bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trichoderma juruarense sp. nov. (Hypocreaceae) a new fungal species from sediments of the Amazonian Juruá River with agricultural potential
Authors: Gwinner Raoni , Sousa Thiago F. , de Sousa Sandra B. , Bandeira Izabel C. , Castro Gleucinei dos S. , Hanada Rogério E. , Faria Jéssica V. , Koolen Hector H. F. , Silva Gilvan Ferreira 
Published: January 2022

Abstract
The species of Trichoderma are the most common fungi to be used as biocontrol agents, and their metabolic arsenal has a wide variety of applications that places this genus among those with the potential to provide biotechnological products. The ubiquitous nature of Trichoderma has favored a rapid increase in the number of described species, and significant efforts have been made towards the taxonomy of Trichoderma in order to improve the accuracy of identification. During a study of cultivable microbiota from the Juruá River, Amazon, Brazil. Isolates with morphological characteristics of the genus Trichoderma were screened for their capacity to control phytopathogens. A total of five Trichoderma isolates were identified using morphological data combined with phylogenetic analysis of the ITS region, and partial sequences of TEF and RPB2. Trichoderma juruarense sp. nov. form a monophyletic clade that is closely related to T. cyanodichotomus, a species that occupies an unresolved position in the Trichoderma taxonomy. T. cyanodichotomus and T. juruarense sp. nov. present an intracellular blue-green pigment in potato dextrose agar (PDA) and differ in conidia and chlamydospores sizes. These data support the proposition of a new species, named here as Trichoderma juruarense. The holotype of T. juruarense INPA0108 presents in vitro inhibition against phytopathogens, such as Colletotrichum siamense (50%), Corynespora cassiicola (43%), Fusarium decemcellulare (61%) and Sclerotium rolfsii (51%), which demonstrates desirable traits that warrant further studies on plant protection. In addition, T. cyanodichotomus and T. juruarense formed a new clade based on the sequence data of the RPB2 gene.
An AI-Enabled Predictive Analytics Dashboard for Acute Neurosurgical Referrals
Authors: Pandit Anand , Jalal Arif , Toma Ahmed , Nachev Parashkev 
Published: January 2022

Abstract
Healthcare dashboards make key information about service and clinical outcomes available to staff in an easy-to-understand format. Most dashboards are limited to providing insights based on group-level inference, rather than individual prediction. Here, we evaluate a dashboard which could analyze and forecast acute neurosurgical referrals based on 10,033 referrals made to a large volume tertiary neurosciences center in central London, U.K., from the start of the Covid-19 pandemic lockdown period until October 2021. As anticipated, referral volumes significantly increased in this period, largely due to an increase in spinal referrals. Applying a range of validated time-series forecasting methods, we found that referrals were projected to increase beyond this time-point. Using a mixed-methods approach, we determined that the dashboard was usable, feasible, and acceptable to key stakeholders. Dashboards provide an effective way of visualizing acute surgical referral data and for predicting future volume without the need for data-science expertise.
Mental health of people living with HIV during the COVID-19 epidemic in Tokyo
Authors: Tanaka Takahiro , Koga Michiko , Senkoji Tomoe , Kubota Megumi , Ikeuchi Kazuhiko , Kikuchi Tadashi , Saito Makoto , Adachi Eisuke , Tsutsumi Takeya , Hosaka Takashi , Yotsuyanagi Hiroshi 
Published: January 2022

Abstract
Background

The COVID-19 pandemic significantly impacts physical health and mental health. People living with HIV (PLWH) have a higher prevalence of psychiatric disorders than the general population. We examined the mental health of PLWH during the COVID-19 pandemic in Japan.
Methods

We retrospectively examined the medical records of PLWHs who underwent the Kessler Psychological Distress Scale-10, the Patient Health Questionnaire-9, and the Generalized Anxiety Disorder-7 at an HIV referral hospital in Tokyo. Stringency Index (SI) values were used to measure the intensity of social infection control measures.
Results

Between February 2020-May 2021, 30 PLWH were examined at least once. The median age was 49 years, 29 PLWH were on antiretroviral therapy, and the median CD4 count was 580.5/µL. A total of 30% of the patients experienced distress, 45% depression, and 21.4% generalized anxiety disorder. Fourteen PLWH were taken for a median of four tests (IQR:2.0-7.3) and classified into three types: 1) Moderate distress or mild depression or anxiety at the beginning that decreased gradually (six patients, 43%), 2) persistent severe distress, but moderate depression or anxiety gradually decreased (six patients, 43%), and 3) extremely severe distress and depression or anxiety continued to syncope with the SI values (two patients, 14%). Having no partners, unemployment, and a history of psychiatric diseases were more commonly observed in the highly severe mental health groups.
Conclusions

PLWH are more vulnerable to the COVID-19 pandemic than the general population, especially those with substantial social isolation. Attention should be paid to the mental health of PLWH.
Simulating Wheat Production Potential Under Near-future Climate Change in Arid Regions of Northeast Iran
Authors: Saberali Seyed Farhad , Shirmohammadi-Aliakbarkhani Zahra , Nasrabadi Hossein Nastari 
Published: January 2022

Abstract
Water scarcity is the key challenge in arid regions, which exacerbates under climate change (CC) and must be considered to assess the impacts of CC on cropping systems. A climate-crop modelling approach was employed by using the CSM-CERES-Wheat model in some arid regions of northeast Iran to project the effects of CC on irrigated wheat production. Current climate data for 1990-2019 and climate projections of three climate models for 2021–2050 under RCP4.5 and RCP8.5 emission scenarios were used to run the crop model. Two irrigation scenarios with different irrigation efficiencies were also simulated to investigate the impacts of water scarcity associated with changing climate and irrigation management on wheat productivity. Results indicated that mean temperature is projected to increase at the rates of 1.74–2.73 °C during the reproductive growth period of winter wheat over the study areas. The precipitation projections also indicated that the precipitation rates would decrease over most of the wheat-growing period. The length of the vegetative growth period will extend in some regions and shorten in others under the near future climate. However, the grain filling duration will reduce by about 2–4 days across all regions. The mean seasonal PET is expected to decrease by about 11 mm from 2021 to 2050 over the study areas. A mean overall reduction in winter wheat yield due to future climate conditions would be about 12.3 % across the study areas. However, an increase of 15-30% in the irrigation efficiency will be able to offset yield reductions associated with limited water supply under future climate scenarios. The results suggest that CC will exacerbate limited irrigation water availability, so implementing high-efficiency irrigation systems should be a priority to adapt to climate change in an arid cropping system.
Genetic Dissection of Grain Zinc and Iron Concentration, Protein Content, Test Weight and Thousand Kernel Weight in Wheat (Triticum Aestivum L.) through Genome Wide Association Study
Authors: D Rathan N , Krishna Hari , Ellur Ranjith Kumar , Sehgal Deepamala , Govindan Velu , Ahlawat Arvind Kumar , Krishnappa Gopalareddy , Jaiswal Jai Prakash , Singh Jang Bahadur , V Saiprasad S , Ambati Divya , Singh Sumit Kumar , Bajpai Kriti , Singh Anju Mahendru 
Published: January 2022

Abstract
Malnutrition due to micronutrients and protein deficiency is recognized among the major global health issues. Genetic biofortification of wheat varieties is both cost-effective and sustainable strategy to contain global micronutrient and protein malnutrition. Genomic regions governing grain zinc concentration (GZnC), grain iron concentration (GFeC), grain protein content (GPC), test weight (TW), and thousand kernel weight (TKW) were investigated in a set of 183 diverse bread wheat genotypes through genome wide association study (GWAS). The RIL population was genotyped using Breeders' 35K Axiom Array and phenotyped in three environments during 2019-2020. A total of 55 marker-trait associations (MTAs) were identified, of which four significant MTAs for GFeC on chromosome 2B, 3A, 3B, 6A and two for GZnC on chromosomes 1A and 7B. Further, a stable SNP was detected for TKW and also identified pleiotropic regions controlling GPC and TKW. In silico analysis revealed a few important putative candidate genes viz., F-box-like domain superfamily, Zinc finger CCCH-type proteins, Serine-threonine/tyrosine-protein kinase, Histone deacetylase domain superfamily and SANT/Myb domain superfamily proteins, etc. The identified novel MTAs will be validated to estimate their effects on different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
Effects of COVID-19 Lockdown on Managing Diabetes Mellitus Among Sudanese Insulin Pump Users, A Cross-Sectional Study
Authors: Salih Esraa Hassan , Ahmed Khabab Abbasher Hussien Mohamed , Babiker Omer Osman Osman , Mohamed Malaz Tarig Abdalla , Omer Mohammed Eltahier Abdalla , Salih Zeinab Mohammed Amara 
Published: January 2022

Abstract
Background
COVID-19 lockdown has affected diabetes management among the insulin pump users by changing their life style, affected their mental health, limited diabetes and insulin pump supplies and more difficult communication with the healthcare providers
Objectives
The aim of this research is to study the effects of COVID-19 lockdown on managing diabetes mellitus among Sudanese insulin pump users, Sudan (March- September 2020).
Methodology:
This is a descriptive cross-sectional community based study which was done in contact with Shimaa medical CO. LTD. 26 insulin pump users were chosen by total coverage and the data was collected throughout phone call interviews. All statistical analyses were performed using IBM SPSS Statistics software, version 20.
Results
The mean age of 22 participants was 25.3 ± 17.2 years, and the majorities (63.6%) were females. The average duration of diabetes was 6.9 ± 3.9 years, and the average duration of insulin pump use was 3 ± 1 years. Of the 22 patients (90.9%) used glucometer for monitoring blood sugar. 9 (40.9%) were less subjective to depression, 9 (40.9%) had moderate susceptibility to have depression. 8 patients (36.4%) reported weight gain, 12 patients (54.5%) reported no weight changes, while 2 patients (9.1%) reported weight loss. The level of physical activity decreased in 10 patients (45.5%), and the dietary habits remained unchanged in 50%. Moreover, participants who reported a decrease in physical activity levels were more likely to report weight gain (P = 0.004) compared with those who reported an increase in physical activity levels. Most of the patients have unchanged behaviors regarding experiencing hyper and hypoglycemic symptoms 45.5%, 72.7% respectively. Most of the patients have unchanged adherence to the insulin pump behaviors, carb counting (63.6%), bolus wizard during mealtime (68.2%), and bolus wizard for hyperglycemia correction (68.2%), self-monitoring of blood glucose (40.9%). (40.9%) of the patients had scheduled phone call appointments, 5 patients (22.7%) received virtual education (VE) from the insulin pump technician. 12 patients (54.5%) reported difficulty obtaining at least one type of insulin pump supply.
Conclusion
COVID-19 lock down has led to the decrease in physical activity with unchanged dietary habits. Getting the insulin pump supplies was difficult for most of the patient’s, and there was shortage and increase prices for diabetes care supplies. Telemedicine should be considered seriously to ease the communication between the patients and the health care providers.
Nasal Carriage and Associated Factors of Methicillin-Resistant Staphylococcus Aureus Among Medicine and Health Science Students of Arba Minch University, Arba Minch, Ethiopia
Authors: Mekuriya Ermiyas , Manilal Aseer , Aklilu Addis , Woldemariam Melat , Hailu Tadios , Wasihun Biresaw 
Published: January 2022

Abstract
Individuals with Methicillin-Resistant Staphylococcus aureus (MRSA) colonized nasal cavities were at greater risk of developing the infection and can serve as potential reservoirs of transmission. Aim of this study is to determine the extent of nasal carriage and associated factors linked to MRSA in medical and health science students of Arba Minch University (AMU), Ethiopia. An institution based cross-sectional study was conducted at AMU from 01st August through 30th November, 2020. A systematic sampling technique was used to recruit the participants. Socio-demographic data were collected using a structured questionnaire. Nasal swabs were collected and S. aureus were identified following standard microbiological methods. Methicillin resistance was tested using cefoxitin disk and antimicrobial susceptibility tests were performed by Kirby-Bauer disk diffusion. Biofilm forming ability was phenotypically detected by micro-titer plate assay. Descriptive statistics and multivariable logistic regression analysis were done by Statistical Package for Social Service (SPSS) version 25. Overall prevalence of Staphylococcus aureus and MRSA were 27.1% (70/258) and 7.4% (19/258) respectively. Methicillin-Resistant S. aureus carriage was higher among medical interns, 16.9% (11/65); isolates were co-resistant to antibiotics, such as trimethoprim-sulfamethoxazole (63.2%) and tetracycline (48.4%). Multidrug resistance (MDR) was observed among 52.6% (10/19) of the isolates. Besides, 31.4% (6/19) of MRSA were biofilm producers and all of them were MDR. Multivariable analysis showed that students having >2 years of mean exposure to hospital [p= 0.048, AOR: 4.99, 95% CI: 1.01-24.66] and those who share clothing and sports equipment [p=0.017, AOR: 5.43, 95% CI: 1.35-21.83] were statistically significant. The overall prevalence of nasal MRSA among students were comparatively lower than that observed in other studies done in Ethiopia itself. An alarming factor is that, 60% of MDR-MRSA were biofilm producers.
Psychometric Evaluation of the Positive Mental Health (PMH) Scale Using Item Analysis According to the Rasch Model
Authors: Vaganian Lusine , Boecker Maren , Bussmann Sonja , Kusch Michael , Labouvie Hildegard , Margraf Jürgen , Gerlach Alexander L. , Cwik Jan C. 
Published: January 2022

Abstract
Background: The investigation of patient-reported outcomes and psycho-oncological interventions mainly focuses on psychological distress or psychopathology. However, the recognition of the equal importance of positive mental health (PMH) has increased lately. The PMH-scale is a brief questionnaire allowing to assess well-being in individuals in the general population and in patients. Previous studies evaluated the psychometric properties of the PMH-scale using classical test theory (CTT). This study is the first to investigate the PMH-scale in patients with cancer using item analysis according to the Rasch model. Methods: In total, N = 357 cancer patients participated in the study. A Rasch analysis of the PMH-scale was conducted including testing of unidimensionality, local independence, homogeneity and differential item functioning (DIF) with regard to age, gender, type of cancer, the presence of metastases, psycho-oncological support, and duration of disease. Additionally, the ordering of the item thresholds as well as the targeting of the scale were investigated.Results: After excluding one misfitting item and accounting for local dependence by forming superitems, a satisfactory overall fit to the Rasch model was established (χ2 = 30.34, p = 0.21). The new PMH-8 scale proved to be unidimensional, and homogeneity of the scale could be inferred. All items showed ordered thresholds, there was no further item misfit. DIF was found for age, but as the impact of DIF was not substantial, no adjustment related to the age-DIF had to be made. The Person Separation Index (PSI = 0.89) was excellent, indicating excellent discriminatory power between different levels of positive mental health. Overall, the targeting of the PMH-8 was good for the majority of the present sample. However, at both ends of the scale item thresholds are missing as indicated by a slight floor effect (1.4%) and a considerable ceiling effect (9.8%). Conclusion: Overall, the results of the analysis according to the Rasch model support the use of the revised PMH-scale in a psycho-oncological context.
Clinical Validation and Treatment Plan Evaluation Based on Auto-Delineation of the Clinical Target Volume for Prostate Cancer Radiotherapy
Authors: Shen Jing , TAO Yinjie , GUAN Hui , ZHEN Hongnan , HE Lei , DONG Tingting , WANG Shaobin , CHEN Yu , CHEN Qi , LIU Zhikai , ZHANG Fuquan 
Published: January 2022

Abstract
Purpose

Clinical target volumes (CTV) and organs at risk (OAR) could be auto-contoured to save workload. The goal of this study was to assess a convolutional neural network (CNN) for totally automatic and accurate CTV and OAR in prostate cancer, while also comparing anticipated treatment plans based on auto-contouring CTV to clinical plans.
Methods

From January 2013 to January 2019, 217 computed tomography (CT) scans of patients with locally advanced prostate cancer treated at our hospital were collected and analyzed. CTV and OAR were delineated with a deep learning based method, which named CUNet. The performance of this strategy was evaluated using the mean Dice similarity coefficient (DSC), 95th percentile Hausdorff distance (95HD), and subjective evaluation. Treatment plans were graded using predetermined evaluation criteria, and % errors for clinical doses to the planned target volume (PTV) and organs at risk(OARs) were calculated.
Results

The defined CTVs had mean DSC and 95HD values of 0.84 and 5.04 mm, respectively. For one patient's CT scans, the average delineation time was less than 15 seconds. When CTV outlines from CUNetwere blindly chosen and compared to GT, the overall positive rate in clinicians A and B was 53.15% vs 46.85%, and 54.05% vs 45.95%, respectively (P>0.05), demonstrating that our deep machine learning model performed as good as or better than human demarcation Furthermore, 8 testing patients were chosen at random to design the predicted plan based on the auto-courtoring CTV and OAR, demonstrating acceptable agreement with the clinical plan: average absolute dose differences of D2, D50, D98, Dmean for PTV are within 0.74%, and average absolute volume differences of V45, V50 for OARs are within 3.4%. Without statistical significance (p>0.05), the projected findings are comparable to clinical truth.
Conclusion

The experimental results show that the CTV and OARs defined by CUNet for prostate cancer were quite close to the ground reality.CUNet has the potential to cut radiation oncologists' contouring time in half. When compared to clinical plans, the differences between estimated doses to CTV and OAR based on auto-courtoring were small, with no statistical significance, indicating that treatment planning for prostate cancer based on auto-courtoring has potential.
The Combination of Inflammation and Nutrition Factors Reinforces the Prognostic Prediction for Stage III Colorectal Cancer Patients After Curative Resection
Authors: Kato Shinya , Miyoshi Norikatsu , Fujino Shiki , Minami Soichiro , Matsuda Chu , Yasui Masayoshi , Ohue Masayuki , Sekido Yuki , Hata Tsuyoshi , Ogino Takayuki , Takahashi Hidekazu , Uemura Mamoru , Yamamoto Hirofumi , Doki Yuichiro , Eguchi Hidetoshi 
Published: January 2022

Abstract
Purpose
Inflammation and nutritional status are known to be associated with the prognosis of several malignancies. Herein, we attempted to develop inflammation–nutrition scores and predict the prognosis of stage III colorectal cancer (CRC).
Methods
This retrospective study included 262 patients with stage III CRC who underwent curative surgery and were divided into two groups: a training set (TS) of 162 patients and a validation set (VS) of 100 patients. In the TS, clinicopathological factors were tested using a Cox regression model, and the Kansai prognostic score (KPS) was assessed by 1 point each for <3.5 g/dL albumin level, >450 monocyte counts, and <1.65 × 105 platelet counts, which were associated with disease-free survival (DFS). Using KPS, DFS and overall survival (OS) were validated in VS.
Results
The C-indices of KPS to predict DFS and OS in TS were 0.707 and 0.772. It was validated in VS that the C-indices of KPS to predict DFS and OS were 0.618 and 0.708, respectively. A high KPS was a significant predictor of DFS and OS.
Conclusion
KPS serves as a new model for the prognosis of patients with stage III CRC.
GRAP2 is a Prognostic Biomarker and Correlated with Immune Infiltration in Lung Adenocarcinoma
Authors: Song Shimao , Deng Xinzhou , Wang Jincheng , Han Jiahui , Peng Zhen , Lu Ying , Jiang Shan , Shi Mingliang , Yan Yutao , Luo Zhiguo 
Published: January 2022

Abstract
Background: GRAP2 is an adaptor protein involved in leukocyte-specific protein-tyrosine kinase signaling; however, the prognostic value of GRAP2 and its correlation with immune cell infiltration in lung adenocarcinoma (LUAD) remain unclear.Methods: All original data were downloaded from the TCGA database and integrated via R 3.2.2. GRAP2 expression was explored with the TCGA and TIMER databases. We evaluated the influence of GRAP2 on clinical prognosis using the Kaplan-Meier plotter, Gene Expression Omnibus (GEO) database and GEPIA database. Correlations between GRAP2 and cancer immune characteristics were analyzed via TIMER and TISIDB databases. Finally, we confirmed the expression of GRAP2 in LUAD by immunohistochemistry staining.Results: Transcription levels of GRAP2 were significantly lower in several human cancers, including LUAD, than in adjacent normal tissues. We also found that tumor tissues have lower protein expression levels of GRAP2 compared with adjacent normal tissues in LUAD by immunohistochemistry staining. The down-regulated GRAP2 was associated with poorer overall survival, pathologic stage, T stage, N stage and primary therapy outcome in LUAD. Mechanically, we identified a hub gene that included a total of 91 GRAP2 co-expressed genes, which were tightly associated with immune response in LUAD. GRAP2 expression was positively correlated with infiltrating levels of B cells, CD8+ T cells, dendritic cells, eosinophils, macrophages, mast cells, Th2 cells, Th1 cells, Th17 cells, NK cells and neutrophils. GRAP2 expression level also affected the cumulative survival time of B cells and dendritic cells. GRAP2 expression is positively correlated with multiple immune markers, chemokines, chemokine receptors and MHC molecules of LUAD.Conclusions: These findings suggest that GRAP2 is a tumor suppressor gene and can be used as a prognostic biomarker for determining prognosis and immune infiltration in LUAD.