bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enteric reabsorption processes and their impact on drug pharmacokinetics
Authors: Ibarra Manuel , Trocóniz Iñaki F. , Fagiolino Pietro 
Published: March 2021

AbstractEnteric reabsorption occurs when a drug is secreted into the intestinal lumen and reabsorbed into the systemic circulation. This distribution process is evidenced by multiple peaks in pharmacokinetic profiles. Commonly, hepatobiliary drug secretion is assumed to be the underlying mechanism (enterohepatic reabsorption, EHR), neglecting other possible mechanisms such as gastric secretion (enterogastric reabsorption, EGR). In addition, the impact of drug reabsorption on systemic clearance, volume of distribution and bioavailability has been a subject of long-standing discussions. In this work, we propose semi-mechanistic pharmacokinetic models to reflect EHR and EGR and compare their respective impact on primary pharmacokinetic parameters. A simulation-based analysis was carried out considering three drug types with the potential for reabsorption, classified according to their primary route of elimination and their hepatic extraction: (A) hepatic metabolism—low extraction; (B) hepatic metabolism—intermediate/high extraction; (C) renal excretion. Results show that an increase in EHR can significantly reduce the clearance of drugs A and B, increase bioavailability of B drugs, and increase the volume of distribution for all drugs. Conversely, EGR had negligible impact in all pharmacokinetic parameters. Findings provide background to explain and forecast the role that this process can play in pharmacokinetic variability, including drug-drug interactions and disease states.
Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
Authors: Arteche-López A. , Ávila-Fernández A. , Romero R. , Riveiro-Álvarez R. , López-Martínez M. A. , Giménez-Pardo A. , Vélez-Monsalve C. , Gallego-Merlo J. , García-Vara I. , Almoguera Berta , Bustamante-Aragonés A. , Blanco-Kelly F. , Tahsin-Swafiri S. , Rodríguez-Pinilla E. , Minguez P. , Lorda I. , Trujillo-Tiebas M. J. , Ayuso C. 
Published: March 2021

AbstractDespite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger sequencing before reporting. Validation of all NGS variants considerably increases the turnaround time and costs of clinical diagnosis. We comprehensively assessed this need in 1109 variants from 825 clinical exomes, the largest sample set to date assessed using Illumina chemistry reported. With a concordance of 100%, we conclude that Sanger sequencing can be very useful as an internal quality control, but not so much as a verification method for high-quality single-nucleotide and small insertion/deletions variants. Laboratories might validate and establish their own thresholds before discontinuing Sanger confirmation studies. We also expand and validate 23 copy number variations detected by exome sequencing in 20 samples, observing a concordance of 95.65% (22/23).
Determinants of SARS-CoV-2 infection in Italian healthcare workers: a multicenter study
Authors: Boffetta Paolo , Violante Francesco , Durando Paolo , De Palma Giuseppe , Pira Enrico , Vimercati Luigi , Cristaudo Alfonso , Icardi Giancarlo , Sala Emma , Coggiola Maurizio , Tafuri Silvio , Gattini Vittorio , Apostoli Pietro , Spatari Giovanna ,   Working Group on SARS-CoV-2 Infection in Italian Healthcare Workers, De Maria Luigi , Caputi Antonio , Sponselli Stefania , Mastrippolito Carmine , Zunarelli Carlotta , Di Felice Giulia , Visci Giovanni , Albini Elisa , Sansone Emanuele , Tomasi Cesare , Bisioli Andrea , Cipriani Lorenzo , De Bellis Alessandro , Tiraboschi Mara Maria , Paraggio Emilio , Rubino Sofia , Capuzzi Michele , Dini Guglielmo , Bruzzone Bianca , Debarbieri Nicoletta , Montecucco Alfredo , Orsi Andrea , Rahmani Alborz , Ricucci Valentina , Guglielmi Giovanni , Fiorentino Leonardo , Brilli Cinzia , Godono Alessandro , Declementi Michael , Mansour Ihab , Milanesio Nicolò , Garzaro Giacomo , Scarmozzino Antonio , Gullino Attilia 
Published: March 2021

AbstractHealthcare workers (HCWs) are at increased risk of being infected with SARS-CoV-2, yet limited information is available on risk factors of infection. We pooled data on occupational surveillance of 10,654 HCW who were tested for SARS-CoV-2 infection in six Italian centers. Information was available on demographics, job title, department of employment, source of exposure, use of personal protective equipment (PPEs), and COVID-19-related symptoms. We fitted multivariable logistic regression models to calculate odds ratios and 95% confidence intervals of infection. The prevalence of infection ranged from 3.0 to 22.0%, and was correlated with that of the respective areas. Women were at lower risk of infection compared to men. Fever, cough, dyspnea and malaise were the symptoms most strongly associated with infection, together with anosmia and ageusia. No differences in the risk of infection were detected according to job title, or working in a COVID-19 designated department. Reported contact with a patient inside or outside the workplace was a risk factor. Use of a mask was strongly protective against risk of infection as was use of gloves. The use of a mask by the source of exposure (patient or colleague) had an independent effect in reducing infection risk.
Diverse activities and biochemical properties of amylase and proteases from six freshwater fish species
Authors: Champasri Chamaiporn , Phetlum Suthathip , Pornchoo Chanakan 
Published: March 2021

AbstractThis study investigated the biochemical properties, enzyme activities, isoenzyme pattern, and molecular weight of three types of digestive enzyme from six freshwater fish species: Puntius gonionotus (common silver barb), Puntioplites proctozysron (Smith’s barb), Oreochromis niloticus (Nile tilapia), Hemibagrus spilopterus (yellow mystus), Ompok bimaculatus (butter catfish), and Kryptopterus geminus (sheatfish). The optimum pHs for amylase and alkaline protease activities were 7.0–8.0 and 8.0–10.0, and the optimum temperatures were 45–60 °C and 50–55 °C, respectively. A pepsin-like enzyme was detected in all three carnivorous fishes (Ompok bimaculatus, Kryptopterus geminus, and Hemibagrus spilopterus) with optimum reaction pH of 2.0 for each and optimum reaction temperatures 50–55 °C. In optimum reaction conditions, the amylase and alkaline protease from Puntioplites proctozyron showed the highest activities. Lower activities of all enzymes were observed at temperature (29 °C) of Lam Nam Choen swamp than at the optimum reaction temperatures. The fish species contained one to three and five to eight isoforms of amylase and alkaline protease, respectively, with molecular weights from 19.5 to 175 kDa. Both the alkaline proteases and amylases were stable in wide pH and temperature ranges.
PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile
Authors: Mule Simon Ngao , Costa-Martins André Guilherme , Rosa-Fernandes Livia , de Oliveira Gilberto Santos , Rodrigues Carla Monadeli F. , Quina Daniel , Rosein Graziella E. , Teixeira Marta Maria Geraldes , Palmisano Giuseppe 
Published: March 2021

AbstractThe etiological agent of Chagas disease, Trypanosoma cruzi, is a complex of seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution requires understanding the parasite origin and population structure. In this study, we introduce the PhyloQuant approach to infer the evolutionary relationships between organisms based on differential mass spectrometry-based quantitative features. In particular, large scale quantitative bottom-up proteomics features (MS1, iBAQ and LFQ) were analyzed using maximum parsimony, showing a correlation between T. cruzi DTUs and closely related trypanosomes’ protein expression and sequence-based clustering. Character mapping enabled the identification of synapomorphies, herein the proteins and their respective expression profiles that differentiate T. cruzi DTUs and trypanosome species. The distance matrices based on phylogenetics and PhyloQuant clustering showed statistically significant correlation highlighting the complementarity between the two strategies. Moreover, PhyloQuant allows the identification of differentially regulated and strain/DTU/species-specific proteins, and has potential application in the identification of specific biomarkers and candidate therapeutic targets.
Covalent-coordination tandem functionalization of a metal–organic framework (UiO-66) as a hybrid probe for luminescence detection of trans,trans-muconic acid as a biomarker of benzene and Fe3+
Authors: Min Jie , Qu Xiang-Long , Yan Bing 
Published: March 2021

A green fluorescent hybrid Tb3+@UiO-66–SO3H is prepared via post-synthetic coordination and ligand exchange based on UiO-66. It is developed as a fluorescent probe for the sensing of Fe3+ and tt-MA of a biomarker of toxic benzene.
PD-L1 expression in anogenital and oropharyngeal squamous cell carcinomas associated with different clinicopathological features, HPV status and prognosis: a meta-analysis
Authors: Qin Yuan , Luan Jiaochen , Zhou Xiang , Li Ying 
Published: March 2021

Abstract
Background: Little research has been done on clinicopathological characteristics and human papillomavirus (HPV) status of anogenital and oropharyngeal squamous cell carcinomas (SCC) with a strong expression of programmed death ligand 1 (PD-L1) in tumor cells. Therefore, we conducted this meta-analysis. Methods: We performed a comprehensive research in PubMed, Embase and Cochrane databases up to 30 September 2020. The effect size was hazard ratio (HR) with 95% confidence interval (CI) for overall survival (OS), cancer-specific survival (CSS), disease-free survival (DFS). The pooled odds ratio (OR) with 95% CI were used to assess the association between PD-L1 expression and clinicopathological features along with HPV status. Results: A total of 2003 cases (944 anogenital and 1059 oropharynx SCC patients) were included. High PD-L1 expression in anogenital SCC cases were associated with advanced age (OR = 1.63, 95% CI: 1.04–2.58) and HPV negativity (OR = 0.47, 95% CI: 0.31–0.71). Besides, PD-L1 positive anogenital SCC cases held a significantly declined OS (HR = 2.18, 95% CI: 1.37–3.47) and CSS (HR = 2.45, 95% CI: 1.30–4.65). For oropharynx SCC, PD-L1 was more frequent in younger and HPV positive patients (OR = 0.60, 95% CI: 0.37–0.98; OR = 3.01, 95% CI: 1.78–5.09) and PD-L1 expression was relevant to better OS and DFS (HR = 0.76, 95% CI: 0.60–0.97; HR = 0.50, 95% CI: 0.33–0.75). Conclusions: The meta-analysis demonstrated that in anogenital SCC, PD-L1 positivity had to do with a worse outcome, which might attribute to advanced age, higher tumor grade, lymph node metastasis and HPV negativity, while in oropharynx cancer, PD-L1 expression was related to better prognosis for the reason that PD-L1 was less frequent in the aged and negative HPV status.
IL-1R2 expression in human gastric cancer and its clinical significance
Authors: Yuan Maoling , Wang Lei , Huang Hao , Li Yuan , Zheng Xiao , Shao Qi , Jiang Jingting 
Published: March 2021

Abstract
Background: Interleukin-1 receptor type II (IL-1R2), also known as CD121b, is a member of the IL-1 receptor family. IL-1R2 acts as negative regulator of the IL-1 system, modulating IL-1 availability for the signaling receptor. IL-1R2 is abnormally expressed in many human inflammatory diseases and cancers, and has important clinical significance. The present study was designed to investigate IL-1R2 expression in human gastric cancer (GC) tissues and the associated clinical implications. Methods: Immunohistochemistry was used to identify the clinical significance and prognostic value of IL-1R2 expression in GC tissues. We investigated IL-1R2 expression in GC tissues, cells, and serum using real-time PCR (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) assays. Results: IL-1R2 was highly expressed in GC tissues, and the overall survival in patients with advanced GC and high IL-1R2 expression was significantly poorer than that in patients with advanced GC and low IL-1R2 expression. Moreover, IL-1R2 mRNA levels in GC tissues and most GC cells were higher than those in para-cancer tissues and GES1 human gastric mucosal epithelial cells. The level of plasma-soluble IL-1R2 in GC patients was higher than that of the healthy control group. Conclusion: Increased IL-1R2 levels are involved in the initiation and progression of human GC, and IL-1R2 might be employed to develop immunotherapeutic approaches targeting GC.
Resting metabolic rate and its adjustments as predictors of risk protein-energy wasting in hemodialysis patients
Authors: Da Jingjing , Long Yanjun , Li Qian , Yang Xia , Yuan Jing , Zha Yan 
Published: March 2021

Abstract
Background: The purpose of the present study was to explore the association between resting metabolic rate (RMR) and protein-energy wasting (PEW) risk in Chinese hemodialysis patients by age and gender subgroup.
Methods: RMR and body composition (body cell mass (BCM) and fat mass) of 774 patients undergoing hemodialysis were estimated by bio-electrical impedance analysis (BIA). Anthropometric data were collected by a standard measurement protocol, and the upper arm muscle circumference (AMC) was calculated. Biochemical nutritional and dialysis parameters were obtained. Linear regression analysis was used to analyze the relationship among RMR, body composition and nutritional factors.
Results: The mean age was 54.96 ± 15.78 years. RMR level in patients was 1463.0 (1240.5, 1669.0) kcal/d. In multiple linear regression models, BCM, left calf circumference (LCC), fat mass were the determinants association with RMR (P&lt;0.001). Among the patients in the sample, 133 (17.2%) had been diagnosed with PEW per International Society of Renal Nutrition and Metabolism (ISRNM) criteria and 363 (46.9%) were being at risk PEW. The area under the receiver-operating characteristic curve (AUC) of RMR for predicting risk PEW was greater than RMR/BCM and RMR/body surface area (BSA). When the cutoff of RMR was 1481 kcal/d it had the higher sensitivity and specificity (82 and 42%), and the AUC was 0.68 in elderly maintenance hemodialysis (MHD) patients (P&lt;0.001). After adjustment for potential confounders, lowest RMR quartile level (&lt;1239) increased the risk of PEW (OR = 4.71, 95% CI: 1.33–16.64, P=0.016) in all patients.
Conclusions: Older patients with PEW have a lower RMR reduction. RMR and RMR/BCM may play the role in objective screening to detect risk PEW in MHD patients, especially in males.
Development and Validation of a Probe Word List to Assess Speech Motor Skills in Children
Authors: Namasivayam Aravind Kumar , Huynh Anna , Bali Rohan , Granata Francesca , Law Vina , Rampersaud Darshani , Hard Jennifer , Ward Roslyn , Helms-Park Rena , van Lieshout Pascal , Hayden Deborah 
Published: March 2021

PurposeThe aim of the study was to develop and validate a probe word list and scoring system to assess speech motor skills in preschool and school-age children with motor speech disorders.MethodThis article describes the development of a probe word list and scoring system using a modified word complexity measure and principles based on the hierarchical development of speech motor control known as the Motor Speech Hierarchy (MSH). The probe word list development accounted for factors related to word (i.e., motoric) complexity, linguistic variables, and content familiarity. The probe word list and scoring system was administered to 48 preschool and school-age children with moderate-to-severe speech motor delay at clinical centers in Ontario, Canada, and then evaluated for reliability and validity.ResultsOne-way analyses of variance revealed that the motor complexity of the probe words increased significantly for each MSH stage, while no significant differences in the linguistic complexity were found for neighborhood density, mean biphone frequency, or log word frequency. The probe word list and scoring system yielded high reliability on measures of internal consistency and intrarater reliability. Interrater reliability indicated moderate agreement across the MSH stages, with the exception of MSH Stage V, which yielded substantial agreement. The probe word list and scoring system demonstrated high content, construct (unidimensionality, convergent validity, and discriminant validity), and criterion-related (concurrent and predictive) validity.ConclusionsThe probe word list and scoring system described in the current study provide a standardized method that speech-language pathologists can use in the assessment of speech motor control. It can support clinicians in identifying speech motor difficulties in preschool and school-age children, set appropriate goals, and potentially measure changes in these goals across time and/or after intervention.
Fractional pilot reuse and max k‐cut based pilot decontamination scheme for multi‐cell TDD massive MIMO systems
Authors: Zeng Wenbo , He Yigang , Li Bing , Wang Shudong 
Published: March 2021

AbstractIn multi‐cell massive multiple‐input multiple‐output (MIMO) cellular networks, pilot contamination (PC) caused by ineluctable pilot reuse severely restricts the system performance in the effectiveness and reliability of transmission. To deal with this problem, an efficient pilot assignment scheme based on fractional pilot reuse and max k‐cut (FPR‐MKC) is therefore proposed in this study. Specifically, first, the measure of susceptibility to interference for each user is designed, and based on this, an innovative boundary is determined for properly selecting the edge users who could employ the unique pilot sequences. Subsequently, the process of allocating reused pilots is innovatively treated as the partition of the vertices of a graph. Building on this idea, an edge‐weighted undirected graph is constructed to present the potential interference intensity among users, and eventually, the max k‐cut (MKC) strategy is executed, which aims to partition centre users into a desired number of mutually exclusive subsets with maximizing the total weight of the edges between the disjoint subsets. Compared with some existing pilot assignment schemes, the proposed FPR‐MKC scheme can adequately mitigate the PC with significantly enhanced quality of service for edge users, which is verified by theoretical analysis and numerical simulation results.
Synthetic wideband range profiling method for moving targets based on phase‐derived velocity measurement
Authors: Li Wenji , Fan Huayu , Ren Lixiang , Mao Erke 
Published: March 2021

AbstractSynthetic wideband signals can obtain a wide spectrum and thus achieve a high range resolution by synthesizing separately emitted signals. A synthetic wideband range profiling method for moving targets based on phase‐derived velocity measurement is proposed. Highly accurate velocity measurement results are obtained by analysing the echo phase information of a moving target, and the accuracy of the velocity estimation results can meet the requirement of the velocity compensation in the synthetic wideband range profiling process. After analysis of the spectrum envelope and the phase of a moving target, a method for synthesizing wideband signals in the frequency domain, thus obtaining a high‐resolution range profile, is developed. The constraint conditions for the motion compensation and synthesis process are analysed and discussed by simulation, and the effectiveness of the proposed method is verified under various circumstances.
Coverage improvement using Voronoi diagrams in directional sensor networks
Authors: Zarei Zahra , Bag‐Mohammadi Mozafar 
Published: March 2021

AbstractRecently, the area coverage problem has emerged in the directional sensor network (DSN), where the sensor's sensed area depends on its working direction and viewing angle. This study has proposed a new algorithm based on the Voronoi diagram, called prioritized geometric area coverage (PGAC), to increase DSN's covered area. In a Voronoi diagram, all internal points of a convex polygon (cell) formed around a sensor are closer to the sensor than any other sensor. Therefore, the best sensor for covering a Voronoi cell area is the corresponding sensor of the cell. In contrast to similar approaches, PGAC considers the relation between the cell area and the sensor's covered area when selecting a sensor's working direction. It categorizes Voronoi cells, based on their geometric sizes, into three categories. In each category, PGAC adjusts the sensor's working direction to maximize the covered area and minimize the overlapping between adjacent cells. It also turns off redundant sensors for extending the network lifetime. Our simulation results showed that PGAC increases the covered area and decreases the number of active sensors compared to similar methods.
Assessing the reliability of the Bisous filament finder
Authors: Muru Moorits Mihkel , Tempel Elmo 
Published: March 2021

Context. Recent years have given rise to numerous methods of detecting the cosmic web elements in the large-scale structure of the Universe. All of these methods describe more or less the same features, but each with its nuance. The Bisous filament finder is a stochastic tool for identifying the spines of filaments using galaxy positions.
Aims. This work provides an analysis of how the galaxy number density of the input data affects the filaments detected with the Bisous model and gives estimates of the reliability of the method itself to assess the robustness of the results.
Methods. We applied the Bisous filament finder to MultiDark-Galaxies data, using various magnitude cuts from the catalogue to study the effects of different galaxy number densities on the results and different parameters of the model. We compared the structures by the fraction of galaxies in filaments and the volume filled by filaments, and we analysed the similarities between the results from different cuts based on the overlap between detected filamentary structures. The filament finder was also applied to the exact same data 200 times with the same parameters to study the stochasticity of the results and the correlation between different runs was calculated.
Results. Multiple samples show that galaxies in filaments have preferentially higher luminosity. We found that when a galaxy is in a filament there is a 97% chance that the same galaxy would be in a filament with even more complete input data and about 85% of filaments are persistent when detecting the filamentary network with higher-density input data. Lower galaxy number density inputs mean the Bisous model finds fewer filaments, but the filaments found are persistent even if we use more complete input data for the detection. We calculated the correlation coefficient between 200 Bisous runs on the exact same input, which is 0.98.
Conclusions. This study confirms that increased number density of galaxies is important to obtain a more complete picture of the cosmic web. To overcome the limitation of the spectroscopic surveys, we will develop the Bisous model further to apply this tool to combined spectroscopic and narrow-band photometric redshift surveys, such as the J-PAS.