bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases
Authors: Zolfaghari Emameh Reza , Hosseini Seyed Nezamedin , Parkkila Seppo 
Published: May 2021

AbstractSus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig or Wuzhishan pig (WZSP), which is broadly used in the life and medical sciences. The whole genome of WZSP was sequenced in 2012. Through a bioinformatics study of pig carbonic anhydrase (CA) sequences, we detected some β- and γ-class CAs among the WZSP CAs annotated in databases, while β- or γ-CAs had not previously been described in vertebrates. This finding urged us to analyze the quality of whole genome sequence of WZSP for the possible bacterial contamination. In this study, we used bioinformatics methods and web tools such as UniProt, European Bioinformatics Institute, National Center for Biotechnology Information, Ensembl Genome Browser, Ensembl Bacteria, RSCB PDB and Pseudomonas Genome Database. Our analysis defined that pig has 12 classical α-CAs and 3 CA-related proteins. Meanwhile, it was approved that the detected CAs in WZSP are categorized in the β- and γ-CA families, which belong to Pseudomonas spp. and Acinetobacter spp. The protein structure study revealed that the identified β-CA sequence from WZSP belongs to Pseudomonas aeruginosa with PDB ID: 5JJ8, and the identified γ-CA sequence from WZSP belongs to P. aeruginosa with PDB ID: 3PMO. Bioinformatics and computational methods accompanied with bacterial-specific markers, such as 16S rRNA and β- and γ-class CA sequences, can be used to identify bacterial contamination in mammalian DNA samples.
Variable posttranslational modifications of severe acute respiratory syndrome coronavirus 2 nucleocapsid protein
Authors: Supekar Nitin T , Shajahan Asif , Gleinich Anne S , Rouhani Daniel S , Heiss Christian , Chapla Digantkumar Gopaldas , Moremen Kelley W , Azadi Parastoo 
Published: May 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), started in 2019 in China and quickly spread into a global pandemic. Nucleocapsid protein (N protein) is highly conserved and is the most abundant protein in coronaviruses and is thus a potential target for both vaccine and point-of-care diagnostics. N Protein has been suggested in the literature as having posttranslational modifications (PTMs), and accurately defining these PTMs is critical for its potential use in medicine. Reports of phosphorylation of N protein have failed to provide detailed site-specific information. We have performed comprehensive glycomics, glycoproteomics and proteomics experiments on two different N protein preparations. Both were expressed in HEK293 cells; one was in-house expressed and purified without a signal peptide (SP) sequence, and the other was commercially produced with a SP channeling it through the secretory pathway. Our results show completely different PTMs on the two N protein preparations. The commercial product contained extensive N- and O-linked glycosylation as well as O-phosphorylation on site Thr393. Conversely, the native N Protein model had O-phosphorylation at Ser176 and no glycosylation, highlighting the importance of knowing the provenance of any commercial protein to be used for scientific or clinical studies. Recent studies have indicated that N protein can serve as an important diagnostic marker for COVID-19 and as a major immunogen by priming protective immune responses. Thus, detailed structural characterization of N protein may provide useful insights for understanding the roles of PTMs on viral pathogenesis, vaccine design and development of point-of-care diagnostics.
Universal adaptive stabilization for a class of multivariable Markovian jump linear systems with partially unknown transition rates
Authors: Berdouzi Driss , El Hadri Kamal , El Bouhtouri Abdelmoula 
Published: May 2021

Abstract
In this paper, the problem of universal adaptive stabilization is investigated for a class of multi-input multi-output Markovian jump linear systems (MJLSs) with partially unknown transition rates (TRs). The class of systems that we are considering is characterized only by some structural assumptions. Firstly, we show the high-gain stochastic stabilizability, that is, any system belonging to this class can be stabilized by a mode-dependent output feedback controller, provided that the proportional gain for every mode is sufficiently large. Moreover, a universal adaptive high-gain controller, which is not based on identification or any estimation algorithms, is presented. It is shown that this controller ensures the convergence and the boundedness of the closed-loop system signals in the mean square sense. Finally, simulation results are given to illustrate the performance and effectiveness of the proposed approaches. MJLSs, high-gain stabilizability, universal adaptive control, output feedback, partially unknown TRs.
Ileal Perforation and Enteric Fever: Implications for Burden of Disease Estimation
Authors: Njarekkattuvalappil Swathi Krishna , Thomas Maria , Kapil Arti , Saigal Karnika , Ray Pallab , Anandan Shalini , Nagaraj Savitha , Shastri Jayanthi , Perumal Sulochana Putli bai , Jinka Dasaratha Ramaiah , Thankaraj Shajin , Ismavel Vijayanand , Zachariah Pradeep , Singh Ashita , Gupta Madhu , Ebenezer Sheena Evelyn , Thomas Mathew Santosh , Ghosh Dhruva , Kataria Kamal , Senger Mamta , Balasubramanian Sundaram , Kang Gagandeep , John Jacob 
Published: May 2021

Abstract

Background
Ileal perforation occurs in about 1% of enteric fevers as a complication, with a case fatality risk (CFR) of 20%–30% in the early 1990s that decreased to 15.4% in 2011 in South East Asia. We report nontraumatic ileal perforations and its associated CFR from a 2-year prospective enteric fever surveillance across India.

Methods
The Surveillance for Enteric Fever in India (SEFI) project established a multitiered surveillance system for enteric fever between December 2017 and March 2020. Nontraumatic ileal perforations were surveilled at 8 tertiary care and 6 secondary care hospitals and classified according to etiology.

Results
Of the 158 nontraumatic ileal perforation cases identified,126 were consented and enrolled. Enteric fever (34.7%), tuberculosis (19.0%), malignancy (5.8%), and perforation of Meckel diverticulum (4.9%) were the common etiology. In those with enteric fever ileal perforation, the CFR was 7.1%.

Conclusions
Enteric fever remains the most common cause of nontraumatic ileal perforation in India, followed by tuberculosis. Better modalities of establishing etiology are required to classify the illness, and frame management guidelines and preventive measures. CFR data are critical for comprehensive disease burden estimation and policymaking.
Morbidity and Mortality Among Adults Experiencing Homelessness Hospitalized With COVID-19
Authors: Cha Susan , Henry Ankita , Montgomery Martha P , Laws Rebecca L , Pham Huong , Wortham Jonathan , Garg Shikha , Kim Lindsay , Mosites Emily ,   COVID-NET Surveillance Team, Chai Shua J , Kawasaki Breanna , Meek James , Anderson Evan J , Weigel Andrew , Ryan Patricia , Kim Sue , Como-Sabetti Kathryn , Torres Salina , Muse Alison , Bennett Nancy M , Billing Laurie M , Sutton Melissa , Talbot H Keipp , Risk Ilene 
Published: May 2021

Abstract
People experiencing homelessness (PEH) are at higher risk for chronic health conditions, but clinical characteristics and outcomes for PEH hospitalized with coronavirus disease 2019 (COVID-19) are not known. We analyzed population-based surveillance data of COVID-19–associated hospitalizations during 1 March to 31 May 2020. Two percent of the people hospitalized with COVID-19 for whom a housing status was recorded were homeless. Of 199 cases in the analytic sample, most were of racial/ethnic minority groups and had underlying health conditions. Clinical outcomes such as ICU admission, respiratory support including mechanical ventilation, and deaths were documented. Hispanic and non-Hispanic black persons accounted for most mechanical ventilation and deaths. Severe illness was common among persons experiencing homelessness who were hospitalized with COVID-19.
Monoclonal Antibody Requires Immunomodulation for Efficacy Against Acinetobacter baumannii Infection
Authors: Nielsen Travis B , Yan Jun , Luna Brian M , Talyansky Yuli , Slarve Matthew , Bonomo Robert A , Spellberg Brad 
Published: May 2021

Abstract
Monoclonal antibodies (mAbs) are gaining significant momentum as novel therapeutics for infections caused by antibiotic-resistant bacteria. We evaluated the mechanism by which antibacterial mAb therapy protects against Acinetobacter baumannii infections. Anticapsular mAb enhanced macrophage opsonophagocytosis and rescued mice from lethal infections by harnessing complement, macrophages, and neutrophils; however, the degree of bacterial burden did not correlate with survival. Furthermore, mAb therapy reduced proinflammatory (interleukin-1β [IL-1β], IL-6, tumor necrosis factor-α [TNF-α]) and anti-inflammatory (IL-10) cytokines, which correlated inversely with survival. Although disrupting IL-10 abrogated the survival advantage conferred by the mAb, IL-10–knockout mice treated with mAb could still survive if TNF-α production was suppressed directly (via anti–TNF-α neutralizing antibody) or indirectly (via macrophage depletion). Thus, even for a mAb that enhances microbial clearance via opsonophagocytosis, clinical efficacy required modulation of pro- and anti-inflammatory cytokines. These findings may inform future mAb development targeting bacteria that trigger the sepsis cascade.
Consumption of tetracyclines, sulphonamides and trimethoprim, and other antibacterials in the community, European Union/European Economic Area, 1997–2017
Authors: Versporten Ann , Bruyndonckx Robin , Adriaenssens Niels , Hens Niel , Monnet Dominique L , Molenberghs Geert , Goossens Herman , Weist Klaus , Coenen Samuel ,   the ESAC-Net study group, Strauss Reinhild , Vandael Eline , Sabtcheva Stefana , Andrašević Arjana Tambić , Kyriakidou Isavella , Vlček Jiří , Sönksen Ute Wolff , Linask Elviira , Sarvikivi Emmi , Hider-Mlynarz Karima , Blank Hans-Peter , Kontopidou Flora , Benkő Ria , Aspelund Gudrun , Oza Ajay , Fortinguerra Filomena , Rutkovska Ieva , Valintėlienė Rolanda , Bruch Marcel , Zarb Peter , Natsch Stephanie , Blix Hege Salvesen , Olczak-Pieńkowska Anna , Silva Ana , Popescu Gabriel Adrian , Tesař Tomáš , Čižman Milan , Herreras Mayte Alonso , Bergfeldt Vendela , Andrews Amelia 
Published: May 2021

Abstract

Objectives
Data on consumption of tetracyclines, sulphonamides and trimethoprim, and other antibacterials were collected from 30 EU/European Economic Area (EEA) countries over two decades. This article reviews temporal trends, seasonal variation, presence of change-points and changes in the composition of main subgroups of tetracyclines, sulphonamides and trimethoprim and other antibacterials.

Methods
For the period 1997–2017, data on consumption of tetracyclines (ATC group J01A), sulphonamides and trimethoprim (ATC group J01E), and other antibacterials (ATC group J01X) in the community and aggregated at the level of the active substance, were collected using the WHO ATC/DDD methodology (ATC/DDD index 2019). Consumption was expressed in DDD per 1000 inhabitants per day and in packages per 1000 inhabitants per day. Consumption of tetracyclines, sulphonamides and trimethoprim, and other antibacterials was analysed based on ATC-4 subgroups and presented as trends, seasonal variation, presence of change-points and compositional changes.

Results
In 2017, consumption of tetracyclines, sulphonamides and trimethoprim, and other antibacterials in the community expressed in DDD per 1000 inhabitants per day varied considerably between countries. Between 1997 and 2017, consumption of tetracyclines did not change significantly, while its seasonal variation significantly decreased over time. Consumption of sulphonamides and trimethoprim significantly decreased until 2006, and its seasonal variation significantly decreased over time. The consumption of other antibacterials showed no significant change over time or in seasonal variation.

Conclusions
Consumption and composition of tetracyclines, sulphonamides and trimethoprim, and other antibacterials showed wide variations between EU/EEA countries and over time. This represents an opportunity to further reduce consumption of these groups in some countries and improve the quality of their prescription.
A prospective surveillance study to determine the prevalence of 16S rRNA methyltransferase-producing Gram-negative bacteria in the UK
Authors: Taylor Emma , Bal Abhijit M. , Balakrishnan Indran , Brown Nicholas M. , Burns Phillipa , Clark Marilyn , Diggle Mathew , Donaldson Hugo , Eltringham Ian , Folb Jonathan , Gadsby Naomi , Macleod Mairi , Ratnaraja Natasha V. D. V. , Williams Cheryl , Wootton Mandy , Sriskandan Shiranee , Woodford Neil , Hopkins Katie L. 
Published: May 2021

Abstract

Objectives
To determine the prevalence of 16S rRNA methyltransferase- (16S RMTase-) producing Gram-negative bacteria in patients in the UK and to identify potential risk factors for their acquisition.

Methods
A 6 month prospective surveillance study was conducted from 1 May to 31 October 2016, wherein 14 hospital laboratories submitted Acinetobacter baumannii, Enterobacterales and Pseudomonas aeruginosa isolates that displayed high-level amikacin resistance according to their testing methods, e.g. no zone of inhibition with amikacin discs. Isolates were linked to patient travel history, medical care abroad, and previous antibiotic exposure using a surveillance questionnaire. In the reference laboratory, isolates confirmed to grow on Mueller-Hinton agar supplemented with 256 mg/L amikacin were screened by PCR for 16S RMTase genes armA, rmtA–rmtH and npmA, and carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like and blaVIM). STs and total antibiotic resistance gene complement were determined via WGS. Prevalence was determined using denominators for each bacterial species provided by participating hospital laboratories.

Results
Eighty-four isolates (44.7%), among 188 submitted isolates, exhibited high-level amikacin resistance (MIC &gt;256 mg/L), and 79 (94.0%) of these harboured 16S RMTase genes. armA (54.4%, 43/79) was the most common, followed by rmtB (17.7%, 14/79), rmtF (13.9%, 11/79), rmtC (12.7%, 10/79) and armA + rmtF (1.3%, 1/79). The overall period prevalence of 16S RMTase-producing Gram-negative bacteria was 0.1% (79/71 063). Potential risk factors identified through multivariate statistical analysis included being male and polymyxin use.

Conclusions
The UK prevalence of 16S RMTase-producing Gram-negative bacteria is low, but continued surveillance is needed to monitor their spread and inform intervention strategies.
PROMIS Global-10 poorly correlates with legacy outcomes for patients undergoing hip arthroscopy
Authors: Bido Jennifer , Sullivan Spencer W , Dooley Matthew S , Nawabi Danyal H , Ranawat Anil S , Kelly Bryan T , Nwachukwu Benedict U 
Published: May 2021

ABSTRACT
The Patient-Reported Outcomes Measurement Information System (PROMIS) Global-10 assesses generic-related quality of life, but has not been well studied in the orthopaedic literature. The purpose was to compare PROMIS Global-10 and legacy hip-specific patient-reported outcome measures (PROMs) in patients undergoing hip arthroscopy for femoroacetabular impingement syndrome (FAIS). This study included patients who underwent primary hip arthroscopy with complete preoperative and 6-month post-operative follow-up. PROMIS Global-10 Physical (PROMIS-P) and Mental (PROMIS-M) components, as well as the modified Harris hip score (mHHS) and International Hip Outcome Tool-33 (iHOT-33) were assessed. PROM analysis included: post-operative changes, correlations, floor and ceiling effects and responsiveness. Final analysis included 112 patients. Average age and body mass index were 36.1±11.7 years and 24.8±3.9 kg/m2, respectively. All 6-month PROMs, except PROMIS-M, were significantly improved compared to preoperative level (P&lt;0.02). Preoperatively, PROMIS-P was poorly correlated with mHHS and iHOT-33 (rs &lt;0.4) whereas PROMIS-M was only poorly correlated with iHOT-33 (rs &lt;0.4, 95% CI of 0.02–0.37). Post-operatively, the iHOT-33 was poorly correlated with both PROMIS measures (rs &lt;0.4). The mHHS was fairly correlated with both PROMIS measures (rs &lt;0.6) post-operatively. The effect sizes for mHHS and iHOT-33 were high (d=1.2 and 1.40, respectively), whereas the effect sizes for PROMIS Global-10 were small (d&lt;0.3). PROMIS Global-10 demonstrated lower effect sizes and poor to fair correlation with legacy hip-specific PROMs, and appears to have a limited role in the assessment of patients undergoing hip arthroscopy for FAIS. Therefore, the PROMIS Global-10 may have a limited role in assessing patients with FAIS.
Modal Logic With Non-Deterministic Semantics: Part II—Quantified Case
Authors: Coniglio Marcelo E , Fariñasdelcerro Luis , Peron Newton Marques 
Published: May 2021

Abstract
In the first part of this paper we analyzed finite non-deterministic matrix semantics for propositional non-normal modal logics as an alternative to the standard Kripke possible world semantics. This kind of modal system characterized by finite non-deterministic matrices was originally proposed by Ju. Ivlev in the 70s. The aim of this second paper is to introduce a formal non-deterministic semantical framework for the quantified versions of some Ivlev-like non-normal modal logics. It will be shown that several well-known controversial issues of quantified modal logics, relative to the identity predicate, Barcan’s formulas and de re and de dicto modalities, can be tackled from a new angle within the present framework.
Up-regulation of chemokine receptor type 4 expression in the ischemic reperfused heart by alcoholic extract of Cichorium intybus rescue the heart from ischemia injury in male rat
Authors: Sedighi Mehrnoosh , Ghorbanzadeh Vajihe , Abaszadeh Saber , Karimi Arash , Cheraghi Mostafa , Rafieian-Kopaei Mahmoud , Moghimian Maryam , Mohammadi Asghar , Veiskarami Saeid , Mokhayeri Yaser , Nazari Afshin 
Published: May 2021

Abstract

Objectives
Cichorium intybus is used in traditional medicine for various diseases including heart disease. This study aimed at evaluating the chemokine receptor type 4 up-regulation and cardioprotective effects of hydroalcoholic extract of C. intybus in a rat model of ischemic reperfusion.

Methods
Animals in four groups of eight rats each received vehicle or one of three doses of C. intybus (50, 100 or 200 mg/kg/d) for 14 days. Then they were subjected to 30 min of ischemia followed by 7 days of reperfusion. At the end of the experiment, blood specimens were prepared for serum assays. The level of myocardium chemokine receptor type 4 was also measured using RT-PCR.

Key findings
Cichorium intybus (CI-50) improved infarct size, episodes of the ventricular ectopic beat, ventricular tachycardia, and duration of ventricular tachycardia, QTc shortening. It also stabilized the ST segment changes and increased heart rate during ischemia. The blood pressure decreased in CI-50 group in comparison to the control and CI-200 group. C. intybus increased serum superoxide dismutase and reduced lactate dehydrogenase activity, Cardiac Troponin I and malondialdehyde levels. C. intybus led to an increase in the expression of chemokine receptor type 4.

Conclusions
These findings suggest that C. intybus administration before ischemia is able to induce cardioprotective effect against ischemic reperfusion injury, probably through chemokine receptor type 4 over-expression and antioxidant activity.
Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition
Authors: Hartley Gabrielle A , Okhovat Mariam , O’Neill Rachel J , Carbone Lucia 
Published: May 2021

AbstractCentromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.
Seasonal variability in non-consumptive mortality of Arctic zooplankton
Authors: Daase Malin , Søreide Janne E 
Published: May 2021

AbstractRecent observations from high-latitude marine ecosystems indicate that non-consumptive mortality may be particularly high in Arctic zooplankton during the polar night. Here we have estimated the contribution of dead organisms to the mesozooplankton community in the high Arctic (Svalbard 78–81oN) during the polar night (January), in spring (May) and in late summer (end of August). To identify in situ dead organisms, we used Neutral Red Stain. The dead zooplankton fraction consisted mainly of copepods, while the contribution of dead non-copepods was low in all seasons. The absolute abundance of dead copepods varied little between seasons; however, the relative contribution of dead copepods was highest in January with 11–35% of the copepods classified as dead, in contrast to 2–12% in spring and summer. Furthermore, there were species-specific differences: copepods of the genus Calanus contributed more to the dead fraction of the copepod community during the polar night compared to spring and summer, leading to a higher “dead” biomass in winter. We conclude that non-consumptive winter mortality is considerable in calanoid copepods in the Arctic and an important but so far neglected component of the passive carbon flux, providing carbon in larger portions for higher trophic level consumers during the low-productive winter.