bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Hydraulic-Fracture-Geometry Characterization with Low-Frequency Distributed-Acoustic-Sensing Strain Data: Fracture-Height Sensitivity and Field Applications
Authors: Liu Yongzan , Jin Ge , Wu Kan , Moridis George 
Published: November 2021

Summary
Low-frequency distributed acoustic sensing (LF-DAS) has been used for hydraulic fracture monitoring and characterization. Large amounts of DAS data have been acquired across different formations. The low-frequency components of DAS data are highly sensitive to mechanical strain changes. Forward geomechanical modeling has been the focus of current research efforts to better understand LF-DAS signals. Moreover, LF-DAS provides the opportunity to quantify fracture geometry. Recently, Liu et al. (2021a, 2021b) proposed an inversion algorithm to estimate hydraulic-fracture width using LF-DAS data measured during multifracture propagation. The LF-DAS strain data are linked to the fracture widths through a forward model developed based on the displacement discontinuity method. In this study, we first investigated the impacts of fracture height on the inversion results through a numerical case with a four-cluster completion design. Then we discussed how to estimate the fracture height based on the inversion results. Finally, we applied the inversion algorithm to two field examples.
The inverted widths are not sensitive to the fracture height. In the synthetic case, the maximum relative error is less than 10% even when the fracture height is two times the true value. After obtaining the fracture width, the fracture height can be estimated by matching the true strain data under various heights with a strong smooth weight. The error between the calculated strain and true strain decreases as the height approaches the true value. In the two field examples, the temporal evolutions of the width summation of all fractures and the width of each fracture show consistent behaviors with the field LF-DAS measurements. The calculated strain data from the forward model match well with the field LF-DAS strain data. The results demonstrate the robustness and accuracy of the proposed inversion algorithm.
Synthesis of Asphalt Nanoparticles and Their Effects on Drilling Fluid Properties and Shale Dispersion
Authors: Xionghu Z. , Egwu S. B. , Jingen D. , Liujie M. , Xiangru J. 
Published: November 2021

Summary
Asphalt nanoparticles (ANs) were developed by synthesizing asphalt powders with chloroacetic acid (ClCH2COOH). The objective of this synthesis was to develop engineered ANs with a cationic point capable of adsorbing on the net negatively charged clay platelets, thereby improving drilling fluid functionality and pore-plugging performance, reducing shale dispersion, and ultimately enhancing shale stability. Tests carried out to study the performance of the synthesized ANs include particle size analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy, drilling fluid rheology, and filtration rate and shale dispersion tests. FT-IR spectrum results confirming the occurrence of a chemical reaction between asphalt and ClCH2COOH showed a shift in NH vibration from 3,439.95 cm−1 (before synthesis) to 3,435.05 cm−1 (after synthesis). Based on particle size analysis, an average particle size diameter of 92.9 nm was observed, suggesting the tendency of ANs to invade and seal nanopore spaces. The shape of ANs ranged from spherical to irregular, because intercalated structures were observed from the scanning electron microscopic analysis on the interaction between ANs and sodium bentonite (Na-Bent). An increase in attracting force between the Na-Bent particles caused by the adsorption of ANs cationic point on bentonite clay particles led to an increase in drilling fluid rheological properties as the ANs %w/v increased. The drilling fluid filtration rate was, however, not significantly affected by the %w/v increase in ANs because results indicated slight decrease in fluid loss when compared with the base mud (BM). According to the shale dispersion test, the shale cuttings percentage recovery of the 2%w/v ANs sample was 76.5%, owing to the decrease in fluid-rock interaction caused by ionic adsorption and encapsulation of shale surfaces by the ANs. Experimental results from this investigation indicate that the likely mechanisms of the effect of ANs on shale formations would be sealing off nanopore spaces in formations because of its ultratiny particle size; adsorption of the net negatively charged shale cuttings by the ANs cationic point, thereby reducing drilling cuttings dispersion; and improving hole-cleaning performance due to its effect on the drilling fluid rheological properties.
Integrated PCR testing and extended window contact tracing system for COVID-19 to improve comprehensiveness and speed
Authors: Raymenants Joren , Geenen Caspar , Thibaut Jonathan , Gorissen Sarah , Nelissen Klaas , André Emmanuel 
Published: November 2021

Abstract
Testing and contact tracing are standard tools for controlling the spread of COVID-191. Their effectiveness hinges on a sequence of processes encompassing testing coverage and timeliness, testing quality and speed of reporting, contact tracing speed and comprehensiveness and compliance with advice given2–6. We optimized this sequence of processes in the context of a public health program targeting around 33,000 higher education students through a combination of low barrier PCR testing with rapid turn-around-time, close integration of testing and tracing teams and IT infrastructure, community engagement and the implementation of bidirectional contact tracing by extending the contact tracing window from 2 to 7 days before symptom onset or test of the index case. We anticipate this combined intervention to help improve epidemic control.
Duplex RTqPCRs for detection and relative quantification of SARS-CoV-2 variants of concern (VOC)
Authors: Carcereny Albert , Garcia-Pedemonte David , Bosch Albert , Pintó Rosa M , Guix Susana 
Published: November 2021

Abstract

During the evolution of the SARS-CoV-2 pandemic, new variants of the virus have emerged and spread worldwide. The increased transmissibility and proclivity of some of these variants to cause more serious disease threatens public health responses against the virus, and they are classified as variants of concern (Variants of Concern, VOCs). While Next-Generation-Sequencing (NGS) is the gold standard to identify VOC, it cannot always be rapidly implemented in some settings to provide information as an early warning tool. Duplex quantitative real time RTqPCR assays offer a sensitive and easy-to-use tool to detect, discriminate, and estimate relative proportions of SARS-CoV-2 variants containing VOC-specific signature mutations from variants lacking it, using allelic discrimination probes. We developed three multiplexed RTqPCR assays that can detect Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2) VOCs by targeting 22281_22289DelCTTTACTTG, 28262_28263InsAACA and 22029_22034DelAGTTCA deletions/insertions in their genomes, respectively. Beta and Delta deletions are mapped to the S gene (residues 241/243 and 157/158, respectively), while Gamma insertion is located between the end of ORF8 and the beginning of N gene. Our specific duplex RTqPCR assays have been adapted from a previously designed duplex RTqPCR assay used to estimate the relative proportion of genomes containing 21765-21770DelTACATG mutation affecting residues HV69/70, a signature mutation of Alpha VOC (Carcereny et al., 2021). All duplex RTqPCR assays targeting signature mutations of VOCs may be used as a complementary tool to NGS for rapid variant tracking and surveillance in wastewater-based epidemiology.
Protocol for the study of hepatic bilirubin uptake in the isolated perfused rat liver
Authors: Stebel Marco , Medic Nevenka , Pelizzo Paola , Sist Paola , Tramer Federica , Passamonti Sabina 
Published: November 2021

Abstract
We present a protocol for the study of bilirubin uptake in the isolated and perfused rat liver. The liver is perfused with an albumin-free saline buffered solution supplemented with glucose, pyruvate and lactate, in the absence of oxygen, at a physiologically low flow rate. Fractions of the venous effluent are collected and analyzed for bilirubin, bilirubin glucuronide and biomarkers of liver integrity. The liver preparation is viable and intact for 1 h after isolation from the general circulation, with constant levels of both bilirubin and bilirubin glucuronide (< 2 nM) in the effluent. Up to 12 boli of 10 nmol bilirubin can be sequentially injected into the portal vein without and with molecules that target sinusoidal membrane transporters of organic anions. Selective inhibition of bilirubin or bilirubin glucuronide uptake is detected as transient peaks in the effluent (Cmax up 6 to 60 nM). This protocol allows collecting repeated observations in the same liver, thus reducing the animal number by a factor of 10.
Maternal Vaginal Fluids Play A Major Role In The Colonization of The Neonatal Intestinal Microbiota
Authors: Tang Chen , Zhang Xueqin , Xie Jingxian , Zeng Lingyu , Xin Yuntian , Zhang Jie , Lin Yi , Xiao Yunshan , Wu Quanfeng , Shen Heqing 
Published: November 2021

Abstract
Background: Caesarean delivery (CD) is associated with newborns’ health risks due to the blocking of microbiome transfer. To understand the vertical bacterial seeding and reduce CD disadvantages, microbiome transmissions via anal and genital routes were investigated, and the efficiency of vaginal fluid swabbing treatment was evaluated using 16s rDNA sequencing-based techniques.Results: Pregnant women were recruited in the Women and Children’s Hospital, School of Medicine, Xiamen University from June 1st to August 15th, 2017. Maternal faeces (n = 26), maternal vaginal fluids (n = 26), and neonatal transitional stools (n = 26) were collected, while the participants underwent natural delivery (ND) (n = 6), CD (n = 4) and CD with vaginal fluid swabbing (CS) on their newborns (n = 16). 26 mothers with the median age 26.50 (25.00-27.25) years showed no substantial clinical differences. The newborns’ gut microbiota altered among ND, CD and CS, and clustered into two groups (PERMANOVA P < 0.01) of swabbing and no-swabbing exposure. Gut colonization of ND babies majorly originated from maternal vaginal microbes (PERMANOVA P = 0.08), no vertical transmission was observed via anal route in any group. The vaginal transfer partially occurred by swabbing, in which the phyla Firmicutes and Proteobacteria and the genera Lactobacillus, Bacteroides, and Escherichia-Shigella in newborns were similar to their mothers. The recovered taxa predicted KEGG functions of biosynthesis, metabolism, and DNA replication and repair with benefits of low risks of digestive, cardiovascular, and immune diseases.Conclusions: The newborn’s gut microbiota is mainly shaped by maternal vaginal microbiota, and aberrant colonization initiated by CD is partly mitigated by the swabbing treatment.
Ustekinumab Trough Levels Predicting Laboratory and Endoscopic Remission in Patients with Crohn’s Disease
Authors: Hirayana Hisashi , Morita Yasuhiro , Imai Takayuki , Takahashi Kenichiro , Yoshida Atsushi , Bamba Shigeki , Inatomi Osamu , Andoh Akira 
Published: November 2021

Abstract
Backgrounds: Optimal concentration of ustekinumab (UST) predicting endoscopic remission has not been fully investigated in Crohn’s disease (CD). We aimed to identify the optimal UST trough levels predicting clinical, laboratory and endoscopic remission in CD patients. Methods: Twenty-eight patients with CD were enrolled and investigated (27 patients by enteroscopy and 1 by colonoscopy). The endoscopic activity was assessed using the modified Rutgeerts scoring system. Serum UST trough levels and anti-UST antibodies (AUAs) levels were determined by in-house immunoassays. Results: Endoscopic activity was negatively correlated with serum UST trough levels (Spearman’s rank correlation coefficient (ρ) = -0.66, P=0.0001) and serum albumin levels (ρ=-0.60, P=0.0007). The endoscopic activity was positively and significantly correlated with CRP (ρ=0.59, P=0.0009) and ESR (ρ=0.44, P=0.033). There was no significant association between the endoscopic score and AUA levels and/or Crohn’s disease activity index (CDAI). Serum UST trough levels and albumin levels were significantly higher in the endoscopic remission group (scores of 0 and 1) than in the non-endoscopic remission group (UST trough, mean 3.3 vs. 1.8μg/mL). No significant difference was observed in AUAs between the endoscopic remission and non-remission groups. Receiver operation curve (ROC) analysis revealed that the optimal cutoff value of UST trough levels predicting normal CRP and serum albumin levels was 1.7μg/mL for each, and the optimal cutoff value predicting endoscopic remission was 2.0μg/mL (AUC: 0.80, 95%-CI: 0.64-0.96). Conclusion: Endoscopic remission requires higher UST trough levels than those needed to normalize CRP and serum albumin levels.
Structure Control of Novel Hierarchical Porous Carbon Material and its Adsorption Properties
Authors: Cai Li-Feng , Zhan Jie-Min , Liang Jie , Yang Lei , Yin Jie 
Published: November 2021

Abstract
Novel hierarchical porous carbon materials (HPCs) were fabricated via a reactive template-induced in situ hypercrosslinking procedure. The effects of carbonization conditions on the microstructure and morphology of HPC were investigated, and the adsorption of methylene blue (MB) on HPC was explored. The as-prepared HPC has a hierarchical micro-, meso- and macropore structure, which results from the overlap of hollow nanospheres possessing microporous shells and macroporous cavities. The carbonization temperature, carbonization time and carbonization heating rate played important roles in tailoring the nanostructures of HPC. The BET specific surface area and micropore specific surface area can reach 2388 m2·g−1 and 1892 m2·g−1, respectively. Benefitting from the well-developed pore structure, the MB removal efficiency can reach 99% under optimized conditions. The adsorption kinetics and thermodynamics can be well described by a pseudo-second-order model and Langmuir model, respectively. Furthermore, such adsorption is characterized by a spontaneous endothermic process.
Effects of Adding Carbon Sources and Nutrient Salts on the Acidification and Microbial Community Structure of Coal Gangue
Authors: Zhu Qi , Ruan Mengying , Hu Zhenqi , Ye Chun 
Published: November 2021

Abstract
Acidic pollution from gangue oxidation has become a primary environmental problem in coal mining areas in China. The use of microorganisms to remediate acidic pollution in coal gangue piles has been indicated to be effective, but environmental differences and carbon sources in different mining areas have become important factors restricting microbial activity. Instead of the addition of new functional bacteria to gangue piles, carbon sources and nutrient salts were added to recently discharged gangue to enhance the activity of beneficial bacteria in the indigenous microbial community. The changes in pH and electrical conductivity (EC) of the gangue leachate as well as the composition and abundance of the functional microbial community on the surface of the gangue were analyzed by leaching simulation experiments and 16S rRNA sequencing. The results showed that (1) the addition of a carbon source maintained the pH of the gangue leachate at 6.31~6.65, which was significantly higher than that of the control group, but the pH of the leachate decreased significantly after the addition of the carbon source was stopped. (2) The addition of carbon sources and nutrient salts changed the microbial community composition on the surface of the gangue, and the species diversity index decreased. The dominant genera in the experimental group were Listeria, Arthrobacter, and Enterococcus; Thiobacillus was not the dominant genus in any of the treatments. (3) The functional gene types in the experimental and control groups were almost the same, but their relative abundance changed. The abundance of functional genes related to the sulfur cycle increased substantially in the experimental group, and the abundance of genes involved in the nitrogen and carbon cycles also increased, albeit to different degrees.
Virological Non-Suppression and Associated Factors Among Adolescents and Youth Living with HIV in Ethiopia: A Facility-Based Case-Control Study
Authors: Dires Yilkal Muchie , Manyazewal Tsegahun , Charlotte Hanlon 
Published: November 2021

Abstract
Background: Virological non-suppression remains the major cause of treatment failure and mortality among adolescents and youth living with HIV in low- and middle-income countries (LMICs). Behavioral and mental health disorders affect adherence to antiretroviral therapy (ART) and the underlying virological suppression, but evidence from LMICs is relatively limited. We aimed to assess HIV virological non-suppression and associated factors among adolescents and youth attending ART in Ethiopia. Methods: A 1:2 matched facility-based case-control study was conducted at ALERT Hospital, Addis Ababa, Ethiopia, among patients with HIVaged 12-24 years who were on ART and with a viral load > (case) or < (control) than 1000 copies/ml after at least six months on ART. The primary outcome was viral load non-suppression: a plasma viral load > 1000 copies/ ml based on two consecutive viral load measurements every three months. The primary exposure was depressive symptoms as measured using the PHQ-9 (Patient Health Questionnaire, 9-item version). Other variables include adherence to ART and sociodemographic characteristics of participants. Data were collected using structured, blinded lay interviewer-administered questionnaires, and data extraction forms. Conditional multivariable logistic regression was conducted using STATA version 14.2 to test the main hypotheses. Results: The study enrolled 192 participants, with a median age of 18 years and 52.1% males. None of the participants reported smoking or chewing Khat (a leaf that stimulates mood). With the PHQ-9 tool, 47%, 28%, and 25% had minimal or no, probable to mild and moderate to severe depression symptoms, respectively. Having depressive symptoms is associated with a higher conditional likelihood of virological failure (odds ratio [OR] = 1.8, p < 0.001) and the association was stronger among those who have moderate or severe depressive symptoms (adjusted OR = 5, 95% CI [1.7-14.6] )and unadjusted OR = 6.8, 95% CI [3.1-14.8]). Having moderate and severe depression is associated with non-adherence to ART (adjusted OR = 10.5). Conclusion: Non-adherence to ART medications, depressive symptoms, advanced WHO stage on ART initiation, poor social support and orphan status were independently associated with virological failure among HIV-infected adolescents and youths on ART. Having moderate and severe depression has higher odds of non-adherence and virological failure. We recommend integration and task-sharing of mental health and HIV care services to reduce virological failure in this group of people.
WITHDRAWN: Understanding of Comorbidities Using Modeling Techniques on EHR
Authors: Badki Meenal 
Published: November 2021

Abstract
Comorbidities refer to the existence of numerous, co-occurring diseases in medicine. The course of one comorbidity is typically extremely dependent on the course of the other condition due to their co-occurrence, and therapies can have major spill-over effects. Despite the high occurrence of comorbidities among patients, there is no complete statistical framework for modelling comorbidity longitudinal dynamics. We propose a probabilistic approach for studying comorbidity dynamics in patients over time in this paper. This approach is a non-homogenous transition technique/mechanism using Hidden Markov Model called as coupled-HMM. Clinical research influenced the design of our coupled-HMM: (1) It accounts for different disease stages (acute, stable) in disease progression by providing clinically meaningful latent phases. (2) It simulates a relationship between the trajectories of comorbidities and the dynamics of capturing co-evolution. (3) The transition mechanism takes into account between-patient heterogeneity (e.g., risk factors, treatments). Based on 675 health trajectories, we assessed our proposed Coupled-HMM, which investigates the concomitant evolution of diabetes mellitus and chronic liver disease. We find that our Coupled-HMM provides a superior fit when compared to competing models without coupling. We also assess the spill-over impact, or the amount to which diabetic therapies are linked to a shift in chronic liver disease from an acute to a stable condition. Immediate application in treatment planning and clinical research becomes possible as a result of our approach in context of comorbidities.
Ovarian Yolk Sac Tumor in a Postmenopausal Patient with Malignant Müllerian Mixed Tumor: A Case Report and Systematic Review of the Literature
Authors: He Shuqian , zhou ping , Cheng Yuxia , Cui Jing , Qi Huangpeng , Sun Qing 
Published: November 2021

Abstract
Background Yolk sac tumor (YST) is a most common form of malignant ovarian germ cell tumors and typically occur in young women and adolescent. Ovarian YST occurred in postmenopausal women is an extremely rare entity which has an aggressive behavior and worse outcome. The aim of this article was to provide better understanding of clinicopathological characteristics, management, and prognosis of postmenopausal YSTs.Case presentation A 64-year-old woman was admitted to our hepatobiliary surgery department due to a cystic and solid round mass in the lower right abdomen in December 2013. laboratory tests showed a-fetoprotein (AFP), carcinoembryonic antigen (CEA), and cancer antigen 19-9 (CA19-9) to be within normal limits, but serum cancer antigen (CA-125) was elevated. Exploratory laparotomy was performed including tumorectomy, right oophorectomy, partial omentectomy. Postoperatively, pathologic findings showed that the morphologic features and immunohistochemical results were consistent with ovarian YST with malignant Müllerian mixed tumor (MMMT). The patient was admitted again for recurrence of the tumor and metastasis to bilateral supraclavicular lymph nodes in August 2018. The patient underwent total abdominal hysterectomy (TAH), left salpingo-oophorectomy, right salpingectomy, pelvic lymphadenectomy, and partial peritonectomy. The patient received 6 cycles of adjuvant chemotherapy with BEP (bleomycin, etoposide, and cisplatin) postoperatively, and died of disease in August 2019. Conclusion Here, we presented a case of postmenopausal YST with MMMT. Meanwhile, a systematic literature review was conducted in the PubMed database, including case reports and case series. We summarized the clinical characteristics, treatments, and prognosis of all cases. Overall survival was calculated with Kaplan-Meier curves. Univariate analysis was performed with the log-rank test. A Cox model was constructed to determine independent predictors of mortality. As the morphological and immunophenotypical features of postmenopausal YSTs were always overlapped with somatic epithelial carcinomas, pathologists should have a high index of suspicion to diagnose ovarian YSTs in older women. Optimum chemotherapy is essential in improving prognosis of postmenopausal YSTs.