29,414 results match your criteria terms taxonomic


Deep learning analysis and age prediction from shoeprints.

Forensic Sci Int 2021 Aug 30;327:110987. Epub 2021 Aug 30.

Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States. Electronic address:

Human gaits are the patterns of limb movements which involve both the upper and lower body parts. These patterns in terms of step rate, gait speed, stance widening, stride, and bipedal forces are influenced by different factors including environmental (such as social, cultural, and behavioral traits) and physical changes (such as age and health status). These factors are reflected on the imprinted shoeprints generated with body forces, which in turn can be used to predict age, a problem not systematically addressed using any computational approach. Read More

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The spatially resolved transcriptional profile of acute T-cell mediated rejection in a kidney allograft.

Kidney Int 2021 Sep 20. Epub 2021 Sep 20.

Analysis of the transcriptional profile of graft biopsies represents a promising strategy to study T cell mediated-rejection (TCMR), also known as acute cellular rejection. However, bulk RNA sequencing of graft biopsies may not capture the focal nature of acute rejection. Herein, we used the whole exome GeoMX Digital Space Profiling platform to study five tubular and three glomerular regions of interest in the kidney graft biopsy from a patient with a chronic-active TCMR episode and in analogous areas from two different normal kidney control biopsies. Read More

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September 2021

Spatial-Spectral Unified Adaptive Probability Graph Convolutional Networks for Hyperspectral Image Classification.

IEEE Trans Neural Netw Learn Syst 2021 Sep 23;PP. Epub 2021 Sep 23.

In hyperspectral image (HSI) classification task, semisupervised graph convolutional network (GCN)-based methods have received increasing attention. However, two problems still need to be addressed. The first is that the initial graph structure in the GCN-based methods is not sufficiently flexible to encode the homogenous structure similarity of HSI pixels when facing the complex scenarios induced by the spatial variability. Read More

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September 2021

scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding.

Brief Bioinform 2021 Sep 22. Epub 2021 Sep 22.

College of Information Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Single-cell Hi-C data are a common data source for studying the differences in the three-dimensional structure of cell chromosomes. The development of single-cell Hi-C technology makes it possible to obtain batches of single-cell Hi-C data. How to quickly and effectively discriminate cell types has become one hot research field. Read More

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September 2021

A deep neural network approach for P300 detection-based BCI using single-channel EEG scalogram images.

Phys Eng Sci Med 2021 Sep 22. Epub 2021 Sep 22.

Tripura University, Agartala, India.

Brain-computer interfaces (BCIs) acquire electroencephalogram (EEG) signals and interpret them into a command that helps people with severe motor disabilities using single channel. The goal of BCI is to achieve a prototype that supports disabled people to develop the relevant function. Various studies have been implemented in the literature to achieve a superior design using multi-channel EEG signals. Read More

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September 2021

Differences in clinical phenotypes of primary Sjögren's syndrome depending on early or late onset.

Adv Clin Exp Med 2021 Sep 22. Epub 2021 Sep 22.

Department of Rheumatology and Internal Medicine, Wroclaw University Clinical Hospital, Poland.

Background: Previous research suggests that systemic involvement in primary Sjögren's syndrome (pSS) is a marker of disease prognosis.

Objectives: To evaluate pSS disease activity and the clinical phenotype of pSS patients depending on the age at diagnosis with long-term follow-up.

Material And Methods: The study group consisted of patients diagnosed with pSS based on the 2016 pSS classification criteria. Read More

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September 2021

COVID-19 economic vulnerability and resilience indexes: Global evidence.

Int Soc Sci J 2021 Jun 15. Epub 2021 Jun 15.

This study complements the extant literature by constructing COVID-19 economic vulnerability and resilience indexes using a global sample of 150 countries categorised into four principal regions: Africa, Asia-Pacific and the Middle East, America, and Europe. Seven variables are used for the vulnerability index and nine for the resilience index. Both regions and sampled countries are classified in terms of the two proposed and computed indexes. Read More

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Seasonality and Oldowan behavioral variability in East Africa.

J Hum Evol 2021 Sep 18:103070. Epub 2021 Sep 18.

Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, United Kingdom.

The extent, nature, and temporality of early hominin food procurement strategies have been subject to extensive debate. In this article, we examine evidence for the seasonal scheduling of resource procurement and technological investment in the Oldowan, starting with an evaluation of the seasonal signature of underground storage organs, freshwater resources, and terrestrial animal resources in extant primates and modern human hunter-gatherer populations. Subsequently, we use the mortality profiles, taxonomic composition, and taphonomy of the bovid assemblages at Kanjera South (Homa Peninsula, Kenya) and FLK-Zinj (Olduvai Gorge, Tanzania) to illustrate the behavioral flexibility of Oldowan hominins, who were targeting different seasonally vulnerable demographics. Read More

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September 2021

Interpretability-Based Multimodal Convolutional Neural Networks for Skin Lesion Diagnosis.

IEEE Trans Cybern 2021 Sep 21;PP. Epub 2021 Sep 21.

Skin lesion diagnosis is a key step for skin cancer screening, which requires high accuracy and interpretability. Though many computer-aided methods, especially deep learning methods, have made remarkable achievements in skin lesion diagnosis, their generalization and interpretability are still a challenge. To solve this issue, we propose an interpretability-based multimodal convolutional neural network (IM-CNN), which is a multiclass classification model with skin lesion images and metadata of patients as input for skin lesion diagnosis. Read More

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September 2021

Live surgery of colorectal endometriosis broadcasted from a surgeon's routine operating theater is not associated with higher complications rate.

Acta Obstet Gynecol Scand 2021 Sep 21. Epub 2021 Sep 21.

Department of Surgery, Rouen University Hospital, Rouen, France.

Introduction: Although live surgeries are routinely included in surgical congress programs, they are the subject of an ongoing debate in terms of patient safety and teaching value. The goal of our study was to assess the risk of postoperative complications related to live surgery broadcast from the surgeon's routine theater, in patients managed for deep endometriosis infiltrating the digestive tract.

Material And Methods: We report a retrospective comparative study, enrolling women managed for colorectal endometriosis by a gynecologic surgeon, from September 2013 to March 2020 in two referral centers. Read More

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September 2021

Evaluation of ultrasonic fibrosis diagnostic system using convolutional network for ordinal regression.

Int J Comput Assist Radiol Surg 2021 Sep 21. Epub 2021 Sep 21.

Nihon University, Tokyo, Japan.

Purpose: Diagnosis of liver fibrosis is important for establishing treatment and assessing the risk of carcinogenesis. Ultrasound imaging is an excellent diagnostic method as a screening test in terms of non-invasiveness and simplicity. The purpose of this study was to automatically diagnose liver fibrosis using ultrasound images to reduce the burden on physicians. Read More

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September 2021

Gut Microbial Divergence Between Three Hadal Amphipod Species from the Isolated Hadal Trenches.

Microb Ecol 2021 Sep 20. Epub 2021 Sep 20.

Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.

Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Read More

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September 2021

A Multicenter Retrospective Study Comparing Surgical Outcomes Between the Overlap Method and Functional Method for Esophagojejunostomy in Laparoscopic Total Gastrectomy: Analysis Using Propensity Score Matching.

Surg Laparosc Endosc Percutan Tech 2021 Sep 21. Epub 2021 Sep 21.

Department of Gastroenterological Surgery II, Faculty of Medicine, Hokkaido University Division of Minimally Invasive Surgery, Hokkaido University Hospital Department of Surgery, Teine Keijinkai Hospital Department of Surgery, Hokkaido Gastroenterology Hospital Department of Surgery, Tonan Hospital, Sapporo Department of Surgery, Asahikawa City Hospital, Asahikawa Department of Surgery, Obihiro-Kosei General Hospital, Obihiro, Japan.

Background: This study aimed to compare the postoperative outcomes after laparoscopic total gastrectomy (LTG) with esophagojejunostomy (EJS) performed using the overlap method or the functional method in a multicenter retrospective study with propensity score matching.

Methods: We retrospectively enrolled all patients who underwent curative LTG for gastric cancer at 6 institutions between January 2004 and December 2018. Patients were categorized into the overlap group (OG) or functional group (FG) based on the type of anastomosis used in EJS. Read More

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September 2021

[Introduction to the hierarchical taxonomy of psychopathology].

Encephale 2021 Sep 17. Epub 2021 Sep 17.

Service universitaire de médecine du sommeil, CHU de Bordeaux, place Amélie-Raba-Léon, 33076 Bordeaux, France; USR CNRS 3413 SANPSY, université de Bordeaux, CHU Pellegrin, 33076 Bordeaux cédex, France.

Introduction: In clinical practice, the usefulness of diagnosis based on the Diagnostic or Statistical Manual of Mental Disorders (DSM) or the International Classification of Diseases, 11th edition, appears essential from a clinical, research, epidemiological, administrative, economic and political level. However, such diagnostic systems have shortcomings in terms of validity, little consideration of comorbidities and strong intra-class heterogeneity. On a structural level, the operationalization of its criteria is based on a reliability which has been defined a posteriori and which does not lead to improving the validity of the diagnosis but rather to the reification of the diagnostic categories. Read More

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September 2021

STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions.

Genome Biol 2021 Sep 20;22(1):270. Epub 2021 Sep 20.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms. Read More

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September 2021

LightGBM: accelerated genomically designed crop breeding through ensemble learning.

Genome Biol 2021 Sep 20;22(1):271. Epub 2021 Sep 20.

National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.

LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines. LightGBM exhibits superior performance in terms of prediction precision, model stability, and computing efficiency through a series of benchmark tests. Read More

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September 2021

The value of arterial spin labeling imaging in the classification and prognostic evaluation of neonatal hypoxic-ischemic encephalopathy.

Curr Neurovasc Res 2021 Sep 19. Epub 2021 Sep 19.

Department of Radiology, The Second Hospita of Hebei Medical University, Shijiazhuang 050005. China.

Objective: This study aims to investigate the correlation between cerebral blood flow (CBF) values and neonatal behavioral neurological assessment (NBNA) in hypoxic-ischemic encephalopathy (HIE), the relationship between early CBF value changes and the prognosis of neonatal HIE, and the consistency between the clinical grading and magnetic resonance (MR) grading of HIE.

Methods: Forty neonates with HIE were scanned using the three-dimensional arterial spin labeling (ASL) sequencing of the cranial magnetic resonance imaging (MRI). These newborns were classified as having mild, moderate and severe HIE, according to the clinical grading, and as being normal or having mild, moderate, or severe HIE, according to the MRI grading. Read More

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September 2021

Guided structure-based ligand identification and design via artificial intelligence modeling.

Expert Opin Drug Discov 2021 Sep 23:1-8. Epub 2021 Sep 23.

Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.

Introduction: The implementation of Artificial Intelligence (AI) methodologies to drug discovery (DD) are on the rise. Several applications have been developed for structure-based DD, where AI methods provide an alternative framework for the identification of ligands for validated therapeutic targets, as well as the design of ligands through generative models.

Areas Covered: Herein, the authors review the contributions between the 2019 to present period regarding the application of AI methods to structure-based virtual screening (SBVS) which encompasses mainly molecular docking applications - binding pose prediction and binary classification for ligand or hit identification-, as well as drug design driven by machine learning (ML) generative models, and the validation of AI models in structure-based screening. Read More

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September 2021

Biotypic classification of facial profiles using discrete cosine transforms on lateral radiographs.

Arch Oral Biol 2021 Aug 27;131:105249. Epub 2021 Aug 27.

University of Pernambuco, Pernambuco Dental School, Oswaldo Cruz University Hospital, Department of Oral and Maxillofacial Surgery and Traumatology, Recife, PE 50100-130, Brazil. Electronic address:

Objective: The aim of the study was to use discrete cosine transforms to graph soft tissue curves in lateral cephalometric radiographs and, with the obtained mathematical values, to group these curves by both traditional biotypes and cluster systems, in order to evaluate discriminatory capacity in terms of accuracy.

Design: A sample of 625 lateral radiographs of adult patients (319 women and 306 men) was classified by facial biotype based on the ANB angle and mandibular plane angle. The curves of the facial profile were digitized with 50 equidistant points and discrete cosine transform was applied to analyze these curves mathematically for the determination of the accuracy of the classification of traditional biotypes. Read More

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The Effectiveness of Ischemia Modified Albumin in Determining Acute Cholecystitis and its Severity.

Clin Lab 2021 Sep;67(9)

Background: Acute cholecystitis (AC) is caused by chemical and bacterial inflammation of the gallbladder. The use of Tokyo guidelines is recommended in determining the diagnosis of AC and its clinical severity. In the early stages of AC, many cytokines are secreted due to the local inflammatory cell activation, leading to exacerbation of inflammation and organ failure. Read More

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September 2021

WaveICA 2.0: a novel batch effect removal method for untargeted metabolomics data without using batch information.

Metabolomics 2021 Sep 20;17(10):87. Epub 2021 Sep 20.

Interdisciplinary Research Center on Biology and Chemistry, and Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.

Introduction: Untargeted metabolomics based on liquid chromatography-mass spectrometry is inevitably affected by batch effects that are caused by non-biological systematic bias. Previously, we developed a novel method called WaveICA to remove batch effects for untargeted metabolomics data. To detect batch effect information, the method relies on a batch label. Read More

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September 2021

Bayesian inference of dependent kappa for binary ratings.

Stat Med 2021 Sep 20. Epub 2021 Sep 20.

Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA.

In medical and social science research, reliability of testing methods measured through inter- and intraobserver agreement is critical in disease diagnosis. Often comparison of agreement across multiple testing methods is sought in situations where testing is carried out on the same experimental units rendering the outcomes to be correlated. In this article, we first developed a Bayesian method for comparing dependent agreement measures under a grouped data setting. Read More

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September 2021

Nonsquamous Lesions of the Vulvar Skin and Subcutaneous Tissue: A Review (Part 1).

J Low Genit Tract Dis 2021 Oct;25(4):303-311

Department of Pathology, Immunology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, NJ.

Objectives: This article aimed to review "nonsquamous lesions of the vulvar skin and subcutaneous tissue" clinically and pathologically, based on the fifth edition of the World Health Organization tumor classification.

Materials And Methods: A database search of PubMed and Google Scholar was performed between 1970 and 2021, using the search terms "vulva," "lower genital tract," and "nonsquamous lesions." The search was limited to "humans," "gynecopathology," and "dermatopathology. Read More

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October 2021

Compliance with the 4Ds of antimicrobial stewardship practice in a tertiary care centre.

JAC Antimicrob Resist 2021 Sep 15;3(3):dlab135. Epub 2021 Sep 15.

Department of Internal Medicine, All India Institute of Medical Sciences (AIIMS), Rishikesh, Uttarakhand, India.

Background: Antimicrobial stewardship describes the practice of promoting the selection of the right drug, dosage, delivery and duration of antimicrobial therapy (the 4Ds) in order to curtail the emergence of resistant organisms. It is important to quantify the inappropriate use of antimicrobials in terms of percentage adherence to each of the 4Ds mentioned.

Methods: We undertook a prospective review of medical records of patients admitted to the medical wards of a tertiary care centre in North India. Read More

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September 2021

Channel state information estimation for 5G wireless communication systems: recurrent neural networks approach.

PeerJ Comput Sci 2021 26;7:e682. Epub 2021 Aug 26.

Department of Electrical Engineering, College of Engineering, Taif University, Taif, Saudi Arabia.

In this study, a deep learning bidirectional long short-term memory (BiLSTM) recurrent neural network-based channel state information estimator is proposed for 5G orthogonal frequency-division multiplexing systems. The proposed estimator is a pilot-dependent estimator and follows the online learning approach in the training phase and the offline approach in the practical implementation phase. The estimator does not deal with complete certainty for channels' statistics and attains superior performance in the presence of a limited number of pilots. Read More

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Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin.

J Med Imaging (Bellingham) 2020 Jan 18;7(1):012706. Epub 2020 Feb 18.

Oregon Health and Science University, Computational Biology Program, Biomedical Engineering Department, Portland, Oregon, United States.

: Pathologists rely on relevant clinical information, visual inspection of stained tissue slide morphology, and sophisticated molecular diagnostics to accurately infer the biological origin of secondary metastatic cancer. While highly effective, this process is expensive in terms of time and clinical resources. We seek to develop and evaluate a computer vision system designed to reasonably infer metastatic origin of secondary liver cancer directly from digitized histopathological whole slide images of liver biopsy. Read More

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January 2020

Application of Genetic Algorithm-Based Support Vector Machine in Identification of Gene Expression Signatures for Psoriasis Classification: A Hybrid Model.

Biomed Res Int 2021 8;2021:5520710. Epub 2021 Sep 8.

Department of Dermatology, Psoriasis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.

Background: Psoriasis is a chronic autoimmune disease impairing significantly the quality of life of the patient. The diagnosis of the disease is done via a visual inspection of the lesional skin by dermatologists. Classification of psoriasis using gene expression is an important issue for the early and effective treatment of the disease. Read More

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September 2021

Safety of Inguinal Hernia Repair in the Elderly with Perioperative Continuation of Antithrombotic Therapy.

Visc Med 2021 Aug 6;37(4):315-322. Epub 2020 Nov 6.

Department of Gastrointestinal Surgery, Hernia Center, West China Hospital, Sichuan University, Chengdu, China.

Introduction: This study aimed to evaluate the safety of an inguinal hernia repair (IHR) under local anesthesia (LA) in the elderly with a perioperative continuation of antithrombotic therapy (AT).

Methods: A total of 120 patients undergoing elective primary IHR between August 2018 and August 2019 at the West China Hospital of China were prospectively studied, among which 60 patients also had coexisting cardiovascular diseases and had a continuation of AT perioperatively (antithrombotic group); the other 60 patients were not on any prior AT (control group). The primary endpoints were intra- and postoperative hemorrhagic complications, the required interventions for complications based on the Clavien-Dindo classification, and postoperative thromboembolic complications. Read More

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Optimal Positive End Expiratory Pressure Levels in Ventilated Patients Without Acute Respiratory Distress Syndrome: A Bayesian Network Meta-Analysis and Systematic Review of Randomized Controlled Trials.

Front Med (Lausanne) 2021 1;8:730018. Epub 2021 Sep 1.

State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

To find the optimal positive end expiratory pressure (PEEP) in mechanical ventilated patients without Acute Respiratory Distress Syndrome (ARDS), we conducted a Bayesian network meta-analysis and systematic review of randomized controlled trials (RCTs) comparing different level of PEEP based on a novel classification of PEEP level: ZEEP group (PEEP = 0 cm H2O); lower PEEP group (PEEP = 1-6 cm H2O); intermediate PEEP group (PEEP = 7-10 cm H2O); higher PEEP group (PEEP > 10 cm H2O). Twenty eight eligible studies with 2,712 patients were included. There were no significant differences in the duration of mechanical ventilation between higher and intermediate PEEP (MD: 0. Read More

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September 2021

Distribution Patterns of Ciliate Diversity in the South China Sea.

Front Microbiol 2021 3;12:689688. Epub 2021 Sep 3.

Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.

Ciliates are abundant microplankton that are widely distributed in the ocean. In this paper, the distribution patterns of ciliate diversity in the South China Sea (SCS) were analyzed by compiling community data from previous publications. Based on morphological identification, a total of 592 ciliate species have been recorded in the SCS. Read More

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September 2021