bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citric acid concentration tune of structural and magnetic properties in hematite (α−Fe2O3) nanoparticles synthesized by sol−gel method
Authors: Utari  , Maulidina Hikmah , Arilasita Retna , Widiyandari Hendri , Suharno  , Purnama Budi 
Published: February 2023

Abstract
This study synthesized hematite nanoparticles using the sol-gel method. The physical properties are modified by the citric acid concentration used as fuel. The resulting sample’s rhombohedral (hexagonal) structure and space group R3c were revealed by the XRD data. The Scherer formula revealed that the crystallite size at the most substantial peak was 32.14 nm, 24.58 nm, and 23.21 nm with an increase in the citric acid concentration of 0.3 M, 0.4 M, and 0.5 M, respectively. The FTIR spectrum’s absorption band reveals the properties of hematite nanoparticles. Finally, the magnetic properties confirmed from the VSM data revealed a significant decrease in the coercive field at 935 Oe, 610 Oe, and 548 Oe as the effect of citric acid concentration increased.
Tunable band-structures of MSe2/C3N (M = Mo and W) van der Waals Heterojunctions
Authors: Liu Zixiang , Yang Yaxiao , Yang Xiaoyu , Yin Guangqiang , Wang Zhiguo 
Published: February 2023

Abstract
Van der Waals (vdW) heterojunctions constructed using two-dimensional (2D) materials have shown excellent properties for applications in various fields. In this study, the structural and electronic properties of 2D MoSe2/C3N and WSe2/C3N vdW heterojunctions have been investigated using first-principles calculations. The results show that the MoSe2/C3N heterojunction is an indirect bandgap semiconductor with a small bandgap 0.05 eV and the WSe2/C3N heterojunction is a type II heterojunction with an indirect bandgap of 0.26 eV. Strains and external electric fields can effectively modulate the electronic structure of these heterojunctions. The WSe2/C3N heterojunction can become a type III heterojunction under compressive strains, which also becomes a direct bandgap heterojunction with type I band alignment under a negative electric field. Our results may be useful for the design of electronic nanodevices.
Invited Commentary: Modern Epidemiology Confronts COVID-19—Reflections From Psychiatric Epidemiology
Authors: Martínez-Alés Gonzalo , Keyes Katherine 
Published: February 2023

Abstract
Dimitris et al. (Am J Epidemiol. 2022;191(6):980–986) outline how the coronavirus disease 2019 (COVID-19) pandemic has, with mixed results, put epidemiology under the spotlight. While epidemiologic theory and methods have been critical in many successes, the ongoing global death toll from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the sometimes chaotic public messaging underscore that epidemiology as a field has room for improvement. Here, we use examples from psychiatric epidemiologic studies conducted during the COVID-19 era to reflect on errors driven by overlooking specific major methodological advances of modern epidemiology. We focus on: 1) use of nonrepresentative sampling in online surveys, which limits the potential knowledge to be gained from descriptive studies and amplifies collider stratification bias in causal studies; and 2) failure to acknowledge multiple versions of exposures (e.g., lockdown, school closure) and differences in prevalence of effect measure modifiers across contexts, which causes violations of the consistency assumption and lack of effect transportability. We finish by highlighting: 1) the heterogeneity of psychiatric epidemiologic results during the pandemic across place and sociodemographic groups and over time; 2) the importance of following the foundational advancements of modern epidemiology even in emergency settings; and 3) the need to limit the role of political agendas in cherry-picking and reporting epidemiologic evidence.
Heterogeneity of emotion regulation strategies in patients with alcohol use disorder during the first year of abstinence: a clustering analysis
Authors: Nandrino Jean-Louis , Gandolphe Marie-Charlotte , Claisse Caroline , Wawrziczny Emilie , Grynberg Delphine 
Published: February 2023

Abstract

Aims
Studies examining the use of specific emotion regulation (ER) strategies in patients with severe alcohol use disorder (AUD) are mainly focused on intergroup comparisons to the detriment of intragroup variability. Yet, these patients are in fact characterized by emotional deficits of varying severity, and we seek to identify different patterns of ER strategies in people with AUD during their first year of abstinence.

Methods
Based on the ER strategies used by a large sample of patients with AUD, we applied cluster analysis to identify the existence of subgroups using distinct patterns of adaptive and nonadaptive strategies. To characterize these groups, we compared their clinical characteristics and then their emotional regulation strategies to those of control consumers.

Results
A first cluster, representing 61% of the sample, is constituted by individuals with high adaptive strategy scores and high nonadaptive strategy scores; a second cluster, representing 39% of the sample, corresponds to individuals with low adaptive strategy scores and high nonadaptive strategy scores. The individuals in these two clusters differed in terms of anxiety level and abstinence time. Compared with control consumers, the use of nonadaptive ER strategies remained lower for the two clusters, while the use of adaptative strategies differed.

Conclusions
Our results support the idea of considering the heterogeneity of emotional capacities in individuals with AUD during the first year of abstinence. The identification of these profiles suggests either the existence of different adaptive ER capacities at baseline or a specific recovery of adaptive strategies over this period.
SARS-CoV-2 ORF8 dimerization and binding mode analysis with class I MHC: computational approaches to identify COVID-19 inhibitors
Authors: Selvaraj Chandrabose , Dinesh Dhurvas Chandrasekaran , Pedone Emilia Maria , Alothaim Abdulaziz S , Vijayakumar Rajendran , Rudhra Ondippili , Singh Sanjeev Kumar 
Published: February 2023

AbstractSARS-CoV-2 encodes eight accessory proteins, one of which, ORF8, has a poorly conserved sequence with SARS-CoV and its role in viral pathogenicity has recently been identified. ORF8 in SARS-CoV-2 has a unique functional feature that allows it to form a dimer structure linked by a disulfide bridge between Cys20 and Cys20 (S-S). This study provides structural characterization of natural mutant variants as well as the identification of potential drug candidates capable of binding directly to the interchain disulfide bridge. The lead compounds reported in this work have a tendency to settle in the dimeric interfaces by direct interaction with the disulfide bridge. These molecules may disturb the dimer formation and may have an inhibition impact on its potential functional role in host immune evasion and virulence pathogenicity. This work provides detailed insights on the sequence and structural variability through computational mutational studies, as well as potent drug candidates with the ability to interrupt the intermolecular disulfide bridge formed between Cys20 and Cys20. Furthermore, the interactions of ORF8 peptides complexed with MHC-1 is studied, and the binding mode reveals that certain ORF8 peptides bind to MHC-1 in a manner similar to other viral peptides. Overall, this study is a narrative of various computational approaches used to provide detailed structural insights into SARS-CoV-2 ORF8 interchain disulfide bond disruptors.
Regularized adversarial learning for normalization of multi-batch untargeted metabolomics data
Authors: Dmitrenko Andrei , Reid Michelle , Zamboni Nicola 
Published: February 2023

AbstractMotivationUntargeted metabolomics by mass spectrometry is the method of choice for unbiased analysis of molecules in complex samples of biological, clinical or environmental relevance. The exceptional versatility and sensitivity of modern high-resolution instruments allows profiling of thousands of known and unknown molecules in parallel. Inter-batch differences constitute a common and unresolved problem in untargeted metabolomics, and hinder the analysis of multi-batch studies or the intercomparison of experiments.ResultsWe present a new method, Regularized Adversarial Learning Preserving Similarity (RALPS), for the normalization of multi-batch untargeted metabolomics data. RALPS builds on deep adversarial learning with a three-term loss function that mitigates batch effects while preserving biological identity, spectral properties and coefficients of variation. Using two large metabolomics datasets, we showcase the superior performance of RALPS as compared with six state-of-the-art methods for batch correction. Further, we demonstrate that RALPS scales well, is robust, deals with missing values and can handle different experimental designs.Availability and implementationhttps://github.com/zamboni-lab/RALPS.Supplementary informationSupplementary data are available at Bioinformatics online.
MeganServer: facilitating interactive access to metagenomic data on a server
Authors: Gautam Anupam , Zeng Wenhuan , Huson Daniel H 
Published: February 2023

AbstractMotivationMetagenomic projects often involve large numbers of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases have required that the user first download the computed data from the server, an increasingly time-consuming process. Here, we present MeganServer, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis in MEGAN, without requiring prior download of the data. We describe a number of different application scenarios.Availability and implementationMeganServer is provided as a stand-alone program tools/megan-server in the MEGAN software suite, available at https://software-ab.cs.uni-tuebingen.de/download/megan6. Source is available at: https://github.com/husonlab/megan-ce/tree/master/src/megan/ms.Supplementary informationSupplementary data are available at Bioinformatics online.
‘You Say One Thing Wrong, and Your Children Are Gone’: Exploring Trauma-Informed Practices in Foster and Kinship Care
Authors: Cooper Kimberlea , Sadowski Christina , Townsend Rob 
Published: February 2023

Abstract
Trauma-informed care is a growing practice approach in child and family social work. Current policy directions in out-of-home care (OOHC) in Victoria, Australia show an interest in further implementation of trauma-informed care, particularly through training for foster and kinship carers. Drawing upon findings from grounded theory research with sixteen foster and kinship carers, this article considers the application of trauma-informed practices in home-based care in the Central Highlands region of Victoria, Australia. The research reveals that whilst carers utilise principles of trauma-informed care to support children and young people, they do not always experience trauma-informed support from the wider OOHC system. This discrepancy suggests that the implementation of trauma-informed care has the potential to increase pressure on home-based carers if it is only encouraged at the interpersonal level between carers and children, without incorporating associated systems-level change. These findings propose that whilst micro-level support and training for carers are necessary and useful, it is crucial for OOHC systems to move beyond such initiatives to plan and enact macro-level reforms.
Cell therapies for spinal cord injury: a review of the clinical trials and cell-type therapeutic potential
Authors: Ribeiro Beatriz F , da Cruz Bruna C , de Sousa Bárbara M , Correia Patrícia D , David Nuno , Rocha Camila , Almeida Ramiro D , Ribeiro da Cunha Maria , Marques Baptista António A , Vieira Sandra I 
Published: February 2023

AbstractSpinal cord injury (SCI) is an as yet untreatable neuropathology that causes severe dysfunction and disability. Cell-based therapies hold neuroregenerative and neuroprotective potential, but, although being studied in SCI patients for more than two decades, long-term efficacy and safety remain unproven, and which cell types result in higher neurological and functional recovery remains under debate.In a comprehensive scoping review of 142 reports and registries of SCI cell-based clinical trials, we addressed the current therapeutical trends and critically analysed the strengths and limitations of the studies. Schwann cells, olfactory ensheathing cells (OECs), macrophages and various types of stem cells have been tested, as well as combinations of these and other cells. A comparative analysis between the reported outcomes of each cell type was performed, according to gold-standard efficacy outcome measures like the ASIA impairment scale, motor and sensory scores.Most of the trials were in the early phases of clinical development (phase I/II), involved patients with complete chronic injuries of traumatic aetiology and did not display a randomized comparative control arm. Bone marrow stem cells and OECs were the most commonly tested cells, while open surgery and injection were the main methods of delivering cells into the spinal cord or submeningeal spaces. Transplantation of support cells, such as OECs and Schwann cells, resulted in the highest ASIA Impairment Scale (AIS) grade conversion rates (improvements in ∼40% of transplanted patients), which surpassed the spontaneous improvement rate expected for complete chronic SCI patients within 1 year post-injury (5–20%). Some stem cells, such as peripheral blood-isolated and neural stem cells, offer potential for improving patient recovery. Complementary treatments, particularly post-transplantation rehabilitation regimes, may contribute highly to neurological and functional recovery.However, unbiased comparisons between the tested therapies are difficult to draw, given the great heterogeneity of the design and outcome measures used in the SCI cell-based clinical trials and how these are reported. It is therefore crucial to standardize these trials when aiming for higher value clinical evidence-based conclusions.
Cancer-testis non-coding RNA LEF1-AS1 regulates the nuclear translocation of PDCD5 and suppresses its interaction with p53 signaling: a novel target for immunotherapy in esophageal squamous cell carcinoma
Authors: Xiao Zhihan , Si Mingxuan , Cao Jing , Chen Xiru , Wang Zichen , Zhang Tongyu , Zhou Yichan , Li Hai , Dai Juncheng , Wang Cheng , Chen Liang , Xu Jing 
Published: February 2023

Abstract
Despite the improvement of current classical treatment, the prognosis of esophageal squamous cell carcinoma (ESCC) remains poor. Immunotherapy, as a new treatment method, has revolutionized the therapy of various cancer types and created more attractive for ESCC. Cancer-testis genes (CTGs), because of its characteristic expression and immunomodulation property, are considered as the ideal targets for tumor immunotherapy. However, the ESCC-specific CTGs, especially long non-coding RNA (lncRNA), has not been elucidated. In the present study, a systematic strategy was adopted to screen ESCC-specific cancer-testis lncRNA (CT-lncRNA). Collectively, 447 genes were recognized as ESCC-specific CT-lncRNAs, in particularly LEF1-AS1 showed the most aberrantly expression and clinically associated with poor outcome. Functional assays revealed that H3K27 acetylation in LEF1-AS1 promoter might give rise to the activation of LEF1-AS1 during ESCC tumorigenesis. The activated LEF1-AS1 was predominantly localized in the cytoplasm implicated in regulation of apoptosis and proliferation capacities of ESCC cells in vitro and in vivo. Further mechanistic studies unveiled that LEF1-AS1 participated in ESCC by interacting with RNA binding protein PDCD5 through weakened its nuclear translocation binding to TP53, leading to p53 degradation and disruption the transcription of downstream genes. Taken together, our findings suggest that LEF1-AS1 acts as a CT-lncRNA and might be an ideal immunotherapeutic target for clinical intervention for ESCC.
Genomic coevolution of papillomavirus and immune system in placental mammals indicates the role of IFN-γ in the emergence of new variants
Authors: Karamveer  , Tiwary Basant K 
Published: February 2023

Abstract
Papillomaviruses (PVs) are causative agents for warts and cancers in different parts of the body in the mammalian lineage. Therefore, these viruses are proposed as model organisms to study host immune responses to pathogens causing chronic infections. The virus-associated cancer progression depends on two integral processes namely angiogenesis and immune response (AIR). The angiogenesis process aids in tumour progression through vessel formation and maturation but the host immune response, in contrast, makes every attempt to eliminate pathogens and thereby maintain healthy tissues. However, the evolutionary contribution of individual viral genes and host AIR genes in carcinogenesis is yet to be explored. Here, we applied the evolutionary genomics approach to find correlated evolution between six PV genes and 23 host AIR-related genes. We estimated that interferon (IFN)-γ is the only host gene evolving in a correlated manner with all six PV genes under study. Furthermore, three PV genes, such as L2, E6 and E7, are found to interact with two thirds of host AIR-related genes. Moreover, a combined differential gene expression analysis and network analysis showed that inflammatory cytokine IFN-γ is the key regulator of hub genes in the protein–protein interaction network of the differentially expressed genes. Functional enrichment of these hub genes is consistent with their established role in different cancers and viral infections. Overall, we conclude that IFN-γ maintains selective pressure on mammalian PV genes and seems to be a potential biomarker for PV-related cancers. This study demonstrates the evolutionary importance of IFN-γ in deciding the fate of carcinogenic PV variants.
Research on cooling-temperature control strategy of fuel-cell engine test bench
Authors: Du Chang , Ma Tiancai , Lin Weikang , Song Kaihang , Liang Yonghao 
Published: February 2023

AbstractAs one of the important ways to utilize hydrogen energy, fuel cells are receiving more and more attention and research from countries and institutions. To meet the practical needs of testing the performance of high-power fuel-cell systems and simulate the actual application environment as much as possible, a fuel-cell system test bench is usually used to test the system performance, in which the cooling-temperature control of the test bench has a great impact on the results of the performance of the fuel-cell system. This paper studies the cooling-temperature control strategy of a 150-kW-class fuel-cell engine test platform, proposes a new test-bench cooling-system structure with a thermostat and heat exchanger as the main heat-dissipation components, and compares and analyzes the impact of coordinated thermostat and heat-exchanger control on the fuel-cell system test performance. The test results show that the control strategy of the coordinated operation of a thermostat and heat exchanger can maintain the steady-state error to within ±0.3℃ and maintain the temperature variation to within ±1.5℃ during the loading-condition test, so as to avoid the limitation of system output performance due to excessive cooling-temperature fluctuation and ensure that the fuel-cell engine performance-test process is carried out smoothly and efficiently.
CRISPR-gene-engineered CYBB knock-out PLB-985 cells, a useful model to study functional impact of X-linked chronic granulomatous disease mutations: application to the G412E X91+-CGD mutation
Authors: Beaumel Sylvain , Verbrugge Lucile , Fieschi Franck , Stasia Marie José 
Published: February 2023

Abstract
Chronic granulomatous disease (CGD) is a rare primary immune disorder caused by mutations in one of the five subunits of the NADPH oxidase complex expressed in phagocytes. Two-thirds of CGD cases are caused by mutations in CYBB that encodes NOX2 or gp91phox. Some rare X91+-CGD point mutations lead to a loss of function but with a normal expression of the mutated NOX2 protein. It is therefore necessary to ensure that this mutation is indeed responsible for the loss of activity in order to make a safe diagnosis for genetic counselling. We previously used the X-CGD PLB-985 cell model of M.C. Dinauer obtained by homologous recombination in the original PLB-985 human myeloid cell line, in order to study the functional impact of such mutations. Although the PLB-985 cell line was originally described by K.A. Tucker et al. in1987 as a distinct cell line isolated from a patient with acute nonlymphocytic leukemia, it is actually identified as a subclone of the HL-60 cells. In order to use a cellular model that meets the quality standard for the functional study of X91+-CGD mutations in CGD diagnosis, we developed our own model using the CRISPR-Cas9 technology in a certified PLB-985 cell line from DSMZ-German Collection of Microorganisms and Cell Cultures. Thanks to this new X-CGD model, we demonstrated that the G412E mutation in NOX2 found in a X91+-CGD patient prohibits access of the electron donor NADPH to its binding site explaining the absence of superoxide production in his neutrophils.
Crohn’s Disease Patient Experiences and Preferences With Disease Monitoring: An International Qualitative Study
Authors: Rohatinsky Noelle , Zelinsky Sandra , Dolinger Michael , Christensen Britt , Wilkens Rune , Radford Shellie , Dubinsky Marla , Novak Kerri 
Published: February 2023

AbstractBackgroundStrategies incorporating objective disease monitoring in Crohn’s disease (CD), beyond clinical symptoms are important to improve patient outcomes. Little evidence exists to explore patient understanding of CD treatment goals, nor preferences and experiences with monitoring options. This qualitative study aimed to explore patient experiences and preferences of CD monitoring to inform monitoring strategies, improve patient engagement, and optimize a patient-centered approach to care.MethodsThis study used a patient-oriented, qualitative descriptive design. Convenience and snowball sampling were used to recruit adult participants diagnosed with CD who had experience with at least 2 types of disease monitoring. Online focus groups were conducted and data were analyzed using thematic analysis.ResultsThis international study included 37 participants from Australia, Canada, United Kingdom, and the United States. Overall, participants preferred more noninvasive types of monitoring [eg, intestinal ultrasound (IUS)] but were willing to undergo more invasive monitoring (eg, colonoscopy) if required. To improve disease monitoring, participants wanted increased access to IUS, establishment of a patient-centered interdisciplinary team and access to information and self-testing. Participants identified challenges with communication between patients and providers and stressed the importance of participating in shared decision making and being equal team members in their care.ConclusionsIt is imperative to incorporate patient-driven preferences into how we can best structure monitoring strategies, to ensure equitable access to those preferred modalities and embrace a shared decision-making approach to disease management in CD.