bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic Next-generation Sequencing Indicates More Precise Pathogens in patients with pulmonary infection: a retrospective study
Authors: Wu Dengfeng , Wang Wei , Xun Qiufen , Wang Hongluan , Liu Jiarong , Zhong Ziqing , Ouyang Chao , Yang Qing 
Published: February 2022

Abstract
Background: Timely identification of causative pathogens is always an important link for the diagnosis and treat for pulmonary infection. As a novel approach to detect the pathogens, metagenomic next-generation sequencing (mNGS) can directly sequence the nucleic acid of specimens, providing a wide range of microbial profiles. The purpose of this study is to evaluate the diagnostic performance of mNGS of bronchoalveolar lavage fluid (BALF) in patients suspected with pulmonary infection.Methods: From April 2019 to July 2021, 502 patients with suspected pneumonia undergoing both mNGS of BALF and conventional microbiological tests (CMTs) were classified into different groups based on the comorbidities. The diagnostic performance was compared between mNGS and CMTs. Clinical comprehensive analysis was regarded as reference standard. Result: The diagnostic accuracy and sensitivity of mNGS were 74.9% (95% confidence interval [CI], 71.7-78.7%) and 72.5% (95% CI, 68.2-76.8%) respectively, outperformed those of CMTs (36.2% for diagnostic accuracy, 25.4% for sensitivity). In most of the pathogens, the detection rate of mNGS was higher than CMTs. Polymicrobial infections most often occurred in immunocompromised group (22.1%), followed by other comorbidities group (22.1% vs 13.3%, p= 0.13) and bronchiectasis group (22.1% vs 9.7%, p= 0.018). Only 2.3% (95%CI, 0.3%-4.4%) patients developed polymicrobial infection in simple pulmonary infection group. Besides, the spectrums of pathogens also varied in different groups. Importantly, the positive predictive values (PPVs) of mNGS were observed discrepant in different pathogens: 94.9% (95%CI 89.1-100%) for Mycobacterium tuberculosis, 86.2% (95%CI,72.9-99.6%) for Chlamydia psittaci, 86.0% (95%CI, 76.0-96.0%) for Aspergillus, and 67.6% (95%CI, 51.1-84.2%) for Non-mycobacterium tuberculosis, 67.3% (95%,54.1-80.5%) for Pneumocystis jeroveci; as for bacteria, the PPVs also show differences in different types of bacteria. Conclusion: mNGS of BALF can highly enhance the accuracy and detection rate of pathogens in patients with pulmonary infection. Besides, the comorbidities and the types of pathogens should be taken into consideration when interpreting the report of mNGS.
Randomization and Selection of Self-Calibrating Binary Encoders in Neural Systems
Authors: Herbert Alan 
Published: February 2022

Abstract
Zebrafish larvae are able to track and capture prey five days post-fertilization, consistent with a genetic specification of pattern recognition by the nervous system, yet inconsistent with a process that involves tweaking of individual neural connections by processes similar to those currently employed to train artificial neural nets (ANN). Biological neural networks appear extremely efficient and adaptable when compared to ANN. Here I describe self-calibrating randomly initiated binary encoders (SCRIBEs) that produce sparse output and are highly scalable. The self-calibrating nets (SCN) they generate are capable of classifying and tracking objects with high accuracy and fluency by a process based on selection of features offering the best discrimination. Calibration of SCRIBEs depends on array thresholds that vary with their size but can happen without external input during development and sleep. In neural systems, synchronization likely depends on neuromodulator and brainwave status.
Identification of Novel Immune-infiltration Related miRNAs that can Predict the Prognosis of Patients with Hepatocellular Carcinoma
Authors: Liu Yefu , Li Wenxin 
Published: February 2022

Abstract
Background: Although immune checkpoint inhibitors (ICIs) have achieved important breakthroughs in the treatment of liver cancer, most hepatocellular carcinoma (HCC) patients do not respond to ICIs, and their clinical outcome remains unsatisfactory. The tumor microenvironment (TME), which contains immune cells and other molecules, probably influences both the prognosis and the response to immunotherapy in HCC. Here, using integrated bioinformatics analyses, we identified key molecules (immune cells and immune-related microRNAs (miRNAs)) as potential prognostic markers for HCC.Method: MRNA and miRNA expression profiles and clinicopathological data were extracted from the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data collection. A total of 22 immune cell types from HCC patients were assessed using a deconvolution algorithm (known as CIBERSORT). Both Kaplan-Meier analysis and Cox proportional hazards regression were used to evaluate the prognostic value of the immunocytes. The correlations between differentially expressed miRNAs and tumor-infiltrating immune cells were investigated using the Pearson correlation coefficient. Machine learning approaches were employed to identify prognostic miRNAs. The miRTarBase database was used to construct a DEmiRNA-target gene network. Function enrichment analyses were performed using Metascape software. The relationships between two specific miRNAs and the expression of immune markers (antigen presenting machinery (APM) and tumor-infiltrating lymphocytes (TILs)) as well as cell checkpoint markers were also analyzed.Results: A total of 19 T regulatory cell (Treg)-related miRNAs were identified by machine learning approaches (p<0.001, |cor|>0.2). Metascape revealed that Treg-related miRNA-target networks were significantly enriched in biological processes including cellular responses to stress, mitotic cell cycle and myeloid cell differentiation. Using univariate Cox regression analysis on an independent dataset, GSE31384, 19 miRNAs were evaluated for their importance in overall survival (OS). Two hub miRNAs (hsa-miR-877 and hsa-miR-137) were found to significantly impact on OS. Therefore, we assessed the association between these two miRNAs and immune markers (APM, TILs) and cell checkpoint markers (programmed cell death-1 (PD-1), programmed death-ligand 1 (PD-L1), cytotoxic T-lymphocyte antigen-4 (CTLA-4), B- and T-lymphocyte attenuator (BTLA)), and found statistically significant associations in both the TCGA and GSE31384 datasets.Conclusion: Our study showed that hsa-miR-877 and hsa-miR-137 were significantly associated with poor prognosis in HCC through their effects on Tregs and immune checkpoint markers in the TME. These results suggest that hsa-miR-877 and hsa-miR-137 might serve as novel therapeutic targets for HCC.
Construction of axial chirality via asymmetric radical trapping by cobalt under visible light
Authors: Xiao Wen-Jing , Jiang Xuan , Xiong Wei , Deng Shuang , Lu Fu-Dong , Jia Yue , Yang Qian , Xue Li-Yuan , Qi Xiaotian , Tunge Jon A. , Lu Liang-Qiu 
Published: February 2022

Abstract
3d-Metals have been identified as economic and sustainable alternatives to palladium, the frequently used metal in transition-metal-catalyzed cross-couplings. However, cobalt has long stood behind its neighboring elements, nickel and copper, in asymmetric radical couplings, owing to its high catalytic activity in the absence of ligands. Here, we disclose an asymmetric metallaphotoredox catalysis (AMPC) strategy for the dynamic kinetic resolution (DKR) of racemic heterobiaryls, which represents the first example of visible-light-induced, asymmetric radical couplings for the construction of axial chirality. This success can also be extended to the reductive cross-coupling variant featuring on more easily available feedstocks. The keys to these successes are the rational design of a sustainable AMPC system by merging asymmetric cobalt catalysis with organic photoredox catalysis and, perhaps more importantly, the identification of an efficient chiral polydentate ligand.
Comparative proteome analysis of the tegument of male and female adult Schistosoma mansoni
Authors: Winkelmann Franziska , Salazar Manuela Gesell , Hentschker Christian , Michalik Stephan , Macháček Tomáš , Scharf Christian , Reisinger Emil C. , Völker Uwe , Sombetzki Martina 
Published: February 2022

Abstract
The tegument, as the surface layer of adult male and female Schistosoma spp. represents the protective barrier of the worms to the hostile environment of the host bloodstream. Here we present the first comparative analysis of sex-specific tegument proteins of paired or virgin Schistosoma mansoni. We applied a new and highly sensitive workflow, allowing detection of even low abundance proteins. Therefore, a streptavidin-biotin affinity purification technique in combination with single pot solid-phase enhanced sample preparation was established for subsequent LC-MS/MS analysis. We were able to identify 1519 tegument proteins for male and female virgin and paired worms and categorized them by sex. Bioinformatic analysis revealed an involvement of female-specific tegument proteins in signaling pathways of cellular processes and antioxidant mechanisms. Male-specific proteins were found to be enriched in processes linked to phosphorylation and signal transduction. This suggests a task sharing between the sexes that might be necessary for survival in the host. Our datasets provide a basis for further studies to understand and ultimately decipher the strategies of the two worm sexes to evade the immune system.
Cardiac Iron Overload Detection Using Longitudinal Strain in Asymptomatic Children with Beta Thalassemia Major
Authors: CHAMTOURI IKRAM , khalifa Roueida , besbes habib , jomaa walid , abdallah wajih , hamda khaldoun ben , Chouchene Chokri , maatouk faouzi 
Published: February 2022

Abstract
Background.Cardiomyopathy mediated by iron disposition in cardiomyocytes is a dreadful cause of morbidity and mortality in patients with beta thalassemia major (BTM). Conventional transthoracic echocardiography (TTE) parameters are preserved at late stages of cardiomyopathy induced by iron overload. Therefore, cardiac imaging modalities based on myocardial deformation such as strain imaging are used for early detection of cardiac iron overload.Aim.To demonstrate the contribution of longitudinal strain (LS) in early detection of cardiac iron overload in children with BTM.Methods.Sixty children (30 children with BTM and 30 healthy controls) were enrolled in this study. Conventional TTE study was performed in both patient and control groups. LV regional longitudinal strain (RLS) were determined and compared between the two study groups.Results.Mean age was 10.4 ± 5years in BTM group compared to 10.2 ± 5 years in control group (p=0.876). Compared to control group, there was no significant difference in conventional TTE parameters except for indexed left atrium (LA) area and volume. LA was significantly larger in BTM children (27.59 ±13.1ml/m² vs. 18.23 ± 4.33 ml/m², p=0.001). RLS was lower in anterior, septal and inferior walls in basal and middle segments of LV in BTM group while there was no significant difference in RLS in apical segment between the two groups (-27.30 ± 5.1 vs. -28.83 ± 4.33, p=0.22).Conclusion.In asymptomatic BMT children with normal conventional TTE parameters, LS could be used for the detection of subclinical myocardial dysfunction.
Free-electron-driven X-ray caustics from strained van der Waals materials
Authors: Shi Xihang , Shentcis Michael , Kurman Yaniv , Wong Liang Jie , de Abajo F. Javier Garcia , Kaminer Ido 
Published: February 2022

Abstract
Tunable nanoscale shaping of X-ray waves remains as an open challenge of critical importance for applications in high-resolution X-ray spectroscopy and imaging. In contrast to this high photon energy regime, shaping of light waves in the visible and infrared regimes is routinely undertaken in a vast range of applications by means of abundantly available optical components. However, analogous optical elements are scarcer for X-rays. Here, we propose a new paradigm based on van der Waals (vdW) materials for shaping X-ray waves directly at the source. By inducing strain and bending on vdW materials, we control their interaction with free electrons in a manner that tunes the emission of X-rays and forms caustic X-ray beams. The geometry of the vdW material alters the caustic beam properties, including its focal length, spot size, and diffraction-free length. The ability to integrate X-ray shaping into the electron-driven emission process bypasses the efficiency limits of current optical techniques in this spectral regime. Looking forward, by shaping X-ray wave interference at the atomic scale we open new horizons in high-resolution X-ray science.
Nursing risks and preventive strategies of the elderly: an interview-based study with staff at long-term care facilities
Authors: Liu Chang-qing , Ren Hong-fei , Li Jia-ling , Cheng Li-nan , Xie Xiao-feng , Zhang Feng-ying 
Published: February 2022

Abstract
Background: The prevention and control of nursing risks play a critically important role in ensuring safety and maintaining the health of the elderly in long-term care facilities. Methods: In-depth interviews were conducted on participants in 16 long-term care facilities using a semi-structured interview. The transcribed interviews and field notes written during the visits were analyzed inductively following a constant comparative method as described in Grounded Theory. Data were analyzed using framework analysis and domains, and the NVivo 10 software was used to refine themes and build relationships among themes. The authors followed the COREQ guidelines to ensure rigour in the study.Results: A total of 28 participants (18 managers, 5 head nurses, 2 qualified nurses, and 3 healthcare assistants) were interviewed. In the risk warning model, nursing risks (factors that affect risks, consequences), risk early warning intervention measures (risk assessment, training, and education, comprehensive preventive measures), challenges and solutions as potential and observation variables affecting nursing risks, were aimed to reduce nursing risks in long-term care facilities.Conclusions: There are many nursing risk factors in long-term care facilities, among which nursing risk assessment plays an important intermediate role in risk prevention. Comprehensive measures can be formulated and implemented according to relevant nursing risk factors, referred to as the early warning model, to reduce the incidence of nursing risks and promote the safety of the elderly in long-term care facilities.
Coexistence in spatiotemporally fluctuating environments
Authors: Johnson Evan , Hastings Alan 
Published: February 2022

Abstract
Ecologists have put forward many explanations for coexistence, but these are only partial explanations; nature is complex, so it is reasonable to assume that in any given ecological community, multiple mechanisms of coexistence are operating at the same time. Here, we present a methodology for quantifying the relative importance of different explanations for coexistence, based on an extension of Modern Coexistence Theory. Current versions of Modern Coexistence Theory only allow for the analysis of communities that are affected by spatial or temporal environmental variation, but not both. We show how to analyze communities with spatiotemporal fluctuations, how to parse the importance of spatial variation and temporal variation, and how to measure everything with either mathematical expressions or simulation experiments. Our extension of Modern Coexistence Theory shows that many more species can coexist than originally thought. More importantly, it allows empiricists to use realistic models and more data to better infer the mechanisms of coexistence in real communities.
SCARB2 Drives Hepatic Carcinoma Initiation by Supporting Cancer Stem Cell Traits and Enhancing MYC Transcriptional Activity
Authors: Wang Feng , Gao Yang , Xue Situ , Zhao Luyao , Zhang Tingting , Li Yun-Xuan , Zhao Chenxi , Wu Fan , Liu Ying , Wu Jie , Yan Yechao , JIANG JIAN-DONG , Li Ke 
Published: February 2022

Abstract
Cancer stem cells (CSCs) with distinct metabolic features are considered to cause hepatocellular carcinoma (HCC) initiation, metastasis and therapeutic resistance. Here, we performed a metabolic gene CRISPR/Cas9 knockout screen in tumorspheres derived from HCC cells and found that deletion of the scavenger receptor SCARB2 suppressed the CSC traits of HCC cells. Using lineage tracing of the Scarb2 locus in mice, we demonstrated that Scarb2 positive HCC cells showed tumor-initiating activity. Specifically, Cre-mediated recombination with oncogenic MYC expression in Scarb2 positive cells drove HCC tumor formation, as determined by lineage tracing in Scarb2 mice. Knockout of Scarb2 in hepatocytes attenuated HCC initiation and progression by inhibiting CSC self-renewal. Mechanistically, binding of SCARB2 with MYC promoted MYC acetylation by interfering with HDCA3-mediated MYC deacetylation and subsequently enhanced MYC activity. Screening of a database of FDA-approved drugs showed Polymyxin B displayed high binding affinity for SCARB2 protein, disrupted the SCARB2-MYC interaction, decreased MYC activity, and reduced the tumor burden. Our study identifies SCARB2 as a marker and functional driver of HCC CSCs and suggests a targeted therapeutic option for HCC.
Modulation of Inflammatory Cytokines Secretion Response from Stimulated Human PBMCs Following Application of Recombinant Human Cytokines IL-37b and IL-38 Produced in Plants.
Authors: Kolotilin Igor 
Published: February 2022

Abstract
Affordable therapeutics are vitally needed for humans worldwide. Plant-based production of recombinant proteins can potentially enhance, back-up, or even substitute for the manufacturing capacity of the conventional, fermenter-based technologies. We plastome-engineered a tobacco cultivar to express high levels of two “plantakines” - recombinant human cytokines, interleukins IL-37b and IL-38, and confirmed their native conformation and folding. Assessment of their biological functionality was performed ex vivo by analyzing the effects exerted by the plantakines on levels of 11 cytokines secreted from human Peripheral Blood Mononuclear Cells (PBMCs) challenged with an inflammatory agent. Application of the plant-produced IL-37b and IL-38 in PBMCs stimulated with Lipopolysaccharide or Phytohaemagglutinin resulted in significant, dose-dependent modulation of pro-inflammatory cytokines secretion and attenuation of levels of several cytokines involved in inflammatory response. Our results demonstrate feasibility of manufacturing functional recombinant human proteins using scalable, cost-effective and eco-friendly plant-based bioreactors.
"Ethical and Regulatory Issues in Genetic Research Collaboration between Global Pharmaceutical Industry and Low- and Middle-income Countries"
Authors: Sharawy Iman 
Published: February 2022

Abstract
Background:The global pharmaceutical industry (big pharma) is responsible for production, and distribution of drugs. Big pharma revenues have been growing markedly totaling about 1.27 trillion U.S. dollars in 2020. Low- and middle-income countries spend only 1.46% of their Gross Domestic Products (GDP) on research and development necessitating collaboration with big pharma. Genetic research require access to sophisticated laboratories, large-scale genotyping facilities, bioinformatics and statistical expertise which cannot be afforded by low or middle-income countries. Consequently, most of the genetic research is conducted in high-income countries and big pharma. Main body: This paper has three aims: the first aim is to identify ethical and regulatory issues related to genetic research collaboration of big Pharma with low and middle-income countries. The second aim is to explain the impact of non-collaboration of big pharma with low and middle-income countries. The third aim is to propose a future ethical and regulatory framework for genetic research of big pharma with low- and middle-income countries. To accomplish these aims the big pharma revenue and spending was outlined, the necessity of genetic collaboration was highlighted and the resultant ethical and regulatory gaps were elaborated. The COVID-19 mRNA vaccine was mentioned as an illustration for non-collaboration. Then a future ethical and regulatory framework for genetic research of big pharma with low- and middle-income countries at the international, national and research ethics committee levels was proposed.Conclusion:This paper identified several ethical and regulatory issues related to genetic research collaboration and non-collaboration of big Pharma with low and middle-income countries followed by proposing a future ethical and regulatory framework for collaboration at the international, national and research ethics committee levels.
Soil chemical properties, microbial biomass and soil enzyme dynamics on transplanted rice with organic amendments
Authors: Singh Nika Beth , Hamimed Selma 
Published: February 2022

Abstract
A field experiment was conducted at the farm of Tamil Nadu Agricultural University, India, during the Kharif season to study soil chemical properties, microbial biomass and soil enzyme dynamics on transplanted rice with organic amendments. Rice CO(R) 48 was used as a test variety. The experiment was laid out in randomized block design (RBD) with three replications and nine treatments, which are: T1 –100% N through dhaincha + balance P and K through inorganic fertilizers, T2 – 50% N through dhaincha + balance N, P and K through inorganic fertilizers, T3 –100% N through vermicompost + balance P and K through inorganic fertilizers, T4 –50% N through vermicompost + balance N, P and K through inorganic fertilizers, T5 –100% NPK (150: 50: 50 kg ha-1) through inorganic fertilizers, T6 –100% NPK through inorganic fertilizers + 12.5 t farmyard manure, T7 – 100% NPK through inorganic fertilizers + 6.25 t dhaincha, T8 – 100% NPK through inorganic fertilizers + 5 t vermicompost, and T9 – Control. The results revealed that maximum microbial population (bacteria, fungal, and actinomycetes), soil enzyme dynamics (urease, dehydrogenase, and soil phosphatase activity), soil available macronutrients (N, P, K) and micronutrients (Fe, Zn, Mn, and Cu) were significantly influenced with the application of 100% of N through dhaincha + balance P and K through inorganic fertilizers followed by application of 100% NPK through inorganic fertilizers + 6.25 t dhaincha. Most minor enzyme activity, microbial population & soil available nutrients of rice were registered in absolute control.