bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cautionary tale of attenuation in star-forming regions
Authors: Molina Mallory , Ajgaonkar Nikhil , Yan Renbin , Ciardullo Robin , Gronwall Caryl , Eracleous Michael , Boquien Médéric , Schneider Donald P 
Published: March 2020

ABSTRACT
The attenuation of light from star-forming galaxies is correlated with a multitude of physical parameters including star formation rate, metallicity and total dust content. This variation in attenuation is even more evident on kiloparsec scales, which is the relevant size for many current spectroscopic integral field unit surveys. To understand the cause of this variation, we present and analyse Swift/UVOT near-UV (NUV) images and SDSS/MaNGA emission-line maps of 29 nearby (z &lt; 0.084) star-forming galaxies. We resolve kiloparsec-sized star-forming regions within the galaxies and compare their optical nebular attenuation (i.e. the Balmer emission line optical depth, $\tau ^{l}_{B}\equiv \tau _{\textrm {H}\beta }-\tau _{\textrm {H}\alpha }$) and NUV stellar continuum attenuation (via the NUV power-law index, β) to the attenuation law described by Battisti et al. We show the data agree with that model, albeit with significant scatter. We explore the dependence of the scatter of the β–$\tau ^{l}_{B}$ measurements from the star-forming regions on different physical parameters, including distance from the nucleus, star formation rate and total dust content. Finally, we compare the measured $\tau ^{l}_{B}$ and β values for the individual star-forming regions with those of the integrated galaxy light. We find a strong variation in β between the kiloparsec scale and the larger galaxy scale that is not seen in $\tau ^{l}_{B}$. We conclude that the sightline dependence of UV attenuation and the reddening of β due to the light from older stellar populations could contribute to the scatter in the β–$\tau ^{l}_{B}$ relation.
‘Eall swylce þu cwæde’: Translation and Imitation in the Old English Judgement Day II
Authors: Healy Tara Ann 
Published: March 2020

Abstract
This essay posits a new explanation for the placement of a perplexing second-person address in the introduction to the Old English Judgement Day II. I argue that the poet deliberately highlights and problematizes the act of translation from Bede’s De die iudicii, providing the Old English speaker with a poetic identity of his own even as Bede’s authoritative voice is retained. Bede’s second-person address to Acca is therefore echoed with all its original intent, but is simultaneously directed at Bede himself. It is likely that this method finds its roots in an Augustinian mode of conversion narrative which has the polemical advantage of inserting its narrator into a broader Christian tradition. I also demonstrate that the approach to translation in Judgement Day II, while in many ways unique within the known corpus of Old English verse, finds stylistic parallels in Alfredian prose translations in which the translator imposes self-referential meaning upon the existing textual content.
Interleukin-31 promotes pathogenic mechanisms underlying skin and lung fibrosis in scleroderma
Authors: Yaseen Bodoor , Lopez Henry , Taki Zeinab , Zafar Sara , Rosario Henrique , Abdi Bahja Ahmed , Vigneswaran Shivanee , Xing Fiona , Arumalla Nikita , Black Simon , Ahmad Sara , Kumar Kimti , Gul Rabia , Scolamiero Laura , Morris Sian , Bowman Alex , Stainer Anna , Rice Alexandra , Stock Carmel , Renzoni Elisabetta , Denton Christopher P , Venturini Cristina , Brown Max , O’Reilly Steven , Stratton Richard 
Published: March 2020

Abstract

Objectives
Cytokines released by infiltrating T cells may promote mechanisms leading to fibrosis in scleroderma. The aim of this study was to investigate the role of the Th2 cytokine IL-31, and its receptor IL-31RA, in scleroderma skin and lung fibrosis.

Methods
IL-31 was measured by ELISA of plasma, and by immunochemistry of fibrotic skin and lung tissue of scleroderma patients. The receptor, IL-31RA, was assayed by qPCR of tissue resident cells. Next-generation sequencing was used to profile the responses of normal skin fibroblasts to IL-31. In wild-type Balb/c mice, IL-31 was administered by subcutaneous mini pump, with or without additional TGFβ, and the fibrotic reaction measured by histology and ELISA of plasma.

Results
IL-31 was present at high levels in plasma and fibrotic skin and lung lesions in a subset of scleroderma patients, and the receptor overexpressed by downstream cells relevant to the disease process, including skin and lung fibroblasts, through loss of epigenetic regulation by miR326. In skin fibroblasts, IL-31 induced next generation sequencing profiles associated with cellular growth and proliferation, anaerobic metabolism and mineralization, and negatively associated with angiogenesis and vascular repair, as well as promoting phenotype changes including migration and collagen protein release via pSTAT3, resembling the activation state in the disease. In mice, IL-31 induced skin and lung fibrosis. No synergy was seen with TGFβ, which supressed IL-31RA.

Conclusion
IL-31/IL-31RA is confirmed as a candidate pro-fibrotic pathway, which may contribute to skin and lung fibrosis in a subset of scleroderma patients.
Effects of soybean meal concentration in lactating sow diets on sow and litter performance and blood criteria1
Authors: Gourley Kiah M , Woodworth Jason C , DeRouchey Joel M , Tokach Mike D , Dritz Steve S , Goodband Robert D 
Published: March 2020

Abstract
A total of 131 sows (Line 241; DNA, Columbus, NE) were used in a study to evaluate the effect of increasing soybean meal concentration in lactating sow diets on sow and litter performance. Sows were blocked by body weight (BW) within parity on day 112 of gestation and allotted to one of three treatments of increasing dietary soybean meal (25%, 30%, or 35% of the total diet). Diets were formulated to 1.05% standardized ileal digestible lysine (Lys) with L-Lys HCl decreasing as soybean meal increased. All other amino acids and nutrients were formulated to meet nutrient requirement recommendations. Diets were fed from day 112 of gestation until weaning (day 20 ± 2). Litters were cross-fostered up to 48 h after farrowing to equalize litter size. Increasing soybean meal concentration increased (linear, P = 0.017) sow BW loss and tended to increase (quadratic, P = 0.052) sow backfat loss from farrowing to weaning. Sow average daily feed intake (ADFI) from day 0 to 7 was similar (P &gt; 0.10) across dietary treatments. However, from day 7 to 14, 14 to weaning, and overall, ADFI decreased (linear, P = 0.01) as soybean meal concentration increased. Despite the linear response in ADFI, the greatest decrease was observed as soybean meal concentration increased from 30% to 35% of the diet. There was no evidence for difference (P &gt; 0.10) in wean-to-estrus interval, litter size, litter weight, or litter weight gain between dietary treatments. Sow serum urea nitrogen concentrations taken on day 14 of lactation increased (linear, P = 0.001) as soybean meal concentration increased. There was no difference (P &gt; 0.05) for sow creatinine concentration, regardless of dietary treatment, suggesting that the increased urea nitrogen was a reflection of the increased dietary crude protein as opposed to increased protein catabolism. In summary, sow feed intake decreased and weight loss increased as soybean meal concentration of the diet increased, with the greatest decrease observed at 35% of the total diet. Although there were no differences in litter performance, it appeared that 35% soybean meal in the lactation diet negatively affected feed intake.
Dairy cows with mild-moderate mastitis change lying behavior in hospital pens
Authors: Herskin Mette S , Fogsgaard Katrine K , Thomsen Peter T , Houe Hans , Forkman Björn , Jensen Margit B 
Published: March 2020

Abstract
In dairy production, mastitis is a major problem affecting animal welfare, productivity, and economy. Hospital pens are typically not used for cows with mastitis, except for severe cases involving recumbency. This field trial included 47 cows from three Danish herds followed for 8 d, of which days 1–5 involved the experimental housing. After day 5, all cows were kept with the lactating group. We examined lying behavior in dairy cows with naturally occurring, mild-moderate mastitis in hospital pens [single or group (depending on conditions on the farm), all with deep straw bedding] vs. sick cows kept in the group of healthy herd mates. Within a herd, every other cow fulfilling the inclusion criteria regarding mastitis was allocated to each of the two experimental treatments. Clinical data from involved cases were collected. No significant differences between housing treatments were found in the clinical variables or the daily lying time. During the period of experimental housing, cows kept in hospital pens showed a higher frequency of lying bouts compared with control cows. This difference did not persist after reintroduction to the lactating herd mates. These results suggest that aspects of lying behavior of dairy cows with mastitis are sensitive to the environment as the frequency of lying bouts differed between cows kept in hospital pens and cows kept in control treatment. More controlled studies are needed to examine underlying motivations and evaluate consequences in terms of animal welfare. For such studies, the inclusion of healthy cows for comparison will be valuable.
Lactobacillus garii sp. nov., isolated from a fermented cassava product
Authors: Diaz Maria , Sayavedra Lizbeth , Atter Amy , Mayer Melinda J. , Saha Shikha , Amoa-Awua Wisdom , Narbad Arjan 
Published: March 2020

A novel Gram-positive, catalase negative, rod-shaped strain, FI11369T, was isolated from gari, a traditional West African fermented food derived from cassava. Based on 16S rRNA gene sequence similarity, the closest type strains were

Lactobacillus xiangfangensis

LMG 26013T (99.4 % similarity),

Lactobacillus plajomi

NBRC 107333T (99.1 %),

Lactobacillus paraplantarum

DSM 10667T (99.1 %),

Lactobacillus pentosus

DSM 20314T (99.0 %),

Lactobacillus plantarum

subsp.

plantarum

ATCC 14917T (99.0 %),

Lactobacillus modestisalitolerans

NBRC 107235T (98.9 %),

Lactobacillus plantarum

subsp.

argentoratensis

DSM 16365T (98.9 %) and

Lactobacillus daowaiensis

NCIMB 15183T (98.8 %). The genome of strain FI11369T was sequenced and the average nucleotide identity (ANI) was compared with its closest relatives. ANI analysis showed that the closest relative,

L. xiangfangensis

DSM 27103T, had only a 82.4 % similarity. The main fatty acids of FI11369T were saturated C16 : 0 (18.2 %), unsaturated C18 : 1
ω9c (43.8 %) and cyclopropane C19 : 0 cyclo (ω10c and/or ω6; 22.5 %). Based on the genotypic and phenotypic data obtained in this study, a novel

Lactobacillus

species,

Lactobacillus garii

sp. nov., with the type strain FI11369T (=NCIMB 15148=DSM 108249), is proposed.
Targeted adaptive isolation strategy for Covid-19 pandemic
Authors: Neufeld Zoltan , Khataee Hamid , Czirok Andras 
Published: March 2020

AbstractWe investigate the effects of social distancing in controlling the impact of the COVID-19 epidemic using a simple susceptible-infected-removed epidemic model. We show that an alternative or complementary approach based on targeted isolation of the vulnerable subpopulation may provide a more efficient and robust strategy at a lower economic and social cost within a shorter timeframe resulting in a collectively immune population.
Contesting the evidence for gene expression in lower oceanic crust
Authors: Orsi William D. 
Published: March 2020

AbstractLiet al[Nature579, 250–255 (2020)] report microbial gene expression in deep ocean crust, from microbial communities that have concentrations as low as 100 cell per cubic cm. This would be incredible, since that would be the lowest biomass sample ever analyzed for gene expression for a deep biosphere sample by several orders of magnitude. However, I have reanalyzed the data and show that the author’s data are derived from contamination via seawater, humans, human skin associated bacteria, drilling fluid, and molecular reagent kits. The method that the authors used to produce their gene expression data is highly sensitive to DNA contamination, which is the case here. The authors claim thatPseudomonas, a known widespread contaminant in molecular reagent kits, is one of the most active groups in their lower crust samples and base their metabolic analysis on this contaminating organism. Here, I show that the gene expression data are derived from contaminatingPseudomonas(as well as other groups), and I show that the groups claimed as being active in the rock samples are also present in the negative controls at similar or higher relative abundance. For example, methane production in long term incubations was reported but gene expression from methanogens was 10 times higher in the drill fluid negative controls compared to the rock samples, demonstrating that the methane measured is likely derived from methanogen contaminants introduced from the drill fluid. There are no signs of active life here, but lipid biomarkers were found preserved in the rocks. Thus, the authors have sampled a fossilized biosphere, not a living one.
The diagnostic evaluation of Convolutional Neural Network (CNN) for the assessment of chest X-ray of patients infected with COVID-19
Authors: Bukhari Syed Usama Khalid , Bukhari Syed Safwan Khalid , Syed Asmara , Shah Syed Sajid Hussain 
Published: March 2020

AbstractIntroductionThe main target of COVID-19 is the lungs where it may cause pneumonia in severely ill patients. Chest X-ray is an important diagnostic test to assess the lung for the damaging effects of COVID-19. Many other microbial pathogens can also cause damage to lungs leading to pneumonia but there are certain radiological features which can favor the diagnosis of pneumonia caused by COVID-19. With the rising number of cases of COVID-19, it would be imperative to develop computer programs which may assist the health professionals in the prevailing scenario.Materials & MethodsA total of two hundred and seventy eight (278) images of chest X-rays have been assessed by applying ResNet-50 convolutional neural network architectures in the present study. The digital images were acquired from the public repositories provided by University of Montreal and National Institutes of Health. These digital images of Chest X-rays were divided into three groups labeled as normal, pneumonia and COVID-19. The third group contains digital images of chest X-rays of patients diagnosed with COVID-19 infection while the second group contains images of lung with pneumonia caused by other pathogens.ResultsThe radiological images included in the data set are 89 images of lungs with COVID-19 infection, 93 images of lungs without any radiological abnormality and 96 images of patient with pneumonia caused by other pathogens. In this data set, 80% of the images were employed for training, and 20% for testing. A pre-trained (on ImageNet data set) ResNet-50 architecture was used to diagnose the cases of COVID-19 infections on lung X-ray images. The analysis of the data revealed that computer vision based program achieved diagnostic accuracy of 98.18 %, and F1-score of 98.19.ConclusionThe performance of convolutional neural network regarding the differentiation of pulmonary changes caused by COVID-19 from the other type of pneumonias on digital images of the chest X-rays is excellent and it may be an extremely useful adjunct tool for the health professionals.
Determination of daily reproduction numbers of SARS-CoV2 based on death cases suggests more rapid initial spread in Italy and the United States
Authors: Ensser Armin , Überla Klaus 
Published: March 2020

Population density, behaviour and cultural habits strongly influence the spread of pathogens. Consequently, key epidemiological parameters may vary from country to country. Confirmed COVID-19 cases in in China have been used to estimate those parameters, that vary largely (reviewed in 1). The estimates also depend on testing frequency and case definitions that are prone to change during ongoing epidemics, providing additional uncertainties. The rise in fatal cases due to SARS-CoV2 could be a more reliable parameter, since missing of deaths is less likely. In the absence of changes in the management of severe COVID-19 cases, the rise in death cases should be proportional to the rise in virus infections. Although the fluctuating low numbers of fatal cases very early in the epidemic may lead to some uncertainty, more than 100 deaths per day are reported since 10.03.2020 in Italy and since 21.03.2020 in the US. Therefore, the dynamics of deaths were analysed to estimate the daily reproduction numbers (Rt) and the effectiveness of control measures.Thus, our analysis provides evidence that basic epidemiological parameters differ between countries to an extent compromising epidemiological predictions of the pandemic. It also suggests that suppression of spread in Italy and the US may be more difficult to achieve. Although we assume that variations in social behaviour are responsible for the different estimates of R0, selection of more rapidly spreading variants of SARS-CoV-2 cannot be excluded. Despite uncertainty in the reliability of the data used and lack of information on possible changes in the effectiveness of registration of COVID-19 deaths during the observation period, our findings should be considered as a working hypothesis demanding further investigations. As the number of deaths rapidly increases worldwide, we encourage more sophisticated modelling of the epidemic based on the dynamics of death cases by experts in the field.
Human keratinocyte (HaCaT) stimulation and healing effect of the methanol fraction from the decoction from leaf fromSideroxylon obtusifolium(Roem. & Schult.) T.D. Penn on experimental burn wound model
Authors: de Fátima Goebel de Souza Tamiris , Pierdoná Taiana Magalhães , Macedo Fernanda Soares , de Aquino Pedro Everson Alexandre , de Fátima Pinheiro Rangel Gisele , Duarte Rebeca Silva , de Barros Viana Glauce Socorro , Alves Ana Paula Negreiros Nunes , Montenegro Raquel Carvalho , Wilke Diego Veras , Silveira Edilberto Rocha , de Alencar Nylane Maria Nunes 
Published: March 2020

AbstractThe larger number of plants, with therapeutic potential, popularly used in Northeastern Brazil is due to their easy access and the great Brazilian biodiversity. Previously, was demonstrated that the methanol fraction fromSideroxylon obtusifolium(MFSOL) promoted an anti-inflammatory and healing activity in excisional wounds. Thus, this work aimed to investigate the healing effects of MFSOL on human keratinocytes cells (HaCaT) and experimental burn model injuries. HaCaT cells were used to investigate migration and proliferation of cell rates. Female Swiss mice were subjected to second-degree superficial burn protocol and divided into four treatment groups: Vehicle (cream-base), 1.0% Silver Sulfadiazine (Sulfa), and 0.5% or 1.0% MFSOL cream (CrMFSOL). Samples were collected for quantification of the inflammatory mediators and histological analyses after 3, 7 and 14 days on evaluation. As result, MFSOL (50 μg/ml) stimulated HaCaT cells by increasing proliferation and migration rates. Moreover, CrMFSOL 0.5% attenuated myeloperoxidase (MPO) activity and also stimulated the release of IL-1β and IL-10, after 3 days with treatment. CrMFSOL 0.5% enhanced wound contraction, promoted tissue remodeling improvement and highest collagen production after 7 days, and VEGF release after 14 days. Therefore, MFSOL evidenced the stimulation of human keratinocyte (HaCaT) cells and improvements on wound healing via inflammatory modulation on burn injuries.
REINDEER: efficient indexing ofk-mer presence and abundance in sequencing datasets
Authors: Marchet Camille , Iqbal Zamin , Gautheret Daniel , Salson Mikael , Chikhi Rayan 
Published: March 2020

AbstractMotivationIn this work we present REINDEER, a novel computational method that performs indexing of sequences and records their abundances across a collection of datasets. To the best of our knowledge, other indexing methods have so far been unable to record abundances efficiently across large datasets.ResultsWe used REINDEER to index the abundances of sequences within 2,585 human RNA-seq experiments in 45 hours using only 56 GB of RAM. This makes REINDEER the first method able to record abundances at the scale of 4 billion distinctk-mers across 2,585 datasets. REINDEER also supports exact presence/absence queries ofk-mers. Briefly, REINDEER constructs the compacted de Bruijn graph (DBG) of each dataset, then conceptually merges those DBGs into a single global one. Then, REINDEER constructs and indexesmonotigs, which in a nutshell are groups ofk-mers of similar abundances.Availabilityhttps://github.com/kamimrcht/REINDEERContactcamille.marchet@univ-lille.fr
Subcortical rather than cortical sources of the frequency-following response (FFR) relate to speech-in-noise perception
Authors: Bidelman Gavin M. , Momtaz Sara 
Published: March 2020

ABSTRACTScalp-recorded frequency-following responses (FFRs) reflect a mixture of phase-locked activity across the auditory pathway. FFRs have been widely used as a neural barometer of complex listening skills, especially speech-in noise (SIN) perception. Applying individually optimized source reconstruction to speech-FFRs recorded via EEG (FFREEG), we assessed the relative contributions of subcortical [auditory nerve (AN), brainstem/midbrain (BS)] and cortical [bilateral primary auditory cortex, PAC] source generators with the aim of identifying which source(s) drive the brain-behavior relation between FFRs and SIN listening skills. We found FFR strength declined precipitously from AN to PAC, consistent with diminishing phase-locking along the ascending auditory neuroaxis. FFRs to the speech fundamental (F0) were robust to noise across sources, but were largest in subcortical sources (BS > AN > PAC). PAC FFRs were only weakly observed above the noise floor and only at the low pitch of speech (F0≈100 Hz). Brain-behavior regressions revealed (i) AN and BS FFRs were sufficient to describe listeners’ QuickSIN scores and (ii) contrary to neuromagnetic (MEG) FFRs, neither left nor right PAC FFREEGpredicted SIN performance. Our preliminary findings suggest subcortical sources not only dominate the electrical FFR but also the link between speech-FFRs and SIN processing as observed in previous EEG studies.