bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic Analysis of The Poultry Red Mite, Dermanyssus Gallinae, Across All Stages of The Lifecycle.
Authors: Bartley Kathryn , Chen Wan , Mills Richard Lloyd , Nunn Francesca , Price Daniel , Rombauts Stephane , de Peer Yves Van , Roy Lise , Nisbet Alasdair , Burgess Stewart 
Published: January 2021

Abstract
Background: The blood feeding poultry red mite (PRM), Dermanyssus gallinae, causes substantial economic damage to the egg laying industry worldwide, and is serious welfare concern for laying hens and poultry house workers. In this study we have investigated the temporal gene expression across the 6 stages/sexes (egg, larvae, protonymph and deutonymph, adult male and adult female) of this neglected parasite in order to understand the temporal expression associated with development, parasitic lifestyle, reproduction and allergen expression. Results: RNA-seq transcript data for the 6 stages was mapped to the PRM genome creating a publicly available gene expression atlas (on the OrcAE platform in conjunction with the PRM genome). Network analysis and clustering of stage-enriched gene expression in PRM resulted in 17 superclusters with stage-specific or multi-stage expression profiles. The 6 stage specific superclusters were clearly demarked from each other and the adult female supercluster contained the most stage specific transcripts (2,725), whilst the protonymph supercluster the fewest (165). Fifteen pairwise comparisons performed between the different stages resulting in a total of 6025 Differentially Expressed Genes (DEGs) (P>0.99). These data were evaluated alongside a Venn/Euler analysis of the top 100 most abundant genes in each stage. An expanded set of cuticle proteins and enzymes (chitinase and metallacarboxypeptidases) were identified in larvae and underpin cuticle formation and ecdysis to the protonymph stage. Two mucin/peritrophic-A salivary proteins (DEGAL6771g00070, DEGAL6824g00220) were highly expressed in the blood-feeding stages, indicating peritrophic membrane formation during feeding. Reproduction-associated vitellogenins were the most abundant transcripts in adult females, whilst in adult males, an expanded set of serine and cysteine proteinases and an epididymal protein (DEGAL6668g00010) were highly abundant. Assessment of the expression patterns of putative homologues of 32 allergen groups described for the house dust mites indicated a bias in expression towards the non-feeding larval stage.Conclusions: This study is the first evaluation of temporal gene expression across all stages of PRM and has provided insight into developmental, feeding, reproduction and survival strategies employed by this mite. The publicly available PRM resource on OrcAE offers an invaluable tool for researchers investigating the biology and novel interventions of this parasite.
Time to Detection of Anemia and Its Predictors Among Children Receiving Antiretroviral Therapy at Debre Tabor Referral Hospital and University of Gonder Compressive Specialized Hospital, 2020: A Multicenter Retrospective Follow-Up Study
Authors: Chanie Ermias , feleke Dejen , Alemayehu Sintayehu ehu , GebreEyesus Fisha , Tesfaw Aragaw , Bayih Wubet , Tigabu Agimasie , Ayinalem Yared , Amare Aberham , Mesfine Demeke , Dagnaw Fentaw , Abate Bruk 
Published: January 2021

Abstract
Background: Although antiretroviral therapy access for HIV infected children increased dramatically, anemia have been continued as a challenge regardless of cluster of differentiation (CD4) count and viral load. Hence, this study aimed to assess the time to detection of anemia and its predictors among children receiving antiretroviral therapy at Debre Tabor referral hospital and University of Gonder Compressive Specialized hospital, 2020.Methods: A retrospective follow-up study was conducted from January 2010 to December 2018. A total of 372 children under the age of 15 who had received ART were included in the study. Data were collected from children’s medical charts and ART registration logbook using a standard checklist. Besides, the data were entered into EPi data 4.2.2 and then exported to Stata 14.0 for further analysis. The Cox regression model, the variables having P-value ≤.05 with 95% CIs in multivariable analysis were declared as a statistically significant for anemia Result: The mean (±SD) of follow-up periods were 56.6 ±1.7 SD months. The overall median survival time free from anemia was 137 months, and the incidence rate of anemia was 6.9 per 100 PYO (95% CI: 5.3, 7.8). Moreover, WHO clinical staging of III/IV [AHR: 4.2, 95% CI: 1.80, 11.1], low CD4 count below threshold [AHR: 1.9, 95% CI: 1.09, 3.37], cotrimoxazole preventive therapy non-users, and poor level of adherence [(AHR: 2.4, 95% CI: 1.20, 4.85] were the main predictors of anemia. Conclusion: The incidence rate of anemia was found to be high. Monitor hemoglobin levels routinely with concurrently CD4 cell count levels, WHO clinical stage, and level of adherence. Hence, preventing and correcting of those predictors in a systematic manner in ongoing basis is crucial. Moreover, strategies need to be strengthened cotrimoxazole preventive therapy supplementation
Automated Measurement of Iris Surface Smoothness Using Anterior Segment Optical Coherence Tomography&nbsp;&nbsp;
Authors: Zarei Mohammad , Mahmudi Tahereh , Riazi-Esfahani Hamid , Mousavi Behnam , Ebrahimiadib Nazanin , Yaseri Mehdi , Pour Elias Khalili , Arabalibeik Hossein 
Published: January 2021

Abstract
Fuchs uveitis (FU) is a chronic and often unilateral ocular inflammation and characteristic iris atrophic changes, other than heterochromia, are common in FU and are key to the correct diagnosis in many cases. With the advent of anterior segment optical coherence tomography (AS-OCT), some investigators attempted to quantitatively study these atrophic changes; mostly by introducing various methods to measure iris thickness in AS-OCT images. We aimed to present an automated method in a observational case series to measure the smoothness index (SI) of iris surface in AS-OCT images. The ratio of the length of the straight line connecting the most peripheral and central points of the anterior iris border (in nasal and temporal sides) to the actual length of this border on AS-OCT images, was defined as SI. In a uveitis referral center twenty-two eyes of 11 patients with unilateral Fuchs uveitis (FU) (7 female) and 22 eyes of 11 healthy control subjects underwent AS-OCT imaging. Image J and a newly developed MATLAB algorithm were used for manual and automated SI measurements, respectively. Agreement between manual and automated measurements was evaluated with Bland-Altman analysis and interclass correlation coefficient. The inter-eye difference of SI was compared between FU group and control group. Automated mean overall SI was 0.868 ± 0.037 and 0.840 ± 0.039 in FU and healthy fellow eyes, respectively (estimated mean difference = -0.028, 95% CI [-0.038, -0.018], p<0.001). Bland- Altman plots showed good agreement between two methods in both healthy and FU eyes. Interclass correlation coefficient between the manual and automated measurements in the FU and healthy fellow eyes was 0.958 and 0.964, respectively. Inter-eye difference of overall SI was 0.029 ± 0.015 and 0.012 ± 0.008 in FU group and control group, respectively (p=0.01). We concluded that he automated algorithm can rapidly and conveniently measure SI with results comparable to manual method.
Irrigation Schedules and Crop Water Requirements for Some Main Crops in Saudi Arabia
Authors: Khan Waseem , Y. Mogtaba , Rahman Jamshaid , Elbashir Murtada , AlHussain Ziyad , Farooq Umer 
Published: January 2021

Abstract
The Food and Agriculture Organization (FAO) CROPWAT 8.0 standard software and the CLIMWAT 2.0 tool affixed to it have been utilized in this study for Qassim Region of Saudi Arabia to find CWRs and irrigation plans for numerous extremely valuable crops of KSA. We were used CROPWAT P. M. method for find out the ETo and (USAD) S. C. method utilized to determine roughly effective rainfall. The analysis demonstrated that ETo change over from 2.84 mm/day in January to reach maximum 9.61 mm/day in July due to high temperature in summer with annual mean was 6.33 mm/day, effective rainfall changes from 0 mm to 53.4 mm. The total IWRs were 308.3 mm/dec, 335.9 mm/dec, 343.6 mm/dec, 853 mm/dec and 1479.6 mm/dec for Barley, Wheat, Maize, Rice and Citrus, respectively. Due to low demand in winter and high demand in summer, the total net irrigation and total gross irrigations are 210.6 mm and 147.4 mm, 176.6 mm and 123.6 mm, 204.5 mm and 143.2 mm, 163.9 mm and 114.7mm for Wheat, Barley, Citrus, and Maize respectively except rice crop. These results showed that Wheat, Barley, Citrus, Maize and Rice crops have 4, 4, 12, 4 and 12 irrigation schedules respectively in a year.
Gender Differences in Refraction Prediction Error of Five Formulas for Cataract Surgery
Authors: Zhang Yibing , Li Tingyang , Reddy Aparna , Nallasamy Nambi 
Published: January 2021

Abstract
Objectives: To evaluate gender differences in optical biometry measurements and lens power calculations. Methods: 8431 eyes of 5519 patients who underwent cataract surgery at University of Michigan’s Kellogg Eye Center were included in this retrospective study. Data including age, gender, optical biometry, postoperative refraction, implanted intraocular lens (IOL) power, and IOL formula refraction predictions were gathered and/or calculated utilizing the Sight Outcomes Research Collaborative (SOURCE) database and analyzed.Results: There was a statistical difference between every optical biometry measure between genders. Despite lens constant optimization, mean signed prediction errors (SPEs) of modern IOL formulas differed significantly between genders, with predictions skewed more hyperopic for males and myopic for females for all 5 of the modern IOL formulas tested. Optimization of lens constants by gender significantly decreased prediction error for 2 of the 5 modern IOL formulas tested.Conclusions: Gender was found to be an independent predictor of refraction prediction error for all 5 formulas studied. Optimization of lens constants by gender can decrease refraction prediction error for certain modern IOL formulas.
Increased Serum Ferritin Levels in Type 2 Diabetes Mellitus Patients: A Hospital Based Cross-Sectional Study
Authors: Chaudhari Rajendra , Niraula Apeksha , Gelal Basanta , Baranwal Jouslin , Sarraf Deependra , Maskey Robin , Lamsal Madhab 
Published: January 2021

Abstract
Background: Type 2 diabetes mellitus is a metabolic disorder of multiple etiology characterized by chronic hyperglycemia with a derangement in carbohydrate, fat and protein metabolism resulting from defects in insulin secretion and action. Ferritin is a ubiquitous intracellular protein complex that reflects the iron stores of the body. Studies have shown that the increased body iron stores are associated with the development of glucose intolerance often leading to metabolic syndrome and type 2 diabetes (T2DM). The objective of the study was to find out association of serum ferritin level with T2DM and assess the correlation between serum ferritin and HbA1c. Methods: A hospital based comparative cross-sectional study was conducted in 43 diabetic patients and 42 age and sex matched healthy controls. Fasting blood glucose (FBG), postprandial blood glucose (PBG), Glycated hemoglobin (HbA1c) and serum ferritin were estimated in cobas c311 autoanalyser using standard protocol. Results: Mean age of healthy control and T2DM were found 54.83 ± 6.48 and 55.95±10.92 years respectively. Mean FPG (mg/dl) (170.41 ± 71.7 v/s 98.38 ± 9.7), PBG (mg/dl) (266.16 ± 110.09 v/s 123.20 ± 17.0), HbA1c (%) (8.17 ± 1.83 v/s 4.9 ± 0.29 and median ferritin (μg/L) 207.90 (138, 306.0) v/s 127.95 (85.75, 210.25) were significantly higher in T2DM compared to the healthy controls. Spearman’s correlation depicted that ferritin level was positively correlated with HbA1c level but the correlation was statistically insignificant. Conclusion: Serum ferritin level was found significantly increased in T2DM compared to healthy age and sex matched controls in our study.
Implementation of Transbronchial Lung Cryobiopsy in a Tertiary Referral Center for Interstitial Lung Diseases – A Cohort Study on Diagnostic Yield, Complications, and Learning Curves
Authors: Davidsen Jesper , Skov Inge , Louw Ida , Laursen Christian 
Published: January 2021

Abstract
BackgroundTransbronchial lung cryobiopsy (TBLC) has been introduced as an alternative to surgical lung biopsy (SLB) in the diagnostics of interstitial lung diseases (ILD). Despite controversy on safety, TBLC is increasingly implemented in ILD centers with an apparent diagnostic yield comparable to SLB. The aim of this study was to assess TBLC implementation experiences from a tertiary Danish ILD center regarding diagnosis, complications, and learning curves for TBLC performance.MethodsTBLC was prospectively performed in a cohort of patients with unclassifiable ILD based on a preceding multidisciplinary clinical and radiological revision. TBLC was performed as an outpatient procedure with the patients in general anesthesia using a flexible bronchoscope with 1.9 or 2.4 mm cryoprobes. Learning curves for TBLC performance were calculated using cumulated sum (CUSUM) scores for diagnostic yield, pneumothorax, and bleeding.Results From February 2017 to March 2020 141 patients (86 (61%) men, median age 69 years [IQR, 60 years to 74 years]) had TBLC performed. A histological and confirmative diagnosis was made in 101 patients (75.2%) and 124 patients (87.9%, i.e. clinical diagnostic yield), respectively, in whom idiopathic interstitial pneumonias constituted the majority (67.3%) of the clinical diagnoses. We observed 2 deaths (1.4%) within 30 days of TBLC, but no procedure-related mortality or severe bleeding. Moderate bleeding occurred in 23 patients (16.3%), pneumothorax in 21 patients (14.9%) with only 14 patients (9.9%) requiring a pleural drain. Based on the CUSUM score analysis, the diagnostic yield obtained was satisfactory throughout the period.ConclusionThis study reports experiences of outpatient TBLC implementation in a tertiary referral ILD center from the largest investigated TBLC cohort in Scandinavia The diagnostic yield and prevalence of complications obtained by TBLC from this single center study on unclassifiable ILD support outpatient TBLC as a valuable and safe alternative to SLB to diagnose ILD in well-selected patients. The learning curves for TBLC were acceptable in the hands of experienced bronchoscopists.Of note, the majority of the abstract details have been presented as a poster at the European Respiratory Society’s Congress in Madrid, Spain in 2019 (European Respiratory Journal 2019 54: PA3107; DOI: 10.1183/13993003.congress-2019.PA3107).
Estimation of Moisture Ratio and Specific Energy Consumption for Apple Slices Drying by Convective and Microwave Methods using Neural Network Modeling
Authors: Sharabiani Vali Rasooli , Roozbeh Abdi , Kaveh Mohammad , Szymanek Mariusz , Tanaś Wojciech 
Published: January 2021

Abstract
Two different drying methods were applied for dehydration of apple, i.e., convection drying (CD) and microwave drying (MD). The process of convection drying through divergent temperatures; 50, 60 and 70°C at 1.0 m/s air velocity and three different levels of microwave power (90, 180, and 360 W) were studied. In the analysis of the performance of our approach on moisture ratio of apple slices, artificial neural networks (ANNs) was used to provide with a background for further discussion and evaluation. In order to evaluate the models mentioned in the literature, the Midilli et al. model was proper for dehydrating of apple slices in both MD and CD. The microwave drying technology enhanced the drying rate when compared with convective drying significantly. Effective diffusivity of moisture in CD drying (1.95×10−7 - 4.09×10−7 m2/s) was found to be lower than that observed in MD (2.94×10−7–8.21×10−7 m2/s). The Ea values of convective drying and microwave drying were 122.28- 125 kJ/mol and 14.01- 15.03 W/g respectively. The MD had the lowest SEC as compared to CD drying methods. According to ANN results, the best values for predication of MR in CD and MD were 0.9993 and 0.9990, respectively.
Altruism in the time of COVID-19: We are all in this together, but who is we?
Authors: Grimalda Gianluca , Buchan Nancy , Ozturk Orgul , Pinate Adriana , Urso Giulia , Brewer Marilynn 
Published: January 2021

Abstract
Theory posits that in situations of existential threat, selfish motivations will be outweighed by altruistic ones, and cooperation will be parochial. Yet, the global character of the COVID-19 pandemic makes unclear which level of group inclusiveness individuals will privilege. In an online experiment, participants from the U.S. and Italy chose to allocate a monetary bonus to a charity active in COVID-19 relief efforts at the local, national, or international level, or to keep the bonus for themselves. We found that personal exposure to COVID-19 increased donations relative to those not exposed, even as levels of environmental exposure (numbers of cases locally) had no effect. Only one-third of individuals acted entirely selfishly. Donors predominantly benefitted the local level (state in the U.S., region in Italy); donations toward country and world levels were half as large. Social identity was a moderating factor in both countries. These results confirm and qualify existing theories.
Robust Denoising of Cryo-EM Images via β-GAN
Authors: Gu Hanlin , Unarta Ilona , Huang Xuhui , Yao Yuan 
Published: January 2021

Abstract
The cryo-electron microscopy (Cryo-EM) becomes popular for macromolecular structure determination. However, the 2D images which Cryo-EM detects are of high noise and often mixed with multiple heterogeneous conformations and contamination, imposing a challenge for denoising. Traditional image denoising methods and simple Denoising Autoencoder can not remove Cryo-EM image noise well when the signal-noise-ratio (SNR) of images is meager and contamination distribution is complex. Thus it is desired to develop new effective denoising techniques to facilitate further research such as 3D reconstruction, 2D conformation classification, and so on. In this paper, we approach the robust denoising problem for Cryo-EM images by introducing a family of Generative Adversarial Networks (GAN), called β-GAN, which is able to achieve robust estimate of certain distributional parameters under Huber contamination model with statistical optimality. To address the challenge of robust denoising where the traditional image generative model might be contaminated by a small portion of unknown outliers, β-GANs are exploited to enhance the robustness of denoising Autoencoder. The method is evaluated by both a simulated dataset on the Thermus aquaticus RNA Polymerase (RNAP) and a real dataset on the Plasmodium falciparum 80S ribosome dataset (EMPIRE-10028), in terms of Mean Square Error (MSE), Peak Signal to Noise Ratio (PSNR), Structural Similarity Index Measure (SSIM) and 3D Reconstruction as well. The results show that equipped with some designs of β-GANs and the robust ℓ1-Autoencoder, one can stabilize the training of GANs and achieve the state-of-the-art performance of robust denoising with low SNR data and against possible information contamination. Our proposed methodology thus provides an effective tool for robust denoising of Cryo-EM 2D images, which is helpful for 3D structure reconstruction.
Long-Term Analysis of Day-To-Day Equatorial IHFACs Variations During Solar Cycle 23-24
Authors: Ranasinghe Manjula , Fujimoto Akiko , Yoshikawa Akimasa , Jayaratne Chandana 
Published: January 2021

Abstract
The east-west ward variation of MAGDAS/CPMN magnetometer 1-hour time resolution data at Davao (Philippines) station operated by International Center for Space Weather Science and Education, Kyushu University from August 1998 to July 2020 are used to investigate the characteristics of the long-term Inter-hemispheric field-aligned currents (IHFACs). The recent in-situ satellite and ground-based observations have reported the dusk-side current polarity of IHFACs are often inconsistent with the Fukushima’s IHFACs model. We investigated whether the dusk-side IHFACs polarity is consistent or not with the current direction predicted by Fukushima’s IHFACs model, by analyzing the time-series data of the day-to-day IHFACs variations. We confirmed that the solstices dusk IHFACs flow the same direction of noon IHFACs and the equinoxes dusk IHFACs disagree with Fukushima’s model. Seasonal IHFACs variations exhibited remarkable asymmetry in both dawn and noon sectors. By contrast, the profile of dusk-side IHFACs intensity was symmetry. We presented that solar cycle dependence can be seen in the peak-to-peak amplitude, monthly average and yearly integral intensity of IHFACs. However, while the dawn and noon IHFACs intensity decreased with year by year, the dusk intensity tended to increase year-to-year. In contrast to annual variations of IHFACs polarity in the dawn/noon sectors, there were multiple periodicities in the dusk sector: annual variation during the declining phase of solar cycle and semiannual or terannual variations during the increasing and maximum phase. The dusk-side day-to-day IHFACs variations were more coherent with F10.7 variability compared with the dawn and noon sectors. It suggests that the dusk IHFACs is affected by the solar cycle activities.
Effects of Fermented Mushroom Residue&nbsp;Feed on Growth Performance and Rumen Microorganisms of Goats
Authors: Zhang Yao , Dou Mengying , Chen Xinzhu , Huang Xiaoyun , Huang Qinlou , Huang Xiusheng 
Published: January 2021

Abstract
Background: The high content of fiber and macromolecular substances in mushroom residue limits its utilization potential. After we fermented seafood mushroom residue with microorganisms, we found that its palatability and utilization have been greatly improved.The purpose of this study was to investigate the effects of feed containing fermented seafood mushroom residue on the growth performance and rumen microorganisms of goats. Methods: Forty-eight Jianyang big-ear goats with similar weight and good health were selected and randomly divided into 4 groups with 12 goats in each group. The control group (C) was fed a basic diet, and the experimental group 1 (L), 2 (M), and 3 (H) were fed diets supplemented with 20%, 30% and 40% fermented seafood mushroom residue.Results: Incorporating 20% fermented mushroom residue significantly increased the average daily gain (ADG) and average daily feed intake (ADFI) and reduced feed to gain ratio (F/G). Incorporating 30% in the diet significantly increased both ADFI and F/G. Growth performance was reduced when greater than 30% fermented mushroom residue was added. The beta diversity of the rumen flora was significantly increased with the 20% fermented mushroom residue diet. The relative abundance of Veillonellaceae, Ruminococcaceae, and Prevotellaceae increased, and the KEGG pathways related to metabolism of cofactors and vitamins, lipid metabolism, and xenobiotics biodegradation and metabolism were enhanced. Forty-nine KEGG pathways significantly associated with ADG were identified. Twenty-six pathways, including protein kinases, mineral absorption, propanoate metabolism, and biosynthesis of unsaturated fatty acids, were positively correlated with ADG. The remaining pathways, including pathogenic Escherichia coli infection, phenylpropanoid biosynthesis, shigellosis, and cyanoamino acid metabolism, were negatively correlated with ADG.Conclusions: These results show that adding 20% fermented seafood mushroom residue can improve the growth performance of goats and have a positive effect on goat rumen microorganisms.