bluuebunny/crossref_metadata_2025_split huggingface dataset:
AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance
Authors: Huber Sebastiaan P. , Zoupanos Spyros , Uhrin Martin , Talirz Leopold , Kahle Leonid , Häuselmann Rico , Gresch Dominik , Müller Tiziano , Yakutovich Aliaksandr V. , Andersen Casper W. , Ramirez Francisco F. , Adorf Carl S. , Gargiulo Fernando , Kumbhar Snehal , Passaro Elsa , Johnston Conrad , Merkys Andrius , Cepellotti Andrea , Mounet Nicolas , Marzari Nicola , Kozinsky Boris , Pizzi Giovanni 
Published: September 2020

AbstractThe ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA’s workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with external simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.
Assessing the role of inter-facility patient transfer in the spread of carbapenemase-producing Enterobacteriaceae: the case of France between 2012 and 2015
Authors: Nekkab Narimane , Crépey Pascal , Astagneau Pascal , Opatowski Lulla , Temime Laura 
Published: September 2020

AbstractThe spread of carbapenemase-producing Enterobacteriaceae (CPE) in healthcare settings is a major public health threat that has been associated with cross-border and local patient transfers between healthcare facilities. Since the impact of transfers on spread may vary, our study aimed to assess the contribution of a patient transfer network on CPE incidence and spread at a countrywide level, with a case study of France from 2012 to 2015. Our results suggest a transition in 2013 from a CPE epidemic sustained by internationally imported episodes to an epidemic sustained by local transmission events through patient transfers. Incident episodes tend to occur within close spatial distance of their potential infector. We also observe an increasing frequency of multiple spreading events, originating from a limited number of regional hubs. Consequently, coordinated prevention and infection control strategies should focus on transfers of carriers of CPE to reduce regional and inter-regional transmission.
Ethnic variation of oral microbiota in children
Authors: Premaraj Thyagaseely S. , Vella Raven , Chung Jennifer , Lin Qingqi , Hunter Panier , Underwood Kori , Premaraj Sundaralingam , Zhou Yanjiao 
Published: September 2020

AbstractDespite widely used preventive measures such as sealant programs to control caries prevalence, disparities are seen among ethnic groups. Supragingival plaque harbors hundreds of bacterial species, playing a significant role in oral health and disease. It is unknown whether the ethnic variation influences the supragingival microbiota in children. In our study, variations in microbiota of the supragingival plaque was investigated from 96 children between 6 and 11 years old in four ethnic groups (African American, Burmese, Caucasian, and Hispanic) from the same geographic location by 16S rRNA gene sequencing. We found that the microbial alpha and beta diversity of supragingival microbiota significantly differed between ethnic groups. The supragingival plaque microbiota had the most complex microbial community in Burmese children. Within-group microbiota similarity in Burmese or Caucasian children was significantly higher than between-groups similarity. We identified seven ethnic group-specific bacterial taxa after adjusting for dental plaque index, decayed missing filled teeth (DMFT) and the frequency of brushing. Children with high plaque index and high DMFT values were more similar to each other in the overall microbial community, compared to low plaque index or low DMFT groups in which inter-subject variation is high. Several bacterial taxa associated with high plaque index or high DMFT were ethnic group-specific. These results demonstrated that supragingival microbiota differed among ethnicity groups in children.
Exact quasi-relativistic wavefunctions of Hydrogen-like atoms
Authors: Grave de Peralta Luis 
Published: September 2020

AbstractExact solutions of a novel quasi-relativistic quantum mechanical wave equation are found for Hydrogen-like atoms. This includes both, an exact analytical expression for the energies of the bound states, and exact analytical expressions for the wavefunctions, which successfully describe quantum particles with mass and spin-0 up to energies comparable to the energy associated to the mass of the particle. These quasi-relativistic atomic orbitals may be used for improving ab-initio software packages dedicated to numerical simulations in physical-chemistry and atomic and solid-state physics.
Near wall Prandtl number effects on velocity gradient invariants and flow topologies in turbulent Rayleigh–Bénard convection
Authors: Yigit Sahin , Hasslberger Josef , Klein Markus , Chakraborty Nilanjan 
Published: September 2020

AbstractThe statistical behaviours of the invariants of the velocity gradient tensor and flow topologies for Rayleigh–Bénard convection of Newtonian fluids in cubic enclosures have been analysed using Direct Numerical Simulations (DNS) for a range of different values of Rayleigh (i.e. $$Ra=10^7-10^9$$

R
a
=

10
7

-

10
9

) and Prandtl (i.e. $$Pr=1$$

P
r
=
1

and 320) numbers. The behaviours of second and third invariants of the velocity gradient tensor suggest that the bulk region of the flow at the core of the domain is vorticity-dominated whereas the regions in the vicinity of cold and hot walls, in particular in the boundary layers, are found to be strain rate-dominated and this behaviour has been found to be independent of the choice of Ra and Pr values within the range considered here. Accordingly, it has been found that the focal topologies S1 and S4 remain predominant in the bulk region of the flow and the volume fraction of nodal topologies increases in the vicinity of the active hot and cold walls for all cases considered here. However, remarkable differences in the behaviours of the joint probability density functions (PDFs) between second and third invariants of the velocity gradient tensor (i.e. Q and R) have been found in response to the variations of Pr. The classical teardrop shape of the joint PDF between Q and R has been observed away from active walls for all values of Pr, but this behavior changes close to the heated and cooled walls for high values of Pr (e.g. $$Pr=320$$

P
r
=
320

) where the joint PDF exhibits a shape mirrored at the vertical Q-axis. It has been demonstrated that the junctions at the edges of convection cells are responsible for this behaviour for $$Pr=320$$

P
r
=
320

, which also increases the probability of finding S3 topologies with large negative magnitudes of Q and R. By contrast, this behaviour is not observed in the $$Pr=1$$

P
r
=
1

case and these differences between flow topology distributions in Rayleigh–Bénard convection in response to Pr suggest that the modelling strategy for turbulent natural convection of gaseous fluids may not be equally well suited for simulations of turbulent natural convection of liquids with high values of Pr.
Development of a probabilistic early health warning system based on meteorological parameters
Authors: Sahai A. K. , Mandal Raju , Joseph Susmitha , Saha Shubhayu , Awate Pradip , Dutta Somenath , Dey Avijit , Chattopadhyay Rajib , Phani R. , Pattanaik D. R. , Despande Sunil 
Published: September 2020

AbstractAmong the other diseases, malaria and diarrhoea have a large disease burden in India, especially among children. Changes in rainfall and temperature patterns likely play a major role in the increased incidence of these diseases across geographical locations. This study proposes a method for probabilistic forecasting of the disease incidences in extended range time scale (2–3 weeks in advance) over India based on an unsupervised pattern recognition technique that uses meteorological parameters as inputs and which can be applied to any geographical location over India. To verify the robustness of this newly developed early warning system, detailed analysis has been made in the incidence of malaria and diarrhoea over two districts of the State of Maharashtra. It is found that the increased probabilities of high (less) rainfall, high (low) minimum temperature and low (moderate) maximum temperature are more (less) conducive for both diseases over these locations, but have different thresholds. With the categorical probabilistic forecasts of disease incidences, this early health warning system is found to be a useful tool with reasonable skill to provide the climate-health outlook about possible disease incidence at least 2 weeks in advance for any location or grid over India.
Deficiency of the SMOC2 matricellular protein impairs bone healing and produces age-dependent bone loss
Authors: Morkmued Supawich , Clauss François , Schuhbaur Brigitte , Fraulob Valérie , Mathieu Eric , Hemmerlé Joseph , Clevers Hans , Koo Bon-Kyoung , Dollé Pascal , Bloch-Zupan Agnès , Niederreither Karen 
Published: September 2020

AbstractSecreted extracellular matrix components which regulate craniofacial development could be reactivated and play roles in adult wound healing. We report a patient with a loss-of-function of the secreted matricellular protein SMOC2 (SPARC related modular calcium binding 2) presenting severe oligodontia, microdontia, tooth root deficiencies, alveolar bone hypoplasia, and a range of skeletal malformations. Turning to a mouse model, Smoc2-GFP reporter expression indicates SMOC2 dynamically marks a range of dental and bone progenitors. While germline Smoc2 homozygous mutants are viable, tooth number anomalies, reduced tooth size, altered enamel prism patterning, and spontaneous age-induced periodontal bone and root loss are observed in this mouse model. Whole-genome RNA-sequencing analysis of embryonic day (E) 14.5 cap stage molars revealed reductions in early expressed enamel matrix components (Odontogenic ameloblast-associated protein) and dentin dysplasia targets (Dentin matrix acidic phosphoprotein 1). We tested if like other matricellular proteins SMOC2 was required for regenerative repair. We found that the Smoc2-GFP reporter was reactivated in adjacent periodontal tissues 4 days after tooth avulsion injury. Following maxillary tooth injury, Smoc2−/− mutants had increased osteoclast activity and bone resorption surrounding the extracted molar. Interestingly, a 10-day treatment with the cyclooxygenase 2 (COX2) inhibitor ibuprofen (30 mg/kg body weight) blocked tooth injury-induced bone loss in Smoc2−/− mutants, reducing matrix metalloprotease (Mmp)9. Collectively, our results indicate that endogenous SMOC2 blocks injury-induced jaw bone osteonecrosis and offsets age-induced periodontal decay.
Multiplexed detection and isolation of viable low-frequency cytokine-secreting human B cells using cytokine secretion assay and flow cytometry (CSA-Flow)
Authors: Rezk Ayman , Li Rui , Bar-Or Amit 
Published: September 2020

AbstractThe ability to functionally characterize cytokine-secreting immune cells has broad implications in both health and a range of immune-mediated and auto-immune diseases. Low-frequency cytokine-defined immune-cell subsets can play key immune-regulatory roles, yet their detailed study is often hampered by limited clinical sample availability. Commonly used techniques including intracellular cytokine staining require cell fixation, precluding subsequent functional interrogation. The cytokine-secretion assay (CSA) can overcome this limitation, though has mostly been used for detection of relatively high-frequency, single-cytokine secreting cells. We examined how adaptation of the CSA in combination with multiparametric flow-cytometry (CSA-Flow) may enable simultaneous isolation of multiple, low-frequency, cytokine-secreting cells. Focusing on human B cells (traditionally recognized as harder to assay than T cells), we show that single-capture CSA-Flow allows for isolation of highly-purified populations of both low-frequency (IL-10+; GM-CSF+) and high-frequency (TNF+) cytokine-defined B cells. Simultaneous detection and isolation of up to three viable and highly-purified cytokine-secreting B-cell subpopulations is feasible, albeit with some signal loss, with fractions subsequently amenable to gene expression analysis and in vitro cell culture. This multiplexing CSA-Flow approach will be of interest in many human cellular immunology contexts aiming to functionally characterize cytokine-secreting immune cells, especially when sample volumes and cell numbers are limited.
Catalytic specificity of the Lactobacillus plantarum cystathionine γ-lyase presumed by the crystallographic analysis
Authors: Matoba Yasuyuki , Noda Masafumi , Yoshida Tomoki , Oda Kosuke , Ezumi Yuka , Yasutake Chiaki , Izuhara-Kihara Hisae , Danshiitsoodol Narandarai , Kumagai Takanori , Sugiyama Masanori 
Published: September 2020

AbstractThe reverse transsulfuration pathway, which is composed of cystathionine β-synthase (CBS) and cystathionine γ-lyase (CGL), plays a role to synthesize l-cysteine using l-serine and the sulfur atom in l-methionine. A plant-derived lactic acid bacterium Lactobacillus plantarum SN35N has been previously found to harbor the gene cluster encoding the CBS- and CGL-like enzymes. In addition, it has been demonstrated that the L. plantarum CBS can synthesize cystathionine from O-acetyl-l-serine and l-homocysteine. The aim of this study is to characterize the enzymatic functions of the L. plantarum CGL. We have found that the enzyme has the high γ-lyase activity toward cystathionine to generate l-cysteine, together with the β-lyase activity toward l-cystine to generate l-cysteine persulfide. By the crystallographic analysis of the inactive CGL K194A mutant complexed with cystathionine, we have found the residues which recognize the distal amino and carboxyl groups of cystathionine or l-cystine. The PLP-bound substrates at the active site may take either the binding pose for the γ- or β-elimination reaction, with the former being the major reaction in the case of cystathionine.
Palpitation was associated with clinical outcomes in patients with hypertrophic cardiomyopathy
Authors: Hu Tingting , Wang Tao , Zhang Xiwen 
Published: September 2020

AbstractHypertrophic cardiomyopathy (HCM) is a common genetic heart disease with diversified clinical presentation and it is important to identify new predictors of clinical outcomes and survival in HCM patients. In our study, 206 HCM patients were compared with respect to major adverse cardiovascular and cerebrovascular events. By multivariable logistic analysis, we determined that palpitation, together with chronic heart failure (CHF) > 1 year, was an independent predictor of major adverse cardiovascular and cerebral events (MACCE) in HCM patients (OR 3.24, 95% CI 1.60–6.57, P = 0.001). Specially, palpitation was related to higher prevalence of rehospitalization (OR 3.86, 95% CI 2.08–7.08, P < 0.001), cardiac death (OR 2.96, 95% CI 1.05–8.32, P = 0.04) and heart failure exacerbation (OR 4.07, 95% CI 2.04–8.13, P < 0.001). However, patients presented with palpitation did not show a significantly different cardiac phenotype and function. Finally, palpitation predicted a poor prognosis in HCM patients without atrial fibrillation by utilizing Kaplan–Meier analysis (P = 0.041). In conclusion, palpitation could be a new predictor of clinical outcomes and overall survival in HCM patients.
A role of color vision in emmetropization in C57BL/6J mice
Authors: Yang Jinglei , Yang Li , Chen Rongfang , Zhu Yun , Wang Siyao , Hou Xueqin , Wei Bei , Wang Qiongsi , Liu Yue , Qu Jia , Zhou Xiangtian 
Published: September 2020

AbstractSpectral composition affects emmetropization in both humans and animal models. Because color vision interacts the effects of chromatic defocus, we developed a method to bypass the effects of longitudinal chromatic aberration by placing a spectral filter behind the optics of the eye, using genetic tools. Newborn C57BL/6J (B6) mice were reared in quasi-monochromatic red (585–660 nm) or blue (410–510 nm) light beginning before eye-opening. Refractive states and ocular dimensions were compared at 4, 6, 8, and 10 weeks with mice reared in normal white light. Cre recombinase-dependent Ai9 reporter mice were crossed with Chx10-Cre to obtain Chx10-Cre;Ai9 mice, expressing red fluorescent protein in retinal Cre-positive cells. Ai9 offsprings, with and without Cre, were reared under a normal visual environment. Refraction and axial components were measured as described above. Expression levels of M and S opsin were quantified by western blotting at 10 weeks. Compared with those reared in white light, B6 mice reared in red light developed relative hyperopia, principally characterized by flattening of corneal curvature. Emmetropization was not affected by blue light, possibly because the reduction in vitreous chamber depth compensated for the increase in corneal curvature. Compared with Cre-negative littermates, the refraction and axial dimensions of Chx10-Cre;Ai9 mice were not significantly different at the follow-up timepoints. M opsin levels were higher in Chx10-Cre;Ai9 mice at 10 weeks while S opsin levels were not different. Red light induced a hyperopic shift in mouse refractive development. Emmetropization was not impacted in mice with perturbed color vision caused by intrinsic red-fluorescent protein, suggesting that color vision may not be necessary in mouse emmetropization when other mechanisms are present.
Relative blood volume changes during haemodialysis estimated from haemoconcentration markers
Authors: Pstras L. , Waniewski J. , Wojcik-Zaluska A. , Zaluska W. 
Published: September 2020

AbstractRelative blood volume (RBV) monitoring is frequently used in haemodialysis patients to help guide fluid management and improve cardiovascular stability. RBV changes are typically estimated based on online measurements of certain haemoconcentration markers, such as haematocrit (HCT), haemoglobin (HGB) or total blood protein concentration (TBP). The beginning of a haemodialysis procedure, i.e. filling the extracorporeal circuit with the patient’s blood (with the priming saline being infused to the patient or discarded) may be associated with relatively dynamic changes in the circulation, and hence the observed RBV changes may depend on the exact moment of starting the measurements. The aim of this study was to use a mathematical model to assess this issue quantitatively. The model-based simulations indicate that when the priming saline is not discarded but infused to the patient, a few-minute difference in the moment of starting RBV tracking through measurements of HCT, HGB or TBP may substantially affect the RBV changes observed throughout the dialysis session, especially with large priming volumes. A possible overestimation of the actual RBV changes is the highest when the measurements are started within a couple of minutes after the infusion of priming saline is completed.
Personal familiarity of music and its cerebral effect on subsequent speech processing
Authors: Castro Maïté , L’héritier Fanny , Plailly Jane , Saive Anne-Lise , Corneyllie Alexandra , Tillmann Barbara , Perrin Fabien 
Published: September 2020

AbstractDespite the obvious personal relevance of some musical pieces, the cerebral mechanisms associated with listening to personally familiar music and its effects on subsequent brain functioning have not been specifically evaluated yet. We measured cerebral correlates with functional magnetic resonance imaging (fMRI) while composers listened to three types of musical excerpts varying in personal familiarity and self (familiar own/composition, familiar other/favorite or unfamiliar other/unknown music) followed by sequences of names of individuals also varying in personal familiarity and self (familiar own/own name, familiar other/close friend and unfamiliar other/unknown name). Listening to music with autobiographical contents (familiar own and/or other) recruited a fronto-parietal network including mainly the dorsolateral prefrontal cortex, the supramarginal/angular gyri and the precuneus. Additionally, while listening to familiar other music (favorite) was associated with the activation of reward and emotion networks (e.g. the striatum), familiar own music (compositions) engaged brain regions underpinning self-reference (e.g. the medial prefrontal cortex) and visuo-motor imagery. The present findings further suggested that familiar music with self-related reference (compositions) leads to an enhanced activation of the autobiographical network during subsequent familiar name processing (as compared to music without self-related reference); among these structures, the precuneus seems to play a central role in personally familiar processing.
A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.)
Authors: Sun Yuyan , Zhang Huiqing , Fan Min , He Yanjun , Guo Pingan 
Published: September 2020

AbstractDwarf architecture is an important trait associated with plant yield, lodging resistance and labor cost. Here, we aimed to identify a gene causing dwarfism in watermelon. The ‘w106’ (dwarf) and ‘Charleston Gray’ (vine) were used as parents to construct F1 and F2 progeny. Dwarf architecture of ‘w106’ was mainly caused by longitudinal cell length reduction and was controlled by a single recessive gene. Whole-genome sequencing of two parents and two bulk DNAs of F2 population localized this gene to a 2.63-Mb region on chromosome 9; this was further narrowed to a 541-kb region. Within this region, Cla015407, encoding a gibberellin 3β-hydroxylase (GA3ox), was the candidate gene. Cla015407 had a SNP mutation (G → A) in the splice acceptor site of the intron, leading to altered splicing event and generating two splicing isoforms in dwarf plants. One splicing isoform retained the intron sequences, while the other had a 13-bp deletion in the second exon of GA3ox transcript, both resulting in truncated proteins and loss of the functional Fe2OG dioxygenase domain in dwarf plants. RNA-Seq analysis indicated that expression of Cla015407 and other GA biosynthetic and metabolic genes were mostly up-regulated in the shoots of dwarf plants compared with vine plants in F2 population. Measurement of endogenous GA levels indicated that bioactive GA4 was significantly decreased in the shoots of dwarf plants. Moreover, the dwarf phenotype can be rescued by exogenous applications of GA3 or GA4+7, with the latter having a more distinct effect than the former. Subcellular localization analyses of GA3ox proteins from two parents revealed their subcellular targeting in nucleus and cytosol. Here, a GA3ox gene controlling dwarf architecture was identified, and loss function of GA3ox leads to GA4 reduction and dwarfism phenotype in watermelon.