bluuebunny/crossref_metadata_2025 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

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

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

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

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

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

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

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

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

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

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

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.
A Low-power 2D Active Pixel Sensor Matrix with Spectral Uniformity, High Dynamic Range, Fast Reset, and De-noising Capabilities
Authors: Dodda Akhil , Jayachandran Darsith , Pannone Andrew , Trainor Nicholas , Stepanoff Sergei , Steves Megan , Radhakrishnan Shiva Subbulakshmi , Bachu Saiphaneendra , Ordonez Claudio , Shallenberger Jeffrey , Redwing Joan , Knappenberger Kenneth , Wolfe Douglas , Das Saptarshi
Published: June 2022

Development of low-power and smart vision sensors is critical for many emerging applications including the acceleration of edge intelligence. In this article, we introduce an active pixel sensor (APS) technology with in-sensor compute capability based on atomically thin two-dimensional (2D) semiconducting material such as monolayer MoS2. The presented 2D APS uses only one programmable phototransistor (1T cell), which significantly reduces the area overhead allowing one to fit 900 pixels in ~0.09 cm2. Phototransistors in the array exploit gate tunable persistent photoconductivity to exhibit high responsivity (~3.6×107 A/W), high specific detectivity (~5.6×1013 Jones), spectral uniformity, and high dynamic range (~80 dB) and electrical programmability to achieve fast reset (~ 100 µs) and in-sensor de-noising capabilities. Commonly encountered problems in the field of 2D material based vision sensors are also resolved by showing near-ideal yield and low device-to-device variation in photoresponse owing to high quality growth, damage-free transfer, and relatively clean fabrication process flow. Remarkably, the energy expenditure by 2D APS was found to be miniscule and in the range of hundreds of femto Joules per pixel. We believe, our low-power 2D APS technology with in-sensor image processing capabilities can be transformative for many edge applications.
Male Gender, Smoking, Younger Age, and Preoperative Pain Found to Increase Postoperative Opioid Requirements in 592 Elective Colorectal Resections
Authors: Karlsdottir Bergljot R. , Zhou Peige P. , Wahba Joyce , Mott Sarah L. , Goffredo Paolo , Hrabe Jennifer , Hassan Imran , Kapadia Muneera R. , Gribovskaja-Rupp Irena
Published: June 2022

Purpose
With increased awareness of the opioid epidemic, understanding contributing factors to postoperative opioid use is important. The purpose of this study was to evaluate patient and perioperative factors that contribute to postoperative opioid use after colorectal resections and their relation to pre-existing pain conditions and psychiatric diagnoses.
Methods
A retrospective review was conducted identifying adult patients who underwent elective colorectal resection at a single tertiary center between 2015 and 2018. Patient demographics, preoperative factors, surgical approach, and perioperative pain management were evaluated to determine standard conversion morphine milligram equivalents required for postoperative days 0 to 3 and total hospital stay.
Results
Five hundred and ninety-two patients: 46% male, median age 58 years undergoing colorectal resections for indications including cancer, inflammatory bowel disease, and diverticulitis were identified. Less opioid use was found to be associated with female gender (β = -42), patients who received perioperative lidocaine infusion (β = -30), and older adults (equivalents/year) (β = -4, all p < 0.01). Preoperative opioid use, preoperative abdominal pain, epidural use and smoking were all independently associated with increased postoperative opioid requirements.
Conclusions
In this study of patients undergoing elective colorectal resection, factors that were associated with higher perioperative opioid use included male gender, smoking, younger age, preoperative opioid use, preoperative abdominal pain, and epidural use. Perioperative administration of lidocaine was associated with decreased opioid requirements. Understanding risk factors and stratifying postoperative pain regimens may aid in improved pain control and decrease long-term dependency.
Analysis of viral integration reveals new insights of oncogenic mechanism in HBV infected- intrahepatic cholangiocarcinoma and combined hepatocellular-cholangiocarcinoma
Authors: Zhao Linghao , Wang Yuyouye , Tian Tao , Rao Xinjie , Dong Wei , Zhang Jinmin , Yang Yuan , Tao Qifei , Peng Fang , Shen Chenhang , Wang Songbo , Liu Hui , Zeng Xi , Zhou Weiping
Published: June 2022

Background:Integration of HBV DNA into the human genome could progressively contributes to hepatocarcinogenesis. Both Intrahepatic cholangiocarcinoma (ICC) and Combined hepatocellular-cholangiocarcinoma (CHC) are known to be associated with HBV infection. However, the integration of HBV and mechanism of HBV-induced carcinogenesis in ICC and CHC remains unclear.Methods:41 patients with ICC and 20 patients with CHC were recruited in the study. We conducted HIVID analysis on these 61 samples to identify HBV integration sites in both the tumor tissues and adjacent non-tumor liver tissues. To further explore the effect of HBV integration on gene expression, we selected paired tumors and adjacent non-tumor liver tissues from 3 ICC and 4 CHC patients for RNA-seq and WGS.Results:We detected 493 HBV integration sites in ICC patients, of which 417 were from tumor samples, 76 were from non-tumor samples. And 246 HBV integration sites were detected in CHC patients, of which 156 were located in the genome of tumor samples and 90 were in non-tumor samples. Recurrent HBV integration events were detected in ICC including TERT, ZMAT4, MET, ANKFN1, PLXNB2, and in CHC like TERT, ALKBH5. Together with our established data of HBV-infected hepatocellular carcinoma, we found HBV preferentially integrates into the specific regions which may affect the gene expression and regulation in cells and induce carcinogenesis. We further performed genomic and transcriptomic sequencing of three ICC and four CHC patients and found that HBV fragments could integrate near some important oncogene like TERT, causing large-scale genome variations on nearby genomic sequences, and at the same time changing the expression level of the oncogene genes.Conclusion:Comparative analysis demonstrates numerous newly discovered mutational events in ICC and CHC resulting from HBV insertions in the host genome. Our study provides an in-depth biological and clinical insights into HBV-induced ICC and CHC.
First record of monogeneans from Schilbe intermedius in South Africa
Authors: Smit Willem J. , Matla Matsoele M. , Luus-Powell Wilmien J.
Published: June 2022

The present study deals with the survey of monogeneans from Schilbe intermedius Rüppell, 1832 (silver catfish). Surveys were carried out at six localities in the northern region of South Africa where fish were collected and examined for monogenean gill parasites. There are presently no records of monogeneans from this fish species from South Africa. Fourteen monogenean species of Schilbetrema Paperna and Thurston, 1968 and two species of Schilbetrematoides Kritsky and Kulo, 1992 have been recorded from African schilbeids. Three species of the Schilbetrema were recorded during this study with variation in infestation: Schilbetrema quadricornis Paperna and Thurston, 1968 from all localities; Schilbetrema acornis Paperna and Thurston, 1968 from four localities; Schilbetrema undinula Kritsky and Kulo, 1992 recorded from one locality.
Comparison of the Protective Efficacy of Intratympanic Oxytocin and Dexamethasone in Cisplatin-induced Ototoxicity
Authors: Taş Burak Mustafa , Özel Gökçe , Azman Musa , Karaer Işıl Çakmak , Kılıç Rahmi
Published: June 2022

Purpose: In this study, we aimed to investigate the efficacy of intratympanic resveratrol and intratympanic dexamethasone treatment in cisplatin-induced ototoxicity. We also compared intratympanic atosiban (oxytocin antagonist) and oxytocin in cisplatin ototoxicity. Methods: In this study, 30 rats (60 ears) were used by separating into 5 groups. Cisplatin was administered intraperitoneally to the first group (n=6). On the second group (n=6), oxytocin were administered intratympanically. On the third group (n=6), dexamethasone were administered intratympanically. On the fourth group (n=6), atosiban were administered intratympanically. On the fifth group (n=6), 0.9% NaCl were administered intratympanically. In Groups 2, 3, 4 and 5, cisplatin was given 30 minute after the administration of medication. ABR and DPOAE tests were performed on all groups before and 72 h after the procedure. Results: The post-treatment ABR I, ABR IV and ABR threshold values of the groups were found to be significantly higher than the pre-treatment values (p<0.001). There was no significant prolongation of the post-treatment ABR I-IV interval in the oxytocin and dexamethasone groups (p>0.05). Pre-treatment values were higher than post-treatment values in all groups. There was no significant decrease in the frequencies of 2832 and 4004 after treatment in the oxytocin and dexamethasone group compared to pre-treatment. No difference was found between the oxytocin and dexamethasone groups (p>0.05). Conclusion: As a result, it has been shown that intratympanic oxytocin may be an option that can be used in the treatment, although it is not as effective as dexamethasone in preventing cisplatin ototoxicity.
Epithelial tumor compartment- and adjacent stromal compartment-specific expression of PARP1 in different anatomical sites in patients with HGSOC
Authors: BERKEL CAGLAR , CACAN Ercan
Published: June 2022

High-grade serous ovarian carcinoma (HGSOC) is responsible for the majority of ovarian cancer-associated deaths. PARP (Poly-(ADP-ribose) polymerase) inhibitors (PARPi) (olaparib, rucaparib and niraparib) have been approved in recent years to be used in both the frontline setting as maintenance therapy and in the recurrent setting for patients with ovarian cancer (OC). Previous studies have reported increased expression of PARP1, a sensor for DNA damage, in OC; however, its compartment (epithelial tumor vs stroma)-, anatomical site (fallopian tube, omentum, ovary and serous tubal in situ carcinoma)- and histotype-specific expression have not been studied. Here, we showed that PARP1 protein levels are higher in epithelial tumors compared to adjacent stroma at four different anatomical locations in HGSOC, with the most significant difference in PARP1 levels in omental metastases. Furthermore, we found that PARP1 protein levels are higher in tumors compared to normal tissue in fallopian tube, omentum and ovary in patients with HGSOC, again with the most significant difference in omentum. We showed that S100A4 and CLDN7, transcriptional targets of PARP1, have the highest copy numbers in serous OC among all cancer types, showing the potential OC-specific roles of these two proteins. We also showed that PARP1 expression is increased in malignant and invasive stage in mouse ovarian surface epithelium cells, and that PARP1 mRNA levels are lower in mucinous histotype compared to serous histotype of epithelial OC. These findings indicate that a better understanding of compartment-, anatomical location- and histotype-specific changes in PARP1 levels in OC is needed, since PARP inhibitors which work by preventing DNA repair in cancer cells are currently being used in the treatment of patients with OC.
Improved chromosome genome assembly, structural variation insight, and annotation of Gossypium barbadense L. 'Pima-S6'
Authors: Herrera-Estrella Luis
Published: June 2022

Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome-assemblies. The analyses revealed important differences on structural variations and annotated proteins between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses reveals chromosomal rearrangements between Pima-S6 and other Gossypium genomes on several chromosomes. Analyses of the re-assembled and re-annotated genome of the close relative G. barbadenses Pima 3–74 using our Pima-S6 assembly, suggest that contig placement of the most recent G. barbadense assemblies might have been unduly influenced by the use of the G. hirsutum TM-1 genome as the anchoring reference. The Pima-S6 reference genome provides a valuable genomic resource and offers new insights of genomic structure and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts.
The effect of roasting on the antioxidant and antibacterial capacity of coffee cherry husk extract
Authors: Mesfin Korsa , Admassu Habtamu , Gobena Feyera , Belayneh Tilahun
Published: June 2022

The coffee cherry process generates huge amounts of byproducts which are disposed of on the land, causing a serious environmental problem. The coffee cherry husk is one of the main byproducts generated from dry coffee processing, which contains many high-value and exhibits antioxidative and antimicrobial properties biomolecules including phenols, tannins and flavonoids. The primary goal of this study was to investigate the effects of roasting temperatures (150–200 °C) and times (10–25 minutes) on the yield, total phenol, tannin, and flavonoid content, as well as the antioxidant and antimicrobial capacity of an ethanol extract obtained from the coffee cherry husk using an automatic solvent extractor. In this study, the extract yield, total phenol and flavonoid content, as well as the antioxidant and antimicrobial capacity of roasted coffee cherry husk extract were enhanced by roasting. The extract yield ranged between 6.22 ± 0.08–16.37 ± 0.61%. The total phenol and flavonoid content ranged from 9.00 ± 0.03–123.49 ± 0.21 mg gallic acid equivalent/g and 2.69 ± 0.26–35.34 ± 0.13 mg quercetin equivalent/g, respectively. As roasting temperature and time increased, total tannin decreased from 42.45 ± 0.20 to 0.27 ± 0.04 mg tannic acid equivalent/g. The 2, 2-diphenyl-1-picrylhydrazyl radical and hydrogen peroxide scavenging capacities extended from 24.68 ± 0.05–93.83 ± 0.11% and 14.45 ± 0.19–76.07 ± 0.16% respectively, while the ferric reducing capacity ranged from 10.85 ± 0.09–47.02 ± 0.20 mg ascorbic acid equivalent/g. The bacterial inhibition zones extended from 7.03 ± 0.56–21.30 ± 0.27 mm and 6.00 ± 0.00–15.77 ± 0.25 mm for Escherichia coli and Staphylococcus aureus, respectively.
Evaluating the performance of Bayesian and Frequentist Approaches for longitudinal modeling: Application to Alzheimer's Disease
Authors: Pérez-Millan Agnès , Contador José , Tudela Raúl , Niñerola-Baizán Aida , Setoain Xavier , Lladó Albert , Sánchez-Valle Raquel , Sala-Llonch Roser
Published: June 2022

Linear Mixed Effects (LME) modelling under both frequentist and Bayesian frameworks have been suggested to study longitudinal trajectories. We studied the performance of both approaches on different dataset configurations using hippocampal volumes from longitudinal MRI data across groups - healthy controls (HC), mild cognitive impairment (MCI) and Alzheimer’s Disease (AD) patients -, including subjects that converted from MCI to AD. We started from a big database of 1250 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and we created different reduced datasets simulating real-life situations using a random-removal permutation-based approach. The number of subjects needed to differentiate groups and to detect conversion to AD was 147 and 115 respectively. The Bayesian approach allowed estimating the LME model even with very sparse databases, with high number of missing points, which was not possible with the frequentist approach. Our results indicate that the frequentist approach is computationally simpler, but it fails in modelling data with high number of missing values.
Does teneligliptin reverse the non-glycemic effects among the non-diabetic obesity subjects?
Authors: Pelluri Ranakishor , Kongara Srikanth , Nagasubramanian Vanitha Rani , Mahadevan Shriraam , Chimakurthy Jithendra
Published: June 2022

Incretins (GLP-1, GIP, DPP-4) are secreted in response to meal. The GLP-1 has very shorter half-life (1–2 min), meanwhile it was degraded by DPP-4 enzyme. The present novel, Teneligliptin which has greatest receptor selectivity and has longer half-life compared to other gliptins. The promising dipp-4 inhibition which can enhance the GLP-1 concentration in the blood. Augmentation of GLP-1 levels are helpful to reduce the weight loss in obesity subjects along with reversing metabolic syndrome components. GLP-1 analogues are gold mine and are succeeded in subjects with obesity. Apart from pharmacotherapy, lifestyle modification in the form of strict diet restrictions and physical exercise are the corner stone intervention for obesity, but subjects are filed to achieve it. Furthermore, there are currently few anti-obesity drugs available, and additional safe and effective therapeutic options for the treatment of obesity are needed. Teneligliptin is developed to treat diabetes, and which do not produce hypoglycaemic effect alone. Hence, considering its safety we are aimed evaluate the non-glycemic effects in non-diabetic obese subjects. The present prospective study was registered in the Clinical trial registry of India, Regd. ID: CTRI/2020/02/023329 [Registered on: 14/02/2020].
Ramming mechanical characteristics of rammed earthen sites
Authors: Pei QiangQiang , Liu Xiaoying , HOU Zhichun , ZHAO Guojing , Zhang Bo , Guo QingLin
Published: June 2022

The ramming technique is a traditional method used to improve the compactness of soil with impact and vibration energy. Based on the measured data of ramming force transmission and dissipation, this study reveals the mechanism of energy transfer and dissipation of single-layer ramming as well as the law of variation with ramming quality, laying thickness, and ramming times. It also establishes the ramming model and empirical formula of ramming quality, laying thickness, and ramming times, introduces the ramming layer changes associated with the constitutive relationship (elastic to elastoplastic parts) as a function of ramming times, and determines the influence depth and horizontal range based on real-time data monitoring. It was found that as the mass of the rammmer increases, the range of influence of the impact stress inside the earth also increases proportionally, and this effect is more pronounced vertically. However, the dissipation rate of energy in horizon direction is much greater than in the vertical direction. The traditional stacked ramming technique of “chong hai wo, hang yin ding” can effectively eliminate the defects of horizontal reversal upwelling impact and unevenness of the ramming layer during the ramming process. The research results provide a theoretical basis for evaluating the quality of the traditional ramming technique.
Determining factors of neonatal kernicterus among neonates treated in NICU in health care centres of West Guji Zone, Suthern, Ethiopia,
Authors: Degavi Girish
Published: June 2022

Background
Kernicterus in infants is a medical challenge that is linked to infant death throughout the world. Extreme jaundice with or without Kernicterus affects roughly one million newborns internationally every year, with overall majority of instances happening in south Asia and Sub-Saharan Africa. There are far more techniques and understanding about the etiology of infant ictrus in Sub-Saharan Africa. It is indeed vital to look into the causes that induce infant kernicterus in order to decrease infant morbidity and mortality rates.
Methodlogy
: A hospital-based unmatched case control study was carried out by evaluating systematically chosen charts of 544 neonates in the neonatal critical care unit of public general hospitals in the West, Guji Zone, Ethiopia. The information was gathered using an extraction format. For analysis, data were entered into epidata management version 4.4.2.1 and exported to SPSS version 20. The binary logistic regression model was employed to assess the relationship between independent and dependent variables.
Results
; A total of 272 neonatal cards were included. Obstetric complication [AOR: 5.77 at 95%CI: 1.85–17.98], low birth weight [AOR: 4.27at 95%CI: 1.579–11.555], birth asphyxia [AOR: 4.83 at 95%CI: 1.617–14.395], RH-incompatibility [AOR: 5.45 at 95%CI: 1.583–18.737], breast feeding [AOR: 6.11at 95%CI: 1.707–21.886], policytemia [AOR: 7.32 at 95%CI: 2.512–21.311], were the determinants of neonatal kernicterus.
Conclusion
Obstetric difficulties, birth hypoxia, breastfeeding, RH-incompatibility, low birth weight, and policytemia are all causes of Neonatal kernicterus. As more than just a consequence, this one was determined that detecting and treating infant kernicterus early on is crucial because it can cause life-threatening complications in newborns.
Cortex or Cancellous —— Which is early for the Decrease of Bone Content for veterbral body in health?
Authors: Bai Lin , Li Jujia , Ren Congcong , Wang Ming , Yang Fan , Li Qian , Zhao Jian , Zhang Ping
Published: June 2022

Objective
To obtained the cortex and cancellous parameter of the vertebral bone of healthy subjects using QCT. To expore which is early and faster for bone loss with age.
Materials and methods
733 physical examiners underwent chest low-dose CT examination were recruited, from January 1, 2021 to December 31, 2021. QCT sequence was used to obtain the bone mineral density of T12-L2 vertebral body without radditional radiation.The mass and area of vertebral cortex and cancellous at the central level of L2 vertebral bodywere measured. The characteristics of vertebral cortex and cancellous with age were analyzed and compared.
Results
Significant differences were found involumetricbone mineral density (vBMD) of T12-L2verterbal body, cortical mass, cancellous mass, cortical area, cortical mass / cancellous mass and cortical area / cancellous area in different age groups, respectively.No significant difference was found in all groups for cancellous area. ThevBMD of T12-L2 vertebral body decreased with age; The cortical mass decreased gradually before 71y.The cancellous mass increased and then decreased with peak at 31-40y.The cortical area decreased gradually before 71y.The cancellous area increasedand then decreased with peak at the age of 41–50.The values of cortical mass/cancellous mass showed a slowly downward trendwith age. The values of cortical area / cancellous area decerased before 61y.
Conclusion
The changes of vertebral BMD, bone content ofcortex and cancellous have different characteristics in different age. The change of cortex may be earlier and faster than that of cancellous with age.
Information Management under uncertain large-scale cloud environment
Authors: OMRI Asma , OMRI Waleed , Benslimane Djamal , OMRI Mohamed-Nazih
Published: June 2022

“Uncertainty” is related to working with inaccurate data, imprecise and incomplete information, and unreliable results that can lead to irrational decisions. Several approaches to managing uncertain data on the web have been proposed in the literature to resolve this problem. These approaches have failed to find the solution to this problem with accuracy and performance. Our study aims to propose a new probabilistic approach to manage web information resources in an uncertain large-scale cloud environment. Our approach is based on three main steps: (1) modeling uncertain web resources, (2) computing HTTP request model, and (3) interpretation and evaluation of uncertain web resources in a context of classic hypertext navigation. The experimental study shows that the analysis of the execution time necessary for the composition of the services, by our approach, is negligible, compared to that of the other studied approaches. The algorithm which deals with the impact of the variation in the number of nodes, which we have proposed, has also been evaluated and checks all the possibilities in polynomial time and can adapt to many possibilities of multiplexing of values.
Dbar-dressing methods to nonlinear defocusing Hirota equation with nonzero boundary conditions
Authors: Huang Yehui , Di Jingjing , Yao Yuqin
Published: June 2022

We study the defocusing Hirota equation with nonzero boundary condition by using Dbar -dressing method. Dbar -problem with non-canonical normalization conditions are introduced. The Lax pair of the defocusing Hirota equation with nonzero boundary condition is derived from an asymptotic expansion method. The N-soliton solutions are constructed under the selected special spectral transformation matrix and the dynamic behavior of soliton solutions are analyzed.