bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin Immunoprecipitation and Sequencing (ChIP‐seq) Optimized for Application in Caenorhabditis elegans
Authors: Sen Ilke , Kavšek Alan , Riedel Christian G.
Published: July 2021

Chromatin immunoprecipitation followed by next‐generation sequencing (ChIP‐seq) has become one of the most popular methods to study protein‐DNA interactions and can be used, for instance, to identify the binding sites of transcription factors or to determine the distributions of histones with specific post‐translational modifications throughout the genome. Although standard ChIP‐seq protocols work well in most experimental systems, there are exceptions, and one of these is the popular model organism Caenorhabditis elegans. Even though this system is very amenable to genetic and cytological methods, biochemical approaches are challenging. This is due to both the animals’ cuticle, which impairs lysis as well as penetration by cross‐linkers, and the rather low protein and chromatin content per body weight. These issues have rendered standard ChIP‐seq protocols inefficient in C. elegans and raised a need for their improvement. Here, we describe improved protocols, with the most important advances being the efficient breakage of the C. elegans cuticle by freeze‐grinding and the use of a very sensitive sequencing library construction procedure, optimized for the relatively low DNA content per body weight of C. elegans. The protocols should therefore improve the reproducibility, sensitivity, and uniformity across tissues of ChIP‐seq in this organism. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Growth and harvesting of synchronized Caenorhabditis elegans

Basic Protocol 2: Chromatin immunoprecipitation (ChIP)

Basic Protocol 3: Library construction for Illumina sequencing
Computational Approach for Rapidly Predicting Temperature‐Dependent Polymer Solubilities Using Molecular‐Scale Models
Authors: Zhou Panzheng , Sánchez‐Rivera Kevin L. , Huber George W. , Van Lehn Reid C.
Published: July 2021

One promising approach to recycle multicomponent plastic waste (e. g., multilayer plastic films) is selective dissolution. Selective dissolution is a solvent‐mediated process in which differences in polymer solubility in a carefully chosen solvent system are exploited to recover a target polymer. Here, a computational approach was developed that rapidly predicts temperature‐dependent polymer solubilities to guide the design of solvent systems for solvent‐mediated polymer recycling. Polymer conformations were obtained from molecular dynamics simulations by modeling the polymer as a short oligomer and then used as input to the conductor‐like screening model for real solvents (COSMO‐RS) for solubility predictions. Using polyethylene (PE) and ethylene vinyl alcohol (EVOH) as representative polymers, the effect of simulation parameters was systematically studied, and predicted solubilities were found to be in good agreement with experimental measurements. The applicability of the approach was demonstrated by identifying selective solvents for PE and EVOH dissolution from a library of 524 solvents.
Ring signature and improved multi‐transaction mode consortium blockchain‐based private information retrieval for privacy‐preserving smart parking system
Authors: Singh Swathi , Satish Divya , Lakshmi Sree Rathna
Published: July 2021

In big cities, the drivers face a major problem in identifying an optimal vacant parking space for their vehicles as the number of vehicles has rapidly grown over the recent years. This objective of determining the available parking space results in wastage of time, air pollution, and traffic congestion. Smart parking systems facilitate the driver to book parking slots and attain real‐time parking information. However, the existing smart parking solutions necessitate the disclosure of sensitive information like desired destination from the vehicle drivers. Moreover, the current smart parking solutions are highly centralized, making them vulnerable for launching privacy breaches by service providers and resulting in the issues of single‐point failure. In this paper, ring signature and improved multi‐transaction mode consortium blockchain‐based private information retrieval (RS‐IMTMCB‐PIR) scheme is proposed for privacy preserving in smart parking system. This RS‐IMTMCB‐PIR scheme initially utilizes an improved multi‐transaction mode consortium blockchain constructed by different number of parking lot owners in order to achieve maximized parking offers based on the factor of availability, transparency, and security. It incorporates an improved private information retrieval approach for protecting the location privacy of drivers and secretly retrieving the offers of parking from the improved multi‐transaction mode consortium blockchain. It further utilizes the benefits of ring signature for permitting the drivers in a potential anonymous authentication process that aids in available parking slot reservation. The simulation results of this proposed RS‐IMTMCB‐PIR scheme portrayed a predominant performance in ensuring maximized degree of drivers' privacy with reduced computation and communication overheads.
Effects of deubiquitylases on the biological behaviors of neural stem cells
Authors: Zhao Qiqi , Li Yixin , Du Xixun , Chen Xi , Jiao Qian , Jiang Hong
Published: July 2021

New neurons are generated throughout life in distinct regions of the mammalian brain due to the proliferation and differentiation of neural stem cells (NSCs). Ubiquitin, a post‐translational modification of cellular proteins, is an important factor in regulating neurogenesis. Deubiquitination is a biochemical process that mediates the removal of ubiquitin moieties from ubiquitin‐conjugated substrates. Recent studies have provided growing evidence that deubiquitylases (DUBs) which reverse ubiquitylation process play critical roles in NSCs maintenance, differentiation and maturation. This review mainly focused on the relationship of DUBs and NSCs, and further summarized recent advances in our understanding of DUBs on regulating NSCs biological behaviors.
Young adult mental health sequelae of eating and body image disturbances in adolescence
Authors: Linardon Jake , Greenwood Christopher J. , Fuller‐Tyszkiewicz Matthew , Macdonald Jacqui A. , Spry Elizabeth , Hutchinson Delyse M. , Youssef George J. , Sanson Ann , Wertheim Eleanor H. , McIntosh Jennifer E. , Le Grange Daniel , Letcher Primrose , Olsson Craig A.
Published: July 2021

Objective

There has been interest in the antecedents and mental health impacts of eating and body image disturbances in adolescence. Less is known about longer‐term mental health impacts into young adulthood, as longitudinal studies with data spanning this developmental period are rare. We capitalize on mental health data collected across adolescence and young adulthood from a population‐based cohort study that has been following >2000 Australian children and their families from infancy to young adulthood.

Method

This sample comprised 1,568 participants who completed the Eating Disorder Inventory drive for thinness and bulimic behavior (the severity of binge‐purge patterns) subscales, and a modified version of the body dissatisfaction subscale in mid‐adolescence (15–16 years), or the Depression Anxiety Stress Scales in young adulthood (19–20, 23–24, and 27–28 years).

Results

After adjusting for baseline demographic and prior mental health factors (<13 years of age), all three indices of eating and body image disturbances in adolescence predicted each mental health outcome in young adulthood. Mental health risks associated with adolescent body dissatisfaction and bulimic behavior scores remained stable across young adulthood, with men having more pronounced problems associated with bulimic behavior scores than women. In contrast, mental health risks associated with adolescent drive for thinness scores diminished across this period similarly for men and women.

Discussion

Findings suggest that adolescent eating and body image disturbances may have long‐term mental health impacts that extend into young adulthood. This underscores the need for early preventative intervention, and longer‐term monitoring and support for body image and eating disturbances.
Iron(III) Complexation with Galactodendritic Porphyrin Species and Hydrocarbons’ Oxidative Transformations
Authors: Castro Kelly A. D. F. , Westrup Kátia C. M. , Silva Sandrina , Pereira Patrícia M. R. , Simões Mário M. Q. , Neves Maria da Graça P. M. S. , Cavaleiro José A. S. , Tomé João P. C. , Nakagaki Shirley
Published: July 2021

The iron metalation of the known free‐base porphyrins H2P2 and H2P3, obtained by structural modification of the well‐known TPPF20 (H2P1) with galactose dendritic units, gave the corresponding iron(III) porphyrin complex FeP2 and the solid hybrid material FeP3S. Their synthesis, characterization and catalytic efficacy toward the oxidation of the organic substrates (Z)‐cyclooctene, cyclohexane and heptane, are reported. In this work, the possibility to modulate selectivity and chemical efficiency of the catalytic system by using simple and more sophisticated metalloporphyrins is demonstrated. Furthermore, the presence of the galactose dendrimer units at the meso‐porphyrin ring positions can tune the oxidation at the terminal positions in linear alkanes. In addition, the FeP3S material was easily recovered and reused at least 3 times for the cyclooctene oxidation. The catalytic performance of material FeP3S, associated with their possibility of reuse, makes this material a promising catalyst.
Improvement in pain interference and function by an allied health pain management program: Results of a randomized trial
Authors: Vandermost Margaret , Bagraith Karl S. , Kennedy Hannah , Doherty Darren , Kilner Simon , Sterling Michele , Henry David , Jones Mark
Published: July 2021

Background

Chronic pain is a significant health problem worldwide and requires a biopsychosocial treatment approach. Access to traditional pain medicine specialist services is limited and innovative treatment models are required to support patients in tertiary care. The study evaluated the clinical effectiveness and safety of the Treatment Access Pathway (TAP), an allied health expanded scope model of care which included innovative group assessment and collaboration with patients to create individualized treatment plans.

Methods

One hundred and eighty‐one patients referred to a tertiary level chronic pain service were randomly allocated to either the TAP or the waitlist study groups. Primary (pain interference) and secondary outcome measures were collected at recruitment and again at 6 months. Per‐protocol analyses were utilized due to high participant attrition (46% across groups).

Results

The TAP group reported greater reductions in pain interference at 6 months than waitlist group (0.9, 95% CI: 0.2–1.6), with more than half of the TAP group (52%) reporting clinically significant improvement. In addition, statistically significant differences between the TAP and waitlist groups were observed for objective measurements of walking endurance (5.4 m, 95% CI: 1.7–9.1); and global impressions of change (1.4 unit decrease, 95% CI: 1–1.9). Nil adverse events were recorded.

Conclusions

The study suggests that an expanded scope allied health model of care prioritizing patient choice and group‐based interventions provides modest benefits for tertiary‐referral chronic pain patients. TAP warrants further investigation as a potentially viable alternative for tertiary healthcare where traditional pain services are unavailable or have long waiting lists.

Significance

The study tests effectiveness and safety of an expanded scope allied health‐led chronic pain program. Despite a high attrition rate, the study showed reduced pain interference and increased physical function in those who completed the protocol. The results are promising and support introduction of this model as an adjunct to existing traditional chronic pain models of care, with a particular focus on improving participant retention in the program. Additionally, the model of care can be used as a standalone chronic pain model of care where no other pain management resources are available.

The study was registered on ANZCTR (Trial ID: ACTRN12617001284358).
Conceptual design and optimization of cogeneration system based on small modular lead‐cooled fast reactor
Authors: Xu Chi , Khan Muhammad Salman , Kong Fanli , Yu Dali , Yu Jie , Li Taosheng
Published: July 2021

Cogeneration system based on Small Modular Lead‐cooled Fast Reactor (SMLFR) becomes attractive due to its good characteristics of flexible location, safety, thermal efficiency, and economy. The conventional cogeneration systems using coal, gas, or renewable energy as the thermal resource have lower thermal performance as compared to LFR based cogeneration systems due to lack of sustainable energy resources. A modified concept design of cogeneration system based on a 35‐MWth SMLFR has been proposed to improve the thermal performance. A new concept of District Heating (DH) structure layout along with optimization based on the exhaust steam/water drainage position. The thermodynamic model based on energy and exergy methods has been used to design and calculate the energy losses of the cogeneration system components. The energy utilization rate can be increased significantly by optimizing the DH. The thermal efficiency of the proposed system reaches up to 73.64% with an increase of 3.51% and the exergy efficiency reaches up to 59.31% with an increase of 5.01%. The increase of thermal performance under the different heating demands will lead to better energy conservation and environmental safety. This study can be further used as the reference for the design and optimization of SMLFR cogeneration system based on thermodynamic and exergy analysis.
RETRACTED: Exploring the prophylactic role of soy isoflavones against polycystic ovarian syndrome
Authors: Manzar Nishaf , khan Safwan Ahmad , Fatima Najum , Nisa Mehr un , Ahmad Muhammad Haseeb , Afzal Muhammad Inam , Saeed Hafiz Fahad Ullah , Imran Muhammad , Anjum Faqir Muhammad , Arshad Muhammad Sajid
Published: July 2021

Soy isoflavones (SI) have strong estrogenic effect in tissues by binding to estrogen receptors and might be beneficial for women with polycystic ovarian syndrome (PCOS) by reduction in testosterone, cholesterol, insulin, weight gain, inflammatory markers, and oxidative stress. The study was planned to examine the effect of various levels of SI on nutrient intake, digestibility, lipid profile, insulin, and reproductive hormones of estradiol valerate (4 mg/rat/IM) PCOS induced rat models. Thirty‐six Wistar 45 days old rats weighing 95 ± 5 g were divided into 4 groups, each having 9 rats: C (control: without SF), SF10 (SF 0.10 g/kg BW), SF15 (SF 0.15 g/kg BW), and SF20 (SF 0.20 g/kg BW). SF was given through the oral gavage. Food and water were offered ad libitum, and intake was recorded daily. During last week of trial, collected feces by total collection method and blood samples were used to calculate nutrient digestibility and biochemical analysis, respectively. Estrogen, progesterone, and prolactin were (p < .05) high in rats fed SF diet that was 4% and 30% increase from C, respectively. Insulin, testosterone, FSH, and LH were lowest in rats fed diet SF20. Significant (p < .05) reduction in cholesterol was observed in rats fed SF15 and SF20 as compared to C. Serum HDL was improved (p < .05) in all SIF0.10, SIF0.15, and SIF0.20 in comparison with PC. Serum LDL was significantly reduced to 68.89 ± 4.36 (mg/dl) in SIF0.20 and to 108.20 ± 4.14 (mg/dl) in SIF0.15, whereas insignificant reduction was observed in SIF0.10 as compared to PC. Highly significant reduction was noted in triglycerides level in SIF0.20; however, significant reduction was observed in both SIF0.10 and SIF0.15 as compared to PC after 3 months of treatment with soy isoflavones.
Calotropis procera (leaves) supplementation exerts curative effects on promoting functional recovery in a mouse model of peripheral nerve injury
Authors: Zafar Shamaila , Rasul Azhar , Iqbal Javed , Anwar Haseeb , Imran Ali , Jabeen Farhat , Shabbir Asghar , Akram Rabia , Maqbool Javeria , Sajid Faiqa , Arshad Muhammad Umair , Hussain Ghulam , Islam Saiful
Published: July 2021

Peripheral nerve injuries are among those complicated medical conditions, which are still waiting for their highly effective first‐line therapies. In this study, the role of Calotropis procera crude leaves was evaluated at different doses for their effectiveness in improving functional recovery following sciatic nerve injury‐induced in the mouse model. Thirty‐two healthy albino mice were divided into four groups as Normal chow group (control, n = 8) and C. procera chow groups (50 mg/kg (n = 8), 100 mg/kg (n = 8) and 200 mg/kg (n = 8)). Behavioral analyses were performed to assess and compare improved functional recovery along with skeletal muscle mass measurement in all groups. Serum samples were analyzed for oxidative stress markers. Results showed that C. procera leaves at dose‐dependent manner showed statistically prominent (p < .05) increase in sensorimotor functions reclamation as confirmed by behavioral analyses along with muscle mass restoration and prominent decline in TOS and momentous increase in TAC along with the augmented activity of antioxidative enzymes.
Nutritional and lifestyle changes required for minimizing the recovery period in home quarantined COVID‐19 patients of Punjab, Pakistan
Authors: Rabail Roshina , Saleem Javeria , Tanveer Zunera , Patching Simon G. , Khalid Abdur Rauf , Sultan Muhammad Tauseef , Manzoor Muhammad Faisal , Karrar Emad , Inam‐Ur‐Raheem Muhammad , Shabbir Muhammad Asim , Aadil Rana Muhammad
Published: July 2021

The COVID‐19 pandemic has introduced a new battle in human history for a safe and fearless life. Therefore, this cross‐sectional survey was conducted (Punjab, Pakistan) on healthy recovered, home quarantined COVID‐19 patients to draw conclusive health support guidelines in the fight against this pandemic. COVID‐19 recovered patients (n = 80) of age ≥14 years were randomly selected during the period November 2020 to February 2021. A nutrition and lifestyle changes questionnaire, containing ten sections and seventy questions, was completed through the telephone/WhatsApp. Data were transferred into an Excel spreadsheet and statistically analyzed by applying chi‐square, correlation, and a t test of independent values using SPSS‐16 software. The patients had an age range of 14 to 80 years, of which 52 (65%) were male and 28 (35%) were female, and 32 (40%) had a normal BMI. The patients had a peak COVID‐19 recovery period of 2 weeks, and a mean recovery period of 2.8 ± 1.4 weeks. Certain variables, including gender (males), age (>40 years), sleep (≤5 hr), less/no physical activity, obesity, diabetes mellitus, and autoimmune diseases, were significantly associated with delayed recovery. Poor nutritional outcomes, including lower intakes of water, legumes, nuts, meat, and milk/yogurt; and higher consumption of fast/fried/junk/spicy foods and cold water/drinks, were also significantly associated with a longer recovery period. The results were similar for not taking daily doses of multivitamins, and vitamins C, D, E, and zinc. This study identified that staying physically active, maintaining sensible body weight, having a sleep of 7 hr, consuming more foods of plant origin especially plant‐based proteins from nuts and legumes, taking supplemental doses of multivitamins, vitamin D, E, and zinc, along with drinking ≥2 L of water daily can provide a significant role in early and safe recovery from COVID‐19.
Glutamine for prevention and alleviation of radiation‐induced oral mucositis in patients with head and neck squamous cell cancer: Systematic review and meta‐analysis of controlled trials
Authors: Alsubaie Hemail M. , Alsini Albaraa Y. , Alsubaie Khaled M. , Abu‐Zaid Ahmed , Alzahrani Faisal R. , Sayed Suhail , Pathak Alok K. , Alqahtani Khaled H.
Published: July 2021

We conducted a systematic review and meta‐analysis of randomized controlled trials (RCTs) that investigated glutamine efficacy in preventing and alleviating radiation‐induced oral mucositis (OM) among patients with head and neck (H&N) cancer. We screened five databases from inception till February 4, 2021 and followed the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines. We included 11 RCTs, comprising 922 patients (458 and 464 patients were assigned to glutamine and control group, respectively). The incidence and onset of radiation‐induced OM of any grade did not substantially differ between both groups. However, glutamine substantially reduced the severity of radiation‐induced OM, as reflected by the reduced incidence of severe OM and reduced mean maximal OM grade score. Additionally, glutamine significantly decreased the rates of analgesic opioid use, nasogastric tube feeding, and therapy interruptions. Oral glutamine supplementation demonstrated various therapeutic benefits in preventing and ameliorating radiation‐induced OM among patients with H&N cancer.
Heat transfer performance of wet porous solar collectors under periodic conditions
Authors: Xue Dawei , Liu Yi , Li Ling
Published: July 2021

Fourier's law was often used to study the heat transfer of collector plates. However, some scholars have found that under time‐varying periodic boundary conditions, using Fourier's law for research will produce certain deviations. In the current work, periodic boundary conditions are used, so the effect of non‐Fourier efficiency on the heat transfer of the collector plate needs to be considered. Based on the Cattaneo–Vernotte equation, a heat transfer model of the solar collector plate with a limited heat transfer rate is constructed, and the problem is solved by the lattice Boltzmann method. On this basis, the influence of radiation, porous media, humidity, and relaxation time on solar collectors is considered. And the average efficiency, tip temperature, and exergy loss of the collectors are quantitatively analyzed. The results show that when the non‐Fourier effect is considered, the tip temperature of the collector plate decreases, the average efficiency and the exergy loss increase. Moreover, with the increase of relaxation time, the tip temperature is lower, the efficiency and the exergy loss are greater. As the humidity and radiation increase, the tip temperature decreases, and the exergy loss and average efficiency increase. When other factors remain unchanged, the average efficiency, tip temperature, and exergy loss increased with an increase in porosity.
Impact of dissipative heat and radiative heat on MHD viscous flow through a slandering stretching sheet with temperature‐dependent variable viscosity
Authors: Sharma Ram Prakash , Ibrahim S. M. , Mishra S. R. , Tinker Seema
Published: July 2021

The purpose of the current investigation is to discuss the varying physical properties, that is, thermal conductivity and viscosity of a viscous time‐independent flow past a slandering stretching surface. The heat transfer phenomenon is enhanced by the inclusion of an external heat source under the action of dissipative heat energy and thermal radiation. The implementation of convective boundary conditions affects the heat and solutal transfer phenomena with the inclusion of chemical reactions. The flow characteristic is directed by the system of differential equations that are converted to nonlinear ordinary type by appropriate assumptions of similarity variables and stream function. Furthermore, the “homotopy analysis method” is deployed to simplify the system. The convergence of the methodology is also discussed with their various order of approximations. The conformity of the solution is presented along with validation in tabular form. Moreover, the effect of the parameters on flow profiles is explained graphically, and the major contribution of few important parameters is laid down. The rate of shear stress along with the longitudinal velocity profile augments with the enhanced variable viscosity. Furthermore, the reverse impact is rendered for the augmented values of the variable viscosity.
The prognostic value of myocardial injury in COVID‐19 patients and associated characteristics
Authors: He Jian , Zhang Bicheng , Zhou Quan , Yang Wenjing , Xu Jing , Liu Tingting , Zhang Haijun , Wu Zhiyong , Li Dong , Zhou Qing , Yan Jie , Zhang Cuizhen , Qian Haiyan , Lu Minjie , Zhou Xiaoyang
Published: July 2021

Background

Since December 2019, coronavirus disease 2019 (COVID‐19) has emerged as an international pandemic. COVID‐19 patients with myocardial injury might need special attention. However, an understanding on this aspect remains unclear. This study aimed to illustrate clinical characteristics and the prognostic value of myocardial injury to COVID‐19 patients.

Methods

This retrospective, single‐center study finally included 304 hospitalized COVID‐19 cases confirmed by real‐time reverse‐transcriptase polymerase chain reaction from January 11 to March 25, 2020. Myocardial injury was determined by serum high‐sensitivity troponin I (Hs‐TnI). The primary endpoint was COVID‐19‐associated mortality.

Results

Of 304 COVID‐19 patients (median age, 65 years; 52.6% males), 88 patients (27.3%) died (61 patients with myocardial injury, 27 patients without myocardial injury on admission). COVID‐19 patients with myocardial injury had more comorbidities (hypertension, chronic obstructive pulmonary disease, cardiovascular disease, and cerebrovascular disease); lower lymphocyte counts, higher C‐reactive protein (CRP; median, 84.9 vs. 28.5 mg/L; p < .001), procalcitonin levels (median, 0.29 vs. 0.06 ng/ml; p < .001), inflammatory and immune response markers; more frequent need for noninvasive ventilation, invasive mechanical ventilation; and was associated with higher mortality incidence (hazard ratio [HR] = 7.02; 95% confidence interval [CI], 4.45–11.08; p < .001) than those without myocardial injury. Myocardial injury (HR = 4.55; 95% CI, 2.49–8.31; p < .001), senior age, CRP levels, and novel coronavirus pneumonia types on admission were independent predictors to mortality in COVID‐19 patients.

Conclusions

COVID‐19 patients with myocardial injury on admission is associated with more severe clinical presentation and biomarkers. Myocardial injury and higher Hs‐TnI are both strongest independent predictors to COVID‐19‐related mortality after adjusting confounding factors.
Pictorial guide to canine and feline blood smears. Part 1: normal cells
Authors: Papasouliotis Kostas , Murphy Kate
Published: July 2021

Background: It is important for practitioner's to be able to examine blood smears as part of a patient's haematological assessment. In order to be able to recognise the presence of abnormal cells, it is essential that practitioners can first identify the morphological characteristics of normal blood cells.

Aim of the article: This is the first of three articles on practical haematology. The aim of this article is to increase confidence in identifying normal red blood cells, white blood cells and platelets in cats and dogs. The following articles, to be published in subsequent issues, will focus on recognising common haematological abnormalities that can be seen during microscopic examination of blood smears.
Uncertain Kingdom: Nowcasting Gross Domestic Product and its revisions
Authors: Anesti Nikoleta , Galvão Ana Beatriz , Miranda‐Agrippino Silvia
Published: July 2021

We propose a release‐augmented dynamic factor model (RA‐DFM) that allows to quantify the role of a country's data flow in nowcasting both early Gross Domestic Product (GDP) releases and subsequent revisions of official estimates. We use the RA‐DFM to study UK GDP early revision rounds and assemble a comprehensive and novel mixed‐frequency dataset that features 12 years of real‐time data vintages. The RA‐DFM improves over the standard DFM in real time when forecasting the first release each quarter. Economic and survey data help to predict the first revision round.
Knockdown of lncRNA MALAT1 ameliorates acute kidney injury by mediating the miR‐204/APOL1 pathway
Authors: Lu Hai‐Yuan , Wang Guo‐Yi , Zhao Jin‐Wen , Jiang Hai‐Tao
Published: July 2021

Background

Acute kidney injury (AKI) was characterized by loss of renal function, associated with chronic kidney disease, end‐stage renal disease, and length of hospital stay. Long non‐coding RNAs (lncRNAs) participated in AKI development and progression. Here, we aimed to investigate the roles and mechanisms of lncRNA MALAT1 in AKI.

Methods

AKI serum samples were obtained from 129 AKI patients. ROC analysis was conducted to confirm the diagnostic value of MALAT1 in differentiating AKI from healthy volunteers. After hypoxic treatment on HK‐2 cells, the expressions of inflammatory cytokines, MALAT1, miR‐204, APOL1, p65, and p‐p65, were measured by RT‐qPCR and Western blot assays. The targeted relationship between miR‐204 and MALAT1 or miR‐204 and APOL1 was determined by luciferase reporter assay and RNA pull‐down analysis. After transfection, CCK‐8, flow cytometry, and TUNEL staining assays were performed to evaluate the effects of MALAT1 and miR‐204 on AKI progression.

Results

From the results, lncRNA MALAT1 was strongly elevated in serum samples from AKI patients, with the high sensitivity and specificity concerning differentiating AKI patients from healthy controls. In vitro, we established the AKI cell model after hypoxic treatment. After experiencing hypoxia, we found significantly increased MALAT1, IL‐1β, IL‐6, and TNF‐α expressions along with decreased miR‐204 level. Moreover, the targeted relationship between MALAT1 and miR‐204 was confirmed. Silencing of MALAT1 could reverse hypoxia‐triggered promotion of HK‐2 cell apoptosis. Meanwhile, the increase of IL‐1β, IL‐6, and TNF‐α after hypoxia treatment could be repressed by MALAT1 knockdown as well. After co‐transfection with MALAT1 silencing and miR‐204 inhibition, we found that miR‐204 could counteract the effects of MALAT1 on HK‐2 cell progression and inflammation after under hypoxic conditions. Finally, NF‐κB signaling was inactivated while APOL1 expression was increased in HK‐2 cells after hypoxia treatment, and lncRNA MALAT1 inhibition reactivated NF‐κB signaling while suppressed APOL1 expression by sponging miR‐204.

Conclusions

Collectively, these results illustrated that knockdown of lncRNA MALAT1 could ameliorate AKI progression and inflammation by targeting miR‐204 through APOL1/NF‐κB signaling.
Post‐COVID‐19 Liver Injury: Comprehensive Imaging With Multiparametric Ultrasound
Authors: Radzina Maija , Putrins Davis Simanis , Micena Arta , Vanaga Ieva , Kolesova Oksana , Platkajis Ardis , Viksna Ludmila
Published: July 2021

Objectives

This study aimed to define patterns of liver injury after severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection using multiparametric ultrasound (mpUS) in a variable patient population with differing severities of COVID‐19.

Methods

Ninety patients were enrolled into the study: 56 had SARS‐CoV‐2 3–9 months prior to enrolment; 34 served as a clinically healthy control group. All patients underwent an mpUS evaluation of the liver (elastography, dispersion and attenuation imaging). Seventy‐six patients had abdominal magnetic resonance (MR) and noncontrast enhanced thoracic computed tomography (CT) scans performed at the same day. All patients were screened for biochemical markers of liver injury.

Results

Liver elasticity, viscosity, and steatosis values were significantly altered in patients after COVID‐19, with particularly higher fibrosis scores compared to the control group (P < .001). Increased biochemical markers of liver injury correlated with changes in mpUS (P < .05), but not with findings on CT or MR findings. Seventeen of 34 hospitalized patients had a moderate or severe course of the disease course with more pronounced changes in mpUS. Increased body mass index was found to influence liver injury and correlated with more severe forms of COVID‐19 (P < .001).

Conclusions

COVID‐19 can cause liver injury observable using mpUS. More severe forms of COVID‐19 and patient obesity are related to increased values of liver damage observed. In comparison to MRI and CT, mpUS appears to be more sensitive to involvement of liver parenchyma. Further research is warranted to establish this promising method for evaluating post‐COVID‐19 liver involvement in the aftermath of the pandemic.
Design of 3‐dB parallel‐line coupler using the substrate integrated double‐strip coaxial line with performance enhancement
Authors: Ho Min‐Hua , Lee Keh‐Yi , Hong Wanchu , Su Gwan‐Wei
Published: July 2021

The contribution of this work is to propose a 3‐dB parallel‐line coupler design using the novel substrate integrated double‐strip coaxial line (SIDSCL). The SIDSCL is composed of three substrates with two signal strips embedded in the center of the SIDSCL tunnel. The proposed coupler's coupled‐line section formed by the SIDSCL's two broad‐side‐faced strips resolves the very difficult‐to‐achieved 3‐dB tight coupling task and possesses an extremely wide operating bandwidth. Its flexible circuit layout diversity allows the through‐ and coupled‐port to be laid either on the same side or on the opposite side. A patch capacitance is attached to each branch‐line to compensate for the parasitic inductance and capacitance that are arisen near the branch junction. As a result, the isolation and impedance matching are greatly improved.
Local versus global stress constraint strategies in topology optimization: A comparative study
Authors: da Silva Gustavo Assis , Aage Niels , Beck André Teófilo , Sigmund Ole
Published: July 2021

Stress‐constrained topology optimization requires techniques for handling thousands to millions of stress constraints. This work presents a comprehensive numerical study comparing local and global stress constraint strategies in topology optimization. Four local and four global solution strategies are presented and investigated. The local strategies are based on either the augmented Lagrangian or the pure exterior penalty method, whereas the global strategies are based on the P‐mean aggregation function. Extensive parametric studies are carried out on the L‐shaped design problem to identify the most promising parameters for each solution strategy. It is found that (1) the local strategies are less sensitive to the continuation procedure employed in standard density‐based topology optimization, allowing achievement of better quality results using less iterations when compared with the global strategies; (2) the global strategies become competitive when P values larger than 100 are employed, but for this to be possible a very slow continuation procedure should be used; (3) the local strategies based on the augmented Lagrangian method provide the best compromise between computational cost and performance, being able to achieve optimized topologies at the level of a pure P‐continuation global strategy with , but using less iterations.
Triple extraction method enables high quality mass spectrometry‐based proteomics and phospho‐proteomics for eventual multi‐omics integration studies
Authors: Sanchez‐Quiles Virginia , Shi Ming‐Jun , Dingli Florent , Krucker Clémentine , Loew Damarys , Bernard‐Pierrot Isabelle , Radvanyi François
Published: July 2021

Large‐scale multi‐omic analysis allows a thorough understanding of different physiological or pathological conditions, particularly cancer. Here, an extraction method simultaneously yielding DNA, RNA and protein (thereby referred to as “triple extraction”, TEx) was tested for its suitability to unbiased, system‐wide proteomic investigation. Largely proven efficient for transcriptomic and genomic studies, we aimed at exploring TEx compatibility with mass spectrometry‐based proteomics and phospho‐proteomics, as compared to a standard urea extraction. TEx is suitable for the shotgun investigation of proteomes, providing similar results as urea‐based protocol both at the qualitative and quantitative levels. TEx is likewise compatible with the exploration of phosphorylation events, actually providing a higher number of correctly localized sites than urea, although the nature of extracted modifications appears somewhat distinct between both techniques. These results highlight that the presented protocol is well suited for the examination of the proteome and modified proteome of this bladder cancer cell model, as efficiently as other more widely used workflows for mass spectrometry‐based analysis. Potentially applicable to other mammalian cell types and tissues, TEx represents an advantageous strategy for multi‐omics on scarce and/or heterogenous samples.
Primary angle closure glaucoma is characterized by altered extracellular matrix homeostasis in the iris
Authors: Semba Richard D. , Zhang Pingbo , Dufresne Craig , Gao Tianshun , Al‐Jadaan Ibrahim , Craven Earl R. , Qian Jiang , Edward Deepak P. , Mahale Alka
Published: July 2021

Purpose

To characterize the proteome of the iris in primary angle closure glaucoma (PACG).

Experimental Design

In this cross‐sectional study, iris samples were obtained from surgical iridectomy of 48 adults with PACG and five normal controls. Peptides from iris were analysed using liquid chromatography‐tandem mass spectrometry on an Orbitrap Q Exactive Plus mass spectrometer. Verification of proteins of interest was conducted using selected reaction monitoring on a triple quadrupole mass spectrometer. The main outcome was proteins with a log2 two‐fold difference in expression in iris between PACG and controls.

Results

There were 3,446 non‐redundant proteins identified in human iris, of which 416 proteins were upregulated and 251 proteins were downregulated in PACG compared with controls. Thirty‐two upregulated proteins were either components of the extracellular matrix (ECM) (fibrillar collagens, EMILIN‐2, fibrinogen, fibronectin, matrilin‐2), matricellular proteins (thrombospondin‐1), proteins involved in cell‐matrix interactions (integrins, laminin, histidine‐rich glycoprotein, paxillin), or protease inhibitors known to modulate ECM turnover (α‐2 macroglobulin, tissue factor pathway inhibitor 2, papilin). Two giant proteins, titin and obscurin, were up‐ and down‐regulated, respectively, in the iris in PACG compared with controls.

Conclusions and Clinical Relevance

This proteomic study shows that ECM composition and homeostasis are altered in the iris in PACG.
Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites
Authors: Hassan Sameer , Töpel Mats , Aronsson Henrik
Published: July 2021

Interaction between protein and ligands are ubiquitous in a biological cell, and understanding these interactions at the atom level in protein–ligand complexes is crucial for structural bioinformatics and drug discovery. Here, we present a web‐based protein–ligand interaction application named Ligand Binding Site Comparison (LiBiSCo) for comparing the amino acid residues interacting with atoms of a ligand molecule between different protein–ligand complexes available in the Protein Data Bank (PDB) database. The comparison is performed at the ligand atom level irrespectively of having binding site similarity or not between the protein structures of interest. The input used in LiBiSCo is one or several PDB IDs of protein–ligand complex(es) and the tool returns a list of identified interactions at ligand atom level including both bonded and non‐bonded interactions. A sequence profile for the interaction for each ligand atoms is provided as a WebLogo. The LiBiSco is useful in understanding ligand binding specificity and structural promiscuity among families that are structurally unrelated. The LiBiSCo tool can be accessed through https://albiorix.bioenv.gu.se/LiBiSCo/HomePage.py.
Prevalence, environmental fate, treatment strategies, and future challenges for wastewater contaminated with SARS‐CoV‐2
Authors: Kuzniewski Saleha
Published: July 2021

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been detected in untreated and treated wastewater and studies have shown that the concentration of SARS‐CoV‐2 is proportional to the prevalence of the coronavirus disease 2019 (COVID‐19) in communities. This article presents a literature review of the prevalence of SARS‐CoV‐2 in wastewater, its environmental fate, recommended treatment strategies for contaminated wastewater, and treatment challenges to be faced in the future. The environmental fate of SARS‐CoV‐2 in wastewater is not straightforward because it can be a source of infection when present in the treated wastewater depending on the permeability of the wastewater treatment plant containment area, and can also leach into aquifers, which may serve as drinking water supplies. Secondly, there are different practices that can mitigate the SARS‐CoV‐2 infection rate from infected feces and urine. The World Health Organization has recommended the use of ultraviolet radiation (UV), disinfection, and filtration for wastewater contaminated with SARS‐CoV‐2, processes also common in wastewater treatment facilities. This article discusses these strategies referencing studies performed with surrogate viruses and shows that SARS‐CoV‐2 treatment can be complicated due to the interference from other aqueous chemical and physical factors. Considering that COVID‐19 is not the first and certainly not the last pandemic, it is imperative to develop an effective multitreatment strategy for wastewater contaminated with contagious viruses and, preferably, those that are compatible with current wastewater treatment methods.
Precision Bayesian phase I‐II dose‐finding based on utilities tailored to prognostic subgroups
Authors: Lee Juhee , Thall Peter F. , Msaouel Pavlos
Published: July 2021

A Bayesian phase I‐II design is presented that optimizes the dose of a new agent within predefined prognostic subgroups. The design is motivated by a trial to evaluate targeted agents for treating metastatic clear cell renal carcinoma, where a prognostic risk score defined by clinical variables and biomarkers is well established. Two clinical outcomes are used for dose‐finding, time‐to‐toxicity during a prespecified follow‐up period, and efficacy characterized by ordinal disease status evaluated at the end of follow‐up. A joint probability model is constructed for these outcomes as functions of dose and subgroup. The model performs adaptive clustering of adjacent subgroups having similar dose‐outcome distributions to facilitate borrowing information across subgroups. To quantify toxicity‐efficacy risk‐benefit trade‐offs that may differ between subgroups, the objective function is based on outcome utilities elicited separately for each subgroup. In the context of the renal cancer trial, a design is constructed and a simulation study is presented to evaluate the design's reliability, safety, and robustness, and to compare it to designs that either ignore subgroups or run a separate trial within each subgroup.
Synthesis and Performance Analysis of New Hybrid Polymer Gel Based on Carboxymethyl Cellulose for Preventing Spontaneous Coal Combustion
Authors: Liu Dong , Wang Junpeng , Zhou Gang , Jiang Wenjing , Duan Jinjie , Tian Fuchao , Xu Hongze
Published: July 2021

Because of the great risk of spontaneous combustion of coal, new gel materials are used for fire prevention and firefighting in coal mines. In this study, sodium alginate (SA), polyacrylamide (CPAM), and carboxymethyl cellulose (CMC) were used as matrices to prepare three different types of fireproof gel: SA‐Al3+/WG, CPAM‐Al3+/WG, and CMC‐Al3+/WG, respectively. Their thermal stabilities were analyzed using thermogravimetric analysis. The microstructures of these gels were observed using scanning electron microscopy, and their chemical bond breakages and combinations were analyzed using Fourier‐transform infrared spectroscopy. The CMC‐Al3+/WG hydrogel had the best water retention capacity, water absorption capacity, compressive strength, and inhibition characteristics according to the results of the water retention rate tests, swelling kinetics experiments, mechanics, and fire extinguishing experiments. It was proven that CMC‐Al3+/WG gel is an ideal fire‐extinguishing material.
Design, Synthesis and Biological Evaluation of New 5‐(2‐Nitrophenyl)‐1‐aryl‐1H‐pyrazoles as Topoisomerase Inhibitors
Authors: Kaur Manpreet , Mehta Vikrant , Arora Sahil , Munshi Anjana , Singh Sandeep , Kumar Raj
Published: July 2021

5‐(2‐Nitrophenyl)‐1‐aryl‐1H‐pyrazoles are designed as topoisomerase (Topo) inhibitors, synthesised and assessed for their anticancer properties against breast (MDA‐MB‐231 and MCF7), lung (A549), and colorectal (HCT116) cancer cell lines. All the compounds induced significant cytotoxicity at low micromolar concentration. The compound 5e exerted potential anticancer effects on breast cancer cell lines at a low micromolar level (IC50<2 μM), and showed negligible toxicity towards normal cells. Compound 5 e reduced reactive oxygen species (ROS) level in breast cancer cells, altered mitochondrial membrane potential and induced the cell cycle arrest at the G2/M phase. This was accompanied by downregulation of oncogenic p‐Akt and upregulation of p‐PTEN along with modulation of apoptotic markers suggesting multiple mechanisms to reduce cancer cell viability. Finally, the topoisomerase inhibition assay revealed the inhibitory activity of 5 e against Topo I and Topo II.
Novel 2‐Pyrazolin‐5‐one Derivative through Unforeseen Orthoamide Intermediate: Mechanistic Insights on Isocyanide Based [4+1] Cycloaddition
Authors: Leyton Ariel , Rabanal‐León Walter A. , Murillo‐López Juliana Andrea , Belmar Julio , Concepción Odette , de la Torre Alexander F. , Muñiz Francisco M. , Báez Reynier , Jiménez Claudio A.
Published: July 2021

This work relates a unique one‐pot procedure to assembly novel 2‐pyrazolin‐5‐one derivative functionalized through an isocyanide based formal [4+1] cycloaddition. A new, unexpected multicomponent reaction occurred when a pyrazolone was condensed with an aldehyde, an isocyanide, and water or alcohol components. Nine novel molecules with an embedded alkyl carboxamide group were obtained in moderate yield. Surprisingly, an unforeseen orthoamide intermediate was isolated and characterized, proving the plausible mechanism for the opened imidate obtained by formal [4+1] cycloaddition. This one‐pot approach to pyrazolone derivatives functionalized with amides stands as a significant advance for preparing this class of molecules.
Haemoproteosis and avian malaria in Columbidae and Corvidae from Iran
Authors: Nourani Leila , Baghkheirati Amir Asghari , Zargar Mostafa , Karimi Vahid , Djadid Navid Dinparast
Published: July 2021

Avian malaria (Plasmodium) and related genera (Haemoproteus and Leucocytozoon) are diverse and widespread parasites. Despite the extent of knowledge on avian haemosporidian parasites, information about domestic and wild bird's blood parasites is overall insufficient in Iran. Prevalence of the haemosporidian parasites’ and phylogenetic relationship of lineages are studied by using molecular and morphological results of 152 examined hosts belonging to 17 species. Molecular analysis for haemosporidian detections demonstrated overall prevalence 22.36%. Inspected hosts mostly belonging to Common Pigeons (Columba livia) parasitized by Haemoproteus spp., and Hooded Crows (Corvus cornix) and Carrion Crow (C. corone) were identified as hosting Plasmodium spp. Detected lineages COLIV03, COQUI05, LINN01, ROFI04 and SGS01 are identified as new reports from Iran. We detected no evidence of Leucocytozoon lineages, while the high prevalence of H. columbae was found in Common Pigeons. Such investigation on avian blood parasites contributes to providing new information on the prevalence, epidemiology and geographical distribution of haemosporidian parasites circulating in domestic, pets and wild birds.