bluuebunny/crossref_metadata_2025_split huggingface dataset:
Food Insecurity and T-cell Dysregulation in Women Living With Human Immunodeficiency Virus on Antiretroviral Therapy
Authors: Peters Brandilyn A , Sheira Lila A , Hanna David B , Qi Qibin , Sharma Anjali , Adedimeji Adebola , Wilson Tracey , Merenstein Daniel , Tien Phyllis C , Cohen Mardge , Wentz Eryka L , Kinslow Jennifer , Landay Alan L , Weiser Sheri D 
Published: November 2020

AbstractBackgroundFood insecurity is associated with increased morbidity and mortality in people with human immunodeficiency virus (HIV) on antiretroviral therapy, but its relationship with immune dysregulation, a hallmark of HIV infection and comorbidity, is unknown.MethodsIn 241 women participating in the Women’s Interagency HIV Study, peripheral blood mononuclear cells were characterized by flow cytometry to identify cell subsets, comprising surface markers of activation (%CD38+HLADR+), senescence (%CD57+CD28−), exhaustion (%PD-1+), and co-stimulation (%CD57− CD28+) on CD4+ and CD8+ T cells. Mixed-effects linear regression models were used to assess the relationships of food insecurity with immune outcomes, accounting for repeated measures at ≤3 study visits and adjusting for sociodemographic and clinical factors.ResultsAt the baseline study visit, 71% of participants identified as non-Hispanic Black, 75% were virally suppressed, and 43% experienced food insecurity. Food insecurity was associated with increased activation of CD4+ and CD8+ T cells, increased senescence of CD8+ T cells, and decreased co-stimulation of CD4+ and CD8+ T cells (all P &lt; .05), adjusting for age, race/ethnicity, income, education, substance use, smoking, HIV viral load, and CD4 count. In stratified analyses, the association of food insecurity with CD4+ T-cell activation was more pronounced in women with uncontrolled HIV (viral load &gt;40 copies/mL and CD4 &lt;500 cells/mm3) but remained statistically significant in those with controlled HIV.ConclusionsFood insecurity may contribute to the persistent immune activation and senescence in women with HIV on antiretroviral therapy, independently of HIV control. Reducing food insecurity may be important for decreasing non–AIDS-related disease risk in this population.
The Mediterranean mussel Mytilus galloprovincialis: responses to climate change scenarios as a function of the original habitat
Authors: Lassoued Jihene , Padín X A , Comeau Luc A , Bejaoui Nejla , Pérez Fiz F , Babarro Jose M F 
Published: November 2020

Abstract
The impact of simulated seawater acidification and warming conditions on specimens of the mussel Mytilus galloprovincialis locally adapted to very distinct, widely separated sites in the Mediterranean Sea (Tunisia) and Atlantic Sea (Galicia, NW Spain) was evaluated in relation to key behavioural and eco-physiological parameters. Over the 2-month exposure to the experimental conditions, mussels were fed optimally to ensure that there are no synergistic interactions between climate change drivers and energetic status of the individuals. In general, regardless of origin (Atlantic or Mediterranean), the mussels were rather resilient to acidification for most of the parameters considered and they were able to grow in strongly acidified seawater through an increased feeding activity. However, shell strength decreased (40%) consistently in both mussel populations held in moderately and highly acidified seawater. The observed reduction in shell strength was not explained by slight alterations in organic matter, shell thickness or aragonite:calcite ratio. The combined effects of high acidification and warming on the key response of byssus strength caused a strong decline in mussel performance, although only in Galician mussels, in which the valve opening time decreased sharply as well as condition index (soft tissue state) and shell growth. By contrast, the observed negative effect of highly acidified scenario on the strength of Tunisian mussel shells was (partly but not totally) counterbalanced by the higher seawater temperature. Eco-physiological and behavioural interactions in mussels in relation to climate change are complex, and future scenarios for the ecology of the species and also the feasibility of cultivating them in Atlantic and Mediterranean zones are discussed.
Using claws to compare reproduction, stress and diet of female bearded and ringed seals in the Bering and Chukchi seas, Alaska, between 1953–1968 and 1998–2014
Authors: Crain Danielle D , Karpovich Shawna A , Quakenbush Lori , Polasek Lori 
Published: November 2020

Abstract
Rapid climate warming is decreasing sea ice thickness, extent and duration. Marine mammals such as bearded (Erignathus barbatus) and ringed (Pusa hispida) seals, which use sea ice for pupping, molting and resting, may be negatively affected. Claws from bearded and ringed seals store up to 14 and 12 years of sequential analyte data, respectively. These data can be used to compare reproduction, stress and diet across decades. In this study, we compare progesterone, cortisol and carbon and nitrogen stable isotopes in female bearded and ringed seals during 1953–1968 (pre-1968, a period prior to sea ice decline) to 1998–2014 (post-1998, a period during sea ice decline). When comparing these periods, bearded seals had statistically higher cortisol concentrations post-1998, and for both species δ13C was more negative post-1998, while progesterone and δ15N did not change. There was a positive relationship between progesterone and cortisol Z-scores for both species, except for ringed seals post-1998. There was a negative relationship between cortisol Z-scores and δ13C for bearded seals evident in post-1998 indicating that higher cortisol Z-scores are associated with more negative δ13C in bearded seals in recent years. This negative relationship between cortisol and δ13C in bearded seals suggests a shift to higher prey diversity, possibly due to changes in sea ice in the Pacific Arctic evident post 1998. Progesterone Z-scores corresponded to expected differences among non-pregnant, unimplanted, implanted and post-partum individuals. Using these data, pregnancy history was determined for reproductive years for each individual female sampled, which could allow for yearly pregnancy rates to be calculated given a large enough representative sample of the population. These results combine decades of observational studies with hormones and stable isotopes to infer changes in reproduction, stress and diet, as well as the connection between these life history parameters.
Transcriptional profiling of theL. monocytogenesPrfA regulon identifies six novel putative PrfA-regulated genes
Authors: Henderson L O , Gaballa A , Orsi R H , Boor K J , Wiedmann M , Guariglia-Oropeza V 
Published: November 2020

ABSTRACTThe transcriptional activator Positive Regulatory Factor A (PrfA) regulates expression of genes essential for virulence in Listeria monocytogenes. To define the PrfA regulon, the 10403S wildtype (WT) strain, a constitutively active prfA* mutant, and an isogenic ∆prfA mutant were grown under PrfA-inducing conditions in a medium containing glucose-1-phosphate and pre-treated with 0.2% activated charcoal. RNA-seq-generated transcript levels were compared as follows: (i) prfA* and WT; (ii) WT and ∆prfA and (iii) prfA* and ∆prfA. Significantly higher transcript levels in the induced WT or constitutively active PrfA* were identified for 18 genes and 2 ncRNAs in at least one of the three comparisons. These genes included: (i) 10/12 of the genes previously identified as directly PrfA-regulated; (ii) 2 genes previously identified as PrfA-regulated, albeit likely indirectly; and (iii) 6 genes newly identified as PrfA-regulated, including one (LMRG_0 2046) with a σA-dependent promoter and PrfA box located within an upstream open reading frame. LMRG_0 2046, which encodes a putative cyanate permease, is reported to be downregulated by a σB-dependent anti-sense RNA. This newly identified overlap between the σB and PrfA regulons highlights the complexity of regulatory networks important for fine-tuning bacterial gene expression in response to the rapidly changing environmental conditions associated with infection.
Effect of capsaicin on the protozoan parasite Trypanosoma cruzi
Authors: Valera-Vera Edward A , Reigada Chantal , Sayé Melisa , Digirolamo Fabio A , Galceran Facundo , Miranda Mariana R , Pereira Claudio A 
Published: November 2020

ABSTRACT
Trypanosoma cruzi is the causative agent of Chagas disease. There are only two approved treatments, both of them unsuitable for the chronic phase, therefore the development of new drugs is a priority. Trypanosoma cruzi arginine kinase (TcAK) is a promising drug target since it is absent in humans and it is involved in cellular stress responses. In a previous study, possible TcAK inhibitors were identified through computer simulations resulting the best compounds capsaicin and cyanidin derivatives. Here, we evaluate the effect of capsaicin on TcAK activity and its trypanocidal effect. Although capsaicin produced a weak enzyme inhibition, it had a strong trypanocidal effect on epimastigotes and trypomastigotes (IC50 = 6.26 µM and 0.26 µM, respectively) being 20-fold more active on trypomastigotes than mammalian cells. Capsaicin was also active on the intracellular cycle reducing by half the burst of trypomastigotes at approximately 2 µM. Considering the difference between the concentrations at which parasite death and TcAK inhibition occur, other possible targets were predicted.
Capsaicin is a selective trypanocidal agent active in nanomolar concentrations, with an IC50 57-fold lower than benznidazole, the drug currently used for treating Chagas disease.
GrimAge Outperforms Other Epigenetic Clocks in the Prediction of Age-Related Clinical Phenotypes and All-Cause Mortality
Authors: McCrory Cathal , Fiorito Giovanni , Hernandez Belinda , Polidoro Silvia , O’Halloran Aisling M , Hever Ann , Ni Cheallaigh Cliona , Lu Ake T , Horvath Steve , Vineis Paolo , Kenny Rose Anne 
Published: November 2020

Abstract
The aging process is characterized by the presence of high interindividual variation between individuals of the same chronical age prompting a search for biomarkers that capture this heterogeneity. Epigenetic clocks measure changes in DNA methylation levels at specific CpG sites that are highly correlated with calendar age. The discrepancy resulting from the regression of DNA methylation age on calendar age is hypothesized to represent a measure of biological aging with a positive/negative residual signifying age acceleration (AA)/deceleration, respectively. The present study examines the associations of 4 epigenetic clocks—Horvath, Hannum, PhenoAge, GrimAge—with a wide range of clinical phenotypes (walking speed, grip strength, Fried frailty, polypharmacy, Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MOCA), Sustained Attention Reaction Time, 2-choice reaction time), and with all-cause mortality at up to 10-year follow-up, in a sample of 490 participants in the Irish Longitudinal Study on Ageing (TILDA). HorvathAA and HannumAA were not predictive of health; PhenoAgeAA was associated with 4/9 outcomes (walking speed, frailty MOCA, MMSE) in minimally adjusted models, but not when adjusted for other social and lifestyle factors. GrimAgeAA by contrast was associated with 8/9 outcomes (all except grip strength) in minimally adjusted models, and remained a significant predictor of walking speed, .polypharmacy, frailty, and mortality in fully adjusted models. Results indicate that the GrimAge clock represents a step-improvement in the predictive utility of the epigenetic clocks for identifying age-related decline in an array of clinical phenotypes promising to advance precision medicine.
Why IACUCs Need Ethicists
Authors: Nobis Nathan 
Published: November 2020

Abstract
Some animal research is arguably morally wrong, and some animal research is morally bad but could be improved. Who is most likely to be able to identify wrong or bad animal research and advocate for improvements? I argue that philosophical ethicists have the expertise that makes them the likely best candidates for these tasks. I review the skills, knowledge, and perspectives that philosophical ethicists tend to have that makes them ethical experts. I argue that, insofar as Institutional Animal Care and Use Committees are expected to ensure that research is ethical, they must have philosophical ethicists as members.
An R848-Conjugated Influenza Virus Vaccine Elicits Robust Immunoglobulin G to Hemagglutinin Stem in a Newborn Nonhuman Primate Model
Authors: Clemens Elene A , Holbrook Beth C , Kanekiyo Masaru , Yewdell Jonathan W , Graham Barney S , Alexander-Miller Martha A 
Published: November 2020

AbstractEliciting broadly protective antibodies is a critical goal for the development of more effective vaccines against influenza. Optimizing protection is of particular importance in newborns, who are highly vulnerable to severe disease following infection. An effective vaccination strategy for this population must surmount the challenges associated with the neonatal immune system as well as mitigate the inherent immune subdominance of conserved influenza virus epitopes, responses to which can provide broader protection. Here, we show that prime-boost vaccination with a TLR7/8 agonist (R848)-conjugated influenza A virus vaccine elicits antibody responses to the highly conserved hemagglutinin stem and promotes rapid induction of virus neutralizing stem-specific antibodies following viral challenge. These findings support the efficacy of R848 as an effective adjuvant for newborns and demonstrate its ability to enhance antibody responses to subdominant antigenic sites in this at-risk population.
Investigation of a Large Diphtheria Outbreak and Cocirculation of Corynebacterium pseudodiphtheriticum Among Forcibly Displaced Myanmar Nationals, 2017–2019
Authors: Weil Lauren M , Williams Margaret M , Shirin Tahmina , Lawrence Marlon , Habib Zakir H , Aneke Janessa S , Tondella Maria L , Zaki Quazi , Cassiday Pamela K , Lonsway David , Farrque Mirza , Hossen Tanvir , Feldstein Leora R , Cook Nicholas , Maldonado-Quiles Gladys , Alam Ahmed N , Muraduzzaman A K M , Akram Arifa , Conklin Laura , Doan Stephanie , Friedman Michael , Acosta Anna M , Hariri Susan , Fox LeAnne M , Tiwari Tejpratap S P , Flora Meerjady S 
Published: November 2020

Abstract

Background
Diphtheria, a life-threatening respiratory disease, is caused mainly by toxin-producing strains of Corynebacterium diphtheriae, while nontoxigenic corynebacteria (eg, Corynebacterium pseudodiphtheriticum) rarely causes diphtheria-like illness. Recently, global diphtheria outbreaks have resulted from breakdown of health care infrastructures, particularly in countries experiencing political conflict. This report summarizes a laboratory and epidemiological investigation of a diphtheria outbreak among forcibly displaced Myanmar nationals in Bangladesh.

Methods
Specimens and clinical information were collected from patients presenting at diphtheria treatment centers. Swabs were tested for toxin gene (tox)-bearing C. diphtheriae by real-time polymerase chain reaction (RT-PCR) and culture. The isolation of another Corynebacterium species prompted further laboratory investigation.

Results
Among 382 patients, 153 (40%) tested tox positive for C. diphtheriae by RT-PCR; 31 (20%) PCR-positive swabs were culture confirmed. RT-PCR revealed 78% (298/382) of patients tested positive for C. pseudodiphtheriticum. Of patients positive for only C. diphtheriae, 63% (17/27) had severe disease compared to 55% (69/126) positive for both Corynebacterium species, and 38% (66/172) for only C. pseudodiphtheriticum.

Conclusions
We report confirmation of a diphtheria outbreak and identification of a cocirculating Corynebacterium species. The high proportion of C. pseudodiphtheriticum codetection may explain why many suspected patients testing negative for C. diphtheriae presented with diphtheria-like symptoms.
Variability in carbapenemase activity of intrinsic OxaAb (OXA-51-like) β-lactamase enzymes inAcinetobacter baumannii
Authors: Takebayashi Yuiko , Findlay Jacqueline , Heesom Kate J , Warburton Philip J , Avison Matthew B , Evans Benjamin A 
Published: November 2020

AbstractObjectivesTo measure the variability in carbapenem susceptibility conferred by different OxaAb variants, characterize the molecular evolution of oxaAb and elucidate the contribution of OxaAb and other possible carbapenem resistance factors in the clinical isolates using WGS and LC–MS/MS.MethodsAntimicrobial susceptibility tests were performed on 10 clinical Acinetobacter baumannii isolates. Carbapenem MICs were evaluated for all oxaAb variants cloned into A. baumannii CIP70.10 and BM4547, with and without their natural promoters. Molecular evolution analysis of the oxaAb variants was performed using FastTree and SplitsTree4. Resistance determinants were studied in the clinical isolates using WGS and LC–MS/MS.ResultsOnly the OxaAb variants with I129L and L167V substitutions, OxaAb(82), OxaAb(83), OxaAb(107) and OxaAb(110) increased carbapenem MICs when expressed in susceptible A. baumannii backgrounds without an upstream IS element. Carbapenem resistance was conferred with the addition of their natural upstream ISAba1 promoter. LC–MS/MS analysis on the original clinical isolates confirmed overexpression of the four I129L and L167V variants. No other differences in expression levels of proteins commonly associated with carbapenem resistance were detected.ConclusionsElevated carbapenem MICs were observed by expression of OxaAb variants carrying clinically prevalent substitutions I129L and L167V. To drive carbapenem resistance, these variants required overexpression by their upstream ISAba1 promoter. This study clearly demonstrates that a combination of IS-driven overexpression of oxaAb and the presence of particular amino acid substitutions in the active site to improve carbapenem capture is key in conferring carbapenem resistance in A. baumannii and other mechanisms are not required.
Navigating treatment approaches for presumed ESBL-producing infections
Authors: Tamma Pranita D , Mathers Amy J 
Published: November 2020

Abstract
ESBL-producing Enterobacterales (ESBL-E) remain a significant global threat. In several regions of the world, ESBLs are produced by over half of Escherichia coli or Klebsiella pneumoniae infections, contributing to significant morbidity and mortality. Though it is accepted that carbapenems are effective for the treatment of invasive ESBL-E infections, controversy remains as to whether carbapenem alternatives can be considered in select cases. Indiscriminate carbapenem use for the treatment of ESBL-E infections will likely further the international antimicrobial resistance crisis, underscoring the importance of investigating the role of non-carbapenem options. In this issue of JAC-Antimicrobial Resistance, we present a PRO/CON debate exploring whether carbapenems are necessary for all infections caused by ceftriaxone-resistant Enterobacterales.
Conceptual considerations for using EHR-based activity logs to measure clinician burnout and its effects
Authors: Kannampallil Thomas , Abraham Joanna , Lou Sunny S , Payne Philip R.O 
Published: November 2020

Abstract
Electronic health records (EHR) use is often considered a significant contributor to clinician burnout. Informatics researchers often measure clinical workload using EHR-derived audit logs and use it for quantifying the contribution of EHR use to clinician burnout. However, translating clinician workload measured using EHR-based audit logs into a meaningful burnout metric requires an alignment with the conceptual and theoretical principles of burnout. In this perspective, we describe a systems-oriented conceptual framework to achieve such an alignment and describe the pragmatic realization of this conceptual framework using 3 key dimensions: standardizing the measurement of EHR-based clinical work activities, implementing complementary measurements, and using appropriate instruments to assess burnout and its downstream outcomes. We discuss how careful considerations of such dimensions can help in augmenting EHR-based audit logs to measure factors that contribute to burnout and for meaningfully assessing downstream patient safety outcomes.
A High-Resolution Melting Analysis with an Unlabeled Probe for CRISPR/Cas9-Induced ZBED6 Knockout Pigs Detection
Authors: Liu Xiaofei , Qiu Songyin , Mei Lin , Jing Hongli , Lin Xiangmei , Wang Qin 
Published: November 2020

Abstract

Background
The zinc finger BED-type containing six knockout (ZBED6-KO) pigs were created to improve economic traits by increasing the expression of insulin-like growth factor 2. They were generated by CRISPR/CRISPR-associated protein 9 (Cas9) technology and a single-base deletion of ZBED6 was found. An efficient and rapid method was needed to detect this type of pig.

Objective
This study aimed to develop a high-resolution melting (HRM) method to detect ZBED6-KO pigs.

Methods
An unlabeled probe and two primers were designed to develop the HRM method. The limit of detection, specificity, and accuracy of the established method were tested by the constructed plasmid and DNA extracts of tissue specimens.

Results
The limit of detection by the established method was 102 copies/µL. The HRM method with an unlabeled probe showed good specificity and high accuracy.

Conclusions
The established HRM analysis with an unlabeled probe showed it to be a highly effective, rapid, and reliable method to distinguish ZBED6-KO pigs from wild-type pigs.

Highlights
It is the first time that HRM analysis with an unlabeled probe has been used in the detection of genome editing pigs by the CRISPR/Cas9 technology.
Edible Fruit Plant Species in the Amazon Forest Rely Mostly on Bees and Beetles as Pollinators
Authors: Paz Fabricia Sousa , Pinto Carlos Eduardo , de Brito Rafael Melo , Imperatriz-Fonseca Vera Lucia , Giannini Tereza Cristina 
Published: November 2020

AbstractEdible fruit plants of tropical forests are important for the subsistence of traditional communities. Understanding the most important pollinators related to fruit and seed production of these plants is a necessary step to protect their pollination service and assure the food security of these communities. However, there are many important knowledge gaps related to floral biology and pollination in megadiverse tropical rainforests, such as the Amazon Forest, due mainly to the high number of plant species. Our study aims to indicate the main pollinators of edible plants (mainly fruits) of the Amazon forest. For this, we adopted a threefold strategy: we built a list of edible plant species, determined the pollination syndrome of each species, and performed a review on the scientific literature searching for their pollinator/visitors. The list of plant species was determined from two specialized publications on Amazon fruit plants, totaling 188 species. The pollination syndrome was determined for 161 species. The syndromes most frequently found among the analyzed species were melittophily (bee pollination), which was found in 101 of the analyzed plant species (54%) and cantharophily (beetle pollination; 26 species; 14%). We also found 238 pollinator/visitor taxa quoted for 52 (28%) plant species in previous publications, with 124 taxa belonging to Apidae family (bees; 52%), mainly from Meliponini tribe (58 taxa; 47%). Knowledge about pollinators is an important step to help on preserving their ecosystem services and maintaining the productivity of fruit trees in the Amazon.