scholarly journals OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

2017 ◽  
Vol 15 (6) ◽  
pp. 361-370 ◽  
Author(s):  
Soheil Jahangiri-Tazehkand ◽  
Limsoon Wong ◽  
Changiz Eslahchi
Keyword(s):  
Accurate Identification ◽  
Gene Neighborhood

Immunolabelling of glomerular deposits in kidney biopsies routinely fixed in glutaraldehyde

1989 ◽  
Vol 47 ◽  
pp. 910-911
Author(s):  
Ś Lhoták ◽  
I. Alexopoulou ◽  
G. T. Simon
Keyword(s):  
Uv Light ◽  
Kidney Diseases ◽  
Light Chains ◽  
Microscopical Level ◽  
Accurate Identification ◽  
Light Microscopical Level ◽  
Dense Deposits ◽  
Cacodylate Buffer ◽  
Glomerular Deposits ◽  
Prognostic Importance

Various kidney diseases are characterized by the presence of dense deposits in the glomeruli. The type(s) of immunoglobulins (Igs) present in the dense deposits are characteristic of the disease. The accurate Identification of the deposits is therefore of utmost diagnostic and prognostic importance. Immunofluorescence (IF) used routinely at the light microscopical level is unable to detect and characterize small deposits found in early stages of glomerulonephritis. Although conventional TEM is able to localize such deposits, it is not capable of determining their nature. It was therefore attempted to immunolabel at EM level IgG, IgA IgM, C3, fibrinogen and kappa and lambda Ig light chains commonly found in glomerular deposits on routinely fixed ( 2% glutaraldehyde (GA) in 0.1M cacodylate buffer) kidney biopsies.The unosmicated tissue was embedded in LR White resin polymerized by UV light at -10°C. A postembedding immunogold technique was employed

Project BRAIN: Working Together to Improve Educational Outcomes for Students With Traumatic Brain Injury

2012 ◽  
Vol 22 (3) ◽  
pp. 106-118 ◽  
Author(s):  
Paula Denslow ◽  
Jean Doster ◽  
Kristin King ◽  
Jennifer Rayman
Keyword(s):  
Traumatic Brain Injury ◽  
At Risk ◽  
Brain Injury ◽  
Educational Outcomes ◽  
School Personnel ◽  
Department Of Education ◽  
Health Providers ◽  
Accurate Identification ◽  
Transition Intervention ◽  
Working Together

Children and youth who sustain traumatic brain injury (TBI) are at risk for being unidentified or misidentified and, even if appropriately identified, are at risk of encountering professionals who are ill-equipped to address their unique needs. A comparison of the number of people in Tennessee ages 3–21 years incurring brain injury compared to the number of students ages 3–21 years being categorized and served as TBI by the Department of Education (DOE) motivated us to create this program. Identified needs addressed by the program include the following: (a) accurate identification of students with TBI; (b) training of school personnel; (c) development of linkages and training of hospital personnel; and (d) hospital-school transition intervention. Funded by Health Services and Resources Administration (HRSA) grants with support from the Tennessee DOE, Project BRAIN focuses on improving educational outcomes for students with TBI through the provision of specialized group training and ongoing education for educators, families, and health professionals who support students with TBI. The program seeks to link families, hospitals, and community health providers with school professionals such as speech-language pathologists (SLPs) to identify and address the needs of students with brain injury.

Dangerous Warrants

2017 ◽  
Author(s):  
Nirej Sekhon
Keyword(s):  
Supreme Court ◽  
Fourth Amendment ◽  
Constitutional Rights ◽  
Police Discretion ◽  
Accurate Identification ◽  
Race And Class ◽  
The Supreme Court ◽  
Local Courts ◽  
State And Local ◽  
Municipal Court

The Supreme Court has cast judicial warrants as the Fourth Amendment gold standard for regulating police discretion. It has embraced a "warrant preference" on the premise that requiring police to obtain advance judicial approval for searches and seizures encourages accurate identification of evidence and suspects while minimizing interference with constitutional rights. The Court and commentators have overlooked the fact that most outstanding warrants do none of these things. Most outstanding warrants are what this article terms "non-compliance warrants": summarily issued arrest warrants for failures to comply with a court or police order. State and local courts are profligate in issuing such warrants for minor offenses. For example, the Department of Justice found that the municipal court in Ferguson, Missouri issued one warrant for every two of its residents. When issued as wantonly as this, warrants are dangerous because they generate police discretion rather than restrain it. Nonetheless, the Supreme Court has, most recently in Utah v. Strieff, treated non-compliance warrants as if no different from the traditional warrants that gave rise to the Fourth Amendment warrant preference. This article argues that non-compliance warrants pose unique dangers, constitutional and otherwise. Non-compliance warrants create powerful incentives for the police to conduct unconstitutional stops, particularly in poor and minority neighborhoods. Their enforcement also generates race and class feedback loops. Outstanding warrants beget arrests and arrests beget more warrants. Over time, this dynamic amplifies race and class disparities in criminal justice. The article concludes by prescribing a Fourth Amendment remedy to deter unconstitutional warrant checks. More importantly, the article identifies steps state and local courts might take to stem the continued proliferation of non-compliance warrants.

Recent Advances in Computational Methods for Identifying Anticancer Peptides

2019 ◽  
Vol 20 (5) ◽  
pp. 481-487 ◽  
Author(s):  
Pengmian Feng ◽  
Zhenyi Wang
Keyword(s):  
Computational Methods ◽  
Clinical Applications ◽  
Future Perspectives ◽  
Small Peptides ◽  
Accurate Identification ◽  
Normal Cells ◽  
Anticancer Peptide ◽  
Anticancer Peptides ◽  
Computational Identification ◽  
Reliable Methods

Anticancer peptide (ACP) is a kind of small peptides that can kill cancer cells without damaging normal cells. In recent years, ACP has been pre-clinically used for cancer treatment. Therefore, accurate identification of ACPs will promote their clinical applications. In contrast to labor-intensive experimental techniques, a series of computational methods have been proposed for identifying ACPs. In this review, we briefly summarized the current progress in computational identification of ACPs. The challenges and future perspectives in developing reliable methods for identification of ACPs were also discussed. We anticipate that this review could provide novel insights into future researches on anticancer peptides.

Seeing wood because of the trees? A case of failure in reverse-engineering

1998 ◽  
Vol 21 (4) ◽  
pp. 468-468
Author(s):  
Philip J. Benson
Keyword(s):  
Reverse Engineering ◽  
Semantic Information ◽  
Complex Representation ◽  
Linguistic Terms ◽  
Accurate Identification

Failure to take note of distinctive attributes in the distal stimulus leads to an inadequate proximal encoding. Representation of similarities in Chorus suffers in this regard. Distinctive qualities may require additional complex representation (e.g., reference to linguistic terms) in order to facilitate discrimination. Additional semantic information, which configures proximal attributes, permits accurate identification of true veridical stimuli.

scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

scholarly journals Assessment of Knowledge, Attitudes, and Practices Regarding Dengue among Physicians: A Web-Based Cross-Sectional Survey

2021 ◽  
Vol 11 (8) ◽  
pp. 105
Author(s):  
Kranthi Swaroop Koonisetty ◽  
Ubydul Haque ◽  
Rajesh Nandy ◽  
Nasrin Aghamohammadi ◽  
Tamanna Urmi ◽  
...  
Keyword(s):  
Dengue Fever ◽  
Viral Infections ◽  
Diagnosis And Treatment ◽  
Cross Sectional Survey ◽  
Accurate Identification ◽  
Cross Sectional ◽  
Web Based ◽  
Attitudes And Practices ◽  
Aedes Mosquitoes ◽  
Knowledge Attitudes And Practices

Dengue fever is one of the most important viral infections transmitted by Aedes mosquitoes and a major cause of morbidity and mortality globally. Accurate identification of cases and treatment of dengue patients at the early stages can reduce medical complications and dengue mortality rate. This survey aims to determine the knowledge, attitude, and practices (KAP) among physicians in dengue diagnosis and treatment. This study was conducted among physicians in Turkey as one nonendemic country and Bangladesh, India, and Malaysia as three dengue-endemic countries. The dosing frequencies, maximum doses, and contraindications in dengue fever were examined. The results found that physicians from Bangladesh, India, and Malaysia have higher KAP scores in dengue diagnosis and treatment compared to physicians in Turkey. This may be due to a lack of physician’s exposure to a dengue patient as Turkey is considered a nonendemic country. This assessment may help establish a guideline for intervention strategies among physicians to have successful treatment outcomes and reduce dengue mortality.

scholarly journals DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

2021 ◽  
Author(s):  
Yanrong Ji ◽  
Zhihan Zhou ◽  
Han Liu ◽  
Ramana V Davuluri
Keyword(s):  
Dna Sequences ◽  
Regulatory Elements ◽  
Ease Of Use ◽  
Fine Tuning ◽  
Supplementary Information ◽  
Sequence Motifs ◽  
Semantic Relationship ◽  
Accurate Identification ◽  
Conserved Sequence ◽  
Genome Wide

Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios. Results To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks. Availability and implementation The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT). Supplementary information Supplementary data are available at Bioinformatics online.

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