bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fecal Microbiota Alterations Associated With Clinical and Endoscopic Response to Infliximab Therapy in Crohn’s Disease
Authors: Zhuang Xiaojun , Tian Zhenyi , Feng Rui , Li Manying , Li Tong , Zhou Gaoshi , Qiu Yun , Chen Baili , He Yao , Chen Minhu , Zeng Zhirong , Zhang Shenghong 
Published: October 2020

Abstract

Background
Gut microbiota dysbiosis is associated with the occurrence and development of Crohn disease (CD). Currently, infliximab (IFX) is used more and more to treat CD; however, gut microbiota alterations during IFX therapy are variable and sometimes even contradictory. We longitudinally identified microbial changes during IFX therapy associated with the clinical and endoscopic response to IFX treatment in CD.

Methods
Fecal-associated microbiota was analyzed using 16S sequencing in 49 patients with active CD who were prospectively recruited at baseline, week 6, and week 30, respectively. Moreover, a model trained on the gut microbiota alterations at week 6 was developed to investigate their potential to predict clinical and endoscopic responses to IFX therapy at weeks 14 and 30.

Results
Characteristics of fecal microbiota composition in patients with CD after IFX treatment displayed an increased diversity and richness, a significant gain in short-chain fatty acid -producing bacteria, and a loss of pathogenic bacteria. Furthermore, certain functional profiles of Kyoto Encyclopedia of Genes and Genomes pathways were predictably altered during the treatment period. Increased proportions of Lachnospiraceae and Blautia were associated with IFX efficacy; the combined increase of these taxa at week 6 showed 83.4% and 84.2% accuracy in predicting clinical response at weeks 14 and 30, respectively, with a predictive value of 89.1% in predicting endoscopic response at week 30.

Conclusions
We found that IFX diminished CD-related gut microbial dysbiosis by modifying microbiota composition and function. Specifically, increased Lachnospiraceae and Blautia at week 6 are associated with the clinical and endoscopic response to IFX, providing potentially predictive biomarkers for IFX treatment decision-making.
Solving multiobjective optimal control problems using an improved scalarization method
Authors: Askarirobati Gholam Hosein , Borzabadi Akbar Hashemi , Heydari Aghileh 
Published: October 2020

Abstract
Detecting the Pareto optimal points on the Pareto frontier is one of the most important topics in multiobjective optimal control problems (MOCPs). This paper presents a scalarization technique to construct an approximate Pareto frontier of MOCPs, using an improved normal boundary intersection (NBI) scalarization strategy. For this purpose, MOCP is first discretized and then using a grid of weights, a sequence of single objective optimal control problems is solved to achieve a uniform distribution of Pareto optimal solutions on the Pareto frontier. The aim is to achieve a more even distribution of Pareto optimal solutions on the Pareto frontier and improve the efficiency of the algorithm. It is shown that in contrast to the NBI method, where Pareto optimality of solutions is not guaranteed, the obtained optimal solution of the scalarized problem is a Pareto optimal solution of the MOCP. Finally, the ability of the proposed method is evaluated and compared with other approaches using several practical MOCPs. The numerical results indicate that the proposed method is more efficient and provides more uniform distribution of solutions on the Pareto frontier than the other methods, such a weighted sum, normalized normal constraint and NBI.
Necrotizing Enterocolitis and the Microbiome: Current Status and Future Directions
Authors: Thänert Robert , Keen Eric C , Dantas Gautam , Warner Barbara B , Tarr Phillip I 
Published: October 2020

Abstract
Decades of research have failed to define the pathophysiology of necrotizing enterocolitis (NEC), a devastating pediatric gastrointestinal disorder of preterm infants. However, evidence suggests that host-microbiota interactions, in which microbial dysbiosis is followed by loss of barrier integrity, inflammation, and necrosis, are central to NEC development. Thus, greater knowledge of the preterm infant microbiome could accelerate attempts to diagnose, treat, and prevent NEC. In this article, we summarize clinical characteristics of and risk factors for NEC, the structure of the pre-event NEC microbiome, how this community interfaces with host immunology, and microbiome-based approaches that might prevent or lessen the severity of NEC in this very vulnerable population.
No Changes in Human Immunodeficiency Virus (HIV) Suppression and Inflammatory Markers in Cerebrospinal Fluid in Patients Randomly Switched to Dolutegravir Plus Lamivudine (Spanish HIV/AIDS Research Network, PreEC/RIS 62)
Authors: Tiraboschi Juan M , Rojas Jhon , Zetterberg Henrik , Blennow Kaj , Niubo Jordi , Gostner Johanna , Navarro-Alcaraz Antonio , Piatti Camila , Fuchs Dietmar , Gisslén Magnus , Rigo-Bonnin Raul , Martinez Esteban , Podzamczer Daniel 
Published: October 2020

Abstract
A major concern of human immunodeficiency virus (HIV) dual therapy is a potentially lower efficacy in viral reservoirs, especially in the central nervous system (CNS). We evaluated HIV RNA, neuronal injury, and inflammatory biomarkers and dolutegravir (DTG) exposure in cerebrospinal fluid (CSF) in patients switching to DTG plus lamivudine (3TC). All participants maintained viral suppression in plasma and CSF at week 48. We observed no increase in CSF markers of inflammation or neuronal injury. Median (interquartile range) total and unbound DTG in CSF were 7.3 (5.9–8.4) and 1.7 (1.2–1.9) ng/mL, respectively. DTG+3TC may maintain viral control without changes in inflammatory/injury markers within the CNS reservoir.
Complement Activation in the Disease Course of Coronavirus Disease 2019 and Its Effects on Clinical Outcomes
Authors: de Nooijer Aline H , Grondman Inge , Janssen Nico A F , Netea Mihai G , Willems Loek , van de Veerdonk Frank L , Giamarellos-Bourboulis Evangelos J , Toonen Erik J M , Joosten Leo A B ,   RCI-COVID-19 study group, Jaeger Martin , Dijkstra Helga , Lemmers Heidi , van Emst Liesbeth , Schraa Kiki , Jacobs Cor , Hijmans Anneke , Jansen Trees , Weren Fieke , Fransman Liz , Gerretsen Jelle , van de Maat Josephine , Nijman Gerine , Moorlag Simone , Taks Esther , Debisarun Priya , Kouijzer Ilse , Wertheim Heiman , Hopman Joost , Rahamat-Langendoen Janette , Bleeker-Rovers Chantal , ten Oever Jaap , van Crevel Reinout , Hoogerwerf Jacobien , de Mast Quirijn , van der Hoeven Hans , Pickkers Peter , Kox Matthijs , Frenzel Tim , Schouten Jeroen , Hemelaar Pleun , Beunders Remi , van der Velde Sjef , Kooistra Emma , Waalders Nicole , Claassen Wout , Heesakkers Hidde , van Schaik Tirsa , van der Eng Hetty , Rovers Noortje , Klop-Riehl Margreet 
Published: October 2020

Abstract

Background
Excessive activation of immune responses in coronavirus disease 2019 (COVID-19) is considered to be related to disease severity, complications, and mortality rate. The complement system is an important component of innate immunity and can stimulate inflammation, but its role in COVID-19 is unknown.

Methods
A prospective, longitudinal, single center study was performed in hospitalized patients with COVID-19. Plasma concentrations of complement factors C3a, C3c, and terminal complement complex (TCC) were assessed at baseline and during hospital admission. In parallel, routine laboratory and clinical parameters were collected from medical files and analyzed.

Results
Complement factors C3a, C3c, and TCC were significantly increased in plasma of patients with COVID-19 compared with healthy controls (P &lt; .05). These complement factors were especially elevated in intensive care unit patients during the entire disease course (P &lt; .005 for C3a and TCC). More intense complement activation was observed in patients who died and in those with thromboembolic events.

Conclusions
Patients with COVID-19 demonstrate activation of the complement system, which is related to disease severity. This pathway may be involved in the dysregulated proinflammatory response associated with increased mortality rate and thromboembolic complications. Components of the complement system might have potential as prognostic markers for disease severity and as therapeutic targets in COVID-19.
Low Inducibility of Latent Human Immunodeficiency Virus Type 1 Proviruses as a Major Barrier to Cure
Authors: Siliciano Janet D , Siliciano Robert F 
Published: October 2020

Abstract
The latent reservoir for human immunodeficiency virus type 1 (HIV-1) in resting CD4+ T cells is a major barrier to cure. The dimensions of the reservoir problem can be defined with 2 assays. A definitive minimal estimate of the frequency of latently infected cells is provided by the quantitative viral outgrowth assay (QVOA), which detects cells that can be induced by T-cell activation to release infectious virus. In contrast, the intact proviral DNA assay (IPDA) detects all genetically intact proviruses and provides a more accurate upper limit on reservoir size than standard single-amplicon polymerase chain reaction assays which mainly detect defective proviruses. The frequency of cells capable of initiating viral rebound on interruption of antiretroviral therapy lies between the values produced by the QVOA and the IPDA. We argue here that the 1–2-log difference between QVOA and IPDA values in part reflects that the fact that many replication-competent proviruses are not readily induced by T-cell activation. Findings of earlier studies suggest that latently infected cells can be activated to proliferate in vivo without expressing viral genes. The proliferating cells nevertheless retain the ability to produce virus on subsequent stimulation. The low inducibility of latent proviruses is a major problem for the shock-and-kill strategy for curing HIV-1 infection, which uses latency-reversing agents to induce viral gene expression and render infected cells susceptible to immune clearance. The latency-reversing agents developed to date are much less effective at reversing latency than T-cell activation. Taken together, these results indicate that HIV-1 eradication will require the discovery of much more effective ways to induce viral gene expression.
Singular patterns of skull shape and brain size change in the domestication of South American camelids
Authors: Balcarcel A M , Sánchez-Villagra M R , Segura V , Evin A 
Published: October 2020

AbstractPatterns of selection in South American camelids (Lamini) and their unique demographic history establish the llama and alpaca as remarkable cases of domestication among large herd animals. Skull shape is implicated in many changes reported between wild and domestic taxa. We apply 3D geometric morphometric methods to describe skull shape, form, and size, differences among the four species of Lamini. In so doing, we test if domesticated Lamini exhibit changes similar to those in other domesticated groups: not only in the skull, but also in brain and body size. In contrast to other domesticated artiodactyls, very little change has occurred in domestic alpacas and llamas compared to their wild counterparts. Nevertheless, their differences are statistically significant and include a flatter cranium, inclined palate and increased airorhynchy in the domestics. Selection pressures that contrast with those on other herd animals, as well as recent population bottlenecks, likely have influenced the morphological patterns we note in Lamini. High-resolution 3D morphospace allows skull size, shape, and form (shape + size), to discriminate all four species, with form providing the greatest separation. These results help differentiate morphologically the Lamini, which in nature are distinguished mainly by body size, and provide an additional tool to archaeologists for distinction of wild and domestic remains. Most of our shape analyses suggest a marginally closer relationship between the alpaca and vicuña, to the exclusion of the guanaco, supporting the genetic relationships for this group. The expected brain size change between wild and domestic populations is lower than previously thought, with a 15.4% reduction in llama, and 6.8% reduction in alpaca. This is the lowest reduction in brain size thus far reported among domesticated Artiodactyla.
High-resolution spectroscopy of SN 2017hcc and its blueshifted line profiles from post-shock dust formation
Authors: Smith Nathan , Andrews Jennifer E 
Published: October 2020

ABSTRACT
SN 2017hcc was remarkable for being a nearby and strongly polarized superluminous Type IIn supernova (SN). We obtained high-resolution Echelle spectra that we combine with other spectra to investigate its line-profile evolution. All epochs reveal narrow P Cygni components from pre-shock circumstellar material (CSM), indicating an axisymmetric outflow from the progenitor of 40–50 km s−1. Broad and intermediate-width components exhibit the classic evolution seen in luminous SNe IIn: symmetric Lorentzian profiles from pre-shock CSM lines broadened by electron scattering at early times, transitioning at late times to multicomponent, irregular profiles coming from the SN ejecta and post-shock shell. As in many SNe IIn, profiles show a progressively increasing blueshift, with a clear flux deficit in red wings of the intermediate and broad velocity components after day 200. This blueshift develops after the continuum luminosity fades, and in the intermediate-width component, persists at late times even after the SN ejecta fade. In SN 2017hcc, the blueshift cannot be explained as occultation by the SN photosphere, pre-shock acceleration of CSM, or a lopsided explosion of CSM. Instead, the blueshift arises from dust formation in the post-shock shell and in the SN ejecta. The effect has a wavelength dependence characteristic of dust, exhibiting an extinction law consistent with large grains. Thus, SN 2017hcc experienced post-shock dust formation and had a mildly bipolar CSM shell, similar to SN 2010jl. Like other superluminous SNe IIn, the progenitor lost around 10 M⊙ due to extreme eruptive mass-loss in the decade before exploding.
Superfluid vortex-mediated mutual friction in non-homogeneous neutron star interiors
Authors: Antonelli M , Haskell B 
Published: October 2020

ABSTRACT
Understanding the average motion of a multitude of superfluid vortices in the interior of a neutron star is a key ingredient for most theories of pulsar glitches. In this paper, we propose a kinetic approach to compute the mutual friction force that is responsible for the momentum exchange between the normal and superfluid components in a neutron star, where the mutual friction is extracted from a suitable average over the motion of many vortex lines. As a first step towards a better modelling of the repinning and depinning processes of many vortex lines in a neutron star, we consider here only straight and non-interacting vortices: we adopt a minimal model for the dynamics of an ensemble of point vortices in two dimensions immersed in a non-homogeneous medium that acts as a pinning landscape. Since the degree of disorder in the inner crust or outer core of a neutron star is unknown, we compare the two possible scenarios of periodic and disordered pinscapes. This approach allows us to extract the mutual friction between the superfluid and the normal component in the star when, in addition to the usual Magnus and drag forces acting on vortex lines, also a pinning force is at work. The effect of disorder on the depinning transition is also discussed.
Eta carinae and the homunculus: far infrared/submillimetre spectral lines detected with the Herschel Space Observatory
Authors: Gull T R , Morris P W , Black J H , Nielsen K E , Barlow M J , Royer P , Swinyard B M 
Published: October 2020

ABSTRACT
The evolved massive binary star η Carinae underwent eruptive mass-loss events that formed the complex bi-polar ‘Homunculus’ nebula harbouring tens of solar masses of unusually nitrogen-rich gas and dust. Despite expectations for the presence of a significant molecular component to the gas, detections have been observationally challenged by limited access to the far-infrared and the intense thermal continuum. A spectral survey of the atomic and rotational molecular transitions was carried out with the Herschel Space Observatory, revealing a rich spectrum of broad emission lines originating in the ejecta. Velocity profiles of selected PACS lines correlate well with known substructures: H i in the central core; NH and weak [C ii] within the Homunculus; and [N ii] emissions in fast-moving structures external to the Homunculus. We have identified transitions from [O i], H i, and 18 separate light C- and O-bearing molecules including CO, CH, CH+, and OH, and a wide set of N-bearing molecules: NH, NH+, N2H+, NH2, NH3, HCN, HNC, CN, and N2H+. Half of these are new detections unprecedented for any early-type massive star environment. A very low ratio [12C/13C] ≤ 4 is estimated from five molecules and their isotopologues. We demonstrate that non-LTE effects due to the strong continuum are significant. Abundance patterns are consistent with line formation in regions of carbon and oxygen depletions with nitrogen enhancements, reflecting an evolved state of the erupting star with efficient transport of CNO-processed material to the outer layers. The results offer many opportunities for further observational and theoretical investigations of the molecular chemistry under extreme physical and chemical conditions around massive stars in their final stages of evolution.
Ensembl 2021
Authors: Howe Kevin L , Achuthan Premanand , Allen James , Allen Jamie , Alvarez-Jarreta Jorge , Amode M Ridwan , Armean Irina M , Azov Andrey G , Bennett Ruth , Bhai Jyothish , Billis Konstantinos , Boddu Sanjay , Charkhchi Mehrnaz , Cummins Carla , Da Rin Fioretto Luca , Davidson Claire , Dodiya Kamalkumar , El Houdaigui Bilal , Fatima Reham , Gall Astrid , Garcia Giron Carlos , Grego Tiago , Guijarro-Clarke Cristina , Haggerty Leanne , Hemrom Anmol , Hourlier Thibaut , Izuogu Osagie G , Juettemann Thomas , Kaikala Vinay , Kay Mike , Lavidas Ilias , Le Tuan , Lemos Diana , Gonzalez Martinez Jose , Marugán José Carlos , Maurel Thomas , McMahon Aoife C , Mohanan Shamika , Moore Benjamin , Muffato Matthieu , Oheh Denye N , Paraschas Dimitrios , Parker Anne , Parton Andrew , Prosovetskaia Irina , Sakthivel Manoj P , Salam Ahamed I Abdul , Schmitt Bianca M , Schuilenburg Helen , Sheppard Dan , Steed Emily , Szpak Michal , Szuba Marek , Taylor Kieron , Thormann Anja , Threadgold Glen , Walts Brandon , Winterbottom Andrea , Chakiachvili Marc , Chaubal Ameya , De Silva Nishadi , Flint Bethany , Frankish Adam , Hunt Sarah E , IIsley Garth R , Langridge Nick , Loveland Jane E , Martin Fergal J , Mudge Jonathan M , Morales Joanella , Perry Emily , Ruffier Magali , Tate John , Thybert David , Trevanion Stephen J , Cunningham Fiona , Yates Andrew D , Zerbino Daniel R , Flicek Paul 
Published: October 2020

Abstract
The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
Development and validation of a risk score for the prediction of cardiovascular disease in living donor kidney transplant recipients
Authors: Ueki Kenji , Tsuchimoto Akihiro , Matsukuma Yuta , Nakagawa Kaneyasu , Tsujikawa Hiroaki , Masutani Kosuke , Tanaka Shigeru , Kaku Keizo , Noguchi Hiroshi , Okabe Yasuhiro , Unagami Kohei , Kakuta Yoichi , Okumi Masayoshi , Nakamura Masafumi , Tsuruya Kazuhiko , Nakano Toshiaki , Tanabe Kazunari , Kitazono Takanari ,   Japan Academic Consortium of Kidney Transplantation investigators
Published: October 2020

Abstract

Background
Cardiovascular disease (CVD) is a major cause of death in kidney transplant (KT) recipients. To improve their long-term survival, it is clinically important to estimate the risk of CVD after living donor KT via adequate pre-transplant CVD screening.

Methods
A derivation cohort containing 331 KT recipients underwent living donor KT at Kyushu University Hospital from January 2006 to December 2012. A prediction model was retrospectively developed and risk scores were investigated via a Cox proportional hazards regression model. The discrimination and calibration capacities of the prediction model were estimated via the c-statistic and the Hosmer–Lemeshow goodness of fit test. External validation was estimated via the same statistical methods by applying the model to a validation cohort of 300 KT recipients who underwent living donor KT at Tokyo Women’s Medical University Hospital.

Results
In the derivation cohort, 28 patients (8.5%) had CVD events during the observation period. Recipient age, CVD history, diabetic nephropathy, dialysis vintage, serum albumin and proteinuria at 12 months after KT were significant predictors of CVD. A prediction model consisting of integer risk scores demonstrated good discrimination (c-statistic 0.88) and goodness of fit (Hosmer–Lemeshow test P = 0.18). In a validation cohort, the model demonstrated moderate discrimination (c-statistic 0.77) and goodness of fit (Hosmer–Lemeshow test P = 0.15), suggesting external validity.

Conclusions
The above-described simple model for predicting CVD after living donor KT was accurate and useful in clinical situations.
Policing, State Repression, and the Pro-Democracy Movement in Hong Kong
Authors: Maguire Edward R 
Published: October 2020

Abstract
Stott and his coauthors report on findings from their study of the police response to protests in Hong Kong. Their analysis is based on the Elaborated Social Identity Model (ESIM), a powerful framework for understanding the dynamic interplay between protesters and police. They find that by responding in an overly forceful and indiscriminate manner, the police triggered psychological changes among protesters that intensified these events and led to greater levels of disorder. In this reaction essay, I comment on the findings of Stott and his coauthors. I also note how the coercive policing practices used by Hong Kong’s police during the protests harm their relationships with the public, diminish the perceived legitimacy of the police, and undermine human rights.