

Development of a femoral template for computer-assisted tunnel placement in anatomical double-bundle ACL reconstruction.

PubMed

Luites, J W H; Wymenga, A B; Blankevoort, L; Kooloos, J M G; Verdonschot, N

2011-01-01

Femoral graft placement is an important factor in the success of anterior cruciate ligament (ACL) reconstruction. In addition to improving the accuracy of femoral tunnel placement, Computer Assisted Surgery (CAS) can be used to determine the anatomic location. This is achieved by using a 3D femoral template which indicates the position of the anatomical ACL center based on endoscopically measurable landmarks. This study describes the development and application of this method. The template is generated through statistical shape analysis of the ACL insertion, with respect to the anteromedial (AM) and posterolateral (PL) bundles. The ligament insertion data, together with the osteocartilage edge on the lateral notch, were mapped onto a cylinder fitted to the intercondylar notch surface (n = 33). Anatomic variation, in terms of standard variation of the positions of the ligament centers in the template, was within 2.2 mm. The resulting template was programmed in a computer-assisted navigation system for ACL replacement and its accuracy and precision were determined on 31 femora. It was found that with the navigation system the AM and PL tunnels could be positioned with an accuracy of 2.5 mm relative to the anatomic insertion centers; the precision was 2.4 mm. This system consists of a template that can easily be implemented in 3D computer navigation software. Requiring no preoperative images and planning, the system provides adequate accuracy and precision to position the entrance of the femoral tunnels for anatomical single- or double-bundle ACL reconstruction.

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome

PubMed Central

Krawitz, Peter M; Schiska, Daniela; Krüger, Ulrike; Appelt, Sandra; Heinrich, Verena; Parkhomchuk, Dmitri; Timmermann, Bernd; Millan, Jose M; Robinson, Peter N; Mundlos, Stefan; Hecht, Jochen; Gross, Manfred

2014-01-01

Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield. PMID:25333064

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome.

PubMed

Krawitz, Peter M; Schiska, Daniela; Krüger, Ulrike; Appelt, Sandra; Heinrich, Verena; Parkhomchuk, Dmitri; Timmermann, Bernd; Millan, Jose M; Robinson, Peter N; Mundlos, Stefan; Hecht, Jochen; Gross, Manfred

2014-09-01

Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield.

Accurate measurement of transgene copy number in crop plants using droplet digital PCR

USDA-ARS?s Scientific Manuscript database

Technical abstract: Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently ...

Accurate measure of transgene copy number in crop plants using droplet digital PCR

USDA-ARS?s Scientific Manuscript database

Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy numb...

2 CFR 176.200 - Procedure.

Code of Federal Regulations, 2012 CFR

2012-01-01

... AND BUDGET GOVERNMENTWIDE GUIDANCE FOR GRANTS AND AGREEMENTS NATIONAL POLICY REQUIREMENTS AWARD TERMS..., PUBLIC LAW 111-5 Single Audit Information for Recipients of Recovery Act Funds § 176.200 Procedure. The award official shall insert the standard award term in this subpart in all awards funded in whole or in...

2 CFR 176.200 - Procedure.

Code of Federal Regulations, 2013 CFR

2013-01-01

... AND BUDGET GOVERNMENTWIDE GUIDANCE FOR GRANTS AND AGREEMENTS NATIONAL POLICY REQUIREMENTS AWARD TERMS..., PUBLIC LAW 111-5 Single Audit Information for Recipients of Recovery Act Funds § 176.200 Procedure. The award official shall insert the standard award term in this subpart in all awards funded in whole or in...

2 CFR 176.200 - Procedure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Reserved AWARD TERMS FOR ASSISTANCE AGREEMENTS THAT INCLUDE FUNDS UNDER THE AMERICAN RECOVERY AND REINVESTMENT ACT OF 2009, PUBLIC LAW 111-5 Single Audit Information for Recipients of Recovery Act Funds § 176.200 Procedure. The award official shall insert the standard award term in this subpart in all awards...

2 CFR 176.200 - Procedure.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Single Audit Information for Recipients of Recovery Act Funds § 176.200 Procedure. The award official shall insert the standard award term in this subpart in all awards funded in whole or in part with... AND BUDGET GOVERNMENTWIDE GUIDANCE FOR GRANTS AND AGREEMENTS [Reserved] AWARD TERMS FOR ASSISTANCE...

Extending Single-Molecule Microscopy Using Optical Fourier Processing

PubMed Central

2015-01-01

This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules. PMID:24745862

Extending single-molecule microscopy using optical Fourier processing.

PubMed

Backer, Adam S; Moerner, W E

2014-07-17

This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules.

A data-driven soft sensor for needle deflection in heterogeneous tissue using just-in-time modelling.

PubMed

Rossa, Carlos; Lehmann, Thomas; Sloboda, Ronald; Usmani, Nawaid; Tavakoli, Mahdi

2017-08-01

Global modelling has traditionally been the approach taken to estimate needle deflection in soft tissue. In this paper, we propose a new method based on local data-driven modelling of needle deflection. External measurement of needle-tissue interactions is collected from several insertions in ex vivo tissue to form a cloud of data. Inputs to the system are the needle insertion depth, axial rotations, and the forces and torques measured at the needle base by a force sensor. When a new insertion is performed, the just-in-time learning method estimates the model outputs given the current inputs to the needle-tissue system and the historical database. The query is compared to every observation in the database and is given weights according to some similarity criteria. Only a subset of historical data that is most relevant to the query is selected and a local linear model is fit to the selected points to estimate the query output. The model outputs the 3D deflection of the needle tip and the needle insertion force. The proposed approach is validated in ex vivo multilayered biological tissue in different needle insertion scenarios. Experimental results in five different case studies indicate an accuracy in predicting needle deflection of 0.81 and 1.24 mm in the horizontal and vertical lanes, respectively, and an accuracy of 0.5 N in predicting the needle insertion force over 216 needle insertions.

A MEMS disk resonator-based band pass filter electrical equivalent circuit simulation

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

Sundaram, G. M.; Angira, Mahesh; Gupta, Navneet

In this paper, coupled beam bandpass Disk filter is designed for 1 MHz bandwidth. Filter electrical equivalent circuit simulation is performed using circuit simulators. Important filter parameters such as insertion loss, shape factor and Q factor aresetimated using coventorware simulation. Disk resonator based radial contour mode filter provides 1.5 MHz bandwidth and unloaded quality factor of resonator and filter as 233480, 21797 respectively. From the simulation result it’s found that insertion loss minimum is 151.49 dB, insertion loss maximum is 213.94 dB, and 40 dB shape factor is 4.17.

Alternative method for predicting optimal insertion depth of the laryngeal tube in children.

PubMed

Kim, J T; Jeon, S Y; Kim, C S; Kim, S D; Kim, H S

2007-11-01

Little information is available about the accuracy of the teeth mark on the laryngeal tube (LT) as a guide to correct placement in children. The aim of this crossover study was to evaluate three methods for optimal insertion depth of the size (#) 2 tube in children weighing 12-25 kg. In 24 children, the LT #2 was consecutively inserted by three different methods: (A) until the thick teeth mark on the tube was aligned with the upper incisors, (B) until resistance was felt, and (C) by inserting to a depth, previously measured, of the curved distance between the cricoid cartilage and the upper incisor. In each case, the depth of insertion, the degree of effective ventilation, the presence of leakage, and the fibreoptic view were assessed. Insertion based on the teeth mark led to a shorter insertion depth and a greater incidence of inadequate ventilation compared with the other two methods. There was no difference in the adequacy of ventilation between methods B and C. The vocal cords were more easily identified with methods B (62.5%) and C (75%) than with method A (12.5%). Insertion of the LT #2 aligned with the teeth mark can result in a shallow insertion depth and inadequate ventilation. The measured distance from the cricoid cartilage to the upper incisor offers alternative guidance for correct LT insertion.