bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 Pneumonia Detection Using Optimized Deep Learning Techniques
Authors: Bashar Abul , Latif Ghazanfar , Ben Brahim Ghassen , Mohammad Nazeeruddin , Alghazo Jaafar
Published: October 2021

It became apparent that mankind has to learn to live with and adapt to COVID-19, especially because the developed vaccines thus far do not prevent the infection but rather just reduce the severity of the symptoms. The manual classification and diagnosis of COVID-19 pneumonia requires specialized personnel and is time consuming and very costly. On the other hand, automatic diagnosis would allow for real-time diagnosis without human intervention resulting in reduced costs. Therefore, the objective of this research is to propose a novel optimized Deep Learning (DL) approach for the automatic classification and diagnosis of COVID-19 pneumonia using X-ray images. For this purpose, a publicly available dataset of chest X-rays on Kaggle was used in this study. The dataset was developed over three stages in a quest to have a unified COVID-19 entities dataset available for researchers. The dataset consists of 21,165 anterior-to-posterior and posterior-to-anterior chest X-ray images classified as: Normal (48%), COVID-19 (17%), Lung Opacity (28%) and Viral Pneumonia (6%). Data Augmentation was also applied to increase the dataset size to enhance the reliability of results by preventing overfitting. An optimized DL approach is implemented in which chest X-ray images go through a three-stage process. Image Enhancement is performed in the first stage, followed by Data Augmentation stage and in the final stage the results are fed to the Transfer Learning algorithms (AlexNet, GoogleNet, VGG16, VGG19, and DenseNet) where the images are classified and diagnosed. Extensive experiments were performed under various scenarios, which led to achieving the highest classification accuracy of 95.63% through the application of VGG16 transfer learning algorithm on the augmented enhanced dataset with freeze weights. This accuracy was found to be better as compared to the results reported by other methods in the recent literature. Thus, the proposed approach proved superior in performance as compared with that of other similar approaches in the extant literature, and it made a valuable contribution to the body of knowledge. Although the results achieved so far are promising, further work is planned to correlate the results of the proposed approach with clinical observations to further enhance the efficiency and accuracy of COVID-19 diagnosis.
Organisational Structure and Created Values. Review of Methods of Studying Collective Intelligence in Policymaking
Authors: Olszowski Rafał , Pięta Piotr , Baran Sebastian , Chmielowski Marcin
Published: October 2021

The domain of policymaking, which used to be limited to small groups of specialists, is now increasingly opening up to the participation of wide collectives, which are not only influencing government decisions, but also enhancing citizen engagement and transparency, improving service delivery and gathering the distributed wisdom of diverse participants. Although collective intelligence has become a more common approach to policymaking, the studies on this subject have not been conducted in a systematic way. Nevertheless, we hypothesized that methods and strategies specific to different types of studies in this field could be identified and analyzed. Based on a systematic literature review, as well as qualitative and statistical analyses, we identified 15 methods and revealed the dependencies between them. The review indicated the most popular approaches, and the underrepresented ones that can inspire future research.
Joint Early Stopping Criterions for Protograph LDPC Codes-Based JSCC System in Images Transmission
Authors: Xu Zhiping , Wang Lin , Hong Shaohua
Published: October 2021

In this paper, a joint early stopping criterion based on cross entropy (CE), named joint CE criterion, is presented for double-protograph low-density parity-check (DP-LDPC) codes-based joint source-channel coding (JSCC) systems in images transmission to reduce the decoding complexity and decrease the decoding delay. The proposed early stopping criterion adopts the CE from the output likelihood ratios (LLRs) of the joint decoder. Moreover, a special phenomenon named asymmetry oscillation-like convergence (AOLC) in the changing process of CE is uncovered in the source decoder and channel decoder of this system meanwhile, and the proposed joint CE criterion can reduce the impact from the AOLC phenomenon. Comparing to the counterparts, the results show that the joint CE criterion can perform well in the decoding complexity and decoding latency in the low–moderate signal-to-noise ratio (SNR) region and achieve performance improvement in the high SNR region with appropriate parameters, which also demonstrates that this system with joint CE is a low-latency and low-power system.
Evaluation of Electric Dynamic Performance of an Electric Vehicle System Using Different Control Techniques
Authors: Hassan Mohamed R. M. , Mossa Mahmoud A. , Dousoky Gamal M.
Published: October 2021

This paper introduces a comprehensive analysis of the dynamic performance of an electric vehicle system using different control algorithms. The complete mathematical models of the electric vehicle and its motor drive system are described in a systematic manner. Furthermore, the vehicle dynamics are tested with several control topologies to investigate the most appropriate one. The adopted control topologies were the direct torque control (DTC), the model predictive direct torque control (MP DTC), and the predictive voltage control (PVC). The obtained results showed that the dynamics of the electric drive system of the vehicle under the PVC system were enhanced compared to the other control schemes.
Design and Implementation of a Single-Stage PFC Active-Clamp Flyback Converter with Dual Transformers
Authors: Wu Sen-Tung , Cheng Yu-Ting
Published: October 2021

This paper proposes an AC/DC single-stage structure by integrating a boost topology and an active clamp flyback (ACF) circuit with power-factor-correction (PFC) function. The PFC function can be achieved by controlling a boost PFC topology operated in the discontinuous conduction mode. With the coordination of active clamping components, a resonant technique is obtained and zero-voltage-switching (ZVS) can be achieved. The proposed converter is combined with the advantages of: (1) compared with two-stage circuit, a single stage circuit decreases the component of the main circuit and reduces the complexity of the control circuit; (2) a boost topology with PFC function operated in discontinuous conduction mode can be accomplished without adding any current detecting technique or detecting input signal; (3) by using the inductor from the PFC stage, ZVS function can be achieved without any additional inductor; (4) the increment of switching frequency facilitates the optimization of power density; (5) the conducting loss at the secondary side can be reduced by adding the synchronous rectification; (6) in this proposed scheme, the dual transformers with series-parallel connection are utilized, the current at the secondary side can be shared for lowering the conduction loss of the synchronous transistors. Finally, a prototype converter with AC 110 V input and DC 19 V/6.32 A (120 W) output under 300 kHz switching frequency is implemented. The efficiency of the proposed converter reaches 88.20% and 0.984 power factor in full load condition.
Reliability Assessment of MV Power Connections
Authors: Hoduń Piotr , Borecki Michał
Published: October 2021

This article presents an analysis of the reliability of the power grid using data on the failure rate of the medium voltage (MV) power grid from the last five years. The analysis of the state of the power grid was based on the data provided by the grid operator. The purpose of this article is to analyze the reliability assessment of the medium voltage (MV) power connections using various analytical methods, a simulation model and reliability indicators. The analysis was performed based on the defined categories of power outages in terms of their duration. This made it possible to determine the energy quality indicators in a selected power grid. Then, a more complex analysis was carried out to assess the convergence of the applied analytical models of reliability assessment with the actual results obtained for the power grid. Moreover, using ANSYS Multiphysics, a numerical model of the cable head was developed to analyze the processes taking place in this element of the power grid for various exploitation cases.
New Experimental Approach for the Determination of the Heat Generation in a Li-Ion Battery Cell
Authors: Christen Rouven , Martin Björn , Rizzo Gerhard
Published: October 2021

With regard to safety, efficiency and lifetime of battery systems, the thermal behavior of battery cells is of great interest. The use of models describing the thermoelectric behavior of battery cells improves the understanding of heat generation mechanisms and enables the development of optimized thermal management systems. In this work, a novel experimental approach is presented to determine both the irreversible heat due to ohmic losses and the reversible heat due to entropy changes directly via heat flow measurements. No additional information about thermal properties of the battery cell, such as heat capacity or thermal conductivity, are required. Thus, the exothermic and endothermic nature of reversible heat generated in a complete charge/discharge cycle can be investigated. Moreover, the results of the proposed method can potentially be used to provide an additional constraint during the identification process of the equivalent circuit model parameters. The described method is applied to a 23 Ah lithium titanate cell and the corresponding results are presented.
Gene Therapies for Monogenic Autism Spectrum Disorders
Authors: Weuring Wout , Geerligs Jeroen , Koeleman Bobby P. C.
Published: October 2021

Novel genome editing and transient gene therapies have been developed the past ten years, resulting in the first in-human clinical trials for monogenic disorders. Syndromic autism spectrum disorders can be caused by mutations in a single gene. Given the monogenic aspect and severity of syndromic ASD, it is an ideal candidate for gene therapies. Here, we selected 11 monogenic ASD syndromes, validated by animal models, and reviewed current gene therapies for each syndrome. Given the wide variety and novelty of some forms of gene therapy, the best possible option must be decided based on the gene and mutation.
Beyond Trinucleotide Repeat Expansion in Fragile X Syndrome: Rare Coding and Noncoding Variants in FMR1 and Associated Phenotypes
Authors: Tekendo-Ngongang Cedrik , Grochowsky Angela , Solomon Benjamin D. , Yano Sho T.
Published: October 2021

FMR1 (FMRP translational regulator 1) variants other than repeat expansion are known to cause disease phenotypes but can be overlooked if they are not accounted for in genetic testing strategies. We collected and reanalyzed the evidence for pathogenicity of FMR1 coding, noncoding, and copy number variants published to date. There is a spectrum of disease-causing FMR1 variation, with clinical and functional evidence supporting pathogenicity of five splicing, five missense, one in-frame deletion, one nonsense, and four frameshift variants. In addition, FMR1 deletions occur in both mosaic full mutation patients and as constitutional pathogenic alleles. De novo deletions arise not only from full mutation alleles but also alleles with normal-sized CGG repeats in several patients, suggesting that the CGG repeat region may be prone to genomic instability even in the absence of repeat expansion. We conclude that clinical tests for potentially FMR1-related indications such as intellectual disability should include methods capable of detecting small coding, noncoding, and copy number variants.
Greig Cephalopolysyndactyly Contiguous Gene Syndrome: Case Report and Literature Review
Authors: Kozma Kinga , Bembea Marius , Jurca Claudia M. , Ioana Mihai , Streață Ioana , Şoşoi Simona Ş. , Pirvu Andrei , Petchesi Codruța D. , Szilágyi Ariana , Sava Cristian N. , Jurca Alexandru , Ujfalusi Anikó , Szűcs Zsuzsanna , Szakszon Katalin
Published: October 2021

Greig cephalopolysyndactyly syndrome (GCPS) is a rare genetic disorder (about 200 cases reported), characterized by macrocephaly, hypertelorism, and polysyndactyly. Most of the reported GCPS cases are the results of heterozygous loss of function mutations affecting the GLI3 gene (OMIM# 175700), while a small proportion of cases arise from large deletions on chromosome 7p14 encompassing the GLI3 gene. To our knowledge, only 6 patients have been reported to have a deletion with an exact size (given by genomic coordinates) and a gene content larger than 1 Mb involving the GLI3 gene. This report presents a patient with Greig cephalopolysyndactyly contiguous gene syndrome (GCP-CGS) diagnosed with a large, 18 Mb deletion on chromosome 7p14.2-p11.2. Similar cases are reviewed in the literature for a more accurate comparison between genotype and phenotype.
Developmental Acquisition of p53 Functions
Authors: Jaiswal Sushil K. , Raj Sonam , DePamphilis Melvin L.
Published: October 2021

Remarkably, the p53 transcription factor, referred to as “the guardian of the genome”, is not essential for mammalian development. Moreover, efforts to identify p53-dependent developmental events have produced contradictory conclusions. Given the importance of pluripotent stem cells as models of mammalian development, and their applications in regenerative medicine and disease, resolving these conflicts is essential. Here we attempt to reconcile disparate data into justifiable conclusions predicated on reports that p53-dependent transcription is first detected in late mouse blastocysts, that p53 activity first becomes potentially lethal during gastrulation, and that apoptosis does not depend on p53. Furthermore, p53 does not regulate expression of genes required for pluripotency in embryonic stem cells (ESCs); it contributes to ESC genomic stability and differentiation. Depending on conditions, p53 accelerates initiation of apoptosis in ESCs in response to DNA damage, but cell cycle arrest as well as the rate and extent of apoptosis in ESCs are p53-independent. In embryonic fibroblasts, p53 induces cell cycle arrest to allow repair of DNA damage, and cell senescence to prevent proliferation of cells with extensive damage.
Mapping the Diverse and Inclusive Future of Parkinson’s Disease Genetics and Its Widespread Impact
Authors: Elsayed Inas , Martinez-Carrasco Alejandro , Cornejo-Olivas Mario , Bandres-Ciga Sara
Published: October 2021

Over the last decades, genetics has been the engine that has pushed us along on our voyage to understand the etiology of Parkinson’s disease (PD). Although a large number of risk loci and causative mutations for PD have been identified, it is clear that much more needs to be done to solve the missing heritability mystery. Despite remarkable efforts, as a field, we have failed in terms of diversity and inclusivity. The vast majority of genetic studies in PD have focused on individuals of European ancestry, leading to a gap of knowledge on the existing genetic differences across populations and PD as a whole. As we move forward, shedding light on the genetic architecture contributing to PD in non-European populations is essential, and will provide novel insight into the generalized genetic map of the disease. In this review, we discuss how better representation of understudied ancestral groups in PD genetics research requires addressing and resolving all the challenges that hinder the inclusion of these populations. We further provide an overview of PD genetics in the clinics, covering the current challenges and limitations of genetic testing and counseling. Finally, we describe the impact of worldwide collaborative initiatives in the field, shaping the future of the new era of PD genetics as we advance in our understanding of the genetic architecture of PD.
UMOD Polymorphisms Associated with Kidney Function, Serum Uromodulin and Risk of Mortality among Patients with Chronic Kidney Disease, Results from the C-STRIDE Study
Authors: Wang Jinwei , Liu Lili , He Kevin , Gao Bixia , Wang Fang , Zhao Minghui , Zhang Luxia ,   on behalf of the Chinese Cohort Study of Chronic Kidney Disease (C-STRIDE)
Published: October 2021

We aimed to explore associations of several single nucleotide polymorphisms (SNPs) detected by genome-wide association studies in uromodulin (UMOD) gene with phenotypes and prognosis of chronic kidney disease (CKD) among 2731 Chinese patients with CKD stage 1–4. Polymorphisms of rs11864909, rs4293393, rs6497476, and rs13333226 were genotyped using the Sequenom MassARRAY iPLEX platform. The SNPs of rs13333226 and rs4293393 were in complete linkage disequilibrium. Based on the T dominant model, T allele of rs11864909 was associated with levels of estimated glomerular filtration rate (eGFR) and serum uromodulin with linear regression coefficients of 2.68 (95% confidence interval (CI): 0.61, 4.96) and −12.95 (95% CI: −17.59, −7.98), respectively, after adjustment for cardiovascular and kidney-specific risk factors. After a median follow-up of 4.94 years, both G allele of rs4293393/rs13333226 and C allele of rs6497476 were associated with reduced risk of all-cause mortality with multivariable-adjusted hazard ratios of 0.341 (95% CI: 0.105, 0.679) and 0.344 (95% CI: 0.104, 0.671), respectively. However, no associations were found between the variants and slope of eGFR in the linear mix effect model. In summary, the variant of rs11864909 in the UMOD gene was associated with levels of eGFR and serum uromodulin, while those of rs4293393 and rs6497476 were associated with all-cause mortality among patients with CKD.
LGFC-CNN: Prediction of lncRNA-Protein Interactions by Using Multiple Types of Features through Deep Learning
Authors: Huang Lan , Jiao Shaoqing , Yang Sen , Zhang Shuangquan , Zhu Xiaopeng , Guo Rui , Wang Yan
Published: October 2021

Long noncoding RNA (lncRNA) plays a crucial role in many critical biological processes and participates in complex human diseases through interaction with proteins. Considering that identifying lncRNA–protein interactions through experimental methods is expensive and time-consuming, we propose a novel method based on deep learning that combines raw sequence composition features, hand-designed features and structure features, called LGFC-CNN, to predict lncRNA–protein interactions. The two sequence preprocessing methods and CNN modules (GloCNN and LocCNN) are utilized to extract the raw sequence global and local features. Meanwhile, we select hand-designed features by comparing the predictive effect of different lncRNA and protein features combinations. Furthermore, we obtain the structure features and unifying the dimensions through Fourier transform. In the end, the four types of features are integrated to comprehensively predict the lncRNA–protein interactions. Compared with other state-of-the-art methods on three lncRNA–protein interaction datasets, LGFC-CNN achieves the best performance with an accuracy of 94.14%, on RPI21850; an accuracy of 92.94%, on RPI7317; and an accuracy of 98.19% on RPI1847. The results show that our LGFC-CNN can effectively predict the lncRNA–protein interactions by combining raw sequence composition features, hand-designed features and structure features.
Eccentric Dipole Evolution during the Last Reversal, Last Excursions, and Holocene Anomalies. Interpretation Using a 360-Dipole Ring Model
Authors: González-López Alicia , Osete María Luisa , Campuzano Saioa A. , Molina-Cardín Alberto , Rivera Pablo , Pavón-Carrasco Francisco Javier
Published: October 2021

The eccentric dipole (ED) is the next approach of the geomagnetic field after the generally used geocentric dipole. Here, we analyzed the evolution of the ED during extreme events, such as the Matuyama-Brunhes polarity transition (~780 ka), the Laschamp (~41 ka) and Mono Lake (~34 ka) excursions, and during the time of two anomalous features of the geomagnetic field observed during the Holocene: the Levantine Iron Age Anomaly (LIAA, ~1000 BC) and the South Atlantic Anomaly (SAA, analyzed from ~700 AD to present day). The analysis was carried out using the paleoreconstructions that cover the time of the mentioned events (IMMAB4, IMOLEe, LSMOD.2, SHAWQ-Iron Age, and SHAWQ2k). We found that the ED moves around the meridian plane of 0–180° during the reversal and the excursions; it moves towards the region of the LIAA; and it moves away from the SAA. To investigate what information can be extracted from its evolution, we designed a simple model based on 360-point dipoles evenly distributed in a ring close to the inner core boundary that can be reversed and their magnitude changed. We tried to reproduce with our simple model the observed evolution of the ED, and the total field energy at the Earth’s surface. We observed that the modeled ED moves away from the region where we set the dipoles to reverse. If we consider that the ring dipoles could be related to convective columns in the outer core of the Earth, our simple model would indicate the potential of the displacement of the ED to give information about the regions in the outer core where changes start for polarity transitions and for the generation of important anomalies of the geomagnetic field. According to our simple model, the regions in which the most important events of the Holocene occur, or in which the last polarity reversal or excursion begin, are related to the regions of the Core Mantle Boundary (CMB), where the heat flux is low.
Prevalence of Intimate Partner Violence, Substance Use Disorders and Depression among Incarcerated Women in Lima, Perú
Authors: Cyrus Elena , Sanchez Jorge , Madhivanan Purnima , Lama Javier R. , Bazo Andrea Cornejo , Valencia Javier , Leon Segundo R. , Villaran Manuel , Vagenas Panagiotis , Sciaudone Michael , Vu David , Coudray Makella S. , Atice Frederick L.
Published: October 2021

Background: Globally, there is evidence supporting the co-occurrence of intimate partner violence (IPV), substance use disorders (SUD) and mental health disorders among women in prisons, however, there is limited research investigating these domains in the Andean region where rates of female incarceration have increased. The study objective was to explore the prevalence of IPV, SUD and depression among incarcerated women in a Peruvian prison and explore associations among these variables and related correlates. Methods: 249 incarcerated women responded to a questionnaire about IPV, substance use, depression, and sexual behavior, and were screened for HIV/sexually transmitted diseases (STDs). Univariate analysis and logistic regression were used to estimate relative risk and the influence of substance use and depression on IPV rates. Results: Twelve months prior to incarceration, of the women with sexual partners pre-incarceration (n = 212), 69.3% experienced threats of violence, 61.4% experienced ≥1 acts of physical violence, and 28.3% reported ≥1 act of sexual aggression. Pre-incarceration, 68.1% of drug-using women had a SUD, and 61.7% of those who consumed alcohol reported hazardous/harmful drinking. There were 20 (8.0%) HIV/STD cases; and 67.5% of the women reported depressive symptoms. Compared to women with no experiences of physical violence, a greater proportion of women who experienced least l violent act had depressive symptoms and engaged in sex work pre-incarceration. Depression was associated with physical violence (adjusted relative risk = 1.35, 95% confidence interval: 1.14–1.58). Recommendations: The findings provide evidence of a syndemic of IPV, substance abuse and depression among incarcerated women in a Peruvian prison. To help guide policy makers, further research is needed to determine if this is indicative of trends for other at-risk women in the region, and viable options to treat these women during incarceration to prevent recidivism and other long-term negative sequalae.
Surgical Outcomes of Clitoroplasty in Children with Congenital Adrenal Hyperplasia and Clitoral Hypertrophy: A 19-Year Experience of a Single Surgeon
Authors: Jun Jaebeom , Song Sang Hoon , Park Sungchan , Han Jae Hyeon , Kim Kun Suk
Published: October 2021

This study aimed to describe the experience with clitoroplasty for clitoral hypertrophy in patients with congenital adrenal hyperplasia of a single surgeon. The medical records of female pediatric patients with congenital adrenal hyperplasia who underwent clitoroplasty at a tertiary referral hospital between 2002 and 2020 were retrospectively analyzed. Three different surgical techniques were applied for clitoroplasty: recession without reduction, reduction and recession, and girth reduction and recession. A total of 104 patients underwent clitoroplasty for clitoral hypertrophy. The median patient age at the time of surgery was 10 months (range, 4 months to 10 years). The operation time was longer in reduction clitoroplasty than in recession clitoroplasty without reduction (median, 153 vs. 111 min, p = 0.003). The mean postoperative pain score of the patients did not differ among the different clitoroplasty techniques. During the mean follow-up of 37.7 months, nine (8.6%) patients underwent reperformed clitoroplasty. The rate of reperformed operation was significantly higher in patients who underwent reduction clitoroplasty (17.3%) than in those who underwent recession without reduction (2%) or girth reduction and recession (0%) (p = 0.031). Early clitoroplasty in patients with congenital adrenal hyperplasia yielded good mid-term surgical outcomes in terms of cosmesis and recurrence rate, with minimal perioperative complications.
Load-Velocity Relationship in Bench Press and Effects of a Strength-Training Program in Wheelchair Basketball Players: A Team Study
Authors: Romarate Ander , Iturricastillo Aitor , Nakamura Fabio Y. , Loturco Irineu , Rodriguez-Negro Josune , Granados Cristina , Yanci Javier
Published: October 2021

Performance in wheelchair basketball is determined by capabilities, such as strength and power. The study has two aims: first, to analyze the association between speed and acceleration variables (collected in the bench press (BP) exercise) and the distinct percentages of one-repetition maximum (1RM); second, to analyze the effect of a strength training protocol on wheelchair basketball (WB) players according to their functional impairments. Ten Spanish male WB players volunteered to participate in the study. The players did a pretest and posttest (1RM in bench press) with 6-week muscle strength intervention program. The results showed a high association between the %1RM and the mean propulsive velocity (MPV) and the maximum velocity (Vmax), both in the total of the participants, and in each separate group of athletes. After implementing the strength training program, both the players of the IWBF (International Wheelchair Basketball Federation) < 2.5 group and those of IWBF > 2.5 group improved their 1RM (p < 0.01, ES = 0.20 to 0.23). However, the program produced positive effects at submaximal intensities in the MPV reached with 30, 40, 70, and 80 kg and in time to maximum velocity (TVmax) with 30, 40, and 70 kg (ES = −3.24 to 1.32) only in players with greater functional impairments. The high association between %1RM and MPV and Vmax can allow for determination the %1RM of the WB players in the BP using the MPV and the Vmax. The training program was effective in improving 1RM in both groups, while improvements in submaximal values only occurred in the IWBF < 2.5 group.
Effect of UVC and UVA Photocatalytic Processes on Tetracycline Removal Using CuS-Coated Magnetic Activated Carbon Nanocomposite: A Comparative Study
Authors: Nasseh Negin , Khosravi Rasoul , Mazari Moghaddam Narjes sadat , Rezania Shahabaldin
Published: October 2021

In this study, we synthesized a novel MAC nanocomposite using almond’s green hull coated with CuS. The whole set of experiments have been conducted inside a batch (discontinuous reactor system) at room temperature. The effectiveness of different parameters in tetracycline removal pH (3, 5, 7, and 9), pollutant concentration (5–100 mg/L), nanocomposite dosage (0.025–1 g/L), and contact time (5–60 min) using newly synthesized nanocomposite were investigated. Based on the results, in the optimal conditions of pH = 9, nanocomposite dosage of 1 g/L, pollutant concentration of 20 mg/L, contact time of 60 min, and room temperature, 95% removal efficiency was obtained. In MAC/CuS/UVC process, the removal of COD and TOC were 76.89% and 566.84% respectively meanwhile, these values in MAC/CuS/UVA process were 74.19% and 62.11%, respectively. The results of nanocomposite stability and magnetic recovery illustrated that the removal efficiency was reduced by 1.5% in the presence of UVC and 5% in the presence of UVA lights during all six cycles. Therefore, this nanocomposite was highly capable of recycling and reuse. It can be concluded that considering the high potential of the synthesized nanocomposite, the photocatalytic efficiency of the MAC/CuS/UVC process in tetracycline synthesis was higher than MAC/CuS/UVA process.
Evaluation of Residual Infectivity after SARS-CoV-2 Aerosol Transmission in a Controlled Laboratory Setting
Authors: Zupin Luisa , Licen Sabina , Milani Margherita , Clemente Libera , Martello Lorenzo , Semeraro Sabrina , Fontana Francesco , Ruscio Maurizio , Miani Alessandro , Crovella Sergio , Barbieri Pierluigi
Published: October 2021

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is mainly transmitted through respiratory droplets, aerosols, or direct contact with fomites from an infected subject. It has been reported that SARS-CoV-2 is stable and viable in aerosol up to 16 h in controlled laboratory conditions. However, the aerosolization conditions varied a lot between the studies. In this work, an experimental laboratory model of SARS-CoV-2 aerosolization was established, employing an impinger nebulizer, a cylindrical chamber for aerosol travel, and a SKC biosampler for the collection of particles. The efficiency of the system was assessed based on the molecular determination of the viral load in the nebulizer after the aerosolization and in the aerosol collected at the end of the travel. Moreover, the residual infectivity was tested in vitro on the Vero E6 cell line, through the observation of the cytopathic effect (CPE), and the quantification of the viral load in the supernatants at 7 days post inoculation (dpi). A high RNA viral load was found in the SKC biosampler after aerosolization, indicating that it was possible to transport a high virus titer through the 30-cm chamber with all the dilutions (initial 105, 104, 103 plaque forming unit—PFU/mL). At the 7 dpi, an increment of the RNA viral load was determined for the dilutions 105 and 104 PFU/mL tested, while only the initial 105 PFU/mL resulted in visible CPE. Our findings allowed us to achieve the resilience of SARS-CoV-2 in aerosol form, at a concentration comparable to those reported for clinical samples. This mode of transmission should be considered for the mitigation and preventive measures to counteract SARS-CoV-2 spreading.
Non-Targeted Metabolite Profiling Reveals Host Metabolomic Reprogramming during the Interaction of Black Pepper with Phytophthora capsici
Authors: Kattupalli Divya , Pinski Artur , Sreekumar Sweda , Usha Aswathi , Girija Aiswarya , Beckmann Manfred , Mur Luis Alejandro Jose , Eppurathu Vasudevan Soniya
Published: October 2021

Phytophthora capsici is one of the most destructive pathogens causing quick wilt (foot rot) disease in black pepper (Piper nigrum L.) to which no effective resistance has been defined. To better understand the P. nigrum–P. capsici pathosystem, we employed metabolomic approaches based on flow-infusion electrospray–high-resolution mass spectrometry. Changes in the leaf metabolome were assessed in infected and systemic tissues at 24 and 48 hpi. Principal Component Analysis of the derived data indicated that the infected leaves showed a rapid metabolic response by 24 hpi whereas the systemic leaves took 48 hpi to respond to the infection. The major sources of variations between infected leaf and systemic leaf were identified, and enrichment pathway analysis indicated, major shifts in amino acid, tricarboxylic acid cycle, nucleotide and vitamin B6 metabolism upon infection. Moreover, the individual metabolites involved in defensive phytohormone signalling were identified. RT-qPCR analysis of key salicylate and jasmonate biosynthetic genes indicated a transient reduction of expression at 24 hpi but this increased subsequently. Exogenous application of jasmonate and salicylate reduced P. capsici disease symptoms, but this effect was suppressed with the co-application of abscisic acid. The results are consistent with abscisic acid reprogramming, salicylate and jasmonate defences in infected leaves to facilitate the formation of disease. The augmentation of salicylate and jasmonate defences could represent an approach through which quick wilt disease could be controlled in black pepper.
From Primary MSC Culture of Adipose Tissue to Immortalized Cell Line Producing Cytokines for Potential Use in Regenerative Medicine Therapy or Immunotherapy
Authors: Paprocka Maria , Kraskiewicz Honorata , Bielawska-Pohl Aleksandra , Krawczenko Agnieszka , Masłowski Leszek , Czyżewska-Buczyńska Agnieszka , Witkiewicz Wojciech , Dus Danuta , Czarnecka Anna
Published: October 2021

For twenty-five years, attempts have been made to use MSCs in the treatment of various diseases due to their regenerative and immunomodulatory properties. However, the results are not satisfactory. Assuming that MSCs can be replaced in some therapies by the active factors they produce, the immortalized MSCs line was established from human adipose tissue (HATMSC1) to produce conditioned media and test its regenerative potential in vitro in terms of possible clinical application. The production of biologically active factors by primary MSCs was lower compared to the HATMSC1 cell line and several factors were produced only by the cell line. It has been shown that an HATMSC1-conditioned medium increases the proliferation of various cell types, augments the adhesion of cells and improves endothelial cell function. It was found that hypoxia during culture resulted in an augmentation in the pro-angiogenic factors production, such as VEGF, IL-8, Angiogenin and MCP-1. The immunomodulatory factors caused an increase in the production of GM-CSF, IL-5, IL-6, MCP-1, RANTES and IL-8. These data suggest that these factors, produced under different culture conditions, could be used for different medical conditions, such as in regenerative medicine, when an increased concentration of pro-angiogenic factors may be beneficial, or in inflammatory diseases with conditioned media with a high concentration of immunomodulatory factors.
RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair
Authors: Blasiak Janusz , Szczepańska Joanna , Sobczuk Anna , Fila Michal , Pawlowska Elzbieta
Published: October 2021

Replication timing (RT) is a cellular program to coordinate initiation of DNA replication in all origins within the genome. RIF1 (replication timing regulatory factor 1) is a master regulator of RT in human cells. This role of RIF1 is associated with binding G4-quadruplexes and changes in 3D chromatin that may suppress origin activation over a long distance. Many effects of RIF1 in fork reactivation and DNA double-strand (DSB) repair (DSBR) are underlined by its interaction with TP53BP1 (tumor protein p53 binding protein). In G1, RIF1 acts antagonistically to BRCA1 (BRCA1 DNA repair associated), suppressing end resection and homologous recombination repair (HRR) and promoting non-homologous end joining (NHEJ), contributing to DSBR pathway choice. RIF1 is an important element of intra-S-checkpoints to recover damaged replication fork with the involvement of HRR. High-resolution microscopic studies show that RIF1 cooperates with TP53BP1 to preserve 3D structure and epigenetic markers of genomic loci disrupted by DSBs. Apart from TP53BP1, RIF1 interact with many other proteins, including proteins involved in DNA damage response, cell cycle regulation, and chromatin remodeling. As impaired RT, DSBR and fork reactivation are associated with genomic instability, a hallmark of malignant transformation, RIF1 has a diagnostic, prognostic, and therapeutic potential in cancer. Further studies may reveal other aspects of common regulation of RT, DSBR, and fork reactivation by RIF1.
Interference on Cytosolic DNA Activation Attenuates Sepsis Severity: Experiments on Cyclic GMP–AMP Synthase (cGAS) Deficient Mice
Authors: Visitchanakun Peerapat , Kaewduangduen Warerat , Chareonsappakit Awirut , Susantitaphong Paweena , Pisitkun Prapaporn , Ritprajak Patcharee , Townamchai Natavudh , Leelahavanichkul Asada
Published: October 2021

Although the enhanced responses against serum cell-free DNA (cfDNA) in cases of sepsis—a life-threatening organ dysfunction due to systemic infection—are understood, the influence of the cytosolic DNA receptor cGAS (cyclic guanosine monophosphate–adenosine monophosphate (GMP–AMP) synthase) on sepsis is still unclear. Here, experiments on cGAS deficient (cGAS-/-) mice were conducted using cecal ligation and puncture (CLP) and lipopolysaccharide (LPS) injection sepsis models and macrophages. Severity of CLP in cGAS-/- mice was less severe than in wildtype (WT) mice, as indicated by mortality, serum LPS, cfDNA, leukopenia, cytokines (TNF-α, IL-6 and IL-10), organ histology (lung, liver and kidney) and spleen apoptosis. With the LPS injection model, serum cytokines in cGAS-/- mice were lower than in WT mice, despite the similar serum cfDNA level. Likewise, in LPS-activated WT macrophages, the expression of several mitochondria-associated genes (as revealed by RNA sequencing analysis) and a profound reduction in mitochondrial parameters, including maximal respiration (determined by extracellular flux analysis), DNA (mtDNA) and mitochondrial abundance (revealed by fluorescent staining), were demonstrated. These data implied the impact of cfDNA resulting from LPS-induced cell injury. In parallel, an additive effect of bacterial DNA on LPS, seen in comparison with LPS alone, was demonstrated in WT macrophages, but not in cGAS-/- cells, as indicated by supernatant cytokines (TNF-α and IL-6), M1 proinflammatory polarization (iNOS and IL-1β), cGAS, IFN-γ and supernatant cyclic GMP–AMP (cGAMP). In conclusion, cGAS activation by cfDNA from hosts (especially mtDNA) and bacteria was found to induce an additive proinflammatory effect on LPS-activated macrophages which was perhaps responsible for the more pronounced sepsis hyperinflammation observed in WT mice compared with the cGAS-/- group.
The Effect of tRNA[Ser]Sec Isopentenylation on Selenoprotein Expression
Authors: Fradejas-Villar Noelia , Bohleber Simon , Zhao Wenchao , Reuter Uschi , Kotter Annika , Helm Mark , Knoll Rainer , McFarland Robert , Taylor Robert W. , Mo Yufeng , Miyauchi Kenjyo , Sakaguchi Yuriko , Suzuki Tsutomu , Schweizer Ulrich
Published: October 2021

Transfer RNA[Ser]Sec carries multiple post-transcriptional modifications. The A37G mutation in tRNA[Ser]Sec abrogates isopentenylation of base 37 and has a profound effect on selenoprotein expression in mice. Patients with a homozygous pathogenic p.R323Q variant in tRNA-isopentenyl-transferase (TRIT1) show a severe neurological disorder, and hence we wondered whether selenoprotein expression was impaired. Patient fibroblasts with the homozygous p.R323Q variant did not show a general decrease in selenoprotein expression. However, recombinant human TRIT1R323Q had significantly diminished activities towards several tRNA substrates in vitro. We thus engineered mice conditionally deficient in Trit1 in hepatocytes and neurons. Mass-spectrometry revealed that hypermodification of U34 to mcm5Um occurs independently of isopentenylation of A37 in tRNA[Ser]Sec. Western blotting and 75Se metabolic labeling showed only moderate effects on selenoprotein levels and 75Se incorporation. A detailed analysis of Trit1-deficient liver using ribosomal profiling demonstrated that UGA/Sec re-coding was moderately affected in Selenop, Txnrd1, and Sephs2, but not in Gpx1. 2′O-methylation of U34 in tRNA[Ser]Sec depends on FTSJ1, but does not affect UGA/Sec re-coding in selenoprotein translation. Taken together, our results show that a lack of isopentenylation of tRNA[Ser]Sec affects UGA/Sec read-through but differs from a A37G mutation.
Technology Standardization for Innovation: How Google Leverages an Open Digital Platform
Authors: Fukami Yoshiaki , Shimizu Takumi
Published: October 2021

The aim of this study is to investigate firms’ strategies for developing and diffusing technology standards while maintaining a consensus with competitors in their industry. We conducted a case study of information technology (IT) standardization and analysed how Google drives the development and diffusion of HTML5 standards. Accordingly, this study sheds light on two strategic initiatives and two relational practices of standard development and diffusion. Adopting the technologies developed by other firms and forming alliances with other browser vendors are key to influencing the standardization process. Additionally, by building partnerships with developer communities, Google has accelerated the development and diffusion of the HTML5 standards. The mechanisms behind Google’s standardization strategies are also discussed.
Genus-Wide Characterization of Nuclear Mitochondrial DNAs in Bumblebee (Hymenoptera: Apidae) Genomes
Authors: Ding Lele , Sang Huiling , Sun Cheng
Published: October 2021

In eukaryotes, DNA of mitochondria is transferred into the nucleus and forms nuclear mitochondrial DNAs (NUMTs). Taking advantage of the abundant genomic resources for bumblebees, in this study, we de novo generated mitochondrial genomes (mitogenomes) for 11 bumblebee species. Then, we identified and characterized NUMTs in genus-wide bumblebee species. The number of identified NUMTs varies across those species, with numbers ranging from 32 to 72, and nuclear genome size is not positively related to NUMT number. The insertion sites of NUMTs in the nuclear genome are not random, with AT-rich regions harboring more NUMTs. In addition, our results suggest that NUMTs derived from the mitochondrial COX1 gene are most abundant in the bumblebee nuclear genome. Although the majority of NUMTs are found within intergenic regions, some NUMTs do reside within genic regions. Transcripts that contain both the NUMT sequence and its flanking non-NUMT sequences could be found in the bumblebee transcriptome, suggesting a potential domestication of NUMTs in the bumblebee. Taken together, our results shed light on the molecular features of NUMTs in the bumblebee and uncover their contribution to genome innovation.
Identification of Potential Host Plants of Sap-Sucking Insects (Hemiptera: Cicadellidae) Using Anchored Hybrid By-Catch Data
Authors: Cao Yanghui , Dietrich Christopher H.
Published: October 2021

Reliable host plant records are available for only a small fraction of herbivorous insect species, despite their potential agricultural importance. Most available data on insect–plant associations have been obtained through field observations of occurrences of insects on particular plants. Molecular methods have more recently been used to identify potential host plants using DNA extracted from insects, but most prior studies using these methods have focused on chewing insects that ingest tissues expected to contain large quantities of plant DNA. Screening of Illumina data obtained from sap feeders of the hemipteran family Cicadellidae (leafhoppers) using anchored hybrid enrichment indicates that, despite feeding on plant fluids, these insects often contain detectable quantities of plant DNA. Although inclusion of probes for bacterial 16S in the original anchored hybrid probe kit yielded relatively high detection rates for chloroplast 16S, the Illumina short reads also, in some cases, included DNA for various plant barcode genes as “by-catch”. Detection rates were generally only slightly higher for Typhlocybinae, which feed preferentially on parenchyma cell contents, compared to other groups of leafhoppers that feed preferentially on phloem or xylem. These results indicate that next-generation sequencing provides a powerful tool to investigate the specific association between individual insect and plant species.
Evaluation of the Differences in the Expression of Biogenic Amine-Related mRNAs and Proteins in Endometrioid Endometrial Cancer
Authors: Czerwiński Michał , Bednarska-Czerwińska Anna , Zmarzły Nikola , Boroń Dariusz , Oplawski Marcin , Grabarek Beniamin Oskar
Published: October 2021

Biogenic amines, such as adrenaline, noradrenaline, histamine, dopamine, and serotonin are important neurotransmitters that also regulate cell viability. Their detection and analysis are helpful in the diagnosis of many diseases, including cancer. The aim of this study was to determine the expression profile of the biogenic amine-related genes and proteins in endometrioid endometrial cancer compared to the control group. The material consisted of endometrial tissue samples and whole blood collected from 30 endometrioid endometrial cancer patients and 30 cancer-free patients. The gene expression was determined by the mRNA microarrays and validated by qRT-PCR. Protein levels were determined in the serum by the enzyme-linked immunosorbent assay (ELISA). Overexpression of histamine H1–H3 receptors and early growth response 1 and silencing of calmodulin, the histamine H4 receptor, and the dopamine D5 receptor have been reported in endometrioid endometrial cancer. The obtained results indicate disturbances in the signaling activated by histamine and dopamine receptors, which could potentially contribute to the progression of endometrioid endometrial cancer.
Serum Calretinin as a Biomarker in Malignant Mesothelioma
Authors: Zupanc Cita , Franko Alenka , Štrbac Danijela , Dodič Fikfak Metoda , Kovač Viljem , Dolžan Vita , Goričar Katja
Published: October 2021

The early diagnosis of malignant mesothelioma (MM) could improve the prognosis of MM patients. To confirm an MM diagnosis, an immunohistochemical analysis of several tumor tissue markers, including calretinin, is currently required. Our aim is to evaluate serum calretinin as a potential biomarker in asbestos-related diseases, especially in MM. Our study includes 549 subjects: 164 MM patients, 117 subjects with asbestosis, 195 subjects with pleural plaques and 73 occupationally asbestos-exposed subjects without asbestos-related diseases. The serum calretinin concentration was determined with a commercially available enzyme immunoassay. Data on the soluble mesothelin-related peptides (SMRP) concentration are available from previous studies. MM patients had a significantly higher calretinin concentration than subjects without disease, subjects with pleural plaques or subjects with asbestosis (all p < 0.001). The histological type was significantly associated with serum calretinin: patients with sarcomatoid MM had lower calretinin than patients with the epithelioid type (p = 0.001). In a ROC curve analysis, the area under the curve for calretinin concentration predicting MM was 0.826 (95% CI = 0.782–0.869; p < 0.001). At the cutoff value of 0.32 ng/mL, sensitivity was 0.683, while specificity was 0.886. The combination of calretinin and SMRP had the highest predictive value. Calretinin is a useful biomarker that can distinguish MM from other asbestos-related diseases and could, therefore, contribute to an earlier non-invasive diagnosis of MM.