bluuebunny/crossref_metadata_2025_split huggingface dataset:
In chronic pancreatitis CD25+/Foxp3+ regulatory T-cells control pancreatic fibrosis by suppression of the type 2 immune response
Authors: Glaubitz Juliane , Wilden Anika , Golchert Janine , Homuth Georg , Voelker Uwe , Bröker Barbara , Lerch Markus , Mayerle Julia , Aghdassi Ali , Weiss Frank , Sendler Matthias 
Published: July 2021

Abstract
Chronic pancreatitis (CP) is characterized by chronic inflammation and the progressive fibrotic replacement of exocrine and endocrine pancreatic tissue. We identified Tregs as central regulators of the fibroinflammatory reaction by a selective depletion of Foxp3-positive cells in a transgenic mouse model (DEREG-mice) of experimental CP. In Treg-depleted DEREG-mice, the induction of CP resulted in a significantly increased stroma deposition, the development of exocrine insufficiency and significant weight loss starting from day 14 after disease onset. In CP, Foxp3+/CD25+ Tregs suppress the type-2 immune response by a repression of Gata3+ T-helper cells (Th2), Gata3+ innate lymphoid cells type 2 (ILC2) and CD206+ M2-macrophages. A suspected pathomechanism behind the fibrotic tissue replacement may involve an observed dysbalance of Activin A expression in macrophages and of its counter regulator Follistatin. Our study identified Tregs as key regulators of the type-2 immune response and of organ remodeling during CP. The Treg-triggered immune response could be a therapeutic target to prevent fibrosis and preserve functional pancreatic tissue.
Communicating with Mechanically Ventilated Patients Who Are Awake. A Qualitative Study on the Experience of Critical Care Nurses in Cyprus during the COVID-19 Pandemic.
Authors: Kyranou Maria , Cheta Charikleia , Pampoulou Eliada 
Published: July 2021

Abstract
Background: Modern protocols for light sedation in combination with the increased turnover of COVID-19 infected patients hospitalized in Intensive Care Units (ICUs) have increased the number of patients who are mechanically ventilated and awake. Nurses require specific skills to care for this vulnerable group of patients. At the same time, nurses report feeling inadequate and frustrated when they attempt to establish communication with mechanically ventilated, conscious patients. Methods: The purpose of this study was to explore nurses’ experiences taking care of conscious, intubated patients in the intensive care unit. The research questions aimed to identify i. the strategies that nurses use for communicating with patients, and ii. the barriers in communication between nurses and patients. This study employed a qualitative design. Data were collected using semi-structured interviews with 14 intensive care nurses working at ICUs in four different hospitals of Cyprus. The data were analyzed by applying thematic analysis.Results: We identified several strategies of unaided (movements -lips, hands, legs- facial expressions, gestures, touching) and aided forms of communication (pen and paper, boards, tablets, mobiles) used by nurses to communicate with patients. Additionally, barriers in communication were reported by participating nurses mainly pertaining to patients’, nurses’ characteristics and the ICU environment. The health protocols imposed by the pandemic added more barriers in the communication between nurses and patients mostly related to the use of protective health equipment.Conclusions: The results of this study, combined with those of others in different countries, point to the difficulties nurses face when trying to communicate with conscious patients during mechanical ventilation. It appears that the complex communication needs of this group of patients are not being met mainly due to the lack of nurses’ training and of appropriate equipment to facilitate alternative and augmentative communication. Our study is amongst the first to add that the protective health protocols due to the pandemic imposed further communication barriers. Undoubtedly, the recognition of such an important issue creates an urgent need to educate nurses in alternative ways of communication with mechanically ventilated, conscious patients during their ICU stay.
SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis
Authors: Gamaarachchi Hasindu , Samarakoon Hiruna , Jenner Sasha , Ferguson James , Amos Timothy , Hammond Jillian , Saadat Hassaan , Smith Martin , Parameswaran Sri , Deveson Ira 
Published: July 2021

Abstract
Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data – known as FAST5 – that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For example, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.
Complications Associated with Bifocal Bone Transport Using Unilateral External Rail Fixator in the Reconstruction of Femur Defects Caused by Infection: Outcome Analysis of 76 Patients
Authors: Peng Cong , Liu Kai , Tian Qi , Tusunniyazi Maimaitiaili , Kong Weiqi , Luan Haopeng , Liu Xiaokang , Zhao Yan 
Published: July 2021

Abstract
Background: The purpose of this study is to evaluate the outcomes of single-level bone transport in the treatment of femoral bone defects after radical debridement, which were caused by infections.Methods: Clinical and radiographic data of patients with infected femoral nonunion treated with a unilateral external fixator (Orthofix limb reconstruction system, LRS) at our hospital from 2010 to 2019 were analyzed retrospectively. The Association for the Study and Application of the Method of Ilizarov (ASAMI) standard was applied to assess the bone and functional outcomes and postoperative complications evaluated by Paley classification. Results: Seventy-six cases of infected femoral bone defects (31 proximal, 19 intermediate, and 26 distal) were managed by single-level bone transport using a unilateral external fixator with a mean follow-up time of 30.8 (23 to 41) months. There were 58 men (76.3%) and 18 women (23.6%), with a mean age of 38.8 years (range, 23 – 60 years). The bone union was achieved in 76 cases with a mean time of 6.9 months (range, 5-8 months). Complications included 29 cases (38.1%) of pin tract infection, 7 cases (9.2%) of muscle contractures, 3 cases (7.9%) of joint stiffness, 13 cases (17.1%) of axial deviation, 2 cases (2.6%) of delayed union, one case (1.3%) of nonunion, and none (0%) of transport gap re-fracture. One patient (1.3%) was scheduled for knee arthroplasty when bone transport treatment ended.Conclusions: Bone transport in the reconstruction of femoral bone defects using unilateral external rail fixator had a satisfactory rate of bone healing and limb function recovery. Complications of distal femoral bone transport were more severe than other sites, but the complication rate was the least of the three. Complications of the proximal were comparable to the intermediate, and soft-tissue-related complications were more likely to occur in the intermediate transport.
The Expression of Interleukin-1β Is Regulated by DNA Methylation in Microglia of Hippocampus to Participate Postoperative Cognitive Dysfunction in Aged Mice
Authors: Gao Yin , Yang Li , Yang Xiu , Hao Jing-Ru , Shen Xiao-Ran , Li Xu , Liu Yue-Ying , Liu Le , Tong Kun , You Yue , Chen Di-Shi , Sun Nan , Gao Can 
Published: July 2021

Abstract
BackgroundPostoperative cognitive dysfunction (POCD) is one of the common postoperative complications in the elderly. The main clinical manifestation is memory impairment, which can cause permanent damage and even dementia in severe cases. However, the pathogenesis of POCD is still unknown. Age and neuroinflammation are known to be closely related to its occurrence, while DNA methylation is very important for transcriptional silencing and neuroinflammation. Consequently, this study intended to establish a mouse model of POCD to explore the role of DNA methylation in regulating the expression of interleukin-1β which participated POCD in aged mice.MethodsPOCD model was established by exploratory laparotomy and evaluated by new object experiment and Y maze test. In addition, ELISA, RT-PCR, Western blotting, immunofluorescence, microglia isolation and flow cytometry methods were used to detect the inflammatory state of dorsal hippocampal after surgery. Moreover, MSP, MeDIP and IL-1β promoter DNA methylation sequencing were used to explore the regulation of DNA methylation on IL-1β in this model. Finally, Golgi staining and Western blotting were used to further explore the role of IL-1β in POCD and its possible mechanisms. ResultsCognitive impairment was observed in aged but not adult mice at 1 day after surgery. There was a significant correlation between the level of IL-1β in dorsal hippocampus and the performance of cognitive function. The microglia in the dorsal hippocampus was activated and the IL-1β promoter DNA methylation was decreased in the aged mice. The increased expression of IL-1β impaired synaptic plasticity and hippocampus-dependent memory formation. Intracerebroventricular administration of IL-1β receptor antagonist could prevent the cognitive impairment of aged mice after surgery, reverse the decrease of dendritic spine density and synapse-associated protein expression induced by surgery.ConclusionDNA methylation regulation may be an important mechanism for greater susceptibility to POCD in aged mice by regulating the expression of IL-1β. IL-1β inhibiting prevented surgery-induced cognitive decline and synaptic plasticity dysfunction. The research also provided a new target for the clinical prevention of the occurrence of POCD in the elderly.
Can Topical Nasal Steroid Prevent the Loss of Smell in Covid-19?
Authors: Timurkaan Mustafa , Yıldırım Yavuz Sultan Selim 
Published: July 2021

Abstract
Purpose: The purpose of this study is to evaluate the effects of nasal steroid use on the loss of smell in patients diagnosed with Covid-19.Material and Method: 211 patients diagnosed with Covid-19 with positive PCR tests between April 2020 and December 2020 and followed up and treated in the Elazig City Hospital Pandemic Clinic were included in this cross-sectional study. The demographic data, comorbidities and drug use histories of the patients were interviewed face-to-face and recorded.Findings: The average age of the patients was 53.55 ± 17.81 (129 men, 82 women). Regarding the age, gender and comorbidities of the patients, there was no difference between the groups with and without loss of smell in terms of average age and gender. Anosmia developed in 50 patients (23.5%) and hyposmia developed in 84 patients (40%). No decrease or loss of sense of smell was observed in 77 patients. 26 of these patients were using nasal steroids at the time of diagnosis, and none of them had a decrease or loss in sense of smell.Results: With the results of the study, it has presented for the first time to the literature that the use of nasal steroids can prevent the loss of smell, which is one of the common neurological symptoms in Covid-19. The results of our study suggest that the nasal steroid, which plays an immunomodulatory role, can be a shield against loss of smell by creating a local anti-inflammatory effect in the nasal mucosa and around the olfactory nerve.
Impacts of Climate Change on Rainfall Trends Under RCP Scenarios in Johor, Malaysia
Authors: Rahmat Siti Nazahiyah , Tarmizi Aainaa Hatin Ahmad , Tukimat Nurul Nadrah Aqilah 
Published: July 2021

Abstract
Changes in the spatial and temporal rainfall pattern affected by the climate change need to be investigated as its significant characteristics are often used for managing water resources. In this study, the impacts of climate change on rainfall variability in Johor was investigated by using General Circulation Model (GCM) on the availability of daily simulation for three representative concentration pathways (RCP) scenarios, RCP2.6, RCP4.5 and RCP8.5 for interval year of Δ2030, Δ2050 and Δ2080. In addition, the annual future rainfall trend for the first interval year of Δ2030 was also made. Daily rainfall series from eight (8) stations in Johor, Malaysia capturing 30 years period (1988-2017) with less than 10% missing data were chosen. The annual mean rainfall for RCP 2.6, 4.5 and 8.5 was predicted increase by 17.5%, 18.1% and 18.3%, respectively as compared to historical data. Moreover, the Mann-Kendall (MK) test was used to detect the trend and resulted in no trend for RCP2.6. Even so, RCP4.5 showed a significant upward trend in Muar and Kota Tinggi, and for RCP8.5, all regions were detected to have an upwards trend except for Pontian and Kluang. In general, the concentration of greenhouse gases from RCP8.5 gave the highest rainfall in future.
Species Richness Capture Plant Functional and Phylogenetic Diversity Variations Along Different Ecosystems on the Hillsides of Damavand Mountain (Iran)
Authors: sadeghinia majid , gholinejad Bahram , kargar Mansoureh 
Published: July 2021

Abstract
Aims Plants vary in their functional traits and thus in their preference towards edaphic conditions. Plants displaying tougher, long-living leaves, which better conserve nutrients in the tissues, are expected to grow better in acidic soils, which are frequently nutrient poor. Methods We used a trait-based approach, quantifying variations in the Leaf-height-seed (LHS) scheme and functional and phylogenetic indices in semi-arid communities from three different habitats (grasslands, shrubland and mixed habitats). Three traits, including specific leaf area (SLA), Plant height (H) and Seed Mass (SM), in 350 plots across the three habitats in the southern hillsides of Damavand Mountain. We only included the species that occurred in more than 20 plots throughout the dataset for the following analyses (i.e., 44 species). We calculated at the plot scale, community weighted means (CWM) for each trait, species richness, Faith’s phylogenetic diversity index (PD), functional richness (Frich), functional and phylogenetic mean pairwise dissimilarities (MPD) and nutrient concentration. Results The results showed that the higher soil nutrient concentration and pH were significant and positive related with species and functional richness and Faith´s phylogenetic distance, while not significant results were obtained for any functional trait at community level (SLACWM, VHCWM and SMCWM) or for the functional and phylogenetic mean pairwise distance.Conclusiones In addition, the phylogenetic and functional patterns responded more to the taxonomic richness variations than to trait-based assembly processes.
TL-Moments Approach: Application of non-Stationary GEV Model in Flood Frequency Analysis
Authors: Jan Nur Amalina Mat , Shabri Ani , Marsani Muhammad Fadhil , Badyalina Basri 
Published: July 2021

Abstract
The non-stationarity in hydrological records is a significant concerning area of interest within the field of flood risk management. Ignoring the non-stationary behaviour in flood series will result in a substantial bias in floods quantile. Hence, the non-stationary flood frequency analysis appeared to be an appropriate option to maintain the independent and identically distributed (IID) assumptions in sample observation. This paper utilized the Generalized Extreme Value (GEV) distribution to analyze extreme flood series. The time-varying moment technique, namely the L-moment and TL-moment methods are employed to estimate the non-stationary model (GEV 1, GEV 2, and GEV 3) in the flood series. The ADF test, Mann-Kendall trend test, and Spearman’s Rho test showed that two out of ten streamflow stations in Johor, Malaysia demonstrated a non-stationary behaviour in the annual maximum streamflow. Results from the simulation study demonstrate a consistent performance on the non-stationary model. Furthermore, the TL-moments method could efficiently predict the flood event estimated at quantiles of the higher return periods.
Magnitude of Child Sexual Abuse and Its Associated Factors Among High School Female Students in Dire Dawa, Eastern Ethiopia. A Cross-sectional Study
Authors: Natae Legesse Abera , Aliye Abdulahi , Tadesse Kalbesse , Guta Alemu 
Published: July 2021

Abstract
Background: Child sexual abuse means any kind of sexual contact with a child under the age of 18 years. It is a common and serious public health problem affecting millions of people each year worldwide. It is the most neglected and least documented form of violence in Ethiopia among school girls. So, this study aimed to assess the magnitude and its associated factors among high school female students in Dire Dawa, Eastern Ethiopia.Methods: An institutional-based, cross-sectional study was conducted, March, 1-23/2021. A stratified multistage sampling technique was used for quantitative data and 794 participants from selected high schools were included. A pre-tested, self-administered questionnaire was used, and data were analyzed using SPSS software version 24. For qualitative data, sixteen in-depth interviews and five focus group discussion were conducted and analyzed thematically. Result: The magnitude of at least one form of sexual abuse were 384 (48.9%), of these, 150 (19.1%) were rape. Students who live alone 4.3 times (AOR=4.30;95 % CI: 1.81-10.24), those who lives with their friends 5 times (AOR=5.02: 95% CI: 2.24-11.24), and those who lives with their single parent 3 times (AOR=3.31: 95% CI: 1.23-8.89) more likely experience life time sexual abuse than those living with their both parents. The odds of experiencing life time sexual abuse among students of rural residence were 2 times higher than their urban counter part (AOR=2.1; 95% CI: 1.79-3.45). Students who don’t drink alcohol were 70% more protective than those who drink alcohol (AOR=0.70: 95% CI: 0.28-0.97).Conclusion: This study revealed that the magnitude of child sexual abuse among female students in Dire Dawa is high. Lack of discussion about sexual issue with parents, living without both parents, drinking alcohol, being rural residence had significant association with child sexual abuse. Unwanted pregnancy, abortion, and STIs were the most common reproductive consequences of sexual abuse. So, community-based comprehensive awareness creation on sexual and reproductive health issues, are recommended especially, at rural area.
Finite-Time Performance Guaranteed Event-Triggered Adaptive Control for Nonlinear Systems with Unknown Control Direction
Authors: Wang Min , Wang Lixue 
Published: July 2021

Abstract
This paper studies the issue of finite-time performance guaranteed event-triggered (ET) adaptive neural tracking control for strict-feedback nonlinear systems with unknown control direction. A novel finite-time performance function is first constructed to describe the prescribed tracking performance, and then a new lemma is given to show the differentiability and boundedness for the performance function, which is important for the verification of the closed-loop stability. Furthermore, with the help of the error transformation technique, the origin constrained tracking error is transformed into an equivalent unconstrained one. By utilizing the first-order sliding mode differentiator, the issue of ``explosion of complexity'' caused by the backstepping design is adequately addressed. Subsequently, an ingenious adaptive updated law is given to co-design the controller and the ET mechanism by the combination of the Nussbaum-type function, thus effectively handling the influences of the measurement error resulted from the ET mechanism and the challenge of the controller design caused by the unknown control direction. The presented event-triggered control scheme can not only guarantee the prescribed tracking performance, but also alleviate the communication burden simultaneously. Finally, numerical and practical examples are provided to demonstrate the validity of the proposed control strategy.
Data-driven simulation and characterization of gold nanoparticles melting
Authors: Zeni Claudio , Rossi Kevin , Pavloudis Theodore , Kioseoglou Joseph , de Gironcoli Stefano , Palmer Richard , Baletto Francesca 
Published: July 2021

Abstract
We develop efficient, accurate, transferable, and interpretable machine learning force fields for Au nanoparticles, based on data gathered from Density Functional Theory calculations.
We then use them to investigate the thermodynamic stability of Au nanoparticles of different sizes (1 to 6 nm), containing up to 6266 atoms, with respect to a solid-liquid phase change through molecular dynamics simulations.
We predict nanoparticle melting temperatures in good agreement with respect to available experimental data.
Furthermore, we characterize in detail the solid to liquid phase change mechanism employing an unsupervised learning scheme to categorize local atomic environments.
We thus provide a rigorous and data-driven definition of liquid atomic arrangements in the inner and surface regions of a nanoparticle, and employ it to show that melting initiates at the outer layers.
MCEMP1 as a Tumor Microenvironment and Immune Infiltration Related Gene for Prognostic Prediction in Advanced Gastric Cancer
Authors: Wang Daijun , Gu Yanmei , Zhao Yang , Li Yumin 
Published: July 2021

Abstract
Background Tumor microenvironment (TME) has displayed profound clinical significance in cancer progression, prognosis and the efficacy of immunotherapy. However, the overall characteristics of TME in patients with advanced gastric cancer (AGC) have not been intensively studied. In order to get a more comprehensive understanding, this study aimed to investigate TME-related prognostic genes in patients with AGC based on bioinformatics, combined with histological verification.Methods Transcriptome and clinical data on stage III/IV GC were obtained from The Cancer Genome Atlas (TCGA) database. The data of stromal, immune scores and 22 infiltrating immune cells from AGC samples were evaluated by ESTIMATE and CIBERSORT algorithms. Then, mast cell-expressed membrane protein 1 (MCEMP1) was focused by integrated protein-protein interaction (PPI) network and Cox regression. The survival and expression analysis of MCEMP1 was evaluated and verified in tissues by immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR).Results There was a positive correlation between TME scores and pathological grades. A total of 666 TME-related differential genes were screened. MCEMP1 was identified as a predictive factor related to the prognosis of AGC both in TCGA database and tissue samples. Further analysis indicated that MCEMP1 was involved in regulating pathways of immune activities. The results of CIBERSORT demonstrated that MCEMP1 expression was significantly correlated with the proportion of 8 kinds of infiltrating immune cells. Conclusion As a TME-related prognostic gene, MCEMP1 might play a crucial role in remodeling immune infiltrates in AGC patients, which might be a potential immunotherapy target for patients with AGC.