bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic data sharing and artificial intelligence in the era of personalized medicine based on a cross‐sectional analysis of the Saudi human genome program
Authors: Alrefaei Abdulmajeed F. , Hawsawi Yousef M. , Almaleki Deyab , Alafif Tarik , Alzahrani Faisal A. , Bakhrebah Muhammed A. 
Published: January 2022

AbstractThe success of the Saudi Human Genome Program (SHGP), one of the top ten genomic programs worldwide, is highly dependent on the Saudi population embracing the concept of participating in genetic testing. However, genetic data sharing and artificial intelligence (AI) in genomics are critical public issues in medical care and scientific research. The present study was aimed to examine the awareness, knowledge, and attitude of the Saudi society towards the SHGP, the sharing and privacy of genetic data resulting from the SHGP, and the role of AI in genetic data analysis and regulations. Results of a questionnaire survey with 804 respondents revealed moderate awareness and attitude towards the SHGP and minimal knowledge regarding its benefits and applications. Respondents demonstrated a low level of knowledge regarding the privacy of genetic data. A generally positive attitude was found towards the outcomes of the SHGP and genetic data sharing for medical and scientific research. The highest level of knowledge was detected regarding AI use in genetic data analysis and privacy regulation. We recommend that the SHGP’s regulators launch awareness campaigns and educational programs to increase and improve public awareness and knowledge regarding the SHGP’s benefits and applications. Furthermore, we propose a strategy for genetic data sharing which will facilitate genetic data sharing between institutions and advance Personalized Medicine in genetic diseases’ diagnosis and treatment.
COVID-19 reinfections among naturally infected and vaccinated individuals
Authors: Rahman Sezanur , Rahman M. Mahfuzur , Miah Mojnu , Begum Mst Noorjahan , Sarmin Monira , Mahfuz Mustafa , Hossain Mohammad Enayet , Rahman Mohammed Ziaur , Chisti Mohammod Jobayer , Ahmed Tahmeed , Arifeen Shams El , Rahman Mustafizur 
Published: January 2022

AbstractThe protection against emerging SARS-CoV-2 variants by pre-existing antibodies elicited due to the current vaccination or natural infection is a global concern. We aimed to investigate the rate of SARS-CoV-2 infection and its clinical features among infection-naïve, infected, vaccinated, and post-infection-vaccinated individuals. A cohort was designed among icddr,b staff registered for COVID-19 testing by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). Reinfection cases were confirmed by whole-genome sequencing. From 19 March 2020 to 31 March 2021, 1644 (mean age, 38.4 years and 57% male) participants were enrolled; where 1080 (65.7%) were tested negative and added to the negative cohort. The positive cohort included 750 positive patients (564 from baseline and 186 from negative cohort follow-up), of whom 27.6% were hospitalized and 2.5% died. Among hospitalized patients, 45.9% had severe to critical disease and 42.5% required oxygen support. Hypertension and diabetes mellitus were found significantly higher among the hospitalised patients compared to out-patients; risk ratio 1.3 and 1.6 respectively. The risk of infection among positive cohort was 80.2% lower than negative cohort (95% CI 72.6–85.7%; p < 0.001). Genome sequences showed that genetically distinct SARS-CoV-2 strains were responsible for reinfections. Naturally infected populations were less likely to be reinfected by SARS-CoV-2 than the infection-naïve and vaccinated individuals. Although, reinfected individuals did not suffer severe disease, a remarkable proportion of naturally infected or vaccinated individuals were (re)-infected by the emerging variants.
GLUT3 inhibitor discovery through in silico ligand screening and in vivo validation in eukaryotic expression systems
Authors: Iancu Cristina V. , Bocci Giovanni , Ishtikhar Mohd , Khamrai Moumita , Oreb Mislav , Oprea Tudor I. , Choe Jun-yong 
Published: January 2022

AbstractThe passive transport of glucose and related hexoses in human cells is facilitated by members of the glucose transporter family (GLUT, SLC2 gene family). GLUT3 is a high-affinity glucose transporter primarily responsible for glucose entry in neurons. Changes in its expression have been implicated in neurodegenerative diseases and cancer. GLUT3 inhibitors can provide new ways to probe the pathophysiological role of GLUT3 and tackle GLUT3-dependent cancers. Through in silico screening of an ~ 8 million compounds library against the inward- and outward-facing models of GLUT3, we selected ~ 200 ligand candidates. These were tested for in vivo inhibition of GLUT3 expressed in hexose transporter-deficient yeast cells, resulting in six new GLUT3 inhibitors. Examining their specificity for GLUT1-5 revealed that the most potent GLUT3 inhibitor (G3iA, IC50 ~ 7 µM) was most selective for GLUT3, inhibiting less strongly only GLUT2 (IC50 ~ 29 µM). None of the GLUT3 inhibitors affected GLUT5, three inhibited GLUT1 with equal or twofold lower potency, and four showed comparable or two- to fivefold better inhibition of GLUT4. G3iD was a pan-Class 1 GLUT inhibitor with the highest preference for GLUT4 (IC50 ~ 3.9 µM). Given the prevalence of GLUT1 and GLUT3 overexpression in many cancers and multiple myeloma’s reliance on GLUT4, these GLUT3 inhibitors may discriminately hinder glucose entry into various cancer cells, promising novel therapeutic avenues in oncology.
A structured ICA-based process for removing auditory evoked potentials
Authors: Ross Jessica M. , Ozdemir Recep A. , Lian Shu Jing , Fried Peter J. , Schmitt Eva M. , Inouye Sharon K. , Pascual-Leone Alvaro , Shafi Mouhsin M. 
Published: January 2022

AbstractTranscranial magnetic stimulation (TMS)-evoked potentials (TEPs), recorded using electroencephalography (EEG), reflect a combination of TMS-induced cortical activity and multi-sensory responses to TMS. The auditory evoked potential (AEP) is a high-amplitude sensory potential—evoked by the “click” sound produced by every TMS pulse—that can dominate the TEP and obscure observation of other neural components. The AEP is peripherally evoked and therefore should not be stimulation site specific. We address the problem of disentangling the peripherally evoked AEP of the TEP from components evoked by cortical stimulation and ask whether removal of AEP enables more accurate isolation of TEP. We hypothesized that isolation of the AEP using Independent Components Analysis (ICA) would reveal features that are stimulation site specific and unique individual features. In order to improve the effectiveness of ICA for removal of AEP from the TEP, and thus more clearly separate the transcranial-evoked and non-specific TMS-modulated potentials, we merged sham and active TMS datasets representing multiple stimulation conditions, removed the resulting AEP component, and evaluated performance across different sham protocols and clinical populations using reduction in Global and Local Mean Field Power (GMFP/LMFP) and cosine similarity analysis. We show that removing AEPs significantly reduced GMFP and LMFP in the post-stimulation TEP (14 to 400 ms), driven by time windows consistent with the N100 and P200 temporal characteristics of AEPs. Cosine similarity analysis supports that removing AEPs reduces TEP similarity between subjects and reduces TEP similarity between stimulation conditions. Similarity is reduced most in a mid-latency window consistent with the N100 time-course, but nevertheless remains high in this time window. Residual TEP in this window has a time-course and topography unique from AEPs, which follow-up exploratory analyses suggest could be a modulation in the alpha band that is not stimulation site specific but is unique to individual subject. We show, using two datasets and two implementations of sham, evidence in cortical topography, TEP time-course, GMFP/LMFP and cosine similarity analyses that this procedure is effective and conservative in removing the AEP from TEP, and may thus better isolate TMS-evoked activity. We show TEP remaining in early, mid and late latencies. The early response is site and subject specific. Later response may be consistent with TMS-modulated alpha activity that is not site specific but is unique to the individual. TEP remaining after removal of AEP is unique and can provide insight into TMS-evoked potentials and other modulated oscillatory dynamics.
Adsorption behaviors and mechanisms of Cu2+, Zn2+ and Pb2+ by magnetically modified lignite
Authors: Di Junzhen , Ruan Zhen , Zhang Siyi , Dong Yanrong , Fu Saiou , Li Hanzhe , Jiang Guoliang 
Published: January 2022

AbstractThe study aims to solve the problems of limited capacity and difficult recovery of lignite to adsort Cu2+, Zn2+ and Pb2+ in acid mine wastewater (AMD). Magnetically modified lignite (MML) was prepared by the chemical co-precipitation method. Static beaker experiments and dynamic continuous column experiments were set up to explore the adsorption properties of Cu2+, Zn2+ and Pb2+ by lignite and MML. Lignite and MML before and after the adsorption of heavy metal ions were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD) and Fourier transform infrared spectrometer (FTIR). Meanwhile, the adsorption mechanisms of Cu2+, Zn2+ and Pb2+ by lignite and MML were revealed by combining the adsorption isotherm model and the adsorption kinetics model. The results showed that the pH, adsorbent dosage, temperature, initial concentration of heavy metal ions, and contact time had an influence on the adsorption of Cu2+, Zn2+ and Pb2+ by lignite and MML, and the adsorption processes were more in line with the Langmuir model. The adsorption kinetics experiments showed that the adsorption processes were jointly controlled by multiple adsorption stages. The adsorption of heavy metal ions by lignite obeyed the Quasi first-order kinetic model, while the adsorption of MML was chemisorption that obeyed the Quasi second-order kinetic model. The negative ΔG and positive ΔH of Cu2+ and Zn2+ indicated the spontaneous and endothermic nature reaction, while the negative ΔH of Pb2+ indicated the exothermic nature reaction. The dynamic continuous column experiments showed that the average removal rates of Cu2+, Zn2+ and Pb2+ by lignite were 78.00, 76.97 and 78.65%, respectively, and those of heavy metal ions by MML were 82.83, 81.57 and 83.50%, respectively. Compared with lignite, the adsorption effect of MML was better. As shown by SEM, XRD and FTIR tests, Fe3O4 was successfully loaded on the surface of lignite during the magnetic modification, which made the surface morphology of lignite coarser. Lignite and MML removed Cu2+, Zn2+ and Pb2+ from AMD in different forms. In addition, the adsorption process of MML is related to the O–H stretching vibration of carboxylic acid ions and the Fe–O stretching vibration of Fe3O4 particles.
Trimethyloxonium-mediated methylation strategies for the rapid and simultaneous analysis of chlorinated phenols in various soils by electron impact gas chromatography–mass spectrometry
Authors: Valdez Carlos A. , Salazar Edmund P. , Leif Roald N. 
Published: January 2022

AbstractThe efficient methylation of a panel of five industrial and environmentally-relevant chlorophenols (CPs) employing trimethyloxonium tetrafluoroborate (TMO) for their qualitative detection and identification by electron impact gas chromatography–mass spectrometry (EI-GC–MS) is presented. The protocol’s execution is simple and smoothly converts the phenols into their O-methylated counterparts conveniently at ambient temperature. The efficiency of two versions of the protocol was successfully tested in their ability to simultaneously derivatize five CPs (2-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, pentachlorophenol and triclosan) in six distinct, separate soil matrices (Nebraska EPA standard soil, Virginia Type A soil, Ottawa sand, Baker sand, Silt and Georgia EPA standard soil) when present at low levels (~ 10 μgg−1). The first version involves the direct derivatization of the spiked soils with the methylating salt while the second one involves an initial soil extraction step of the CPs followed by methylation. The MDL values for each methylated CP were determined and lower values were found (4.1–13.2 ng.mL−1) for both sand matrices (Ottawa and Baker) as well as for the Georgia EPA standard soil, while larger values (8.2–21.8 ng.mL−1) were found for the Virginia Type soil, Nebraska EPA standard soil and Silt. The presented protocol offers a safer and more practical alternative to the universally employed diazomethane method and can be readily applicable to matrices other than soils. Furthermore, the protocols described herein may find applicability to the methylation of other analytes bearing acidic protons.
Intrinsic topological magnons in arrays of magnetic dipoles
Authors: Mellado Paula 
Published: January 2022

AbstractWe study a simple magnetic system composed of periodically modulated magnetic dipoles with an easy axis. Upon adjusting the geometric modulation amplitude alone, chains and two-dimensional stacked chains exhibit a rich magnon spectrum where frequency gaps and magnon speeds are easily manipulable. The blend of anisotropy due to dipolar interactions between magnets and geometrical modulation induces a magnetic phase with fractional Zak number in infinite chains and end states in open one-dimensional systems. In two dimensions it gives rise to topological modes at the edges of stripes. Tuning the amplitude in two-dimensional lattices causes a band touching, which triggers the exchange of the Chern numbers of the volume bands and switches the sign of the thermal conductivity.
Nematode community structure along elevation gradient in high altitude vegetation cover of Gangotri National Park (Uttarakhand), India
Authors: Kashyap Priyanka , Afzal Shahid , Rizvi Anjum Nasreen , Ahmad Wasim , Uniyal V. P. , Banerjee Dhriti 
Published: January 2022

AbstractThe study was undertaken to understand the dynamics of soil nematode communities association along elevation gradient and associated variables in high-altitude regions of Western Himalaya. The diversity and distribution pattern of soil nematodes were investigated at four elevation ranges (Elv1, Elv2, Elv3, and Elv4 each of 500 m class) along altitudinal gradient (3000–5000 m). The nematode community comprised 58 genera of which 37 genera showed sensitivity towards altitudinal variation and the community structure also varied among elevation classes. It was found that elevation significantly affect the nematodes trophic group, diversity composition, and the nematode indices. Nematode generic richness and evenness index indicated a relatively low biodiversity of soil nematodes is supported at higher altitudes. Moreover, maturity indices reflected lower sustenance of k-strategic nematodes at higher elevations. Structure index depicted fewer connections in the soil food web at higher elevations. Nematode faunal profile showed low nutrient and low disturbance in the region. Carbon footprint of the whole nematode assemblage declined along the elevation. Overall substantial differences in the nematode composition, abundance, trophic structure, and contribution to belowground carbon cycling were observed with change in elevation. These findings could be utilized as useful tool in the long-term monitoring and to understand the region's soil health.
Multiple soil map comparison highlights challenges for predicting topsoil organic carbon concentration at national scale
Authors: Feeney C. J. , Cosby B. J. , Robinson D. A. , Thomas A. , Emmett B. A. , Henrys P. 
Published: January 2022

AbstractSoil organic carbon (SOC) concentration is the fundamental indicator of soil health, underpinning food production and climate change mitigation. SOC storage is highly sensitive to several dynamic environmental drivers, with approximately one third of soils degraded and losing carbon worldwide. Digital soil mapping illuminates where hotspots of SOC storage occur and where losses to the atmosphere are most likely. Yet, attempts to map SOC often disagree. Here we compare national scale SOC concentration map products to reveal agreement of data in mineral soils, with progressively poorer agreement in organo-mineral and organic soils. Divergences in map predictions from each other and survey data widen in the high SOC content land types we stratified. Given the disparities are highest in carbon rich soils, efforts are required to reduce these uncertainties to increase confidence in mapping SOC storage and predicting where change may be important at national to global scales. Our map comparison results could be used to identify SOC risk where concentrations are high and should be conserved, and where uncertainty is high and further monitoring should be targeted. Reducing inter-map uncertainty will rely on addressing statistical limitations and including covariates that capture convergence of physical factors that produce high SOC contents.
Effects of motion paradigm on human perception of tilt and translation
Authors: Clément Gilles , Beaton Kara H. , Reschke Millard F. , Wood Scott J. 
Published: January 2022

AbstractThe effect of varying sinusoidal linear acceleration on perception of human motion was examined using 4 motion paradigms: off-vertical axis rotation, variable radius centrifugation, linear lateral translation, and rotation about an earth-horizontal axis. The motion profiles for each paradigm included 6 frequencies (0.01–0.6 Hz) and 5 tilt amplitudes (5°–20°). Subjects verbally reported the perceived angle of their whole-body tilt and the peak-to-peak translation of their head in space and used a joystick capable of recording 2-axis motion in the sagittal and transversal planes to indicate the phase between the perceived and actual motions. The amplitudes of perceived tilt and translation were expressed in terms of gain, i.e., the ratio of perceived tilt to equivalent tilt angle, and the ratio of perceived translation to equivalent linear displacement. Tilt perception gain decreased, whereas translation perception gain increased, with increasing frequency. During off-vertical axis rotation, the phase of tilt perception and of translation perception did not vary across stimulus frequencies. These motion paradigms elicited similar responses in roll tilt and interaural perception of translation, with differences likely due to the influence of naso-occipital linear accelerations and input to the semicircular canals that varied across motion paradigms.
Modulation of miR-145-5p and miR-146b-5p levels is linked to reduced parasite load in H9C2 Trypanosoma cruzi infected cardiomyoblasts
Authors: Farani Priscila Silva Grijó , Ferreira Beatriz Iandra Silva , Gibaldi Daniel , Lannes-Vieira Joseli , Moreira Otacilio Cruz 
Published: January 2022

AbstractIn the heart tissue of acutely Trypanosoma cruzi-infected mice miR-145-5p and miR-146b-5p are, respectively, downregulated and upregulated. Here, we used the H9C2 rat cardiomyoblast cell line infected with the Colombian T. cruzi strain to investigate the parasite-host cell interplay, focusing on the regulation of miR-145-5p and miR-146b-5p expression. Next, we explored the effects of interventions with the trypanosomicidal drug Benznidazole (Bz) alone or combined with Pentoxifylline (PTX), a methylxanthine derivative shown to modulate immunological and cardiac abnormalities in a model of chronic chagasic cardiomyopathy, on parasite load and expression of miR-145-5p and miR-146b-5p. The infection of H9C2 cells with trypomastigote forms allowed parasite cycle with intracellular forms multiplication and trypomastigote release. After 48 and 144 h of infection, upregulation of miR-145-5p (24 h: 2.38 ± 0.26; 48 h: 3.15 ± 0.9-fold change) and miR-146b-5b (24 h: 2.60 ± 0.46; 48 h: 2.97 ± 0.23-fold change) was detected. The peak of both miRNA levels paralleled with release of trypomastigote forms. Addition of 3 µM and 10 µM of Bz 48 h after infection reduced parasite load but did not interfere with miR-145-5p and miR-146b-5p levels. Addition of PTX did not interfere with Bz-induced parasite control efficacy. Conversely, combined Bz + PTX treatment decreased the levels of both microRNAs, resembling the expression levels detected in non-infected H9C2 cells. Moreover, the use of miR-145-5p and miR-146b-5p mimic/inhibitor systems before infection of H9C2 cells decreased parasite load, 72 h postinfection. When H9C2 cells were treated with miR-145-5p and miR-146b-5p mimic/inhibitor 48 h after infection, all the used systems, except the miR-146b-5p inhibitor, reduced parasite load. Altogether, our data indicate that these microRNAs putatively control signaling pathways crucial for parasite–host cell interaction. Thus, miR-145-5p and miR-146b-5p deserve to be further investigated as biomarkers of parasite control and tools to identify therapeutic adjuvants to etiological treatment in Chagas disease.
The association between steps per day and blood pressure in children
Authors: Weres Aneta , Baran Joanna , Czenczek-Lewandowska Ewelina , Leszczak Justyna , Mazur Artur 
Published: January 2022

AbstractLower levels of physical activity are associated with an increased overall cardiometabolic risk, as well as the risk or being overweight. It is difficult to determine the optimal level of physical activity that protects the needs of children and young people. Studies on the required number of steps, as well as approximating the daily volume of physical activity, are gaining increasing credibility in research and practice. Researchers propose a "rule" of ≥ 11,500 steps per day, for children and teenagers of both sexes. The aim of the study was to assess whether 11,500 steps a day is sufficient to maintain normal blood pressure among children and adolescents. 1002 children and adolescents aged 4–15 were included in the study. To assess physical activity, measured in the number of steps per day, the Actigraph accelerometer wGT3X-BT was used. The normal number of steps was defined as greater than or equal to 11,500 steps per day for children and teenagers, for both girls and boys. In the entire study group, a significantly lower risk of hypertension was observed when the number of steps was normal (OR is 0.45 and the upper confidence limit for OR is 0.71). The study confirmed the beneficial protective role of physical activity against hypertension in older children and adolescents. However, it should be emphasized that no such relationship has been demonstrated in the case of preschool children. The presented norms of the number of steps should be promoted to the wider community to make prevention of cardiovascular diseases even more effective.