bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis
Authors: Wipperman Matthew F. , Bhattarai Shakti K. , Vorkas Charles Kyriakos , Maringati Venkata Suhas , Taur Ying , Mathurin Laurent , McAulay Katherine , Vilbrun Stalz Charles , Francois Daphie , Bean James , Walsh Kathleen F. , Nathan Carl , Fitzgerald Daniel W. , Glickman Michael S. , Bucci Vanni 
Published: February 2021

AbstractThe composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation.
Nuclear spin assisted magnetic field angle sensing
Authors: Qiu Ziwei , Vool Uri , Hamo Assaf , Yacoby Amir 
Published: February 2021

AbstractQuantum sensing exploits the strong sensitivity of quantum systems to measure small external signals. The nitrogen-vacancy (NV) center in diamond is one of the most promising platforms for real-world quantum sensing applications, predominantly used as a magnetometer. However, its magnetic field sensitivity vanishes when a bias magnetic field acts perpendicular to the NV axis. Here, we introduce a different sensing strategy assisted by the nitrogen nuclear spin that uses the entanglement between the electron and nuclear spins to restore the magnetic field sensitivity. This, in turn, allows us to detect small changes in the magnetic field angle relative to the NV axis. Furthermore, based on the same underlying principle, we show that the NV coupling strength to magnetic noise, and hence its coherence time, exhibits a strong asymmetric angle dependence. This allows us to uncover the directional properties of the local magnetic environment and to realize maximal decoupling from anisotropic noise.
Berry curvature origin of the thickness-dependent anomalous Hall effect in a ferromagnetic Weyl semimetal
Authors: Zhang Yao , Yin Yuefeng , Dubuis Guy , Butler Tane , Medhekar Nikhil V. , Granville Simon 
Published: February 2021

AbstractMagnetic Weyl semimetals with spontaneously broken time-reversal symmetry exhibit a large intrinsic anomalous Hall effect originating from the Berry curvature. To employ this large Hall current for room temperature topo-spintronics applications, it is necessary to fabricate these materials as thin or ultrathin films. Here, we experimentally demonstrate that Weyl semimetal Co2MnGa thin films (20–50 nm) show a large anomalous Hall angle ~11.4% at low temperature and ~9.7% at room temperature, which can be ascribed to the non-trivial topology of the band structure with large intrinsic Berry curvature. However, the anomalous Hall angle decreases significantly with thicknesses below 20 nm, which band structure calculations confirm is due to the reduction of the majority spin contribution to the Berry curvature. Our results suggest that Co2MnGa is an excellent material to realize room temperature topo-spintronics applications; however, the significant thickness dependence of the Berry curvature has important implications for thin-film device design.
Quantifying the impact of the COVID-19 lockdown on household water consumption patterns in England
Authors: Abu-Bakar Halidu , Williams Leon , Hallett Stephen H. 
Published: February 2021

AbstractThe COVID-19 lockdown has instigated significant changes in household behaviours across a variety of categories including water consumption, which in the south and east regions of England is at an all-time high. We analysed water consumption data from 11,528 households over 20 weeks from January 2020, revealing clusters of households with distinctive temporal patterns. We present a data-driven household water consumer segmentation characterising households’ unique consumption patterns and we demonstrate how the understanding of the impact of these patterns of behaviour on network demand during the COVID-19 pandemic lockdown can improve the accuracy of demand forecasting. Our results highlight those groupings with the highest and lowest impact on water demand across the network, revealing a significant quantifiable change in water consumption patterns during the COVID-19 lockdown period. The implications of the study to urban water demand forecasting strategies are discussed, along with proposed future research directions.
Imaging atelectrauma in Ventilator-Induced Lung Injury using 4D X-ray microscopy
Authors: Fardin Luca , Broche Ludovic , Lovric Goran , Mittone Alberto , Stephanov Olivier , Larsson Anders , Bravin Alberto , Bayat Sam 
Published: February 2021

AbstractMechanical ventilation can damage the lungs, a condition called Ventilator-Induced Lung Injury (VILI). However, the mechanisms leading to VILI at the microscopic scale remain poorly understood. Here we investigated the within-tidal dynamics of cyclic recruitment/derecruitment (R/D) using synchrotron radiation phase-contrast imaging (PCI), and the relation between R/D and cell infiltration, in a model of Acute Respiratory Distress Syndrome in 6 anaesthetized and mechanically ventilated New-Zealand White rabbits. Dynamic PCI was performed at 22.6 µm voxel size, under protective mechanical ventilation [tidal volume: 6 ml/kg; positive end-expiratory pressure (PEEP): 5 cmH2O]. Videos and quantitative maps of within-tidal R/D showed that injury propagated outwards from non-aerated regions towards adjacent regions where cyclic R/D was present. R/D of peripheral airspaces was both pressure and time-dependent, occurring throughout the respiratory cycle with significant scatter of opening/closing pressures. There was a significant association between R/D and regional lung cellular infiltration (p = 0.04) suggesting that tidal R/D of the lung parenchyma may contribute to regional lung inflammation or capillary-alveolar barrier dysfunction and to the progression of lung injury. PEEP may not fully mitigate this phenomenon even at high levels. Ventilation strategies utilizing the time-dependence of R/D may be helpful in reducing R/D and associated injury.
Uncovering the superior corrosion resistance of iron made via ancient Indian iron-making practice
Authors: Dwivedi Deepak , Mata Jitendra P. , Salvemini Filomena , Rowles Matthew R. , Becker Thomas , Lepková Kateřina 
Published: February 2021

AbstractAncient Indian iron artefacts have always fascinated researchers due to their excellent corrosion resistance, but the scientific explanation of this feature remains to be elucidated. We have investigated corrosion resistance of iron manufactured according to traditional metallurgical processes by the Indian tribes called ‘Agaria’. Iron samples were recovered from central India (Aamadandh, Korba district, Chhattisgarh). Iron artefacts are investigated using a range of correlative microscopic, spectroscopic, diffraction and tomographic techniques to postulate the hidden mechanisms of superlative corrosion resistance. The importance of manufacturing steps, ingredients involved in Agaria’s iron making process, and post-metal treatment using metal-working operation called hot hammering (forging) is highlighted. This study also hypothesizes the probable protective mechanisms of corrosion resistance of iron. Findings are expected to have a broad impact across multiple disciplines such as archaeology, metallurgy and materials science.
Modified conditioning regimen with idarubicin followed by autologous hematopoietic stem cell transplantation for invasive B-cell non-Hodgkin’s lymphoma patients
Authors: Tian Chen , Li Yueyang , Liu Su , Chen Zehui , Zhang Yizhuo , Yu Yong , Yang Hongliang , Zhao Haifeng , Zhao Zhigang , Yuan Tian , Wang Yafei 
Published: February 2021

AbstractHigh-dose chemotherapy followed by autologous hematopoietic stem cell transplantation (ASCT) is still a consolidation treatment choice for relapsed/refractory B-cell non-Hodgkin’s lymphoma (NHL) patients and some aggressive B-cell NHL as frontline therapy. Due to the shortage of carmustine, we switched to idarubicin-substituted BEAC (IEAC) conditioning regimen. We retrospectively compared the outcomes of 72 aggressive B-cell NHL patients treated with IEAC or BEAC regimens followed by ASCT as upfront consolidative treatment. The median time to neutrophil and platelet reconstitution showed no difference between IEAC and BEAC groups. IEAC regimen was well tolerated without increase of adverse events. Transplant-related mortality didn’t occur. The overall survival (OS) and progression-free survival (PFS) of IEAC group (33 and 23 months) were a little longer than that of BEAC group (30 and 18 months). However, due to the small sample numbers, there’s no significant difference in OS and PFS between IEAC and BEAC group with DLBCL or MCL. Multivariate analysis showed that AnnArbor staging, IPI score, lactate dehydrogenase level, remission of disease, modified regimen were related with PFS and OS. In conclusion, IEAC regimen was well tolerated and replacement with idarubicin could be an alternative when carmustine was not available.
Biogeography of the cosmopolitan terrestrial diatom Hantzschia amphioxys sensu lato based on molecular and morphological data
Authors: Maltsev Yevhen , Maltseva Svetlana , Kociolek John Patrick , Jahn Regine , Kulikovskiy Maxim 
Published: February 2021

AbstractUntil now, the reported diversity of representatives from the genus Hantzschia inhabiting soils from different parts of Eurasia was limited to the few species H. amphioxys, H. elongata and H. vivax and some of their infraspecific taxa. We have studied the morphology, ultrastructure and phylogeny of 25 soil diatom strains, which according to published description would be assigned to “H. amphioxys sensu lato” using 18S rDNA, 28S rDNA and rbcL. We show that strains are made up of seven different species of Hantzschia, including five new for science. Five strains were identified as H. abundans. This species has a slight curvature of the raphe near its external proximal ends. Four of the examined strains were represented by different populations of H. amphioxys and their morphological characteristics fully correspond with its isolectotype and epitype. The main specific features of this species include 21–25 striae in 10 μm, 6–11 fibulae in 10 μm, 40–50 areolae in 10 μm and internal proximal raphe endings bent in opposite directions. H. attractiva sp. nov., H. belgica sp. nov., H. parva sp. nov., H. pseudomongolica sp. nov. and H. stepposa sp. nov. were described based on differences in the shape of the valves, significant differences in dimensions, a lower number of striae and areolae in 10 μm and the degree and direction of deflection of the internal central raphe endings. Based on the study of the morphological variability and phylogeny of soil Hantzschia-species from different geographical locations we conclude that while some species such as H. amphioxys are truly cosmopolitan in their distributions, some sympatric populations of pseudocryptic taxa exist in the Holarctic.
Dogs (Canis familiaris) recognize their own body as a physical obstacle
Authors: Lenkei Rita , Faragó Tamás , Zsilák Borbála , Pongrácz Péter 
Published: February 2021

AbstractMental representations of one’s own body provide useful reference when negotiating physical environmental challenges. Body-awareness is a neuro-ontogenetic precursor for higher order self-representation, but there is a lack of an ecologically valid experimental approach to it among nonhuman species. We tested dogs (N = 32) in the ‘body as an obstacle’ task. They had to pick up and give an object to their owner, whilst standing on a small mat. In the test condition we attached the object to the mat, thus the dogs had to leave the mat because otherwise they could not lift the object. Dogs came off the mat more frequently and sooner in the test condition, than in the main control condition, where the object was attached to the ground. This is the first convincing evidence of body awareness through the understanding of the consequence of own actions in a species where previously no higher-order self-representation capacity was found. We urge for an ecologically valid approach, and following of bottom-up methods, in studying modularly constructed self-representation.
Multipronged dental analyses reveal dietary differences in last foragers and first farmers at Grotta Continenza, central Italy (15,500–7000 BP)
Authors: Nava Alessia , Fiorin Elena , Zupancich Andrea , Carra Marialetizia , Ottoni Claudio , Di Carlo Gabriele , Vozza Iole , Brugnoletti Orlando , Alhaique Francesca , Cremonesi Renata Grifoni , Coppa Alfredo , Bondioli Luca , Borić Dušan , Cristiani Emanuela 
Published: February 2021

AbstractThis paper provides results from a suite of analyses made on human dental material from the Late Palaeolithic to Neolithic strata of the cave site of Grotta Continenza situated in the Fucino Basin of the Abruzzo region of central Italy. The available human remains from this site provide a unique possibility to study ways in which forager versus farmer lifeways affected human odonto-skeletal remains. The main aim of our study is to understand palaeodietary patterns and their changes over time as reflected in teeth. These analyses involve a review of metrics and oral pathologies, micro-fossils preserved in the mineralized dental plaque, macrowear, and buccal microwear. Our results suggest that these complementary approaches support the assumption about a critical change in dental conditions and status with the introduction of Neolithic foodstuff and habits. However, we warn that different methodologies applied here provide data at different scales of resolution for detecting such changes and a multipronged approach to the study of dental collections is needed for a more comprehensive and nuanced understanding of diachronic changes.
Severe acute malnutrition morphological patterns in children under five
Authors: Medialdea Laura , Bogin Barry , Thiam Mbeugue , Vargas Antonio , Marrodán María D. , Dossou Nicole I. 
Published: February 2021

AbstractCurrent methods for infant and child nutritional assessment rely on anthropometric measurements, whose implementation faces technical challenges in low- and middle-income countries. Anthropometry is also limited to linear measurements, ignoring important body shape information related to health. This work proposes the use of 2D geometric morphometric techniques applied to a sample of Senegalese participants aged 6–59 months with an optimal nutritional condition or with severe acute malnutrition to address morphometric variations due to nutritional status. Significant differences in shape and size body changes were described according to nutritional status, resulting age, sex and allometric effect crucial factors to establish nutritional morphological patterns. The constructed discriminant functions exhibited the best classification rates in the left arm. A landmark-based template registering body shape could be useful to both assess acute malnutrition and better understand the morphological patterns that nutritional status promotes in children during their first 5 years of growth and development.
A meta-analysis uncovers the first sequence variant conferring risk of Bell’s palsy
Authors: Skuladottir Astros Th. , Bjornsdottir Gyda , Thorleifsson Gudmar , Walters G. Bragi , Nawaz Muhammad Sulaman , Moore Kristjan Helgi Swerford , Olason Pall I. , Thorgeirsson Thorgeir E. , Sigurpalsdottir Brynja , Sveinbjornsson Gardar , Eggertsson Hannes P. , Magnusson Sigurdur H. , Oddsson Asmundur , Bjornsdottir Anna , Vikingsson Arnor , Sveinsson Olafur A. , Hrafnsdottir Maria G. , Sigurdardottir Gudrun R. , Halldorsson Bjarni V. , Hansen Thomas Folkmann , Paarup Helene , Erikstrup Christian , Nielsen Kaspar , Klokker Mads , Bruun Mie Topholm , Sorensen Erik , Banasik Karina , Burgdorf Kristoffer S. , Pedersen Ole Birger , Ullum Henrik , Jonsdottir Ingileif , Stefansson Hreinn , Stefansson Kari 
Published: February 2021

AbstractBell’s palsy is the most common cause of unilateral facial paralysis and is defined as an idiopathic and acute inability to control movements of the facial muscles on the affected side. While the pathogenesis remains unknown, previous studies have implicated post-viral inflammation and resulting compression of the facial nerve. Reported heritability estimates of 4–14% suggest a genetic component in the etiology and an autosomal dominant inheritance has been proposed. Here, we report findings from a meta-analysis of genome-wide association studies uncovering the first unequivocal association with Bell’s palsy (rs9357446-A; P = 6.79 × 10−23, OR = 1.23; Ncases = 4714, Ncontrols = 1,011,520). The variant also confers risk of intervertebral disc disorders (P = 2.99 × 10−11, OR = 1.04) suggesting a common pathogenesis in part or a true pleiotropy.
Flexibility and mobility of SARS-CoV-2-related protein structures
Authors: Römer Rudolf A. , Römer Navodya S. , Wallis A. Katrine 
Published: February 2021

AbstractThe worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein—using its complete homo-trimer configuration with 2905 residues—our method identifies a large-scale opening and closing of the S1 subunit through movement of the S$${}^\text{B}$$

B

domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.
Timescale of hole closure during plasma membrane repair estimated by calcium imaging and numerical modeling
Authors: Klenow Martin Berg , Heitmann Anne Sofie Busk , Nylandsted Jesper , Simonsen Adam Cohen 
Published: February 2021

AbstractPlasma membrane repair is essential for eukaryotic cell life and is triggered by the influx of calcium through membrane wounds. Repair consists of sequential steps, with closure of the membrane hole being the key event that allows the cell to recover, thus identifying the kinetics of hole closure as important for clarifying repair mechanisms and as a quantitative handle on repair efficiency. We implement calcium imaging in MCF7 breast carcinoma cells subject to laser damage, coupled with a model describing the spatio-temporal calcium distribution. The model identifies the time point of hole closure as the time of maximum calcium signal. Analysis of cell data estimates the closure time as: $$\langle t_c \rangle =5.45\pm 2.25$$

⟨

t
c

⟩
=
5.45
±
2.25

s and $$\langle t_c \rangle =6.81\pm 4.69$$

⟨

t
c

⟩
=
6.81
±
4.69

s using GCaMP6s-CAAX and GCaMP6s probes respectively. The timescale was confirmed by independent time-lapse imaging of a hole during sealing. Moreover, the analysis estimates the characteristic time scale of calcium removal, the penetration depth of the calcium wave and the diffusion coefficient. Probing of hole closure times emerges as a strong universal tool for quantification of plasma membrane repair
Evolutionary development of the Homo antecessor scapulae (Gran Dolina site, Atapuerca) suggests a modern-like development for Lower Pleistocene Homo
Authors: García-Martínez Daniel , Green David J. , Bermúdez de Castro José María 
Published: February 2021

AbstractTwo well-preserved, subadult 800 ky scapulae from Gran Dolina belonging toHomo antecessor, provide a unique opportunity to investigate the ontogeny of shoulder morphology in Lower Pleistocene humans. We compared theH. antecessorscapulae with a sample of 98P. troglodytesand 108H. sapiensrepresentatives covering seven growth stages, as well as with the DIK-1-1 (Dikika;Australopithecus afarensis), KNM-WT 15000 (Nariokotome;H. ergaster), and MH2 (Malapa;A. sediba) specimens. We quantified 15 landmarks on each scapula and performed geometric morphometric analyses.H. sapiensscapulae are mediolaterally broader with laterally oriented glenoid fossae relative toPanand Dikika shoulder blades. Accordingly,H. antecessorscapulae shared more morphological affinities with modern humans, KNM-WT 15000, and even MH2. BothH. antecessorand modernHomoshowed significantly more positive scapular growth trajectories thanPan(slopes:P. troglodytes = 0.0012;H. sapiens = 0.0018;H. antecessor = 0.0020). Similarities in ontogenetic trajectories between theH. antecessorand modern human data suggest that Lower Pleistocene hominin scapular development was already modern human-like. At the same time, several morphological features distinguishH. antecessorscapulae from modern humans along the entire trajectory. Future studies should include additionalAustralopithecusspecimens for further comparative assessment of scapular growth trends.
Years of life lost to COVID-19 in 81 countries
Authors: Pifarré i Arolas Héctor , Acosta Enrique , López-Casasnovas Guillem , Lo Adeline , Nicodemo Catia , Riffe Tim , Myrskylä Mikko 
Published: February 2021

AbstractUnderstanding the mortality impact of COVID-19 requires not only counting the dead, but analyzing how premature the deaths are. We calculate years of life lost (YLL) across 81 countries due to COVID-19 attributable deaths, and also conduct an analysis based on estimated excess deaths. We find that over 20.5 million years of life have been lost to COVID-19 globally. As of January 6, 2021, YLL in heavily affected countries are 2–9 times the average seasonal influenza; three quarters of the YLL result from deaths in ages below 75 and almost a third from deaths below 55; and men have lost 45% more life years than women. The results confirm the large mortality impact of COVID-19 among the elderly. They also call for heightened awareness in devising policies that protect vulnerable demographics losing the largest number of life-years.