bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transport properties of crystallized antiferromagnetic MnBi2Te4 thin films grown by magnetron sputtering
Authors: Lu Haoyu , Huang Yiya , Guo Qixun , Wang Kun , He Miaomiao , Yin Zhuo , Wang Dongwei , Liu Tao , Wang Jing , Yu Guanghua , Teng Jiao 
Published: November 2022

Abstract
The intrinsic magnetic topological insulator MnBi2Te4 has drawn great attention due to its novel quantum states, among which the most promising one is the quantum anomalous Hall effect. However, MnBi2Te4 is a metastable phase with a narrow temperature range for synthesis, which remains a challenge to grow uniform and high quality MnBi2Te4 sample. Large-area MnBi2Te4 thin films are mainly prepared by molecular beam epitaxy so far. Here, we report a highly versatile method for growing crystallized MnBi2Te4 films on amorphous SiO2/Si substrates by magnetron sputtering at room temperature and post-annealing. High-quality MnBi2Te4 films with a c-axis perpendicular to the substrate and low surface roughness are realized. MnBi2Te4 films have an antiferromagnetic Néel temperature of 21 K, with low carrier concentration (2.5 × 1019 cm−3) and decent mobility (34 cm2 V−1s−1). The films reveal ferromagnetic at ground state and a typical spin-flop transition at 2–3 T. This work provides a pathway toward the fabrication of sputtered-MnBi2Te4 devices for electronic and spintronic applications.
Spin–orbit coupling, orbitally entangled antiferromagnetic order, and collective spin–orbital excitations in

Sr2VO4
Authors: Mohapatra Shubhajyoti , Kumar Singh Dheeraj , Ray Rajyavardhan , Ghosh Sayandip , Singh Avinash 
Published: November 2022

Abstract
With electron filling n = 1 in the

Sr

2

VO

4

compound, the octahedrally coordinated

t

2

g

orbitals are strongly active when the tetragonal distortion induced crystal field is tuned by external agent such as pressure. Considering the full range of crystal field induced tetragonal splitting in a realistic three-orbital model, collective spin–orbital excitations are investigated using the generalized self-consistent plus fluctuation approach. At ambient pressure, an entangled orbital + antiferromagnetic order is found to be stabilized beyond a critical value (∼30 meV) of spin–orbit coupling which is in the realistic range for 3d ions. The behavior of the calculated energy scales of collective excitations with crystal field is consistent with that of the transition temperatures with pressure as obtained from susceptibility and resistivity anomalies in high-pressure studies.
Role of gas flow direction on monolayer MoS2 growth on patterned surfaces via CVD
Authors: Aras Fikret Gonca , Yeltik Aydan 
Published: November 2022

Abstract
The chemical vapor deposition (CVD) technique has been widely used to grow high quality single layer MoS2 crystals. However, there are still issues that need to be clarified in order to determine the appropriate conditions for the repeatable and scalable process. In this study, we experimentally investigated the effect of flow direction on the size distribution and optical signal of monolayer MoS2 flakes grown on microchannel arrayed surfaces. As an important parameter controlling the CVD process, the carrier gas flow was revealed to be highly sensitive to geometric orientation of the patterned surface. The flow direction parallel to the array yielded larger flakes with narrower size distribution, and enhanced photoluminescence (PL) peak intensities compared to the case with flow normal to the array while the Raman intensities for both the cases are almost the same. The size distributions were obtained as 6 ± 13 and 37 ± 4 µm for the perpendicular and parallel cases, respectively. It was also found that the PL peak intensity increased by approximately 1.5 times when switching to parallel configuration. This study presents an experimental approach to understand the influence of the precursor stream reshaped by the growth surface geometry on the structural and optical properties of monolayer MoS2, which has great potential for use in optoelectronic applications.
Graphene based Nano Gas Sensors: Mechanistic Study
Authors: Jaiswal Monica , Majumdar Neha , Kumar Robin , Mittal Jagjiwan , Jha Pika 
Published: November 2022

Abstract
Selective, sensitive and accurate gas monitoring system can help to control the air pollution, prevent an explosion and injury to industrial workers. Due to very high surface to volume ratio and unique properties, graphene is a highly suitable carbon material to detect toxic gases. As single layer, few layer or multi-layer, graphene either in pure form or after modifications has been studied for the application in gas sensors. Present paper serves as a compendium of research work carried out on graphene and its derivatives in gas sensing applications. Review is mainly concentrated on the sensing of three toxic gases namely nitrogen dioxide (NO2), carbon monoxide (CO) and ammonia (NH3). Special emphasis is done on describing the mechanisms for gas sensing by pristine graphene and after modifications.
Effects of pulse voltage on the droplet formation of glycol ethers solvent ink in a piezoelectric inkjet printing process for fabricating hydrophobic lines on paper substrate
Authors: Dinh Duc Minh Trinh , Le Ngan Nguyen , Lam Phuong Hong , Thi Le Anh Van , Thi Le Mai , Thi Dang Dung My , Thi Nguyen Hiep , Dang Chien Mau 
Published: November 2022

Abstract
Inkjet printing is a fabrication technique which can create designed patterns by ejecting many tiny ink droplets out of nozzles onto substrate. This technique has recently been applied into fabrication process of micro-electro-mechanical systems (MEMS). However, the exact understanding of the effect of pulse voltage on ink droplet is still the focus of many researchers today. Therefore, the goal of this work is to investigate the effect of voltage of phase 1 (V
1) and phase 2 (V
2) of drive waveform on an inkjet printing process to understand how the droplet and satellite droplet have been formed. Solvent ink was prepared from diethylene glycol monobutyl ether (DEGBE) and nonaethylene glycol monododecyl ether (C12E9). Ink droplets were observed by high speed camera which had been installed into our CeraPrinter X-Serie inkjet printer. Results showed that V
1 = −10 V and V
2 = 50 V are suitable for our inkjet printer to achieve stable jetting without the appearance of satellite drops. These optimum values of pulse voltage were confirmed through the printing of our solvent ink on paper substrate for fabricating hydrophobic lines.
The shape-controlled synthesis of alloyed CdSxSe1−x nanocrystals and their applications in LEDs
Authors: Le Na Vo Thi , Ngoc Pham Kim , Tuan Duong Anh , Huong Nguyen Viet , Hai Vu Ngoc , Huu Tuan Nguyen 
Published: November 2022

Abstract
Alloy nanocrystals (NCs) provide access and control of the parameters for nanoscale engineering because their physical and optical properties depend on size, shape, and composition. Here, alloy CdS
x
Se1−x
NCs with different shapes were synthesised via a one-pot method using cadmium acetate, sulfur, and selenium as precursors in trioctylphosphine solution. The luminescence and shapes of NCs were characterised by fluorescence spectroscopy and transmission electron microscopy, respectively. It was found that the modification of precursor concentration resulted in NC shape variation, including branched NCs, long and short nanorods. Consequently, a series of alloy CdS
x
Se1−x
NCs with different shape-based light emitting devices (LEDs) were fabricated and their operation characteristics were also compared. The obtained luminance and luminous efficiency showed that the control of NC shape is the key factor for the improvement of LED performance. We anticipate that this work will provide further insight into the design of CdSxSe1−x NCs-based LEDs with shape variation.
Three key areas in progressing delirium practice and knowledge: recognition and relief of distress, new directions in delirium epidemiology and developing better research assessments
Authors: MacLullich Alasdair M J , Hosie Annmarie , Tieges Zoë , Davis Daniel H J 
Published: November 2022

AbstractDelirium presents formidable challenges: it affects one in four of older hospitalised adults, greatly elevates the risk of multiple short- and long-term complications including dementia and causes significant distress. Delirium care remains generally poor. Yet, there are clear grounds for optimism; the last decade has seen impactful policy advances and a tripling of research output. Here, we highlight three linked areas which have strong potential to transform delirium practice and knowledge in the near term.Delirium-related distress is strikingly underrepresented in practice guidance and research. Proactive recognition combined with effective clinical responses based on good communication provides a critical and largely untapped opportunity to improve care.Delirium epidemiology research is well positioned to produce novel insights through advanced prospective designs in populations such as emergency medical patients with detailed pre-, intra- and post-delirium assessments allied with fluid, imaging and other biomarkers.Research-grade assessment of delirium currently involves a chaotic array of tools, methods and diagnostic algorithms. Areas for development: expand and analytically distinguish the range of features assessed (including distress), optimise feature assessment including use of validated neuropsychological tests where possible, produce standardised algorithms which articulate explicit pathways from features to diagnosis, and create new fine-grained approaches to the measurement of severity.Delirium practice and knowledge show accelerating growth. This is encouraging but much of the necessary progress is still to come. Innovation in these three highlighted areas, as well as many others, will open up exciting possibilities in enhancing the care of patients with this common and often devastating condition.
Critical review of conformational B-cell epitope prediction methods
Authors: Cia Gabriel , Pucci Fabrizio , Rooman Marianne 
Published: November 2022

Abstract
Accurate in silico prediction of conformational B-cell epitopes would lead to major improvements in disease diagnostics, drug design and vaccine development. A variety of computational methods, mainly based on machine learning approaches, have been developed in the last decades to tackle this challenging problem. Here, we rigorously benchmarked nine state-of-the-art conformational B-cell epitope prediction webservers, including generic and antibody-specific methods, on a dataset of over 250 antibody-antigen structures. The results of our assessment and statistical analyses show that all the methods achieve very low performances, and some do not perform better than randomly generated patches of surface residues. In addition, we also found that commonly used consensus strategies that combine the results from multiple webservers are at best only marginally better than random. Finally, we applied all the predictors to the SARS-CoV-2 spike protein as an independent case study, and showed that they perform poorly in general, which largely recapitulates our benchmarking conclusions. We hope that these results will lead to greater caution when using these tools until the biases and issues that limit current methods have been addressed, promote the use of state-of-the-art evaluation methodologies in future publications and suggest new strategies to improve the performance of conformational B-cell epitope prediction methods.
varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data
Authors: Kumar Ajay Anand , Loeys Bart , Van De Beek Gerarda , Peeters Nils , Wuyts Wim , Van Laer Lut , Vandeweyer Geert , Alaerts Maaike 
Published: November 2022

Abstract

Motivation
Computational identification of copy number variants (CNVs) in sequencing data is a challenging task. Existing CNV-detection methods account for various sources of variation and perform different normalization strategies. However, their applicability and predictions are restricted to specific enrichment protocols. Here, we introduce a novel tool named varAmpliCNV, specifically designed for CNV-detection in amplicon-based targeted resequencing data (Haloplex™ enrichment protocol) in the absence of matched controls. VarAmpliCNV utilizes principal component analysis (PCA) and/or metric dimensional scaling (MDS) to control variances of amplicon associated read counts enabling effective detection of CNV signals.

Results
Performance of VarAmpliCNV was compared against three existing methods (ConVaDING, ONCOCNV and DECoN) on data of 167 samples run with an aortic aneurysm gene panel (n = 30), including 9 positive control samples. Additionally, we validated the performance on a large deafness gene panel (n = 145) run on 138 samples, containing 4 positive controls. VarAmpliCNV achieved higher sensitivity (100%) and specificity (99.78%) in comparison to competing methods. In addition, unsupervised clustering of CNV segments and visualization plots of amplicons spanning these regions are included as a downstream strategy to filter out false positives.

Availability and implementation
The tool is freely available through galaxy toolshed and at: https://hub.docker.com/r/cmgantwerpen/varamplicnv. Supplementary Data File S1: https://tinyurl.com/2yzswyhh; Supplementary Data File S2: https://tinyurl.com/ycyf2fb4.

Supplementary information
Supplementary data are available at Bioinformatics online.
Teleonomy as a problem of self-causation
Authors: Gontier Nathalie 
Published: November 2022

AbstractA theoretical framework is provided to explore teleonomy as a problem of self-causation, distinct from upward, downward and reticulate causation. Causality theories in biology are often formulated within hierarchy theories, where causation is conceptualized as running up or down the rungs of a ladder-like hierarchy or, more recently, as moving between multiple hierarchies. Research on the genealogy of cosmologies demonstrates that in addition to hierarchy theories, causality theories also depend upon ideas of time. This paper explores the roots and impact of both time and hierarchy thinking on causal reasoning in the evolutionary sciences. Within evolutionary biology, the Neodarwinian synthesis adheres to a linear notion of time associated with linear hierarchies that portray upward causation. Eco-evo-devo schools recognize the importance of downward causation and consequently receive resistance from the standard view because downward causation is sometimes understood as backward causation, considered impossible by adherents of a linear time model. In contrast, downward causation works with a spatial or presential time notion. Hybridization, lateral gene transfer, infective heredity, symbiosis and symbiogenesis require recognition of reticulate causation occurring in both space and time, or spacetime, between distinct and interacting ontological hierarchies. Teleonomy is distinct from these types of causation because it invokes the problem of self-causation. By asking how the focal level in a hierarchy can persist through time, self-causation raises philosophical concerns on the nature of duration, identity and individuality.
Local brain environment changes associated with epileptogenesis
Authors: Ikoma Yoko , Sasaki Daichi , Matsui Ko 
Published: November 2022

AbstractPlastic change of the neuronal system has traditionally been assumed to be governed primarily by the long-term potentiation/depression mechanisms of synaptic transmission. However, a rather simple shift in the ambient ion, transmitter and metabolite concentrations could have a pivotal role in generating plasticity upon the physiological process of learning and memory. Local brain environment and metabolic changes could also be the cause and consequences of the pathogenesis leading to epilepsy. Governing of the local brain environment is the primal function of astrocytes. The metabolic state of the entire brain is strongly linked to the activity of the lateral hypothalamus. In this study, plastic change of astrocyte reactions in the lateral hypothalamus was examined using epileptogenesis as an extreme form of plasticity. Fluorescent sensors for calcium or pH expressed in astrocytes were examined for up to one week by in vivo fibre photometry in freely moving transgenic male mice. Optical fluctuations on a timescale of seconds is difficult to assess because these signals are heavily influenced by local brain blood volume changes and pH changes. Using a newly devised method for the analysis of the optical signals, changes in Ca2+ and pH in astrocytes and changes in local brain blood volume associated with hippocampal-stimulated epileptic seizures were extracted. Following a transient alkaline shift in the astrocyte triggered by neuronal hyperactivity, a prominent acidic shift appeared in response to intensified seizure which developed with kindling. The acidic shift was unexpected as transient increase in local brain blood volume was observed in response to intensified seizures, which should lead to efficient extrusion of the acidic CO2. The acidic shift could be a result of glutamate transporter activity and/or due to the increased metabolic load of astrocytes leading to increased CO2 and lactate production. This acidic shift may trigger additional gliotransmitter release from astrocytes leading to the exacerbation of epilepsy. As all cellular enzymic reactions are influenced by Ca2+ and pH, changes in these parameters could also have an impact on the neuronal circuit activity. Thus, controlling the astrocyte pH and/or Ca2+ could be a new therapeutic target for treatment of epilepsy or prevention of undesired plasticity associated with epileptogenesis.
Cerebrospinal fluid biomarkers for assessing Huntington disease onset and severity
Authors: Caron Nicholas S , Haqqani Arsalan S , Sandhu Akshdeep , Aly Amirah E , Findlay Black Hailey , Bone Jeffrey N , McBride Jodi L , Abulrob Abedelnasser , Stanimirovic Danica , Leavitt Blair R , Hayden Michael R 
Published: November 2022

Abstract
The identification of molecular biomarkers in CSF from individuals affected by Huntington disease may help improve predictions of disease onset, better define disease progression and could facilitate the evaluation of potential therapies. The primary objective of our study was to investigate novel CSF protein candidates and replicate previously reported protein biomarker changes in CSF from Huntington disease mutation carriers and healthy controls. Our secondary objective was to compare the discriminatory potential of individual protein analytes and combinations of CSF protein markers for stratifying individuals based on the severity of Huntington disease. We conducted a hypothesis-driven analysis of 26 pre-specified protein analytes in CSF from 16 manifest Huntington disease subjects, eight premanifest Huntington disease mutation carriers and eight healthy control individuals using parallel-reaction monitoring mass spectrometry. In addition to reproducing reported changes in previously investigated CSF biomarkers (NEFL, PDYN, and PENK), we also identified novel exploratory CSF proteins (C1QB, CNR1, GNAL, IDO1, IGF2, and PPP1R1B) whose levels were altered in Huntington disease mutation carriers and/or across stages of disease. Moreover, we report strong associations of select CSF proteins with clinical measures of disease severity in manifest Huntington disease subjects (C1QB, CNR1, NEFL, PDYN, PPP1R1B, and TTR) and with years to predicted disease onset in premanifest Huntington disease mutation carriers (ALB, C4B, CTSD, IGHG1, and TTR). Using receiver operating characteristic curve analysis, we identified PENK as being the most discriminant CSF protein for stratifying Huntington disease mutation carriers from controls. We also identified exploratory multi-marker CSF protein panels that improved discrimination of premanifest Huntington disease mutation carriers from controls (PENK, ALB and NEFL), early/mid-stage Huntington disease from premanifest mutation carriers (PPP1R1B, TTR, CHI3L1, and CTSD), and late-stage from early/mid-stage Huntington disease (CNR1, PPP1R1B, BDNF, APOE, and IGHG1) compared with individual CSF proteins. In this study, we demonstrate that combinations of CSF proteins can outperform individual markers for stratifying individuals based on Huntington disease mutation status and disease severity. Moreover, we define exploratory multi-marker CSF protein panels that, if validated, may be used to improve the accuracy of disease-onset predictions, complement existing clinical and imaging biomarkers for monitoring the severity of Huntington disease, and potentially for assessing therapeutic response in clinical trials. Additional studies with CSF collected from larger cohorts of Huntington disease mutation carriers are needed to replicate these exploratory findings.
Ehm2 transcript variant 1 inhibits breast cancer progression and increases E-cadherin stability
Authors: Yin Xin , Li Gen , Fan Dongwei , Ge Zhicheng , Yang Tianshu , Shang Yaxin , Ma Tianyu , Yuan Baowen , Huang Wei , Teng Xu , Yu Hefen 
Published: November 2022

Abstract
Ehm2/1, an Ehm2 transcript variant, regulates the cytoskeleton by binding to plasma membrane proteins. However, the role of Ehm2/1 in breast cancer development remains poorly understood. This study shows that, the expression of Ehm2/1 was decreased in breast cancer and that patients with low Ehm2/1 expression had a significantly poorer prognosis than those with high expression of Ehm2/1. Overexpression of Ehm2/1 in MCF-7 breast cancer cells inhibited cell migration and invasion. Ehm2/1 markedly increased the stability and half-life of E-cadherin. Moreover, Ehm2/1 was collocated with E-cadherin in the plasma membrane of MCF-7 cells. Furthermore, downregulation of Ehm2/1 promoted ubiquitination of E-cadherin, whereas overexpression of Ehm2/1 inhibited ubiquitination of E-cadherin. These results suggest that Ehm2/1 could suppress the migration and invasion of breast cancer cells by increasing E-cadherin stability.
The comprehensive role of apoptosis inhibitor of macrophage (AIM) in pathological conditions
Authors: Yang Huiqing , Luo Yan , Lai Xiaofei 
Published: November 2022

Summary
CD5L/AIM (apoptosis inhibitor of macrophage), as an important component in maintaining tissue homeostasis and inflammation, is mainly produced and secreted by macrophages but partially dissociated and released from blood AIM-IgM. AIM plays a regulatory role in intracellular physiological mechanisms, including lipid metabolism and apoptosis. AIM not only increases in autoimmune diseases, directly targets liver cells in liver cancer and promotes cell clearance in acute kidney injury, but also causes arteriosclerosis and cardiovascular events, and aggravates inflammatory reactions in lung diseases and sepsis. Obviously, AIM plays a pleiotropic role in the body. However, to date, studies have failed to decipher the mechanisms behind its different roles (beneficial or harmful) in inflammatory regulation. The inflammatory response is a “double-edged sword,” and maintaining balance is critical for effective host defense while minimizing the adverse side effects of acute inflammation. Enhancing the understanding of AIM function could provide the theoretical basis for new therapies in these pathological settings. In this review, we discuss recent studies on the roles of AIM in lipid metabolism, autoimmune diseases and organic tissues, such as liver cancer, myocardial infarction, and kidney disease.