bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice
Authors: Zhou Dongrui , Li Na , Yang Fan , Zhang Honglin , Bai Zhimao , Dong Yangyang , Li Mengjie , Zhu Wenyong , Fei Zhongjie , Xiao Pengfeng , Sun Xiao , Lu Zuhong 
Published: January 2021

SummaryTraditional farm environments induce protection from allergic diseases. In this study, farm environmental factors were classified into three categories, environmental microbes, soil, and organic matter. To explore the impact of soil and environmental microorganisms on gut microbiota and immune function, mice were fed sterilized soil, soil microbes (in lieu of environmental microbes), or non-sterilized soil. Metagenomic sequencing results showed the intake of sterile soil i.e. inhaling a small amount of soil microbes in the air increased gut microbial diversity and the abundance of type III secretion system (T3SS) genes, and decreased serum immune globulin E (IgE) levels induced by 2-4-dinitrofluorobenzene(DNFB). The intake of soil microbes increased the abundance of genes involved in the metabolism of short chain fatty acids and amino acid biosynthesis. Meanwhile, the intake of soil increased gut microbial diversity, the abundance of T3SS genes and related infectious elements, and genes associated with the metabolism of short chain fatty acids and amino acid biosynthesis, and decreased serum IgE levels. Therefore, soil may be useful as a potential “prebiotic” promoting the reproduction and growth of some intestinal microorganisms that harbor bacterial secretion system genes, especially those of T3SS, whose abundance was positively and significantly correlated with innate immune function of mice.
DNA metabarcoding reveals adaptive seasonal variation of individual trophic traits in a critically endangered fish
Authors: Villsen Kurt , Corse Emmanuel , Meglécz Emese , Archambaud-Suard Gaït , Vignes Hélène , Ereskovsky Alexander V. , Chappaz Rémi , Dubut Vincent 
Published: January 2021

AbstractDietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fishZingel asperand conducted modelling and simulation analyses to characterize and identify some of the drivers of individual trophic trait variation in this species. We found that intra-specific competition and ontogeny had minor effects on the trophic niche ofZ. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity (in our case, the seasonal variation in the availability of preferred prey types). Overall, our results are in line with the optimal foraging theory and suggest thatZ. asperis specialized on a few ephemeropteran prey species (Baetis fuscatusandEcdyonurus) but adapts its foraging by becoming more opportunistic as its favoured prey seasonally decline. Despite the now widespread usage of metabarcoding, very few studies have attempted to study inter- and intra-populational individual trophic traits variation with metabarcoding data. This study illustrates how metabarcoding data obtained from feces can be combined with modelling and simulation approaches to test hypotheses in the conventional analytic framework of trophic analysis.
Pre-mRNA processing entropy in a mouse model of trauma
Authors: Jentzsch Maximilian S. , Fredericks Alger M. , Machan Jason T. , Ayala Alfred , Monaghan Sean F. 
Published: January 2021

AbstractPurposeNext generation sequencing has expanded our understanding of many disease processes, including trauma and critical illness. Many studies focus identifying a small set of genes or proteins that are aberrantly expressed. Our objective was to determine whether global differences in pre-mRNA processing entropy, or disorder, could offer novel insights in the setting of critical illness.MethodsWe used an established murine model of trauma that consisted of hemorrhagic shock and cecal ligation and puncture. In our first experiment mice exposed to trauma were compared to controls. In our second experiment, survival 14 days after exposure to trauma was studied. Using deep RNA sequencing we determined entropy values for every pre-mRNA processing event identified. We then used principal component analysis (PCA) to conduct unsupervised classification of the data.ResultsMice exposed to trauma separated from controls using PCA. Similarly, mice that did not survive 14 days post exposure clustered closely together on PCA.ConclusionOur results suggest that there is a substantial difference in global pre-mRNA processing entropy in mice exposed to trauma vs. controls, and that pre-mRNA processing entropy may be helpful in predicting mortality. The method introduced here is easily transferrable to other disease processes and samples.
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Authors: Cele Sandile , Gazy Inbal , Jackson Laurelle , Hwa Shi-Hsia , Tegally Houriiyah , Lustig Gila , Giandhari Jennifer , Pillay Sureshnee , Wilkinson Eduan , Naidoo Yeshnee , Karim Farina , Ganga Yashica , Khan Khadija , Bernstein Mallory , Balazs Alejandro B. , Gosnell Bernadett I. , Hanekom Willem , Moosa Mahomed-Yunus S. ,   NGS-SA,   COMMIT-KZN Team, Lessells Richard J. , Oliveira Tulio de , Sigal Alex 
Published: January 2021

AbstractSARS-CoV-2 variants of concern (VOC) have arisen independently at multiple locations and may reduce efficacy of current vaccines targeted at the spike glycoprotein. We re-cently described the emergence of VOC in South Africa (501Y.V2 or PANGO lineage B.1.351) with mutations in the spike receptor-binding domain (RBD) and N-terminal domain (NTD). Here, using a live virus neutralization assay (LVNA), we compared neutralization of a first wave virus (B.1.1.117) versus the 501Y.V2 variant using plasma collected from adults hospitalized with COVID-19 from two South African infection waves, with the second wave dominated by 501Y.V2 infections. Sequencing demonstrated that infections in first wave plasma donors were with viruses harbouring none of the 501Y.V2-defining RBD or NTD mutations, except for one with E484K. 501Y.V2 virus was effectively neutralized by plasma from second wave infections and first wave virus was effectively neutralized by first wave plasma. In cross-neutralization, 501Y.V2 virus was poorly neutralized by first wave plasma, with an 8.4-fold drop in neutralization relative to first wave virus and a 15.1-fold drop relative to 501Y.V2 neutralization by second wave plasma. In contrast, second wave plasma neutralization of first wave virus was more effective, showing 4.1-fold decline relative to 501Y.V2 virus neutralization and 2.3-fold decline relative to first wave plasma neutralization. While we only tested one plasma elicited by E484K alone, this potently neutralized both variants. The observed effective neutralization of first wave virus by 501Y.V2 infection elicited plasma provides preliminary evidence that vaccines based on VOC sequences could retain activity against other circulating SARS-CoV-2 lineages.
The impact of social restrictions during the COVID-19 pandemic on the physical activity levels of older adults: a baseline analysis of the CHARIOT COVID-19 Rapid Response prospective cohort study
Authors: Salman David , Beaney Thomas , Robb Catherine E. , de Jager Loots Celeste A. , Giannakopoulou Parthenia , Udeh-Momoh Chi , Ahmadi-Abhari Sara , Majeed Azeem , Middleton Lefkos T. , McGregor Alison. H. 
Published: January 2021

AbstractObjectivesPhysical inactivity is more common in older adults, is associated with social isolation and loneliness, and contributes to increased morbidity and mortality. We examined the effect of social restrictions, implemented to reduce transmission of COVID-19 in the UK (lockdown), on physical activity (PA) levels of older adults, and the demographic, lifestyle and social predictors of this change.DesignBaseline analysis of a survey-based prospective cohort studySettingAdults enrolled in the Cognitive Health in Ageing Register for Investigational and Observational Trials (CHARIOT) cohort from GP practices in North West London were invited to participate from April to July 2020.Participants6,219 cognitively healthy adults aged 50 to 92 years completed the survey.Main outcome measuresSelf-reported PA before and after lockdown, as measured by Metabolic Equivalent of Task (MET) minutes. Associations of PA with demographic, lifestyle and social factors, mood and frailty.ResultsMean PA was significantly lower following lockdown, from 3,519 MET minutes/week to 3,185 MET minutes/week (p<0.001). After adjustment for confounders and pre-lockdown PA, lower levels of PA after lockdown were found in those who were over 85 years old (640 [95% CI: 246 to 1034] MET minutes/week less); were divorced or single (240 [95% CI: 120 to 360] MET minutes/week less); living alone (277 [95% CI: 152 to 402] MET minutes/week less); reported feeling lonely often (306 [95% CI: 60 to 552] MET minutes/week less); and showed symptoms of depression (1007 [95% CI: 1401 to 612] MET minutes/week less) compared to those aged 50-64 years, married, co-habiting, and not reporting loneliness or depression, respectively.Conclusions and ImplicationsMarkers of social isolation, loneliness and depression were associated with lower PA following lockdown in the UK. Interventions to improve PA in older adults should take account of social and community factors, and targeted strategies to increase physical activity in socially isolated, lonely and depressed older adults should be considered.
Predator‐scale spatial analysis of intra‐patch prey distribution reveals the energetic drivers of rorqual whale super‐group formation
Authors: Cade David E. , Seakamela S. Mduduzi , Findlay Ken P. , Fukunaga Julie , Kahane‐Rapport Shirel R. , Warren Joseph D. , Calambokidis John , Fahlbusch James A. , Friedlaender Ari S. , Hazen Elliott L. , Kotze Deon , McCue Steven , Meÿer Michael , Oestreich William K. , Oudejans Machiel G. , Wilke Christopher , Goldbogen Jeremy A. 
Published: January 2021

Abstract

Animals are distributed relative to the resources they rely upon, often scaling in abundance relative to available resources. Yet, in heterogeneously distributed environments, describing resource availability at relevant spatial scales remains a challenge in ecology, inhibiting understanding of predator distribution and foraging decisions.

We investigated the foraging behaviour of two species of rorqual whales within spatially limited and numerically extraordinary super‐aggregations in two oceans. We additionally described the lognormal distribution of prey data at species‐specific spatial scales that matched the predator's unique lunge‐feeding strategy.

Here we show that both humpback whales off South Africa's west coast and blue whales off the US west coast perform more lunges per unit time within these aggregations than when foraging individually, and that the biomass within gulp‐sized parcels was on average higher and more tightly distributed within super‐group‐associated prey patches, facilitating greater energy intake per feeding event as well as increased feeding rates.

Prey analysis at predator‐specific spatial scales revealed a stronger association of super‐groups with patches containing relatively high geometric mean biomass and low geometric standard deviations than with arithmetic mean biomass, suggesting that the foraging decisions of rorqual whales may be more influenced by the distribution of high‐biomass portions of a patch than total biomass. The hierarchical distribution of prey in spatially restricted, temporally transient, super‐group‐associated patches demonstrated high biomass and less variable distributions that facilitated what are likely near‐minimum intervals between feeding events.

Combining increased biomass with increased foraging rates implied that overall intake rates of whales foraging within super‐groups were approximately double those of whales foraging in other environments. Locating large, high‐quality prey patches via the detection of aggregation hotspots may be an important aspect of rorqual whale foraging, one that may have been suppressed when population sizes were anthropogenically reduced in the 20th century to critical lows.

A free Plain Language Summary can be found within the Supporting Information of this article.
The frequency exponent of artificial sandstone's complex resistivity spectrum
Authors: Jia Jiang , Ke Shizhen , Rezaee Reza , Li Junjian , Wu Feng 
Published: January 2021

ABSTRACTThe complex resistivity spectra of 16 artificial sandstone samples with different physical property at different water and solution saturations were measured and fitted with the Cole–Cole model in the frequency band of 40 Hz to 110 MHz. The frequency exponent in the model indicates the ideal degree of the sample's capacitive property. The experimental result shows that the frequency exponents of the samples are concentrated mainly between 0.82 and 0.88 and present a segmented law that decreases first and then increases with decreasing the water saturation. The minimum frequency exponent has a linear relationship with porosity and cementation index and an exponential relationship with formation factors. The frequency exponent is expected to be used in the study of the oil–water distribution in the reservoir. The frequency exponents of the samples decrease with an increase in clay content. Frequency exponents are independent of the ion type in the solution. Numerical simulation results support that the capacitive property generated by the connected pore‐throat spaces is near ideal, but the capacitive property contributed by the closed pore‐throat spaces is non‐ideal. This could be the possible reason why the frequency exponents of the samples are less than one. The pore‐throats with higher capillary pressure can be blocked and become secondary closed pore‐throat space during the flooding process and result in a decrease in frequency exponent. This can explain the influence of reservoir parameters on frequency exponent and can further clarify the physical significance of the Cole–Cole frequency exponent on the rock's complex resistivity.
Do biochemical parameters and intradialytic symptoms affectpost‐dialysisrecovery time? A prospective, descriptive study
Authors: Ozen Nurten , Cepken Tugba , Tosun Betul 
Published: January 2021

AbstractThe recovery time is defined as the time required to recover from the feelings of lassitude and fatigue. The daily activities of patients are affected by dialysis sessions, requiring significant time for patients to return to their routines. This situation implies a lower quality of life for HD patients. The aim of this study was to investigate the effects of biochemical parameters and intradialytic symptoms on post‐dialysis recovery time in maintenance HD patients. This study was conducted at a private dialysis center during June and August 2019. Data were collected using the “Descriptive Characteristics Form” and the “Dialysis Symptom Index.” “STROBE check‐list” was used for the report of the study. The study was completed with 86 participants. The median post‐dialysis recovery time was 240 min (interquartile range, 120–360 min), and female patients exhibit significantly higher recovery time than male patients. The median BMI was statistically significantly higher in patients whose post‐dialysis recovery time was ≥240 min. Additional findings show that the post‐dialysis recovery time was shortened by 0.230 times for male patients, while intradialytic hypotension (IDH) prolonged the median post‐dialysis recovery time by 3.141 times. Factors underlying the IDH should be determined in order to eradicate the issue. The study was registered inClinicalTrials.govwith the number NCT04274556.
Correlation between vancomycin clearance and cystatin C‐based glomerular filtration rate in paediatric patients
Authors: Oh Yunmi , Park Sojin , Park Esther , Lee Jaehyun , Lee Hukyoung , Kim Jeongmee , Cho Joongbum 
Published: January 2021

AimsBecause of limitations with the serum creatinine‐based glomerular filtration rate (GFRcr), estimates of the serum cystatin C‐based glomerular filtration rate (GFRcys) are getting attention to predict vancomycin clearance (CLvan). We evaluated the correlations between (i) CLvan and GFRcr, and (ii) CLvan and GFRcys in paediatric patients.MethodsWe evaluated a retrospective cohort of patients between 1 and 19 years old admitted to a tertiary hospital between 2017 and 2019. CLvan was estimated using measured vancomycin trough concentrations. We conducted Spearman's correlation analyses between CLvan and 1/creatinine, GFRcr, 1/cystatin C and GFRcys. Subgroup analyses were conducted for the young child, child, adolescent subgroups, intensive care unit patients and low body weight (<10th percentile) patients.ResultsWe analysed 40 patients. GFRcys correlated with CLvan better than GFRcr did (ρ = 0.731, P < 0.001 vs ρ = 0.504, P = 0.001). In the subgroup analyses, the correlation between GFRcys and CLvan was stronger than that between GFRcr and CLvan (child subgroup ρ = 0.712, P = 0.002 vs ρ = 0.282, P = 0.289; intensive care unit patients ρ = 0.772, P < 0.001 vs ρ = 0.540, P = 0.004; low body weight patients ρ = 0.671, P < 0.001 vs ρ = 0.464, P = 0.022).ConclusionsSerum cystatin C‐based GFR strongly correlates with vancomycin clearance, suggesting the possibility of better prediction models than creatinine‐based GFR. Further prospective studies are required for the validation of the prediction model in a large paediatric population.
Genetics and Child Development: Recent Advances and Their Implications for Developmental Research
Authors: Armstrong‐Carter Emma , Wertz Jasmin , Domingue Benjamin W. 
Published: January 2021

AbstractRecent genetic discoveries offer a new lens through which to study cognitive, emotional, behavioral, and social processes that are foundational to children’s development. In this article, we review the latest advances in genomics—genome‐wide association studies and the polygenic scores that have come out of them—and discuss how these techniques can be leveraged to shed light on developmental research questions. Then, we describe how developmental scientists might apply these methods in their own lines of work—for example, in investigations of individual differences in developmental trajectories, intergenerational transmission, peer relationships, and processes of resilience and positive adaptation. Finally, we discuss ethical concerns and limitations of genetics research as they pertain to developmental science.
Immunodeficiency (CVID and CD4 lymphopenia) is associated with a high risk of malignancy among adults with primary immune deficiency
Authors: Shavit R , Maoz-Segal R , Prizinsky S , Haj-Yahia S , Offengenden I , Machnas-Mayan D , Tunisky Y , Iancovici-Kidon M , Agmon-Levin N 
Published: January 2021

Summary
Primary immunodeficiency disorders (PID) are a group of heterogeneous disorders characterized by recurrent infections, autoimmunity, increased lymphoproliferative disorders and other malignancies. PID is classified into cellular or humoral disorders or a combination of both. We evaluated the clinical differences among adult patients with three variants of PID: common variable immunodeficiency (CVID), idiopathic CD4 lymphopenia (ICL) and combined immunodeficiency (CID). We retrospectively compared demographics, immunological characteristics, clinical presentations and outcomes of CVID, CID and ICL patients followed from 2012 to 2018. In our cohort, we identified 44 adult patients diagnosed with CVID (22), CID (11) and ICL (11). Malignancy was associated with CID, as seven of 11 patients in this group were diagnosed with malignancy compared to CVID (three of 22) or ICL (two of 11) (P = 0·002 and 0·03, respectively). Malignancies were also linked to male gender [odds ratio (OR) = 5, 95% confidence interval (CI) = 1·12–22·18) P = 0·0342] and a low ratio of CD4/CD8 &lt; 0·8 (OR = 5·1, 95% CI = 1·22–21·28, P = 0·025). Among CID and ICL, two of 11 patients died in each group, while no death was documented among CVID group (P = 0·04). Autoimmune manifestations did not differ between groups. Similarly, the rate of infections was similar between groups, although infectious agents vary. CID is associated with a high risk of malignancy compare to CVID or ICL. Among adults with PID, male gender, low CD4 and a CD4/CD8 ratio of &lt; 0·8 may serve as risk factors of concomitant malignancy. Surveillance of lymphocyte subpopulations should be considered for all adults.
Biallelic loss of function variant in the unfolded protein response gene PDIA6 is associated with asphyxiating thoracic dystrophy and neonatal‐onset diabetes
Authors: Al‐Fadhli Fatima M. , Afqi Manal , Sairafi Mona Hamza , Almuntashri Makki , Alharby Essa , Alharbi Ghadeer , Abdud Samad Firoz , Hashmi Jamil Amjad , Zaytuni Dimah , Bahashwan Ahmed A. , Choi Jin Huk , Peake Roy W. A. , Beutler Bruce , Almontashiri Naif A. M. 
Published: January 2021

AbstractProtein disulfide isomerase A6 (PDIA6) is an unfolded protein response (UPR)‐regulating protein. PDIA6 regulates the UPR sensing proteins, Inositol requiring enzyme 1, and EIF2AK3. Biallelic inactivation of the two genes in mice and humans resulted in embryonic lethality, diabetes, skeletal defects, and renal insufficiency. We recently showed that PDIA6 inactivation in mice caused embryonic and early lethality, diabetes and immunodeficiency. Here, we present a case with asphyxiating thoracic dystrophy (ATD) syndrome and infantile‐onset diabetes. Whole exome sequencing revealed a homozygous frameshift variant in the PDIA6 gene. RNA expression was reduced in a gene dosage‐dependent manner, supporting a loss‐of‐function effect of this variant. Phenotypic correlation with the mouse model recapitulated the growth defect and delay, early lethality, coagulation, diabetes, immunological, and polycystic kidney disease phenotypes. In general, the phenotype of the current patient is consistent with phenotypes associated with the disruption of PDIA6 and the sensors of UPR in mice and humans. This is the first study to associate ATD to the UPR gene, PDIA6. We recommend screening ATD cases with or without insulin‐dependent diabetes for variants in PDIA6.