bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular determinants of surface colonisation in diarrhoeagenicEscherichia coli(DEC): from bacterial adhesion to biofilm formation
Authors: Ageorges Valentin , Monteiro Ricardo , Leroy Sabine , Burgess Catherine M , Pizza Mariagrazia , Chaucheyras-durand Frédérique , Desvaux Mickaël
Published: March 2020

Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.
Novel Prognostic Biomarkers of Mucosal Healing in Ulcerative Colitis Patients Treated With Anti-TNF: Neutrophil-to-Lymphocyte Ratio and Platelet-to-Lymphocyte Ratio
Authors: Bertani Lorenzo , Rossari Federico , Barberio Brigida , Demarzo Maria Giulia , Tapete Gherardo , Albano Eleonora , Baiano Svizzero Giovanni , Ceccarelli Linda , Mumolo Maria Gloria , Brombin Chiara , de Bortoli Nicola , Bellini Massimo , Marchi Santino , Bodini Giorgia , Savarino Edoardo , Costa Francesco
Published: March 2020

Background

Anti-tumor necrosis factor drugs (anti-TNFs) are widely used for the treatment of ulcerative colitis (UC). However, many patients experience loss of response during the first year of therapy. An early predictor of clinical remission and mucosal healing is needed. The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are markers of subclinical inflammation poorly evaluated in UC patients treated with anti-TNFs. The aim of this multicenter study was to evaluate whether NLR and PLR could be used as prognostic markers of anti-TNF treatment response.

Methods

Patients with UC who started anti-TNF treatment in monotherapy were evaluated. Patients with concomitant corticosteroid treatment ≥20 mg were excluded. We calculated NLR, PLR, and fecal calprotectin before treatment and after induction. The values of NLR and PLR were correlated with clinical remission and mucosal healing at the end of follow-up (54 weeks) using the Mann-Whitney U test and then multivariate analysis was conducted.

Results

Eighty-eight patients were included. Patients who reached mucosal healing after 54 weeks of therapy displayed lower levels of both baseline NLR and PLR (P = 0.0001 and P = 0.04, respectively); similar results were obtained at week 8 (P = 0.0001 and P = 0.001, respectively). Patients who presented with active ulcers at baseline endoscopic evaluation had higher baseline NLR and PLR values compared with those without detected ulcers (P = 0.002 and P = 0.0007, respectively).

Conclusions

BothNLR and PLR showed a promising role as early predictors of therapeutic response to anti-TNF therapy in UC patients. If confirmed in larger studies, classification and regression trees proposed in this article could be useful to guide clinical decisions regarding anti-TNF treatment.
Premobilization of CD133+ progenitors is associated with attenuated inflammation-induced pulmonary dysfunction following extracorporeal circulation in mice
Authors: Luo Dan , Liu Xinhao , Zhang Jie , Du Lei , Bai Lin , Luo Shuhua
Published: March 2020

OBJECTIVES

Progenitor cells mobilized by granulocyte colony-stimulating factor (G-CSF) have been shown to lessen acute kidney injury induced by extracorporeal circulation (ECC). Both acute kidney injury and lung injury are characterized by endothelial dysfunction. Our goal was to examine whether and how G-CSF-mobilized progenitors with endothelial capacity may help mitigate ECC-induced pulmonary dysfunction.

METHODS

G-CSF (10 μg/kg/day) was administered subcutaneously to C57BL/6 mice before or at the initiation of the ECC process, after which lung injury was assessed by measuring neutrophils in the fluid from bronchoalveolar lavage and determining the pathological score in lung tissue. CD133+ progenitors were isolated and injected into C57BL/6 mice before ECC in vivo. We incubated the CD133+ cells with pulmonary monocytes or neutrophils isolated from naïve mice in vitro.

RESULTS

Pretreatment with G-CSF for 2 days significantly decreased the number of neutrophils in the bronchoalveolar lavage fluid, and the pathological score (P < 0.01; n = 5) improved the PaO2/FiO2 ratio [193.4 ± 12.7 (ECC without G-CSF) vs 305.6 ± 22.6 mmHg (ECC with G-CSF); P = 0.03, n = 5] and suppressed neutrophil elastase and tumour necrosis factor-α levels in the circulation; we also observed increases in both circulating and pulmonary populations of CD133+ progenitors. Similar effects were observed in animals pretreated with CD133+ progenitors instead of G-CSF before ECC. The majority of CD133+/CD45− and CD133+/CD45+ progenitors were mobilized in the lung and in the circulation, respectively. Incubating CD133+ progenitors with neutrophils or pulmonary monocytes blocked lipopolysaccharide-induced release of inflammatory factors.

CONCLUSIONS

Our results suggest that pretreatment of G-CSF attenuates ECC-induced pulmonary dysfunction through inhibiting the inflammatory response in lung tissue and in the circulation with associated premobilization of CD133+ progenitors.
Citrullinated fibrinogen is a target of auto-antibodies in interstitial lung disease in mice with collagen-induced arthritis
Authors: Sato Tomomi , Satooka Hiroki , Ichioka Satoko , Maruo Yoshihiro , Hirata Takako
Published: March 2020

Interstitial lung disease (ILD) is a very common and lethal complication of rheumatoid arthritis (RA), yet its pathogenesis is not well understood, in part due to the lack of adequate animal models. Although collagen-induced arthritis (CIA) is the most widely used animal model for RA, the lung involvement occurring in this model has scarcely been studied. To evaluate the suitability of CIA as a model for RA-associated ILD (RA-ILD), we immunized DBA/1 mice with bovine type II collagen and characterized lung disease in this model. Histologic analyses revealed patchy interstitial infiltration of inflammatory cells in the peripheral regions of the lung, notably in the subpleural region, in mice with CIA. This pattern resembled usual interstitial pneumonia in humans, which is the most prevalent pattern in RA-ILD. Among infiltrates in the lung, CD11bhi macrophages of the M2 phenotype were most prominently increased. IgG and C3 were deposited in the subpleural region where inflammatory cells infiltrated. The sera from CIA mice contained auto-antibodies against citrullinated proteins, which are specific and predictive markers for RA. Protein citrullination was enhanced in the lung of CIA mice compared with naive mice, and citrullinated fibrinogen was primarily targeted by these auto-antibodies. The elevation of auto-antibodies against citrullinated proteins and their deposition in the lung with patchy subpleural preponderance suggest that CIA can serve as a model to study the pathogenesis of RA-ILD.
Problems with the problem list: challenges of transparency in an era of patient curation
Authors: Porter Amy S , O’Callaghan Jolene , Englund Kristin A , Lorenz Robert R , Kodish Eric
Published: March 2020

In recent years, the OpenNotes movement and other changes in healthcare have driven institutions to make medical records increasingly transparent. As patients have begun to question and request changes to their Problem Lists, clinicians have come to face the ever more frequent challenge of discerning which changes to make and which to refuse. Now clinicians and patients together choose the list of problems that represent the patient’s current state of health and illness. As the physician’s role slides closer to consultant and the medical paternalism of the twentieth century falls further into the background of our technology-infused present, who holds the power of delineating a patient’s clinical identity? This paper examines the ethical and practical dimensions of this question and proposes a research agenda that aims to answer it. Such explorations are essential to ensuring that the physician remains relevant to patient’s notions of health, illness, intervention, and healing.
Discovery of a retrogradely rotating neutron star in the X-ray pulsar GX 301–2
Authors: Mönkkönen Juhani , Doroshenko Victor , Tsygankov Sergey S , Nabizadeh Armin , Abolmasov Pavel , Poutanen Juri
Published: March 2020

We report on the analysis of the spin evolution of a slow X-ray pulsar GX 301–2 along the orbit using long-term monitoring by Fermi/Gamma-ray Burst Monitor. Based on the observationally confirmed accretion scenario and an analytical model for the accretion of angular momentum, we demonstrate that in this system, the neutron star spins retrogradely, that is, in a direction opposite to the orbital motion. This first-of-a-kind discovery of such a system proves the principal possibility of retrograde rotation in accreting systems with suitable accretion torque, and might have profound consequences for our understanding of the spin evolution of X-ray pulsars, estimates of their initial spin periods, and the ultimate result of their evolution.
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

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 < 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

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

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

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 > 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 > 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 > 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

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.
Phytophthora nicotianae Infection of Citrus Leaves and Host Defense Activation Compared to Root Infection
Authors: Wu Jian , Handique Utpal , Graham James , Johnson Evan
Published: March 2020

Currently, little is known about the host pathogen interaction between Phytophthora spp. and citrus roots versus leaves. Therefore, we compared the molecular events occurring in citrus roots and leaves after zoospore inoculation with Phytophthora nicotianae. We analyzed the physical characteristics and genetic responses to P. nicotianae infection of leaves and roots for susceptible and tolerant citrus rootstocks to examine the potential for leaves to model root responses to P. nicotianae infection. Leaves responded faster and stronger to P. nicotianae infection than roots, and leaves showed greater differential response than roots. In addition to differences in hormonal responses, sugar, phospholipase D (PLD), and phospholipase A (PLA) involvement in the interaction between citrus and P. nicotianae was identified. This work, for the first time, creates a solid P. nicotianae zoospore infection protocol, reports P. nicotianae infection on citrus leaves through stomata, and provides evidence that different host organs respond to the pathogen differentially in timing and magnitude. This work identifies the hormones, sugars, pathogenesis-related genes, PLDs, and PLAs that are involved in the molecular events occurring in citrus under infection of P. nicotianae zoospore, and advances our understanding of the mechanisms underlying the interaction.
Identifying drivers of forest resilience in long-term records from the Neotropics
Authors: Adolf C. , Tovar C. , Kühn N. , Behling H. , Berrío J. C. , Dominguez-Vázquez G. , Figueroa-Rangel B. , Gonzalez-Carranza Z. , Islebe G. A. , Hooghiemstra H. , Neff H. , Olvera-Vargas M. , Whitney B. , Wooller M. J. , Willis K. J.
Published: March 2020

Here, we use 30 long-term, high-resolution palaeoecological records from Mexico, Central and South America to address two hypotheses regarding possible drivers of resilience in tropical forests as measured in terms of recovery rates from previous disturbances. First, we hypothesize that faster recovery rates are associated with regions of higher biodiversity, as suggested by the insurance hypothesis. And second, that resilience is due to intrinsic abiotic factors that are location specific, thus regions presently displaying resilience in terms of persistence to current climatic disturbances should also show higher recovery rates in the past. To test these hypotheses, we applied a threshold approach to identify past disturbances to forests within each sequence. We then compared the recovery rates to these events with pollen richness before the event. We also compared recovery rates of each site with a measure of present resilience in the region as demonstrated by measuring global vegetation persistence to climatic perturbations using satellite imagery. Preliminary results indeed show a positive relationship between pre-disturbance taxonomic richness and faster recovery rates. However, there is less evidence to support the concept that resilience is intrinsic to a region; patterns of resilience apparent in ecosystems presently are not necessarily conservative through time.
Evaluation of scaffold microstructure and comparison of cell seeding methods using micro-computed tomography-based tools
Authors: Palmroth Aleksi , Pitkänen Sanna , Hannula Markus , Paakinaho Kaarlo , Hyttinen Jari , Miettinen Susanna , Kellomäki Minna
Published: March 2020

Micro-computed tomography (micro-CT) provides a means to analyse and model three-dimensional (3D) tissue engineering scaffolds. This study proposes a set of micro-CT-based tools firstly for evaluating the microstructure of scaffolds and secondly for comparing different cell seeding methods. The pore size, porosity and pore interconnectivity of supercritical CO
2
processed poly(
l
-lactide-co-
ɛ
-caprolactone) (PLCL) and PLCL/β-tricalcium phosphate scaffolds were analysed using computational micro-CT models. The models were supplemented with an experimental method, where iron-labelled microspheres were seeded into the scaffolds and micro-CT imaged to assess their infiltration into the scaffolds. After examining the scaffold architecture, human adipose-derived stem cells (hASCs) were seeded into the scaffolds using five different cell seeding methods. Cell viability, number and 3D distribution were evaluated. The distribution of the cells was analysed using micro-CT by labelling the hASCs with ultrasmall paramagnetic iron oxide nanoparticles. Among the tested seeding methods, a forced fluid flow-based technique resulted in an enhanced cell infiltration throughout the scaffolds compared with static seeding. The current study provides an excellent set of tools for the development of scaffolds and for the design of 3D cell culture experiments.
Antarctic petrels ‘on the ice rocks’: wintering strategy of an Antarctic seabird
Authors: Delord K. , Kato A. , Tarroux A. , Orgeret F. , Cotté C. , Ropert-Coudert Y. , Cherel Y. , Descamps S.
Published: March 2020

There is a paucity of information on the foraging ecology, especially individual use of sea-ice features and icebergs, over the non-breeding season in many seabird species. Using geolocators and stable isotopes, we defined the movements, distribution and diet of adult Antarctic petrels
Thalassoica antarctica
from the largest known breeding colony, the inland Svarthamaren, Antarctica. More specifically, we examined how sea-ice concentration and free-drifting icebergs affect the distribution of Antarctic petrels. After breeding, birds moved north to the marginal ice zone (MIZ) in the Weddell sector of the Southern Ocean, following its northward extension during freeze-up in April, and they wintered there in April–August. There, the birds stayed predominantly out of the water (60–80% of the time) suggesting they use icebergs as platforms to stand on and/or to rest. Feather δ
15
N values encompassed one full trophic level, indicating that birds fed on various proportions of crustaceans and fish/squid, most likely Antarctic krill
Euphausia superba
and the myctophid fish
Electrona antarctica
and/or the squid
Psychroteuthis glacialis
. Birds showed strong affinity for the open waters of the northern boundary of the MIZ, an important iceberg transit area, which offers roosting opportunities and rich prey fields. The strong association of Antarctic petrels with sea-ice cycle and icebergs suggests the species can serve, year-round, as a sentinel of environmental changes for this remote region.
Intestinal microbes: an axis of functional diversity among large marine consumers
Authors: Scott Jarrod J. , Adam Thomas C. , Duran Alain , Burkepile Deron E. , Rasher Douglas B.
Published: March 2020

Microbes are ubiquitous throughout the world's oceans, yet the manner and extent of their influence on the ecology and evolution of large, mobile fauna remains poorly understood. Here, we establish the intestinal microbiome as a hidden, and potentially important, ‘functional trait’ of tropical herbivorous fishes—a group of large consumers critical to coral reef resilience. Using field observations, we demonstrate that five common Caribbean fish species display marked differences in where they feed and what they feed on. However, in addition to space use and feeding behaviour—two commonly measured functional traits—we find that interspecific trait differences are even more pronounced when considering the herbivore intestinal microbiome. Microbiome composition was highly species specific. Phylogenetic comparison of the dominant microbiome members to all known microbial taxa suggest that microbiomes are comprised of putative environmental generalists, animal-associates and fish specialists (resident symbionts), the latter of which mapped onto host phylogeny. These putative symbionts are most similar to—among all known microbes—those that occupy the intestines of ecologically and evolutionarily related herbivorous fishes in more distant ocean basins. Our findings therefore suggest that the intestinal microbiome may be an important functional trait among these large-bodied consumers.
Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov.
Authors: Albuquerque Luciana , Castelhano Nadine , Raposo Pedro , Froufe Hugo J. C. , Tiago Igor , Severino Rita , Roxo Inês , Gregório Inês , Barroso Cristina , Egas Conceição , da Costa Milton S.
Published: March 2020

We performed high-quality genome sequencing of eight strains of the species of the genus

Tepidimonas

and examined the genomes of closely related strains from the databases to understand why

Tepidimonas taiwanensis

is the only strain of this genus that utilizes glucose and fructose for growth. We found that the assimilation of these hexoses by

T. taiwanensis

was due to the presence of two transporters that are absent in all other genomes of strains of members of the genus

Tepidimonas

examined. Some strains lack genes coding for glucokinase, but the Embden–Meyerhof–Parnas pathway appears to be otherwise complete. The pentose phosphate pathway has a complete set of genes, but genes of the Entner–Doudoroff pathway were not identified in the genomes of any of the strains examined. Genome analysis using average nucleotide identity (ANIb), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI) and phylogenetic analysis of 400 conserved genes was performed to assess the taxonomic classification of the organisms. Two isolates of the genus

Tepidimonas

from the hot spring at São Pedro do Sul, Portugal, designated SPSP-6T and SPSPC-18 were also examined in this study. These organisms are mixotrophic, have an optimum growth temperature of about 50 ºC, utilize several organic acids and amino acids for growth but do not grow on sugars. Distinctive phenotypic, 16S rRNA gene sequence and genomic characteristics of strains SPSP-6T and SPSPC-18 lead us to propose a novel species based on strain SPSP-6T for which we recommend the name Tepidimonas charontis sp. nov. (=CECT 9683T=LMG 30884T).
Proposal to reclassify Leptotrichia goodfellowii into a novel genus as Pseudoleptotrichia goodfellowii gen. nov., comb. nov.
Authors: Eisenberg Tobias , Glaeser Stefanie P. , Blom Jochen , Kämpfer Peter
Published: March 2020

The reclassification of

Leptotrichia goodfellowii

as Pseudoleptotrichia goodfellowii gen. nov., comb. nov. is proposed because of the separate phylogenetic position on the basis of the results of 16S rRNA gene sequence analysis, the genomic differences from all other

Leptotrichia

species and phenotypic differences from

Leptotrichia

species. The species Pseudoleptotrichia goodfellowii is the type species of the genus. The type strain is LB 57T, CCUG 32286 T, DSM 19756T.
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

We 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

Liet 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

Introduction

The 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 & Methods

A 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.

Results

The 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.

Conclusion

The 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

The 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

Motivation

In 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.

Results

We 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.

Availability

https://github.com/kamimrcht/REINDEER

Contact

camille.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

Scalp-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.
Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020
Authors: Byass Peter
Published: March 2020

Background

The outbreak of COVID-19 in China in early 2020 provides a rich data source for exploring the ecological determinants of this new infection, which may be of relevance elsewhere.

Objectives

Assessing the spread of the COVID-19 across China, in relation to associations between cases and ecological factors including population density, temperature, solar radiation and precipitation.

Methods

Open-access COVID-19 case data include 18,069 geo-located cases in China during January and February 2020, which were mapped onto a 0.25° latitude/longitude grid together with population and weather data (temperature, solar radiation and precipitation). Of 15,539 grid cells, 559 (3.6%) contained at least one case, and these were used to construct a Poisson regression model of cell-weeks. Weather parameters were taken for the preceding week given the established 5-7 day incubation period for COVID-19. The dependent variable in the Poisson model was incident cases per cell-week and exposure was cell population, allowing for clustering of cells over weeks, to give incidence rate ratios.

Results

The overall COVID-19 incidence rate in cells with confirmed cases was 0.12 per 1,000. There was a single case in 113/559 (20.2%) of cells, while two grid cells recorded over 1,000 cases. Weekly means of maximum daily temperature varied from −28.0 to 30.1 °C, minimum daily temperature from −42.4 to 23.0 °C, maximum solar radiation from 0.04 to 2.74 MJm−2 and total precipitation from 0 to 72.6 mm. Adjusted incidence rate ratios suggested brighter, warmer and drier conditions were associated with lower incidence.

Conclusion

Though not demonstrating cause and effect, there were appreciable associations between weather and COVID-19 incidence during the epidemic in China. This does not mean the pandemic will go away with summer weather but demonstrates the importance of using weather conditions in understanding and forecasting the spread of COVID-19.
Access to Scientific Literature by the Conservation Community
Authors: Larios Daisy , Brooks Thomas M. , Macfarlane Nicholas B.W. , Roy Sugoto
Published: March 2020

Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find itnot easyornot at all easyto access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and gender (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work wereConservation Biology, Biological Conservation, Nature, andScience. The majority prefer to read journal articles on screen but prefer to read books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.