bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hox gene expression during development of the phoronid Phoronopsis harmeri
Authors: Gąsiorowski Ludwik , Hejnol Andreas 
Published: January 2020

Abstract
Background: Phoronida is a small group of marine worm-like suspension feeders, which together with brachiopods and bryozoans form the clade Lophophorata. Although their development is well studied on the morphological level, data regarding gene expression during this process are scarce and restricted to the analysis of relatively few transcription factors. Here we present a description of the expression patterns of Hox genes during the embryonic and larval development of the phoronid Phoronopsis harmeri. Results: We identified sequences of eight Hox genes in the transcriptome of Ph. harmeri and determined their expression pattern during embryonic and larval development using whole mount in situ hybridization. We found that none of the Hox genes is expressed during embryonic development. Instead their expression is initiated in the later developmental stages, when the larval body is already formed. In the investigated initial larval stages the Hox genes are expressed in the non-collinear manner in the posterior body of the larvae: in the telotroch and the structures that represent rudiments of the adult worm. Additionally, we found that certain head-specific transcription factors are expressed in the oral hood, apical organ, preoral coelom, anterior digestive system and developing larval tentacles, anterior to the Hox-expressing territories. Conclusions: The lack of Hox gene expression during early development of Ph. harmeri indicates that the larval body develops without positional information from the Hox patterning system. Such phenomenon might be a consequence of the evolutionary intercalation of the larval form into an ancestral life cycle of phoronids. The observed Hox gene expression can also be a consequence of the actinotrocha representing a “head larva”, which is composed of the most anterior body region that is devoid of Hox gene expression. Such interpretation is further supported by the expression of head-specific transcription factors. This implies that the Hox patterning system is used for the positional information of the trunk rudiments and is, therefore, delayed to the later larval stages. We propose that a new body form was intercalated to the phoronid life cycle by precocious development of the anterior structures or by delayed development of the trunk rudiment in the ancestral phoronid larva.
Prevalence, molecular characterization and antimicrobial profiles of Enterohaemorrhagic E. coli O157 isolated from ruminants slaughtered in Al Ain, United Arab Emirates
Authors: Al-Ajmi Dawood , Rahman Shafeeq , Banu Sharmila 
Published: January 2020

Abstract
Background: Shiga toxin-producing Escherichia coli (STEC) are associated with major food illness around the world. E.coli O157, has been widely reported as the most common STEC serogroup, and has emerged as an important enteric pathogen. Further, cattle have been identified as a major E. coli O157:H7 reservoir for human infection; however, the ecology of this organism in camels, sheep and goats is less understood. The current study aims to evaluate the prevalence of E. coli serotype O157 in feces of cattle, camels, sheep and goats slaughtered in United Arab Emirates (UAE) for meat consumption. This study was carried out on fecal samples of healthy cattle (n = 137), camels (n = 140), sheep (n = 141) and goats (n = 150) during the period of September 2017 to August 2018. We have used the traditional sensitive immunomagnetic separation technique (IMS) coupled with a culture plating method for detection of E. coli O157. Non-sorbitol fermenting colonies were assessed via the latex agglutination test and the positive cultures were subjected to PCR for detection of attaching and effacing genes (eaeA), hemolysin A (hlyA) and Shiga toxin-producing genes (stx1 and stx2) and genes specific for E. coli O157:H7 (rfb O157, uid A and flic H7). All E. coli O157 isolates were analyzed for their susceptibility pattern toward 20 select antibiotics.Results: E. coli O157 was present in the fecal samples of goats, camels and cattle at 2%, 3.3%, and 1.6%, respectively. In sheep we failed to detect any E. coli O157 strains. The most prevalent E.coli O157 gene identified across all species’ isolates was stx2, while stx1 was not detected in any of the samples. ­After testing samples from camels, goats and cattle, Cefotaxime (100%), Chloramphenicol (100%), Ciprofloxacin (100%), Norfloxacin (100%) and Polymixin B (100%) showed susceptibility showed susceptibility to all E.coli O157 isolates.Conclusion: This is the first study, to our knowledge, to report on the prevalence of E. coli O157 in the slaughter animals in UAE and clearly demonstrates the presence of these pathogens in slaughtered animals, which could possibly contaminate the meat products intended for human consumption.
Identification and Drug Sensitivity of Aerobic Bacterial Isolates from Diabetic Foot Ulcers of Sudanese Patients: a Cross sectional study
Authors: nour saada Mohamed , Mukhtar Maowia , Elmakk Mohamed , Elshibli Elshibli Mohamed , Elfakey Walyeldin Elnour , Shamad Mahdi , Ibrahim Nuha , Fadul Mohamed yahia , Mohamed Safia 
Published: January 2020

Abstract
Background Diabetic foot ulcer infection cause great morbidity and mortality among diabetic patients and is a major cause of lower extremity amputation worldwide. This study aimed to determine the profile of aerobic bacteria and their antibiotic sensitivity patterns in diabetic foot infections (DFI) among different Wagner's grades. Methods This study was conducted during December 2017 - March 2018 in a Diabetic Center, Sudan. A total of 152 diabetic patients with different grades of foot ulcers were randomly enrolled in the study. The patients were grouped using Wagner's classification. Tissue biopsies and deep swabs were collected from the ulcers for aerobic cultures. The cultured isolates were identified using phenotypic and biochemical properties and their sensitivity to commonly used antibiotics, Colistin, Aikacin, Ciprofloxacin, Augmentin, Ceftazideme, Gentamicin, Clindamycin, Ceftriaxone Meropenum. Cotrimoxazole, Erythomycin, Oxacillin and Vancomycin. Fusidic acid, Imepenem, and Piperacillin was tested using the Kirby Bauer disk diffusion method. Results The mean age of the patients was 54.31 (SD ± 12.1) years, male to female ratio of 8: 1. The mean duration of diabetes was 14 (SD ± 8) years. The ulcers varied in duration from 1 day to 10 years. of 152 samples 181 aerobic bacteria were isolated. Cultures yielded 1-3 isolate per culture. The maximum number was isolated from grade 3 group followed by long standing ulcer LSU group 50.8% and 28% respectively. Polymicrobial infection was higher in LSU (30.4%). The isolates were mostly Gram-negative bacteria. The most frequent were proteus spp. (35.3%), S. aureus MRSA 14.4% and Coliform 12.2% respectively. The most common isolates in grade 3 were P. Mirablis, Staphylococcus and Coliform and in long standing ulcers were P. Mirablis, S. aureus MRSA and Coagulase negative staphylococcus respectively. Conclusion Gram-negative bacteria were more prevalent and the most frequent pathogens were Proteus spp. The most common polymicrobial infections were due to P. mirablis with; P. aerginosa, S. MRSA and Coliform respectively . Gram negative rods were sensitive to Amikacin, (80.6) %) while the highest sensitivity of Gram positive was to Imepnem (85%). Most of the isolates were sensitive to Meropenem. No significant relation between Wagner grades and neuropathy was detected.
Development, reliability and validity of the Safe Use of Mobility Aids Checklist (SUMAC) for 4-wheeled walker use in people living with dementia
Authors: Hunter Susan , Divine Alison , Omana Humberto , Madou Edward , Holmes Jeffrey 
Published: January 2020

Abstract
Background

Balance and gait problems are common and progressive in dementia. Mobility aid use in people with dementia increases the likelihood of falls three-fold. An assessment tool to quantify mobility aid safety in people with dementia does not currently exist. The objectives of this study were: 1) to develop a tool for the evaluation of physical function and safety with use of a 4-wheeled walker in people with dementia, and 2) to evaluate its construct and criterion validity, inter-rater and test-retest reliability and minimal detectable change.

Methods

Healthcare professionals (HCP) experienced in care and rehabilitation of people with dementia participated in focus groups for item generation of the new tool, entitled The Safe Use of Mobility Aid Checklist (SUMAC). The SUMAC evaluates physical function (PF) and safe use of the equipment (EQ) on nine tasks of daily life. Ten individuals with dementia using a 4-wheeled walker were recorded performing the tasks within the SUMAC. Reliability was evaluated by having five HCP score participant videos on two occasions. Inter-rater and test-retest reliability was assessed using intra-class correlation coefficients (ICC). Construct validity was evaluated using scores determined by a consensus panel compared to the individual HCP scores using Spearman’s rank-order correlations. Criterion validity was assessed between SUMAC-PF and the Performance-Oriented Mobility Assessment (POMA) using Spearman’s rank-order correlations.

Results

Three focus groups (n=17) were completed and these generated a tool comprised of nine tasks and the components within each task that the clinicians would observe for physical function and safe use. Inter-rater reliability was statistically significant for the SUMC-PF (ICC=0.72, 95%CI (0.33-0.92), p<0.001) and SUMAC-EQ (ICC=0.40, 95%CI (0.03-0.78), p=0.020). Test-retest reliability was also statistically significant for the SUMAC-PF (ICC=0.69, 95%CI (0.45-0.83), p<0.001) and SUMAC-EQ (ICC=0.73, 95%CI (0.53,0.85), p<0.001). The POMA correlated strongly with the SUMAC-PF (r=0.84), but not EQ (r=0.39).

Conclusions

Each of the scores of the SUMAC, physical function and safe use of the equipment, demonstrated content validity, strong inter-rater and test-retest reliability and strong criterion and concurrent validity for the assessment of mobility aid safety in people with dementia.
Factors Associated with Current and Severe Pain among People Living with HIV: Results from a Statewide Sample
Authors: Joseph Verlin , Jones Abenaa , Canidate Shantrel , Mannes Zachary , Lu Huiyin , Ennis Nicole , Ibanez Gladys , Somboonwit Charurut , Cook Robert 
Published: January 2020

Abstract
Background People living with HIV (PLWH) are more likely to suffer from pain compared to the general public. Pain often clusters with mental health symptoms and substance use. This study sought to evaluate mental health and substance use factors associated with and pain and severe pain intensities among PLWH. Methods Data were derived from HIV+ adults (N=733) recruited from community health centers across Florida who completed questionnaires regarding demographics, chronic pain, HIV clinical outcomes, mental health symptoms, and substance use information. Pain was assessed using the Brief Pain Inventory (BPI) short form. Multivariate logistic regression analysis was utilized to assess the relationship between selected covariates and pain. Results Approximately half (45.0%) of participants reported having current pain. After controlling for covariates, PLWH reporting current symptoms of anxiety or PTSD were 2.49 (CI=1.48, 4.18) and 1.69 (CI= 1.11, 2.57) times as likely to report pain compared to PLWH without those factors respectively. PLWH reporting current symptoms of anxiety and male participants were 2.03 (CI= 1.03, 4.01) and 2.02 (CI= 1.26, 3.24) times as likely to report severe pain compared to PLWH without those factors respectively. Conclusion The relationship between pain and mental health is complex, thus future research is needed to determine if pain treatments may reduce mental health symptoms or if treatments can be targeted to address both issues simultaneously
Protein A/G-based enzyme-linked immunosorbent assay for detection of anti-Pythium insidiosum antibodies in human and animal subjects
Authors: Jaturapaktrarak Chalisa , Payattikul Penpan , Lohnoo Tassanee , Kumsang Yothin , Laikul Aree , Pathomsakulwong Watcharapol , Yurayart Chompoonek , Tonpitak Walaiporn , Krajaejun Theerapong 
Published: January 2020

Abstract
Objectives: Pythiosis is a deadly infectious disease caused by Pythium insidiosum. Reports of both human and animal pythiosis are on the rise worldwide. Prognosis of the pythiosis patients relies on early diagnosis and prompt treatment. There are needs for an immunodiagnostic test that can detect the disease in both humans and animals. This study aims at reporting an optimized protocol for the development of a protein A/G-based enzyme-linked immunosorbent assay (ELISA) for the detection of anti-P. insidiosum antibody in multiple host species. Results: A total of 25 pythiosis and 50 control sera, obtained from humans, horses, dogs, cats, and cows, were recruited for the assay development. With a proper ELISA cutoff point, all pythiosis sera can ultimately be distinguished from the control sera. The successfully-developed protein A/G-based ELISA can detect the anti-P. insidiosum antibodies in serum samples of both humans and animals. It is a versatile and feasible-to-develop immunodiagnostic assay for pythiosis.
Etiologies and Outcomes of Rheumatology Patients with Acute Respiratory Failure Requiring Intensive Care: A Single-Center Cohort Study of 259 Patients
Authors: Shi Yan , Zhao Jiu-liang , Qin Han-yu , Hu Xiao-yun , Jiang Wei , Wang Chun-yao , Weng Li , Wang Qian , Zeng Xiao-feng , Peng Jin-min , Du Bin 
Published: January 2020

Abstract
Background: The etiologies of acute respiratory failure (ARF) in critically ill rheumatology patients remain unknown. We aimed to describe the clinical features, etiologies and outcomes of adult patients with systemic rheumatic diseases (SRDs) who were admitted to intensive care unit (ICU). Methods: We performed a retrospective study of all SRD patients with ARF who were admitted to a medical ICU between 2014 and 2018. We collected data on demographics, clinical characteristics, reasons for ICU admission and outcomes. Etiologies of ARF were classified as infection, SRD exacerbation, and undetermined. Independent predictors of ICU mortality were identified with multivariate logistic regression analysis. Results: A total of 259 patients admitted to ICU due to ARF were included in final analysis. Systemic lupus erythematosus, dermatomyositis/polymyositis (DM/PM), vasculitis and rheumatoid arthritis were the most common SRDs (78% of patients). Etiologies of ARF included infection (n = 209, 80.7%), SRD exacerbation (n = 71, 27.4%), and undetermined (n = 21, 8.1%). The most common pathogen was Pneumocystis jirovecii (39.8%), followed by Aspergillus spp. (33.2%), and cytomegalovirus (23.2%). One hundred and fifty-five patients (59.8%) died during ICU. Higher acute physiology and chronic health evaluation II score (odds ratio [OR] 1.118, 95% confidence interval [CI] 1.054 to 1.186, p < 0.001) and PaO2/FiO2 < 100 mmHg (OR 3.918, 95% CI 2.199 to 6.892, p < 0.001), DM/PM (OR 4.898, 95% CI 1.949 to 12.309, p = 0.001), vasculitis (OR 3.007, 95% CI 1.237 to 7.309, p = 0.015) and Pneumocystis pneumonia (OR 2.345, 95% CI 1.168 to 4.705, p = 0.016) were independent predictors of ICU mortality. Conclusions: Opportunistic infections and SRD exacerbation were the most common etiologies of ARF in patients with SRDs requiring ICU admission, with high ICU mortality. Development of a standard protocol for differential diagnosis in this group of immunocompromised patients might help initiate definitive therapy and improve clinical outcome. Keywords: Infection, Systemic rheumatic disease, Acute respiratory failure, Etiology
Anti-inflammatory Mechanism of Rhein in Treating Asthma Based on Network Pharmacology
Authors: Feng Junfang , Chen Ou , Wang Yibiao 
Published: January 2020

Abstract
BackgroundNetwork pharmacology was used to study Rhein -target-pathway and to clarify its anti-inflammatory mechanism in the treatment of asthma.and provide a new idea for the treatment of asthmaMethodsThis method, which allows using network pharmacology to figure out the operational mechanism of Rhein-Target-Pathway, defines the effect of anti-inflammatory in treating asthma. The platform of Traditional Chinese Medicine Molecular Mechanism Bioinformatics, a web server for network, is used to get the corresponding target of Rhein and permit molecular docking. Cytoscape3.7.1, a kind of network software, is used to construct Rhein-predicted target network and analyse network topology. Search anti-inflammatory targets in the database of TTD and then construct the PPI network as well as create protein interaction networks that are combined with the Rhein-predicted target network. The anti-inflammatory targets of Rhein should be presented. The asthma genes of human being can be attained from the database of NCBI Gene Database and construct correspondence vivo response network model. Find Anti-inflammatory targets of Rhein against asthma, screen anti-inflammatory targets of Rhein related with Pathogenesis of asthma. Enrichr database is used to analyse signal pathway from anti-inflammatory targets of Rhein KEGG.ResultsAccording to the study, Rhein corresponds to 17 target proteins, four anti-inflammatory targets of Rhein related to asthma(MAPK14, EGFR, ERBB2, TNFRSF1A) are probably the most important targets where asthma is treated by Rhein.ConclusionsThese four anti-inflammatory targets of Rhein related to asthma are probably the key targets in the treatment of asthma by using Rhein. For the purpose of preventing the occurrence as well as development of asthma and delaying the progress of the disease, one or some of the four anti-inflammatory targets of Rhein related to asthma can be controlled.
Efficacy of Azithromycin 1% and 1.5% ophthalmic solutions compared to tobramycin 0.3% eye drops: A systematic review and meta-analysis
Authors: Motbaynor Birhanu , Kassie Teshager Worku 
Published: January 2020

Abstract
Background: Azithromycin 1% and 1.5% ophthalmic preparations are used widely in clinical practice for the treatment of signs and symptoms of eye diseases. Despite individual studies, there have been no summarized evidence about the efficacy of azithromycin over tobramycin eye drops. Therefore, the aim of this study was to abridge this gap by rendering conclusive evidence by comparing the efficacy of azithromycin 1% and 1.5% over tobramycin 0.3% ophthalmic solutions for the treatment of eye diseases in short duration in terms of bacterial resolution, cure rate and resolving clinical sign and symptoms of eye diseases. Methods: Systematic searches were performed in both electronic (Medline (Ovid), EMBASE (Ovid), Emcare (Ovid), CINAHL (EBSCOhost), Scopus, PubMed, ProQuest, Web of Science and Cochrane Central Register of Controlled Trials) and other sources (Worldcat, Mednar, Google and Google scholar). Multicenter randomized controlled trial studies conducted in the English language were identified and screened. Joanna Briggs Institute quality assessment checklist for randomized controlled trials was used to critically appraise the methodological quality of studies. Analysis of individual studies was conducted using the OpenMeta-analyst and Review manager Version 5.3 software. The study was reported, according to the PRISMA reporting checklist. Results: Eleven studies were included in the systematic review and meta-analysis. In clinical cure rate, Azithromycin 1% and 1.5% eye drops were more effective than tobramycin 0.3% eye drops in short duration dosing (≤ 5 days) with a twice-a-day regimen (RR=1.138; 95% CI:1.008, 1.284) whereas on increased duration (>5days) azithromycin is almost similarly as effective as tobramycin with (RR=1.007; 95% CI: 0.964, 1.052). There was no significant difference in efficacy of bacterial resolution of azithromycin (1%, 1.5%) eye drops compared to tobramycin (0.3%) eye drops (RR=0.992; 95% CI: 0.967, 1.0183). Conclusion: Azithromycin 1% and 1.5% eye drops are more effective in clinical cure rate than tobramycin 0.3% eye drops for short duration treatment. So that it is recommended to use azithromycin instead of tobramycin eye drops to get good result in short duration dosage. Systematic Review Registration ID : CRD42019139911, registered on October 16,2019; https://www.crd.york.ac.uk/PROSPERO/#recordDetails Keywords: Azithromycin, Tobramycin, Efficacy, Eye drops, Eye diseases
Dynamic monitoring of a migrating and penetrating intracardiac foreign body by echocardiography perioperatively
Authors: Huang HJ , Zhang S , Wang P , Ji XF , Wang ZN , zhao jiaqi 
Published: January 2020

Abstract
Backgroud: Cardiac penetrating injuries caused by migrating foreign bodies are rare. The perioperative locating of these foreign bodies is challenging since their location may change with the continuous beat of the heart. Case presentation: We reported an interesting case of cardiac penetrating injury caused by a self-inflicted needle that migrated from the neck to the heart. The needle was dynamically monitored by both transthoracic echocardiography (TTE) and transesophageal echocardiography (TEE) perioperatively, which showed a significant location change of the needle in the ventricular wall. In a few hours, the needle had moved into the right ventricle with a distance of 2.0cm. An emergency surgery was immediately carried out and the needle was successfully removed without open heart surgery and cardiopulmonary bypass (CPB). If there had been any delay, it would be possible that the needle might enter the right ventricle and was not visible on the surface of the visceral pericardium. The dynamic monitoring of the needle’s location using echocardiography helped clinical decisions and benefited the patient. Conclusions: Foreign bodies with sharp nature have a tendency to migrate though tissues and lead to serious complications. A real-time, continuous and accurate monitoring of cardiac foreign bodies is urgently needed. Echocardiography with a combination of both TTE and TEE help determination of optimal surgical method without radiation hazards, which is worth popularizing in clinical practice.
Hadoop-CNV-RF: a clinically validated and scalable copy number variation detection tool for next-generation sequencing data
Authors: Onsongo Getiria , Lam Ham Ching , Bower Matthew , Thyagarajan Bharat 
Published: January 2020

Abstract
Objective : Detection of small copy number variations (CNVs) in clinically relevant genes is routinely being used to aid diagnosis. We recently developed a tool, CNV-RF , capable of detecting small clinically relevant CNVs. CNV-RF was designed for small gene panels and did not scale well to large gene panels. On large gene panels, CNV-RF routinely failed due to memory limitations. When successful, it took about 2 days to complete a single analysis, making it impractical for routinely analyzing large gene panels. We need a reliable tool capable of detecting CNVs in the clinic that scales well to large gene panels.
Results : We have developed Hadoop-CNV-RF, a scalable implementation of CNV-RF . Hadoop-CNV-RF is a freely available tool capable of rapidly analyzing large gene panels. It takes advantage of Hadoop, a big data framework developed to analyze large amounts of data. Preliminary results show it reduces analysis time from about 2 days to less than 4 hours and can seamlessly scale to large gene panels. Hadoop-CNV-RF has been clinically validated for targeted capture data and is currently being used in a CLIA molecular diagnostics laboratory. Its availability and usage instructions are publicly available at: https://github.com/getiria-onsongo/hadoop-cnvrf-public .