bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic utility and phenotype correlation of serum ASCA and ANCA in pediatric inflammatory bowel disease
Authors: Kim Jeong Min , Choi Young Min , Jung Seung A , Moon Jin Soo , Ko Jae Sung , Yang Hye Ran 
Published: June 2022

Abstract
Background
Both anti-Saccharomyces cerevisiae antibody (ASCA) and anti-neutrophil cytoplasmic antibody (ANCA) are associated with inflammatory bowel disease (IBD); however, the clinical role of these serological biomarkers in pediatric IBD has been poorly investigated. Therefore, this study aimed to evaluate the diagnostic utility and phenotypic correlation of serological biomarkers in pediatric IBD.
Methods
A retrospective review was performed on all pediatric subjects diagnosed with IBD between March 2004 and July 2021. Pediatric patients were recruited and classified as Crohn’s disease (CD), ulcerative colitis (UC), and IBD unclassified (IBD-U) based on the revised Porto criteria. The Paris classification was used to evaluate disease phenotypes. Laboratory markers including fecal calprotectin were also evaluated. Serum levels of ASCA IgG and IgA, anti-proteinase-3 with cytoplasmic ANCA (PR3-ANCA), and anti-myeloperoxidase with perinuclear ANCA (MPO-ANCA) using ELISA, and serum ANCA titer using immunofluorescent test were measured.
Results
In all, 229 pediatric patients with IBD (CD: 147, UC: 53, IBD-U: 29) were included. The ASCA IgG seropositivity was significantly different among the three groups (CD: 75.4%, UC: 17.5%, and IBD-U: 60.0%; p < 0.001) and ASCA IgA seropositivity was also significantly different among the three groups (CD: 23.8%, UC: 2.5%, and IBD-U: 20.0%; p < 0.001). Serum titers of ASCA IgG were significantly difference among the 3 IBD subgroups (CD 32.7 U/mL vs. UC 11.3 U/mL vs. IBD-U 25.30 U/mL; p < 0.001), and ASCA IgA also revealed significant difference (CD 10.2 U/mL vs. UC 6.8 U/mL vs. IBD-U 9.0 U/mL; p < 0.001). Three ANCA antibodies were positive in 1.4%, 32.1%, and 37.9% of CD, UC, and IBD-U patients, respectively (p < 0.001). Perianal disease modifier P1 revealed higher ASCA IgG titers (P1 40.0 U/mL vs. P0 29.4 U/mL, p = 0.001), while showing no differences in age, disease location, and behavior. Using optimal cutoffs determined by ROC analysis, serum IgG and IgA ASCAs showed 68.0% and 63.1% sensitivity, and 67.7% and 64.6% specificity, respectively, in distinguishing CD.
Conclusions
Serological biomarkers of ASCAs IgG and IgA, pANCA, and PR3-ANCA may be effective in the diagnosis and clinical evaluation of disease phenotypes in an Asian pediatric IBD cohort.
Key factors for differential drought tolerance in two contrasting wild materials of Artemisia wellbyi identified using comparative transcriptomics
Authors: Liu Huan , Wang Qiyu , Wang Jinglong , Liu Yunfei , Renzeng Wangdui , Zhao Guiqin , Niu Kuiju 
Published: June 2022

Abstract
Background: Drought is a significant condition that restricts vegetation growth on the Tibetan Plateau. Artemisia wellbyi is one of the most important group species found in the Tibetan Plateau. Understanding the molecular mechanisms of the drought-tolerant material of A. wellbyi is crucial for the conservation of water and soil and for ecological protection; however, they remain unclear. Our study compared the transcriptomic characteristics of drought-tolerant “11” and drought-sensitive “6” material of A. wellbyi under drought stress. Results: A total of 4875 upregulated and 4381 downregulated differentially expressed genes (DEGs) were induced by drought in the tolerant material; however, only 1931 upregulated and 4174 downregulated DEGs were induced by drought in the sensitive material. The photosynthesis and transcriptional regulation differed significantly with respect to the DEGs number and expression level. We found that CDPKs (calmodulin-like domain protein kinases), SOS3 (salt overly sensitive3), MAPKs (mitogen-activated protein kinase cascades), RLKs (receptor like kinase), and LRR-RLKs (repeat leucine-rich receptor kinase) were firstly involved in response to drought stress in drought tolerant A. wellbyi. Positive regulation of genes associated with the metabolism of ABA (abscisic acid), ET (ethylene), and IAA (indole acetic acid) could play a crucial role in the interaction with other transcriptional regulatory factors, such as MYBs (v-myb avian myeloblastosis viral oncogene homolog), AP2/EREBPs (APETALA2/ethylene-responsive element binding protein family), WRKYs, and bHLHs (basic helix-loop-helix family members) and receptor kinases, and regulate downstream genes for defense against drought stress. In addition, HSP70 (heat shock protein70) and MYB73 were considered as the hub genes because of their strong association with other DEGs. Conclusions: Positive transcriptional regulation and negative regulation of photosynthesis could be associated with better growth performance under drought stress in the drought-tolerant material. In addition, the degradation of sucrose and starch in the tolerant A. wellbyi to alleviate osmotic stress and balance excess ROS. These results highlight the candidate genes that are involved in enhancing the performance of drought-tolerant A. wellbyi and provide a theoretical basis for improving the performance of drought-resistant A. wellbyi.
Degree of conversion of 3D printing resins used for splints and orthodontic appliances under different post-polymerization conditions.
Authors: DANTAGNAN Claire-Adeline , FRANÇOIS Philippe , GOFF Stéphane LE , ATTAL Jean-Pierre , DURSUN Elisabeth 
Published: June 2022

Abstract
Objectives: To measure the degree of conversion (DC) of different 3D printing resins usable for splints or orthodontic appliances, manufacturing under different post-polymerization conditions.Materials and Methods: Five 3D printing photopolymer resins were studied. Each resin was analyzed in liquid form (n=15), then cylindrical specimens (n=135) were additively manufactured and post-cured with different times (10, 60 and 90 minutes) and temperatures (20°, 60° and 80°). The degree of conversion of each specimen was measured by Fourier Transformed Infrared Spectroscopy (FTIR). The data were statistically analyzed using a 3-way ANOVA followed by Tukey’s post hoc test.Results: Time and temperature of post-polymerization significantly influenced the DC of each resin: when time and/or temperature increased, the DC increased. For all resins tested, the lowest DC was obtained with a post-curing protocol at 10 min and 20° and the highest DC at 90 min 80°. However, at 80°, samples showed a yellowish color.Conclusions: The time and temperature of post-curing could have an impact on the DC of the 3D printing resins studied. DC of the 3D printing resins could be optimized by adjusting the post-polymerization protocol. Clinical Relevance: Whatever the resin used, it seems that a post-curing at 60 min and 60° would be the minimal time and temperature conditions to obtain a proper polymerization. Beyond that, to boost the DC, it would be preferable to increase the post-curing time
Dynamic behavior and ligand binding properties of the wild type dCK and its characterized gemcitabine-resistant variant: a bioinformatics and computational study
Authors: Rahmati Yasmin , Khalifeh Khosrow , Heshmati Emran 
Published: June 2022

Abstract
In order to control the cell proliferation in various types of cancers, gemcitabine as the analogue of deoxycytidine is being used to perturb the DNA synthesis. The main challenge in using gemcitabine includes resistance of some patients to this compound due to the genetic mutations on deoxycytidine kinase (dCK) that are found in a fraction of human population. Here, we investigated the dynamics behavior and ligand binding properties of the wild type (WT) dCK and its characterized double mutant using a combination of the bioinformatics tools and molecular dynamics (MD) simulation studies. The crystal structure of the WT enzyme was trimmed by the MODELLER program and that of the double mutant was made by this program, and the structures were used as input for MD simulation. Root-mean-square deviation (RMSD) values of the WT and mutant enzyme in complex with both ligands, demonstrated that WT enzyme forms more stable complex with gemcitabine, as compared with its natural ligand (deoxycytidine). However, the stability of the double mutant-deoxycytidine complex is greater, when compared with gemcitabine. It was also found that Arg131 as a critical residue can affect the binding pattern of the enzyme to ligands in a manner that the WT enzyme can interact with both ligands, while, mutant enzyme cannot establish efficient interaction with gemcitabine, and shows high affinity to deoxycytidine. These data together indicate that gemcitabine can interact with the WT enzyme in a competitive manner, while double mutant can be considered as a resistant variant against gemcitabine.
Comparison of weight loss induced by Daily Caloric Restriction versus Intermittent Fasting (DRIFT) in individuals with obesity: Study protocol for a 52-week randomized clinical trial
Authors: Ostendorf Danielle M. , Caldwell Ann E , Zaman Adnin , Pan Zhaoxing , Bing Kristen , Wayland Liza T , Creasy Seth A , Bessesen Daniel H , MacLean Paul , Melanson Edward L , Catenacci Victoria A 
Published: June 2022

Abstract
Background
The standard-of-care for treating overweight and obesity is daily caloric restriction (DCR). While this approach produces modest weight loss, adherence to DCR declines over time and weight regain is common. Intermitting fasting (IMF) is an alternative dietary strategy for reducing energy intake (EI) that involves > 60% energy restriction on 2–3 days per week, or on alternate days, with habitual intake on fed days. While numerous studies have evaluated IMF as a weight loss strategy, there are several limitations including: lack of a standard-of-care DCR control, failure to provide guidelines-based behavioral support, and failure to rigorously evaluate dietary and PA adherence using objective measures. To date, only three longer-term (52-week) trials have evaluated IMF as a weight loss strategy. None of these longer-duration studies reported significant differences between IMF and DCR in changes in weight. However, each of these studies has limitations that prohibit drawing generalizable conclusions about the relative long-term efficacy of IMF vs. DCR for obesity treatment.
Methods
The Daily Caloric Restriction vs. Intermittent Fasting Trial (DRIFT) is a two-arm, 52-week block randomized (1:1) clinical weight loss trial. The two intervention arms (DCR and IMF) are designed to prescribe an equivalent average weekly energy deficit from baseline weight maintenance energy requirements. Both DCR and IMF will be provided guidelines-based behavioral support and a PA prescription. The primary outcome is change in body weight at 52 weeks. Secondary outcomes include changes in body composition (dual energy x-ray absorptiometry (DXA)), metabolic parameters, total daily energy expenditure (TDEE, doubly labeled water (DLW)), EI (DLW intake-balance method, 7-day diet diaries), and patterns of physical activity (PA, activPAL device).
Discussion
Although DCR leads to modest weight loss success in the short-term, there is wide inter-individual variability in weight loss and poor long-term weight loss maintenance. Evidence-based dietary approaches to energy restriction that are effective long-term are needed to provide a range of evidence-based options to individuals seeking weight loss. The DRIFT study will evaluate the long-term effectiveness of IMF vs. DCR on changes in objectively measured weight, EI, and PA, when these approaches are delivered using guidelines-based behavioral support and PA prescriptions.
Trial Registration {2a}:
ClinicalTrials.gov Identifier NCT03411356. Registered trial name: Intermittent Fasting Versus Daily Caloric Restriction for Weight Loss. Registered on January 26, 2018.
Bounding Pandemic Spread By Heat Spread
Authors: Lazebnik Teddy , Itai Uri 
Published: June 2022

Abstract
The beginning of a pandemic is a crucial stage for policymakers. Proper management at this stage can reduce overall health and economical damage. However, knowledge about the pandemic is insufficient. Thus, the use of complex and sophisticated models is challenging. In this study, we propose analytical and stochastic heat spread-based boundaries for the pandemic spread. These are compared with the stochastic Susceptible-Infected-Recovered (SIR) model taking place on an interaction graph. The proposed boundaries are not requiring accurate biological knowledge such as the SIR model does.
Accelerating the Alignment Processing Speed of the Comprehensive End-to-End Whole-Genome Bisulfite Sequencing Pipeline, wg-blimp
Authors: Lehle Jake D. , McCarrey John R. 
Published: June 2022

Abstract
Background
Analyzing whole-genome bisulfite sequencing (WGBS) datasets is a time-intensive process due to the complexity and size of the input raw sequencing files and lengthy read alignment step during downstream data processing. This is particularly challenging with WGBS data because the conversion of all unmethylated Cs to Ts genome-wide renders read alignment a cumbersome computational process that can take up to a full work week of computing time. The objective of the study described here was to modify the read alignment algorithm associated with the wg-blimp pipeline to shorten the time required to complete this phase while retaining overall read alignment accuracy.
Results
Here we report improvements upon the recently published pipeline wg-blimp (whole-genome bisulfite sequencing methylation analysis pipeline) achieved by replacing the use of the bwa-meth aligner with the faster gemBS aligner. This improvement to the wg-blimp pipeline has led to a > 7x acceleration in the processing speed of samples when scaled to larger publicly available FASTQ datasets containing 80–160 million (M) reads. Importantly, this acceleration was achieved while maintaining nearly identical accuracy of properly mapped reads when compared to data from the original pipeline.
Conclusion
The modifications to the wg-blimp pipeline reported here merge the speed and accuracy of the gemBS aligner with the comprehensive analysis and data visualization assets of the wg-blimp pipeline to provide a significantly accelerated pipeline that can produce high-quality data much more rapidly without compromising read accuracy.
Prediction of the need for emergency endoscopic treatment for upper gastrointestinal bleeding and new score model: A retrospective study
Authors: Sasaki Yoshihiro , Abe Tomoko , Kawamura Norio , Keitoku Taisei , Shibata Isamu , Ohno Shiho , Ono Keiichi , Makishima Makoto 
Published: June 2022

Abstract
Background: Gastrointestinal bleeding is one of the major gastrointestinal diseases. In this study, our objective was to compare Glasgow-Blatchford Score (GBS), AIMS65 score, MAP score, Modified GBS, and Iino et al. as outcome measures for upper gastrointestinal bleeding. In addition, we extracted factors associated with hemostatic procedures including endoscopy, and proposed a new robust score model. Methods: From January 2015 to December 2019, patients with symptoms such as hematemesis who visited the National Hospital Organization Disaster Medical Center and underwent urgent upper endoscopy were retrospectively reviewed. The GBS, AIMS65, MAP score, Modified GBS, and Iino et al. scores were evaluated, and the outcomes were those requiring hemostatic treatments at the subsequent emergency endoscopy. We performed logistic regression analysis of factors related to endoscopic hemostasis and upper gastrointestinal bleeding, and created a new score model to evaluate the prediction of hemostatic treatment and mortality in the new score and the existing scores. Results: The factors associated with endoscopic treatment were hematemesis, heart rate, HB (Hemoglobin), blood pressure, BUN (Blood urea nitrogen). Based on these predictors and the partial regression coefficients, a new score named HB was generated. HB score was slightly more discriminatory compared to GBS and Modified GBS (area under the receiver operating characteristic curves [AUROC]: 0.73 versus 0.721 and 0.7128, respectively) in predicting hemostatic treatment in emergency endoscopy. The HB score also showed satisfactory prediction accuracy for subsequent deaths (AUROC: 0.6857. P <0.001).Conclusions: Our new HB score was better performing than the GBS in predicting hemostatic treatment, hemostasis and mortality.
Maternal Dendritic Cells Influence Fetal Allograft Response following Murine In-Utero Hematopoietic Stem Cell Transplantation
Authors: Kandasamy Karthikeyan , Johana Nuryanti Binti , Tan Lay Geok , Tan Yvonne , Li Julie Yeo Su , Zhihui Li , Jiayu Koh , Ginhoux Florent , Chan Jerry KY , Choolani Mahesh A , Mattar Citra NZ 
Published: June 2022

Abstract
Intrauterine hematopoietic cell transplantation (IUT), potentially curative in congenital haematological disease, is limited by subtherapeutic donor cell chimerism. Microchimerism of maternal immune cells trafficked into IUT recipients may directly influence donor-specific alloresponsiveness. We investigated if maternal dendritic cell (DC) depletion affected recipient alloresponsiveness and donor cell chimerism. IUT was performed on fetuses at embryonic day 14 (E-14), after crossing transgenic CD11c.DTR (C57BL/6) female mice and BALB/c male mice, with semi-allogenic BALB/c or C57BL/6, or fully allogenic C3H bone marrow donor cells, following transient maternal DC depletion with diphtheria toxin administered to the dam. We observed reduced maternally trafficked cells in the recipient fetuses particularly following BALB/c donor cell transplantation. IUT enriched trafficked maternal-derived clonotypes which displayed substantially reduced diversity. DC depletion restored maternal clonotype diversity and enhanced donor-specific immunomodulatory changes in the recipient pups, increasing regulatory T-cell subtype and immune-inhibitory protein expression, and inhibiting proinflammatory cytokine and donor-specific antibody production, though it did not affect donor cell chimerism. Functional tolerance acquired after BALB/c donor cell IUT with DC depletion was maintained following postnatal transplantation without immunosuppression, despite diminishing peripheral blood donor chimerism. We show for the first time that trafficked maternal cells influences donor-specific alloresponsiveness to IUT, possibly by expanding alloreactive clonotypes in the recipients, and depleting maternal DC promotes and maintains acquired tolerance independent of donor cell chimerism, presenting a novel approach to improve IUT efficacy.
A Comparative Study on the Mechanical and Physical Properties of Plywood Panels Prepared by Chitosan as Green Composite
Authors: Talaei Aisona , Ashori Alireza , Heidari Vahid 
Published: June 2022

Abstract
The goal of this study is to make green wood products that are acceptable both in terms of mechanical and physical properties using chitosan as a natural binder. Five-layer poplar plywood specimens prepared with two different commercial adhesives namely urea formaldehyde (UF) and methylene diphenyl isocyanate (MDI), and compared with chitosan (CH). For the purpose of evaluation, mechanical properties such as modulus of rupture (MOR), modulus of elasticity (MOE), glue line shear strength (SS), surface soundness and physical properties such as thickness swelling (TS), water absorption (WA) of the samples were studied. Variable parameters were: adhesive type (UF, MDI and CH), adhesive content (2, 4 and 6 wt%), and adhesive spread rate (150 and 180 g/m2). Other parameters such as pressing time (10 min), press pressure (30 kg/m2) and press temperature (140 ºC) were held constant. Based on the findings of this study, MOR properties of the panels slightly increased when the resin content was increased from 150 to 180 g/m2. The results of shear strength and surface soundness showed that boards made with chitosan as a binder, had the same results as the boards made with UF resin. Analysis of data revealed that the mechanical properties were significantly different among the board types. In general, WA and TS decreased (improved) with the increase of resin content. According to the test results, the lowest TS observed in chitosan boards was 4% chitosan with 180 g/m2 spread rate, which is not only better than UF plywood, but also close to the results of MDI specimens. According to the measured parameters, 4% chitosan with spread rate of 180 g/m2 can be considered as the optimal binder composition for plywood manufacturing. Finally, it can be stated that chitosan has potential as replacement resin material for plywood manufacturing.
Challenges Faced by People Living With Lower Limb Amputation Secondary to Type 2 Diabetes Mellitus. A Qualitative Study at Apromase Global Evangelical Hospital-kumasi
Authors: Boakye Dorothy Serwaa , Amoah Vida Maame Kissiwaa , Amoah Christian , Akrasi Spike Asare , Akrugu Peter 
Published: June 2022

Abstract
Background: Considering the burden of diabetes mellitus and its associated complications which includes limb amputation, an investigation into the challenges faced by persons with limb amputation cannot be downplayed. Amputation is a surgical method by which a part or the whole extremity is removed. Objective: The main objective of the study was to explore the challenges faced by people with lower limb amputation secondary to type II diabetes mellitus Method: The study followed a qualitative research approach using an explorative, narrative and descriptive design. Thirteen participants who had their limbs amputated at the Global Evangelical hospital were purposively sampled and interviewed using an interview guide. Data analysis was done using thematic analysis. Result: The study revealed four main themes. All of the participants had an incapacitating physical challenge after amputation of the lower limb. Psychologically/ emotionally, all of the amputees were affected negatively though some had better coping strategies. Socio-economical challenge was common to them all. The males who were bread winners of their families had more serious economic issues than the females. Their coping strategies were mostly, thinking positive, having faith in God as well as social support and rehabilitation. Conclusion: Participants faced enormous challenges from cost of treating diabetes mellitus to limb amputation and associated challenges which include psychological/emotional, physical and socio-economic.