bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Method for Standardizing Inland Fish Community Surveys: Characterizing Habitat Associated with Small-Bodied Fish Species, Abundance, and Size Distributions in a Highly Modified Estuary
Authors: Merz Joseph E. , Camp Meghan J. , Simonis Juniper L. , Thorpe Whitney 
Published: July 2021

Monitoring fish assemblages in estuary environments is often difficult to standardize due to habitat complexity and gear-specific selectivity. This is further compounded by conventional sampling methods which require fish handling that might cause stress or mortality. To ameliorate these issues, we developed the Single-Platform Aquatic Species and Habitat Sampling System (Platform), an integrated and mobile concentrator net and live box prototype, coupled with a range of physical monitoring equipment. The long-term goal of the Platform is to employ non-invasive sampling techniques such as video and eDNA; however, our aim in this study was to test the Platform’s ability to sample across different habitat types and detect differences in fish assemblages. We investigated the utility of the Platform over a short time period (2 mo) in a relatively small and complex embayment within the highly modified San Francisco Estuary, California. We were able to identify clear physical distinctions among estuary/delta habitat types and detect habitat segregation by ecological groups of sampled fishes with the Platform. The Platform also detected discernable ontogenetic shifts (i.e., size differences) within estuary habitats of commonly observed fish species. These initial results demonstrate the Platform’s ability to contrast fish density, size, and species diversity, which sets the stage to advance more passive monitoring techniques, including video and eDNA methods. The Platform has the potential to fill a methodological gap in non-invasive surveying of small-bodied fish across a range of estuarine habitats, warranting further investigation of potential applications.
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
Authors: Honorato Rodrigo V. , Koukos Panagiotis I. , Jiménez-García Brian , Tsaregorodtsev Andrei , Verlato Marco , Giachetti Andrea , Rosato Antonio , Bonvin Alexandre M. J. J. 
Published: July 2021

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending &gt;12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.
Immune Microenvironment Signatures as Biomarkers to Predict Early Recurrence of Stage Ia-b Lung Cancer
Authors: Wang Qiang , Zhou Danting , Wu Fang , Liang Qingchun , He Qiongzhi , Peng Muyun , Yao Tianyu , Hu Yan , Qian Banglun , Tang Jingqun , Wang Xiang , Liu Wenliang , Yu Fenglei , Chen Chen 
Published: July 2021

IntroductionApproximately 30% of patients diagnosed with stage Ia-b NSCLC die of recurrent disease after surgery. This study aimed to identify immune-related biomarkers that might predict tumor recurrence in stage Ia-b NSCLC within 40 months after curative resection.MethodsGene expression data of stage Ia-b NSCLC samples was retrieved from the TCGA database, the GEO databases, and the Second Xiangya hospital (XXEYY) database. 22 types of tumors infiltrating immune cells and the expression of immune-associated genes were investigated using CIBERSORT, immunohistochemical staining, and GSEA analyses in a total of 450 patients (80 in the training cohort and 370 in the validation cohorts). Recurrence-related immune features were selected based on the LASSO Cox regression model.ResultsHigh density of Tregs, Macrophages M0 and M1 cell could be observed in recurrence group while the memory B cell was more frequently enriched in controls, yet Tregs alone was significantly associated with tumor early recurrence in TCGA cohort, XYEYY cohort and GSE37745 dataset. A handful of immune-related genes were identified in the recurrence group. Based on Lasso regression analysis, the expressions of five immune-related genes, RLTPR, SLFN13, MIR4500HG, HYDIN and TPRG1 were closely correlated with tumor early recurrence. In the training cohort (TCGA), the combination of these five genes has sensitivity and specificity of 85% and 85%, with AUC of 0.91 (95% CI 0.84-0.98) for lung cancer early recurrence prediction, whereas in validation cohorts, the sensitivity and specificity using this panel was 61-89% and 54-82%, with AUC of 0.62-0.84.ConclusionOur study demonstrated that the immune microenvironment signatures were closely related to tumor early recurrence. Compared to tumor-infiltrating lymphocytes, the expression of five immune-related genes could be robust biomarkers to predict early recurrence of stage Ia-b NSCLC after curative resection.
Age-Related Differences in the Expression of Most Relevant Mediators of SARS-CoV-2 Infection in Human Respiratory and Gastrointestinal Tract
Authors: Berni Canani Roberto , Comegna Marika , Paparo Lorella , Cernera Gustavo , Bruno Cristina , Strisciuglio Caterina , Zollo Immacolata , Gravina Antonietta Gerarda , Miele Erasmo , Cantone Elena , Gennarelli Nicola , Nocerino Rita , Carucci Laura , Giglio Veronica , Amato Felice , Castaldo Giuseppe 
Published: July 2021

Background: Clinical features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection seem to differ in children compared to that in adults. It has been hypothesized that the lower clinical severity in children could be influenced by differential expression of the main host functional receptor to SARS-CoV-2, the angiotensin-converting enzyme 2 (ACE2), but data are still conflicting. To explore the origin of age-dependent clinical features of coronavirus disease 2019 (COVID-19), we comparatively evaluated the expression in children and adult subjects of the most relevant mediators of the SARS-CoV-2 infection: ACE2, angiotensin-converting enzyme 1 (ACE1), transmembrane serine protease-2 (TMPRSS2), and neuropilin-1 (NRP1), at upper respiratory tract and small intestine level.Methods: The expression of ACE2, ACE1, TMPRSS2, and NRP1 in nasal epithelium and in small intestine epithelium was investigated by quantitative real-time PCR analysis.Results: We found no differences in ACE2, ACE1, and TMPRSS2 expression in the nasal epithelium comparing children and adult subjects. In contrast, nasal epithelium NRP1 expression was lower in children compared to that in adults. Intestinal ACE2 expression was higher in children compared to that in adults, whereas intestinal ACE1 expression was higher in adults. Intestinal TMPRSS2 and NRP1 expression was similar comparing children and adult subjects.Conclusions: The lower severity of SARS-CoV-2 infection observed in children may be due to a different expression of nasal NRP1, that promotes the virus interaction with ACE2. However, the common findings of intestinal symptoms in children could be due to a higher expression of ACE2 at this level. The insights from these data will be useful in determining the treatment policies and preventive measures for COVID-19.
Oxygen Extraction Based on Inspiratory and Expiratory Gas Analysis Identifies Ventilatory Inefficiency in Chronic Obstructive Pulmonary Disease
Authors: Miki Keisuke , Tsujino Kazuyuki , Maekura Ryoji , Matsuki Takanori , Miki Mari , Hashimoto Hisako , Kagawa Hiroyuki , Kawasaki Takahiro , Kuge Tomoki , Kida Hiroshi 
Published: July 2021

Aims: In contrast to cardiovascular disease, low rather than high ventilatory inefficiency, evaluated by the minute ventilation-carbon dioxide output (V'E-V'CO2)-slope, has been recognized as being related to greater disease severity in chronic obstructive pulmonary disease (COPD). To better care for patients with cardiopulmonary disease, understanding the physiological correlation between ventilatory inefficiency and exercise limitation is necessary, but remains inadequate. Given that oxygen uptake (V'O2) evaluated by cardiopulmonary exercise testing (CPET) depends on both the ventilatory capability and oxygen extraction, i.e., the difference between inspiratory and expiratory oxygen concentration (ΔFO2), the aim of this study was to investigate the correlations between V'E-V'CO2-slope and the ΔFO2 during exercise and their physiological implications in patients with COPD.Methods: A total of 156 COPD patients (mean age, 70.9 ± 7.2 years) with Global Initiative for Chronic Obstructive Lung Disease (GOLD) stages I–IV and 16 controls underwent CPET with blood gas analysis.Results: With the progression of COPD, mechanical ventilatory constraints together with a slower respiratory frequency led to exertional respiratory acidosis. In GOLD IV cases, (1) decrease in the dependence of reduced peak V'O2 on V'E led to an increase in its dependence on peak ΔFO2 during exercise; and (2) the ΔFO2-V'CO2-slope became steeper, correlating with the severity of exertional respiratory acidosis (r = 0.6359, p &lt; 0.0001). No significant differences in peak exercise ΔFO2 or V'E-V'CO2-slope were observed among the various GOLD stages. In all subjects, including controls, peak exercise ΔFO2 had the strongest correlation with the V'E-V'CO2-slope (r = −0.8835, p &lt; 0.0001) and correlated well with body mass index (r = 0.3871, p &lt; 0.0001), although it did not correlate with the heart rate-V'CO2-relationship and V'E.Conclusions: Ventilatory efficiency related to CO2 clearance might depend on exertional oxygen extraction in the body. Measuring ΔFO2 might be a key component for identifying ventilatory inefficiency and oxygen availability. Increasing ΔFO2 would help to improve ventilatory inefficiency and exercise tolerance separately from cardiac and ventilatory capability in COPD patients.
Australian Maltreated Infants and Young Children Can Achieve Positive Relational Health With Neurodevelopmentally- and Trauma-Informed Interventions Provided Within Relationally-Positive and Stable Environments
Authors: Cox Allison , Frederico Margarita , Mosse Holly , Radford Lyn , Ambry Dallas , Ryan Clare 
Published: July 2021

Background: Childhood maltreatment such as abuse, neglect and family violence has a profound impact on children's psychological and relational functioning and their lifelong trajectory, with associated adverse physical and mental health outcomes, higher mortality rates and reduced socioeconomic opportunities. The aim of the study was to explore the impact of neurodevelopmentally- and trauma-informed interventions on the relational health of children who have experienced maltreatment.Context: The study was conducted at Berry Street Take Two, an Australian therapeutic service. Take Two provides services to Victorian children aged 0-18 years, to address the impact of the trauma they have experienced from maltreatment. Take Two clinicians use relational and ecological frameworks, neurodevelopmental research and evidence-informed approaches to repair family relationships and develop networks of caring adults that focus on meeting the child's needs. Take Two uses the NMT approach as a framework for clinical intervention-planning and is site-certified in the use of the NMT Clinical Practice tools.Method: The mixed methods study had two components. A cross sectional study of baseline and repeat clinical measure data (HoNOSCA and SDQ) with a cohort of children aged 2–11 years (n = 91), who were clients of Berry Street Take Two between 2014 and 2019, was conducted utilizing SPSS. The quantitative data analysis was supplemented by three case studies of Berry Street Take Two clients, which explored the process of intervention, including intervention type, timing and dosage. The case studies drew on the full case record for each child to illustrate the impact of NMT-informed interventions on the relational health, psychological and behavioral functioning of children.Results: The study found that Take Two intervention was associated with improved relational health, measured by the NMT metric and supported by significant positive changes on the SDQ and HoNOSCA with medium effect sizes (cohen's d). The case study analysis highlighted the importance of intervention addressing individual, family and systems elements to bring about positive change.Conclusions: This study illustrates the value of neurodevelopmental trauma-informed interventions in positively impacting on the relational health and current functioning of maltreated children and the potential to reduce the lifelong impact of maltreatment.
Associations Between the Kynurenine Pathway, Proinflammatory Cytokines, and Brain-Derived Neurotrophic Factor in Hospitalized Patients With Chronic Schizophrenia: A Preliminary Study
Authors: Okamoto Naomichi , Natsuyama Tomoya , Igata Ryohei , Konishi Yuki , Tesen Hirofumi , Ikenouchi Atsuko , Yoshimura Reiji 
Published: July 2021

Purpose: The kynurenine (Kyn) pathway may play a role in the pathophysiology of schizophrenia. This pathway shows crosstalk with proinflammatory cytokines, including interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α), and/or brain-derived neurotrophic factor (BDNF). Moreover, Kyn metabolites affect neurotransmission and cause neurotoxicity. To date, the influence of the Kyn pathway on proinflammatory cytokines and BDNF remains to be fully elucidated. The aim of this study was to investigate the relationships of the Kyn pathway with proinflammatory cytokines, BDNF, and psychiatric symptoms in patients with schizophrenia.Methods: Thirty patients with schizophrenia and ten healthy control participants were recruited for this study. All patients were diagnosed with schizophrenia using the Diagnostic and Statistical Manual for Mental Disorders, Fifth Edition (DSM-5). The healthy controls were those who did not fulfill any of the diagnostic criteria in the DSM-5. The serum levels of Kyn and its metabolites, proinflammatory cytokines, and BDNF were measured in patients with schizophrenia and healthy controls. Patients with schizophrenia were also assessed for psychiatric symptoms using the Positive and Negative Syndrome Scale (PANSS).Results: Patients with schizophrenia and healthy controls showed no significant differences in the levels of Kyn and its metabolites, proinflammatory cytokines, and BDNF. A significant positive correlation was found between the serum levels of TNF-α and Kyn (r = 0.53, p = 0.0026) and the Kyn/tryptophan (Trp) value (r = 0.67, p = 0.000046) in the schizophrenia group, but not in the healthy control group.Conclusion: TNF-α affects the Kyn pathway in patients with chronic schizophrenia, but not in the healthy individuals, although serum TNF-α levels showed no difference between the two groups. Associations between the Kyn pathway and the levels of proinflammatory cytokines and BDNF or psychotic symptoms might be complicated in hospitalized patients with chronic schizophrenia.
SIGIRR and TNFAIP3 Are Differentially Expressed in Both PBMC and TNF-α Secreting Cells of Patients With Major Depressive Disorder
Authors: Lin Chin-Chuen , Huang Tiao-Lai 
Published: July 2021

Background: Major depressive disorder (MDD) is associated with the activation of the immune/inflammatory system. TNF-α is associated with MDD and poor treatment response. Toll-like receptors (TLR) are responsible in innate immune response, and is associated with MDD and antidepressant response. Some negative regulators of TLR pathway such as SOCS1, TOLLIP, SIGIRR, TNFAIP3, and MyD88s, are reported to be differentially expressed in the peripheral blood samples of patients of MDD.Methods: We recruited patients with MDD and healthy controls, collect their demographic data, and measured their mRNA levels of negative TLR regulators, using peripheral blood mononuclear cells (PBMC) and isolated TNF-α secreting cells. Clinical symptoms were evaluated using Halmiton Depression Rating Scale (Ham-D). Some patients were evaluated again after 4 weeks of antidepressant treatment.Results: Forty-seven patients with MDD and 52 healthy controls were recruited. Between the PBMC samples of 37 MDD patients and 42 controls, mRNA levels of SOCS1, SIGIRR, TNFAIP3, and MyD88s were significantly different. Between TNF-α secreting cells of 10 MDD patients and 10 controls, mRNA levels of SIGIRR and TNFAIP3 were significantly different. Change of Ham-D score only correlated significantly with TOLLIP mRNA level after treatment.Conclusion: SIGIRR and TNFAIP3, two negative regulators of TLR immune response pathways, were differentially expressed in both PBMC and TNF-α secreting cells of patients with MDD as compared to healthy controls. The negative regulations of innate immune response could contribute to the underlying mechanism of MDD.
Psychological Distress and Tobacco Use Among Hospital Workers During COVID-19
Authors: Mounir Izza , Menvielle Loick , Perlaza Samir , Chênevert Denis , Planchard Jo-Hanna , Fabre Roxane , Benoit Michel , Benyamina Amine , Rolland Benjamin , Cherikh Faredj , David Renaud 
Published: July 2021

Background and Aims: This work aims to assess the impact of the COVID-19 pandemic on hospital workers' psychological parameters and attitudes toward substance use, before and during the French COVID-19 lockdown.Methods: An online survey was proposed to the staff of the University Hospital of Nice and Sainte-Marie psychiatric hospital in France from May 18 to June 6, 2020 assessing changes in daily habits, psychological distress and changes in substance use, including smoking.Results: A total of 702 respondents (80.3% female) filled out the survey. Overall, most of the workers reported increased stress, irritability, sadness, decreased motivation, and a worse quality of sleep after the beginning of the COVID-19 lockdown. Additionally, hospital workers who were more likely to use tobacco during the COVID-19 lockdown reported increased sadness (OR = 1.23, p &lt; 0.001), loss of motivation (OR = 0.86, p &lt; 0.05), alcohol consumption (OR = 3.12, p &lt; 0.001), lower incomes (OR = 1.69, p &lt; 0.05), living alone (OR = 1.77, p &lt; 0.001) and doing less physical activity (OR = 0.36, p &lt; 0.001).Conclusion: During the first lockdown, significant psychological changes (sadness, distress, irritability) associated with changes in tobacco use and physical activity were reported. Such results should encourage hospital leaders to implement dedicated policies to better accompany hospital workers' psychological distress.
The Efficacy and Safety of <2 cm Micro-Keyhole Microvascular Decompression for Hemifacial Spasm
Authors: Huang Jiashang , Zhan Yan , Li Yi , Jiang Li , Wang Kuan , Wu Zhimin , Xie Yanfeng , Shi Quanhong 
Published: July 2021

Objective: Microvascular decompression (MVD) surgery has been accepted as a minimally invasive surgical modality for the treatment of hemifacial spasm (HFS). However, the size of the bone window does not match the concept of minimally invasive. This study is aimed at evaluating the efficacy and safety of &lt;2 cm micro-keyhole MVD.Methods: A total of 148 patients with HFS diagnosed in the First Affiliated Hospital of Chongqing Medical University from January 1, 2019, to July 1, 2020, who underwent MVD in the neurosurgery department of the hospital were collected. Surgery was performed by a retrosigmoid keyhole approach with the bone hole diameter &lt;2 cm, which was named micro-keyhole MVD. The efficacy and safety of the micro-keyhole MVD were evaluated by statistical analysis of the efficacy of the micro-keyhole MVD and the incidence of postoperative complications.Results: The effect of micro-keyhole MVD was satisfying (cure or partial remission) in 97.2% (n = 144). The failure and recurrence rates were 2.7% (n = 4) and 0.6% (n = 1), respectively. Among them, immediate facial palsy, delayed facial palsy, hearing loss, and cerebrospinal fluid (CSF) leakage were found in 0.6% (n = 1), 8.1% (n = 12), 4.7% (n = 7), and 1.3% (n = 2). Only one patient developed cerebellar infarction, which was complicated by “moyamoya disease.” The micro-keyhole MVD in the treatment of HFS can achieve a high remission rate and reduce the incidence of surgical complications.Conclusion: Micro-keyhole MVD is a safe and effective minimally invasive treatment for HFS. This technique does not increase the incidence of cranial nerve injury. Meanwhile, it reduces the incidence of CSF leakage and hearing loss (HL).
Effects of Ti doping on scintillation properties of CaZrO3 single crystals
Authors: Fukushima Hiroyuki , Nakauchi Daisuke , Kato Takumi , Kawaguchi Noriaki , Yanagida Takayuki 
Published: July 2021

Abstract
The Ti-doped CaZrO3 single crystals were successfully synthesized. All the samples exhibited a high transmittance up to 80% and an absorption edge derived from the doped Ti. Both the photoluminescence (PL) and scintillation spectra revealed a broad emission band. The PL and scintillation decay curves had two emission components, and these decay time constants were less than 1 μs. All the Ti-doped samples exhibited clear photoabsorption peaks, and the light yield of 1370 photons MeV−1 was obtained in the 1% Ti-doped sample.
Ce concentration dependence of optical and scintillation properties on Ce-doped La2Si2O7 crystal
Authors: Kantuptim Prom , Kato Takumi , Nakauchi Daisuke , Kawaguchi Noriaki , Yanagida Takayuki 
Published: July 2021

Abstract
A lanthanum pyrosilicate (La2Si2O7, LaPS) single crystal is successfully grown with a Ce-doped concentration of 0.5 to 20.0% as well as undoped LaPS for reference. The photoluminescence emission map of Ce-doped LaPS has broad emission at 360–410 nm from Ce3+ 5d-4f transition, with a decay time of 20–24 ns. In the scintillation properties, Ce-doped LaPS presents the scintillation peak at 390 nm under X-ray excitation, with the decay time constant at 26–31 ns plus another decay constant caused by the emission from host material at 250–600 ns. The afterglow level at 20 ms after X-ray irradiation is around 30–56 ppm. In the 662 keV γ-ray pulse height spectra, 1.0% Ce-doped LaPS shows a clear photoabsorption peak, with a scintillation light yield of 5400 ph MeV−1. The relationship between γ-ray energy and the photoabsorption peak channel (linearity) is also covered in this study.