bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing the interpretability of transcription factor binding site prediction using attention mechanism
Authors: Park Sungjoon , Koh Yookyung , Jeon Hwisang , Kim Hyunjae , Yeo Yoonsun , Kang Jaewoo
Published: August 2020

Transcription factors (TFs) regulate the gene expression of their target genes by binding to the regulatory sequences of target genes (e.g., promoters and enhancers). To fully understand gene regulatory mechanisms, it is crucial to decipher the relationships between TFs and DNA sequences. Moreover, studies such as GWAS and eQTL have verified that most disease-related variants exist in non-coding regions, and highlighted the necessity to identify such variants that cause diseases by interrupting TF binding mechanisms. To do this, it is necessary to build a prediction model that precisely predicts the binding relationships between TFs and DNA sequences. Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is difficult to interpret the prediction results obtained from the previous models. In addition, the previous models assumed all the sequence regions in the input DNA sequence have the same importance for predicting TF-binding, although sequence regions containing TF-binding-associated signals such as TF-binding motifs should be captured more than other regions. To address these challenges, we propose TBiNet, an attention based interpretable deep neural network for predicting transcription factor binding sites. Using the attention mechanism, our method is able to assign more importance on the actual TF binding sites in the input DNA sequence. TBiNet outperforms the current state-of-the-art methods (DeepSea and DanQ) quantitatively in the TF-DNA binding prediction task. Moreover, TBiNet is more effective than the previous models in discovering known TF-binding motifs.
A single unified model for fitting simple to complex receptor response data
Authors: Buchwald Peter
Published: August 2020

The fitting of complex receptor-response data where fractional response and occupancy do not match is challenging. They encompass important cases including (a) the presence of “receptor reserve” and/or partial agonism, (b) multiple responses assessed at different vantage points along a pathway, (c) responses that are different along diverging downstream pathways (biased agonism), and (d) constitutive activity. For these, simple models such as the well-known Clark or Hill equations cannot be used. Those that can, such as the operational (Black&Leff) model, do not provide a unified approach, have multiple nonintuitive parameters that are challenging to fit in well-defined manner, have difficulties incorporating binding data, and cannot be reduced or connected to simpler forms. We have recently introduced a quantitative receptor model (SABRE) that includes parameters for Signal Amplification (γ), Binding affinity (Kd), Receptor activation Efficacy (ε), and constitutive activity (εR0). It provides a single equation to fit complex cases within a full two-state framework with the possibility of incorporating receptor occupancy data (i.e., experimental Kds). Simpler cases can be fit by using consecutively reduced forms obtained by constraining parameters to specific values, e.g., εR0 = 0: no constitutive activity, γ = 1: no amplification (Emax-type fitting), and ε = 1: no partial agonism (Clark equation). Here, a Hill-type extension is introduced (n ≠ 1), and simulated and experimental receptor-response data from simple to increasingly complex cases are fitted within the unified framework of SABRE with differently constrained parameters.
Update analysis on the association between Methionine synthase rs1805087 A/G variant and risk of prostate cancer
Authors: Zhang Wei , Zhang Ze , Wu Hao , Xu Kai , Yuan Wei , Mi Yuan-Yuan , Shi Li , Zuo Li , Shi Yun-Feng
Published: August 2020

Previous studies have investigated the association of the rs1805087 A/G variant ofMethionine synthasegene with the susceptibility to prostate cancer (PCa). Nevertheless, the conclusions remain divergent. We performed a systemic analysis with odds ratios (ORs) and 95% confidence intervals (95% CIs) to assessMethionine synthasers1805087 A/G variant and PCa risk. Furthermore, we utilized in silico analysis to investigate the relationship betweenMethionine synthaseexpression and the overall survival (OS) time. Totally, 10,666 PCa patients and 40,750 controls were included. We observed thatMethionine synthasers1805087 A/G variant is associated with an elevated risk of PCa (G-allele vs. A-allele: OR = 1.06, 95% CI = 1.01–1.11,P = 0.013; heterozygous model: OR = 1.08, 95% CI = 1.02–1.14,P = 0.009; dominant model: OR = 1.08, 95% CI = 1.02–1.14,P = 0.007). During stratified analysis, similar results were obtained in Asian populations, hospital-based, high quality studies and that with large sample size. Moreover, in silico analysis indicated theMethionine synthaseexpression is down-regulated in both young and old PCa subjects (P < 0.05). Compared with the normal subjects, the down-regulated expression ofMethionine synthasewas found in PCa cases with Gleason score 6 to 9. Our study showed thatMethionine synthasers1805087 A/G variant may be associated with susceptibility of PCa, especially in Asian populations, hospital-based studies and that with high quality and large sample size. Furthermore,Methionine synthasers1805087 A/G variant may be related to the prognosis of PCa.
An ambient temperature collection and stabilization strategy for canine microbiota studies
Authors: Lin Ching-Yen , Cross Tzu-Wen L. , Doukhanine Evgueni , Swanson Kelly S.
Published: August 2020

Similar to humans, the fecal microbiome of dogs may be useful in diagnosing diseases or assessing dietary interventions. The accuracy and reproducibility of microbiome data depend on sample integrity, which can be affected by storage methods. Here, we evaluated the ability of a stabilization device to preserve canine fecal samples under various storage conditions simulating shipping in hot or cold climates. Microbiota data from unstabilized samples stored at room temperature (RT) and samples placed in PERFORMAbiome·GUT collection devices (PB-200) (DNA Genotek, Inc. Ottawa, Canada) and stored at RT, 37 °C, 50 °C, or undergoing repeated freeze–thaw cycles, were compared with freshly extracted samples. Alpha- and beta diversity indices were not affected in stabilized samples, regardless of storage temperature. Unstabilized samples stored at RT, however, had higher alpha diversity. Moreover, the relative abundance of dominant bacterial phyla (Firmicutes, Fusobacteria, Bacteriodetes, and Actinobacteria) and 24 genera were altered in unstabilized samples stored at RT, while microbiota abundance was not significantly changed in stabilized samples stored at RT. Our results suggest that storage method is important in microbiota studies and that the stabilization device may be useful in maintaining microbial profile integrity, especially for samples collected off-site and/or those undergoing temperature changes during shipment or storage.
Early-life stress affects drug abuse susceptibility in adolescent rat model independently of depression vulnerability
Authors: Alves Renata L. , Oliveira Pedro , Lopes Igor M. , Portugal Camila C. , Alves Cecília J. , Barbosa Fernando , Summavielle Teresa , Magalhães Ana
Published: August 2020

The development of substance abuse problems occurs due to a diverse combination of risk factors. Among these risks, studies have reported depression and early-life stress as of importance. These two factors often occur simultaneously, however, there is a lack of understanding of how their combined effect may impact vulnerability to drug abuse in adolescence. The present study used rats with different vulnerability to depression (Wistar and Wistar-Kyoto) to investigate the impact of maternal separation (MS) on emotional state and drug addiction vulnerability during the adolescence period. Mothers and their litters were subjected to MS (180 min/day) from postnatal day 2 to 14. The offspring emotional state was assessed by observing their exploratory behavior. Drug abuse vulnerability was assessed through conditioning to cocaine. MS impacted the emotional state in both strains. Wistar responded with increased exploration, while Wistar-Kyoto increased anxiety-like behaviours. Despite the different coping strategies displayed by the two strains when challenged with the behavioural tests, drug conditioning was equally impacted by MS in both strains. Early-life stress appears to affect drug abuse vulnerability in adolescence independently of a depression background, suggesting emotional state as the main driving risk factor.
Integrated structural and functional analysis of the protective effects of kinetin against oxidative stress in mammalian cellular systems
Authors: Naseem Muhammad , Othman Eman M. , Fathy Moustafa , Iqbal Jibran , Howari Fares M. , AlRemeithi Fatima A. , Kodandaraman Geema , Stopper Helga , Bencurova Elena , Vlachakis Dimitrios , Dandekar Thomas
Published: August 2020

Metabolism and signaling of cytokinins was first established in plants, followed by cytokinin discoveries in all kingdoms of life. However, understanding of their role in mammalian cells is still scarce. Kinetin is a cytokinin that mitigates the effects of oxidative stress in mammalian cells. The effective concentrations of exogenously applied kinetin in invoking various cellular responses are not well standardized. Likewise, the metabolism of kinetin and its cellular targets within the mammalian cells are still not well studied. Applying vitality tests as well as comet assays under normal and hyper-oxidative states, our analysis suggests that kinetin concentrations of 500 nM and above cause cytotoxicity as well as genotoxicity in various cell types. However, concentrations below 100 nM do not cause any toxicity, rather in this range kinetin counteracts oxidative burst and cytotoxicity. We focus here on these effects. To get insights into the cellular targets of kinetin mediating these pro-survival functions and protective effects we applied structural and computational approaches on two previously testified targets for these effects. Our analysis deciphers vital residues in adenine phosphoribosyltransferase (APRT) and adenosine receptor (A2A-R) that facilitate the binding of kinetin to these two important human cellular proteins. We finally discuss how the therapeutic potential of kinetin against oxidative stress helps in various pathophysiological conditions.
A versatile bulk electrotransfection protocol for murine embryonic fibroblasts and iPS cells
Authors: Eghbalsaied Shahin , Hyder Iqbal , Kues Wilfried A.
Published: August 2020

Although electroporation has been widely accepted as the main gene transfer tool, there is still considerable scope to improve the electroporation efficiency of exogenous DNAs into primary cells. Here, we developed a square-wave pulsing protocol using OptiMEM-GlutaMAX for highly efficient transfection of murine embryonic fibroblasts (MEF) and induced pluripotency stem (iPS) cells using reporter genes as well as gRNA/Cas9-encoding plasmids. An electrotransfection efficiency of > 95% was achieved for both MEF and iPS cells using reporter-encoding plasmids. The protocol was efficient for plasmid sizes ranging from 6.2 to 13.5 kb. Inducing the error prone non-homologous end joining repair by gRNA/Cas9 plasmid transfection, a high rate of targeted gene knockouts of up to 98% was produced in transgenic cells carrying a single-copy of Venus reporter. Targeted deletions in the Venus transgene were efficiently (up to 67% deletion rate) performed by co-electroporation of two gRNA-encoding plasmids. We introduced a plasmid electrotransfection protocol which is straight-forward, cost-effective, and efficient for CRISPRing murine primary cells. This protocol is promising to make targeted genetic engineering using the CRISPR/Cas9 plasmid system.
liputils: a Python module to manage individual fatty acid moieties from complex lipids
Authors: Manzini Stefano , Busnelli Marco , Colombo Alice , Kiamehr Mostafa , Chiesa Giulia
Published: August 2020

Lipidomic analyses address the problem of characterizing the lipid components of given cells, tissues and organisms by means of chromatographic separations coupled to high-resolution, tandem mass spectrometry analyses. A number of software tools have been developed to help in the daunting task of mass spectrometry signal processing and cleaning, peak analysis and compound identification, and a typical finished lipidomic dataset contains hundreds to thousands of individual molecular lipid species. To provide researchers without a specific technical expertise in mass spectrometry the possibility of broadening the exploration of lipidomic datasets, we have developed liputils, a Python module that specializes in the extraction of fatty acid moieties from individual molecular lipids. There is no prerequisite data format, as liputils extracts residues from RefMet-compliant textual identifiers and from annotations of other commercially available services. We provide three examples of real-world data processing with liputils, as well as a detailed protocol on how to readily process an existing dataset that can be followed with basic informatics skills.
A randomized, double-blind water taste test to evaluate the equivalence of taste between tap water and filtered water in the Taipei metropolis
Authors: Jhuang Jing-Rong , Lee Wen-Chung , Chan Chang-Chuan
Published: August 2020

High water quality and sufficient water availability are the main concerns of water users. Promoting the efficient use of tap water can contribute to sustainable drinking water management and progress towards Sustainable Development Goals. In many metropolises, water suppliers treat municipal water with appropriate treatment processes and well-maintained distribution infrastructure. Under this circumstance, it is acceptable that municipal water can be a source of drinking water. The presence of residual chlorine in tap water, connected to municipal water supply, inactivates pathogenic microorganisms and prevents recontamination. However, adding chlorine to tap water may affect the organoleptic properties of drinking water. On the other hand, the use of point-of-use (POU) water dispensers, which provides an additional treatment step on tap water, is not energy-efficient. A randomized, double-blind water taste test was conducted in the Taipei metropolis to assess whether tap water from public drinking fountains and filtered water from POU water dispensers have similar organoleptic properties. An odds ratio (OR) and the area under the receiver operating characteristic curve (AUC) were used to measure the participants’ ability to distinguish between the two water varieties. A five-region hypothesis test was conducted to test the OR, and a 95% bootstrap confidence interval of the AUC was calculated. The results of the study showed that the 95% five-region confidence interval of OR equal to (0.5, 1.49), and the 95% bootstrap confidence interval of AUC equal to (0.42, 0.56). These results implied that people in the Taipei metropolis could not distinguish between tap water and filtered water. It is recommended that more drinking fountains be installed and maintained fully functional and clean to achieve excellence in tap water access.
Marine heatwaves and the collapse of marginal North Atlantic kelp forests
Authors: Filbee-Dexter K. , Wernberg T. , Grace S. P. , Thormar J. , Fredriksen S. , Narvaez C. N. , Feehan C. J. , Norderhaug K. M.
Published: August 2020

Extreme climatic events including marine heatwaves (MHWs) are becoming more frequent and severe in the Anthropocene. However, our understanding of how these events affect population dynamics of ecologically important species is limited, in part because extreme events are rare and difficult to predict. Here, we quantified the occurrence and severity of MHWs over 60 years in warm range edge kelp forests on both sides of the North Atlantic. The cumulative annual intensity of MHWs increased two- to four-fold during this period, coinciding with the disappearance of kelps. We experimentally demonstrated a relationship between strong and severe 2018 heatwaves and high kelp mortality in both regions. Patterns of kelp mortality were strongly linked to maximum temperature anomalies, which crossed lethal thresholds in both regions. Translocation and tagging experiments revealed similar kelp mortality rates on reefs dominated by healthy kelp forests and degraded sediment-laden algal ‘turfs’, indicating equal vulnerability to extreme events. These results suggest a mechanistic link between MHWs and broad-scale kelp loss, and highlight how warming can make ecosystem boundaries unstable, forcing shifts to undesirable ecosystem states under episodically extreme climatic conditions.
NOTCH2 participates in Jagged1-induced osteogenic differentiation in human periodontal ligament cells
Authors: Manokawinchoke Jeeranan , Sumrejkanchanakij Piyamas , Boonprakong Lawan , Pavasant Prasit , Egusa Hiroshi , Osathanon Thanaphum
Published: August 2020

Jagged1 activates Notch signaling and subsequently promotes osteogenic differentiation in human periodontal ligament cells (hPDLs). The present study investigated the participation of the Notch receptor, NOTCH2, in the Jagged1-induced osteogenic differentiation in hPDLs. NOTCH2 and NOTCH4 mRNA expression levels increased during hPDL osteogenic differentiation. However, the endogenous NOTCH2 expression levels were markedly higher compared with NOTCH4. NOTCH2 expression knockdown using shRNA in hPDLs did not dramatically alter their proliferation or osteogenic differentiation compared with the shRNA control. After seeding on Jagged1-immobilized surfaces and maintaining the hPDLs in osteogenic medium, HES1 and HEY1 mRNA levels were markedly reduced in the shNOTCH2-transduced cells compared with the shControl group. Further, shNOTCH2-transduced cells exhibited less alkaline phosphatase enzymatic activity and in vitro mineralization than the shControl cells when exposed to Jagged1. MSX2 and COL1A1 mRNA expression after Jagged1 activation were reduced in shNOTCH2-transduced cells. Endogenous Notch signaling inhibition using a γ-secretase inhibitor (DAPT) attenuated mineralization in hPDLs. DAPT treatment significantly promoted TWIST1, but decreased ALP, mRNA expression, compared with the control. In conclusion, Notch signaling is involved in hPDL osteogenic differentiation. Moreover, NOTCH2 participates in the mechanism by which Jagged1 induced osteogenic differentiation in hPDLs.
Glass shape influences drinking behaviours in three laboratory experiments
Authors: Langfield Tess , Pechey Rachel , Gilchrist Philippe T. , Pilling Mark , Marteau Theresa M.
Published: August 2020

Reducing consumption of drinks which contain high levels of sugar and/or alcohol may improve population health. There is increasing interest in health behaviour change approaches which work by changing cues in physical environments (“nudges”). Glassware represents a modifiable cue in the drinking environment that may influence how much we drink. Here, we report three laboratory experiments measuring consumption of soft drinks served in different glasses (straight-sided vs. outward-sloped), using distinct paradigms to measure drinking. In Study 1 (N = 200), though total drinking time was equivalent, participants consumed a soft drink with a more ‘decelerated’ trajectory from outward-sloped tumblers, characterised by a greater amount consumed in the first half of the drinking episode. In Study 2 (N = 72), during a bogus taste test, participants consumed less from straight-sided wine flutes than outward-sloped martini coupes. In Study 3 (N = 40), using facial electromyography to explore a potential mechanism for decreased consumption, straight-sided glasses elicited more ‘pursed’ lip embouchures, which may partly explain reduced consumption from these glasses. Using a combination of methods, including objective measures of volume drunk and physiological measures, these findings suggest that switching to straight-sided glasses may be one intervention contributing to the many needed to reduce consumption of health-harming drinks.
Spectral photon-counting CT imaging of colorectal peritoneal metastases: initial experience in rats
Authors: Thivolet Arnaud , Si-Mohamed Salim , Bonnot Pierre-Emmanuel , Blanchet Christophe , Képénékian Vahan , Boussel Loïc , Douek Philippe , Rousset Pascal
Published: August 2020

Computed tomography imaging plays a major role in the preoperative assessment of tumor burden by providing an accurate mapping of the distribution of peritoneal metastases (PM). Spectral Photon Counting Computed Tomography (SPCCT) is an innovative imaging modality that could overcome the current limitations of conventional CT, offering not only better spatial resolution but also better contrast resolution by allowing the discrimination of multiple contrast agents. Based on this capability, we tested the feasibility of SPCCT in the detection of PM at different time of tumor growth in 16 rats inoculated with CC531 cells using dual-contrast injection protocols in two compartments (i.e. intravenous iodine and intraperitoneal gadolinium or the reverse protocol), compared to surgery. For all peritoneal regions and for both protocols, sensitivity was 69%, specificity was 100% and accuracy was 80%, and the correlation with surgical exploration was strong (p = 0.97; p = 0.0001). No significant difference was found in terms of diagnostic performance, quality of peritoneal opacification or diagnostic quality between the 2 injection protocols. We also showed poor vascularization of peritoneal metastases by measuring low concentrations of contrast agent in the largest lesions using SPCCT, which was confirmed by immunohistochemical analyses. In conclusion, SPCCT using dual-contrast agent injection protocols in 2 compartments is a promising imaging modality to assess the extent of PM in a rat model.
Thermal niche helps to explain the ability of dung beetles to exploit disturbed habitats
Authors: Giménez Gómez Victoria C. , Verdú José R. , Zurita Gustavo A.
Published: August 2020

In terrestrial ecosystems, insects face a wide range of temperatures among habitats and time; consequently, the thermal niche is one of the main determinants of habitat selection and temporal patterns of activity. The replacement of native forests changes micro-climatic conditions and reduces the diversity of dung beetles; however, the physiological mechanisms behind these changes are not clear. We explore the role of the thermal niche in dung beetles to explain the ability of native species to exploit human-created habitats. Using infrared thermography, we measured variables associated with the thermal niche in 17 native species and used linear mixed-effects model and ANOVAs to compare disturbed habitats and the native forest. Endothermy and body mass explained the ability of dung beetles to exploit human-created open habitats. Small and diurnal species with very low endothermy were able to exploit deforested open habitats; evening/nocturnal/crepuscular species showed similar body mass and high endothermy in all habitats. Regarding thermoregulation mechanisms, none of the species (except one) showed defined or efficient mechanisms of physiological thermoregulation. In view of the accelerated process of forest replacement and climate change, a more profound understanding of the physiological requirements of species is essential to predict and mitigate future extinctions.
Granulocyte-macrophage colony stimulating factor (GM-CSF) is fully expressed in the genital tract, seminal plasma and spermatozoa of male pigs
Authors: Padilla Lorena , Martínez-Hernández Jesús , Barranco Isabel , Lucas Xiomara , Pastor Luis M. , Rodriguez-Martínez Heriberto , Roca Jordi , Parrilla Inmaculada
Published: August 2020

Granulocyte-macrophage colony stimulating factor (GM-CSF) is a pro-inflammatory cytokine identified in boar seminal plasma (SP) but until now unexplored in terms of place of production and its association to spermatozoa. This study aimed to explore these aspects by evaluating the presence of GM-CSF in porcine reproductive organs (testes, epididymis and accessory sex glands), SP and mature spermatozoa (from cauda epididymis and ejaculated) using Western blot (WB), immunohistochemistry and immunocytochemistry. Positive labelling was obtained in tissues, SP and spermatozoa. In reproductive organs, WB revealed three forms of GM-CSF with different glycosylation degrees (15, 31 and 40 kDa). In SP and epididymal fluid, the GM-CSF appeared only in its active form while in spermatozoa the GM-CSF form present varied among sperm sources. Non-viable spermatozoa showed more GM-CSF than viable spermatozoa (14.87 ± 1.98 RU vs. 7.25 ± 0.52 RU) of fluorescence intensity. In conclusion, GM-CSF is widely present in the reproductive tract of male pigs, attached to the spermatozoa already in the epididymis as well as verted to SP. Consequently, the GM-CSF ought to regulate male genital tract and sperm function as well as mediating initial inflammatory responses and further mediating later immune actions by the female to semen deposition.
Manganese-contaminated groundwater treatment by novel bacterial isolates: kinetic study and mechanism analysis using synchrotron-based techniques
Authors: Therdkiattikul Nakharin , Ratpukdi Thunyalux , Kidkhunthod Pinit , Chanlek Narong , Siripattanakul-Ratpukdi Sumana
Published: August 2020

The occurrence of manganese in groundwater causes coloured water and pipe rusting in water treatment systems. Consumption of manganese-contaminated water promotes neurotoxicity in humans and animals. Manganese-oxidizing bacteria were isolated from contaminated areas in Thailand for removing manganese from water. The selected bacterium was investigated for its removal kinetics and mechanism using synchrotron-based techniques. Among 21 isolates, Streptomyces violarus strain SBP1 (SBP1) was the best manganese-oxidizing bacterium. At a manganese concentration of 1 mg L−1, SBP1 achieved up to 46% removal. The isolate also successfully removed other metal and metalloid, such as iron (81%) and arsenic (38%). The manganese concentration played a role in manganese removal and bacterial growth. The observed self-substrate inhibition best fit with the Aiba model. Kinetic parameters estimated from the model, including a specific growth rate, half-velocity constant, and inhibitory constant, were 0.095 h−1, 0.453 mg L−1, and 37.975 mg L−1, respectively. The synchrotron-based techniques indicated that SBP1 removed manganese via combination of bio-oxidation (80%) and adsorption (20%). The study is the first report on biological manganese removal mechanism using synchrotron-based techniques. SBP1 effectively removed manganese under board range of manganese concentrations. This result showed the potential use of the isolate for treating manganese-contaminated water.
Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma
Authors: Singh Prithvi , Sharma Archana , Jha Rishabh , Arora Shweta , Ahmad Rafiq , Rahmani Arshad Husain , Almatroodi Saleh A. , Dohare Ravins , Syed Mansoor Ali
Published: August 2020

Asthma is a multifarious disease affecting several million people around the world. It has a heterogeneous risk architecture inclusive of both genetic and environmental factors. This heterogeneity can be utilised to identify differentially expressed biomarkers of the disease, which may ultimately aid in the development of more localized and molecularly targeted therapies. In this respect, our study complies with meta-analysis of microarray datasets containing mRNA expression profiles of both asthmatic and control patients, to identify the critical Differentially Expressed Genes (DEGs) involved in the pathogenesis of asthma. We found a total of 30 DEGs out of which 13 were involved in the pathway and functional enrichment analysis. Moreover, 5 DEGs were identified as the hub genes by network centrality-based analysis. Most hub genes were involved in protease/antiprotease pathways. Also, 26 miRNAs and 20 TFs having an association with these hub genes were found to be intricated in a 3-node miRNA Feed-Forward Loop. Out of these, miR-34b and miR-449c were identified as the key miRNAs regulating the expression of SERPINB2 gene and SMAD4 transcription factor. Thus, our study is suggestive of certain miRNAs and unexplored pathways which may pave a way to unravel critical therapeutic targets in asthma.
No association between proton pump inhibitor use and ALS risk: a nationwide nested case–control study
Authors: Cetin Hakan , Sun Jiangwei , Almqvist Catarina , Reichardt Berthold , Tomschik Matthias , Zimprich Fritz , Fang Fang , Ingre Caroline
Published: August 2020

The use of proton pump inhibitors (PPIs) has been proposed as a potential risk factor for neurodegenerative diseases, but little is known regarding its role in amyotrophic lateral sclerosis (ALS). We therefore aimed to assess the association of PPI use with the subsequent risk of ALS, and performed a register-based nationwide nested case–control study, including 2,484 ALS cases diagnosed during July 2006–December 2013 in Sweden and 10 population controls per case that were individually matched to the case by sex, age, and area of residence. Dispenses and cumulative defined daily doses (cDDDs) of PPIs were extracted from the Swedish Prescribed Drug Register. The association of PPI use with the risk of ALS was assessed using conditional logistic regression, after applying different lag windows to avoid reverse causation. ALS patients were more likely to be dispensed with PPIs before diagnosis than controls. However, previous PPI use was not associated with an increased risk of ALS (OR = 1.08, 95% CI 0.97–1.19), and there was no dose–response relationship between cDDDs of PPIs and ALS risk (p = 0.0874), after excluding dispenses during the year before ALS diagnosis. The results were similar after excluding dispenses during the 2 or 3 years before ALS diagnosis.
Characterization of complex fluvio–deltaic deposits in Northeast China using multi-modal machine learning fusion
Authors: Boateng Cyril D. , Fu Li-Yun , Danuor Sylvester K.
Published: August 2020

Due to the lack of petroleum resources, stratigraphic reservoirs have become an important source of future discoveries. We describe a methodology for predicting reservoir sands from complex reservoir seismic data. Data analysis involves a bio-integrated framework called multi-modal machine learning fusion (MMMLF) based on neural networks. First, acoustic-related seismic attributes from post-stack seismic data were used to characterize the reservoirs. They enhanced the understanding of the structure and spatial distribution of petrophysical properties of lithostratigraphic reservoirs. The attributes were then classified as varied modal inputs into a central fusion engine for prediction. We applied the method to a dataset from Northeast China. Using seismic attributes and rock physics relationships as input data, MMMLF was performed to predict the spatial distribution of lithology in the Upper Guantao substrata. Despite the large scattering in the acoustic-related data properties, the proposed MMMLF methodology predicted the distribution of lithological properties through the gamma ray logs. Moreover, complex stratigraphic traps such as braided fluvial sandstones in the fluvio–deltaic deposits were delineated. These findings can have significant implications for future exploration and production in Northeast China and similar petroleum provinces around the world.
Experimental and numerical investigations on the failure processes and mechanisms of composite coal–rock specimens
Authors: Gao Fuqiang , Kang Hongpu , Yang Lei
Published: August 2020

Brittle failure is a fundamental failure pattern in many different materials, from small nanoscale materials with single crystals to the large earth crust. Many efforts have been dedicated to understanding the brittle failure mechanisms of individual brittle and semi-brittle materials. Limited studies have been conducted on the brittle failure of composite materials with interaction and energy feedback between different materials. Here we investigated the brittle failure pattern of coal–rock composite materials under uniaxial compression by laboratory tests and numerical simulations. We used a high-speed camera to capture the failure of coal–rock specimens. For all three tested coal–rock combined specimens, the rock failed with a splitting pattern that resulted from a single tensile fracture that developed sub-parallel to the loading direction. We regarded this brittle failure as a sliding-induced tensile fracture from frictional drag that was caused by unequal lateral deformation of the rock and coal under identical axial loading. The tensile crack propagated stably at ~ 0.05 times the Rayleigh wave speed cR. We observed an unstable failure pattern of the coal samples that was characterized by the ejection of small pieces from the coal specimen surface. This behavior is attributed to the strain energy that is stored in the rock specimen, which releases when the coal fails. The excessive strain energy transitions into dynamic energy during coal failure. Our findings provide insight into the brittle failure mechanisms of composite materials and have significant implications at scales relevant to seismicity, engineering applications and geohazards.
A computational structural study on the DNA-protecting role of the tardigrade-unique Dsup protein
Authors: Mínguez-Toral Marina , Cuevas-Zuviría Bruno , Garrido-Arandia María , Pacios Luis F.
Published: August 2020

The remarkable ability of tardigrades to withstand a wide range of physical and chemical extremes has attracted a considerable interest in these small invertebrates, with a particular focus on the protective roles of proteins expressed during such conditions. The discovery that a tardigrade-unique protein named Dsup (damage suppressor) protects DNA from damage produced by radiation and radicals, has raised expectations concerning its potential applications in biotechnology and medicine. We present in this paper what might be dubbed a “computational experiment” on the Dsup-DNA system. By means of molecular modelling, calculations of electrostatic potentials and electric fields, and all-atom molecular dynamics simulations, we obtained a dynamic picture of the Dsup-DNA interaction. Our results suggest that the protein is intrinsically disordered, which enables Dsup to adjust its structure to fit DNA shape. Strong electrostatic attractions and high protein flexibility drive the formation of a molecular aggregate in which Dsup shields DNA. While the precise mechanism of DNA protection conferred by Dsup remains to be elucidated, our study provides some molecular clues of their association that could be of interest for further investigation in this line.
Hemispheric asymmetry in hand preference of right-handers for passive vibrotactile perception: an fNIRS study
Authors: Jin Sang Hyeon , Lee Seung Hyun , Yang Seung Tae , An Jinung
Published: August 2020

Hemispheric asymmetry in hand preference for passive cutaneous perception compared to active haptic perception is not well known. A functional near-infrared spectroscopy was used to evaluate the laterality of cortical facilitation when 31 normal right-handed participants were involved in 205 Hz passive vibrotactile cutaneous stimuli on their index fingers of preferred and less-preferred hand. Passive cutaneous perception resulted that preferred (right) hand stimulation was strongly leftward lateralized, whereas less-preferred (left) hand stimulation was less lateralized. This confirms that other manual haptic exploration studies described a higher hemispheric asymmetry in right-handers. Stronger cortical facilitation was found in the right primary somatosensory cortex (S1) and right somatosensory association area (SA) during left-hand stimulation but not right-hand stimulation. This finding suggests that the asymmetric activation in the S1 and SA for less-preferred (left) hand stimulation might contribute to considerably reinforce sensorimotor network just with passive vibrotactile cutaneous stimulation.
The Rnf complex is a Na+ coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima
Authors: Kuhns Martin , Trifunović Dragan , Huber Harald , Müller Volker
Published: August 2020

rnf genes are widespread in bacteria and biochemical and genetic data are in line with the hypothesis that they encode a membrane-bound enzyme that oxidizes reduced ferredoxin and reduces NAD and vice versa, coupled to ion transport across the cytoplasmic membrane. The Rnf complex is of critical importance in many bacteria for energy conservation but also for reverse electron transport to drive ferredoxin reduction. However, the enzyme has never been purified and thus, ion transport could not be demonstrated yet. Here, we have purified the Rnf complex from the anaerobic, fermenting thermophilic bacterium Thermotoga maritima and show that is a primary Na+ pump. These studies provide the proof that the Rnf complex is indeed an ion (Na+) translocating, respiratory enzyme. Together with a Na+-F1FO ATP synthase it builds a simple, two-limb respiratory chain in T. maritima. The physiological role of electron transport phosphorylation in a fermenting bacterium is discussed.
Functional zwitterionic biomaterials for administration of insulin
Authors: Chen Xingyu , Yang Dongqiong
Published: August 2020

This review summarizes the structures and biomedical applications of zwitterionic biomaterials in the administration of insulin.
Substrate-controlled, PBu3-catalyzed annulation of phenacylmalononitriles with allenoates enables tunable access to cyclopentenes
Authors: Vaishanv Narendra Kumar , Chandrasekharan Sanoop P , Zaheer Mohd Khalid , Kant Ruchir , Mohanan Kishor
Published: August 2020

Divergence in the PBu3-catalyzed [3+2] annulation of phenacylmalononitriles with allenoates offers facile access to functionalized cyclopentene carboxamides and cyclopentenols.
Divergent influence of {1 1 1} vs. {1 0 0} crystal planes and Yb3+ dopant on CO oxidation paths in mixed nano-sized oxide Au/Ce1−xYbxO2−x/2 (x = 0 or 0.1) systems
Authors: Woźniak Piotr , Kraszkiewicz Piotr , Małecka Małgorzata A.
Published: August 2020

In this paper, the fundamental information on interactions in systems concerning nanocrystalline gold disperses on the shaped (octahedron-like or cube-like) Ce1−xYbxO2−x/2 (x = 0 or 0.1) support has been discussed.
Gold–palladium colloids as catalysts for hydrogen peroxide synthesis, degradation and methane oxidation: effect of the PVP stabiliser
Authors: Freakley Simon J. , Agarwal Nishtha , McVicker Rebecca U. , Althahban Sultan , Lewis Richard J. , Morgan David J. , Dimitratos Nikolaos , Kiely Christopher J. , Hutchings Graham J.
Published: August 2020

PVP polymer stabilisers effect the reactivity of AuPd nanoparticles towards H2O2 synthesis/decomposition and methane oxidation.
Inserting Co and P into MoS2 photocathodes: enhancing hydrogen evolution reaction catalytic performance by activating edges and basal planes with sulfur vacancies
Authors: Pichaimuthu Karthika , Jena Anirudha , Chang Ho , Su Chaochin , Liu Ru-Shi
Published: August 2020

The production of hydrogen using solar energy via a photoelectrochemical system is an effective technique for meeting present clean energy needs.
Cooking and sensorial quality, nutritional composition and functional properties of cold-extruded rice/white bean gluten-free fettuccine fortified with whole carob fruit flour
Authors: Arribas Claudia , Cabellos Blanca , Guillamón Eva , Pedrosa Mercedes M.
Published: August 2020

A different rice/white bean-based gluten-free fettuccine (rice 0–100%, bean 0–100%) fortified with 10% carob fruit has been developed.
Single-nanostructure bandgap engineering enabled by magnetic-pulling thermal evaporation growth
Authors: Xu Jinyou , Wang Xingyu , Nötzel Richard
Published: August 2020

This review provides an overview of recent advances in single-nanostructure bandgap engineering by magnetic-pulling thermal evaporation.
Highly regioselective bioconversion of ginsenoside Re into 20(S/R)-Rf2 by an optimized culture ofCordyceps sinensis
Authors: Wang Weinan , Liu Jishuang , Xin Yu , He Tianzhu , Qiu Ye , Qu Mo , Song Yan , Qiu Zhidong
Published: August 2020

Highly regioselective hydration of the C24–C25 double bond is discovered during the bioconversion of ginsenoside Re byCordyceps sinensis.
Fabrication and characterization of a Fe3O4/polyvinylpyrrolidone (Fe3O4/PVP) nanocomposite as a coating for carbon steel in saline media
Authors: Bagherzadeh Mojtaba , Mousavi Omid , Shams Ghahfarokhi Zahra
Published: August 2020

Corrosion of carbon steel (CS) is a security and financial concern for numerous industries involving oil, petroleum, and automotive industries.
A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4+ cells
Authors: Zhong Runtao , Hou Liangsheng , Zhao Yingbo , Wang Tianle , Wang Shaohua , Wang Mengyu , Xu Dan , Sun Yeqing
Published: August 2020

A 3D mixing-based portable magnetic device to perform on-chip efficient cell capture and automatic intracellular immunofluorescence (IF) staining is presented.
Synthesis of BaTiO3nanoparticles as shape modified filler for high dielectric constant ceramic–polymer composite
Authors: Kim Taehee , Lim Hanwhuy , Lee Youngkwan , Kim Baek-Jin
Published: August 2020

Coral-like structured barium titanate (BaTiO3) nanoparticles were synthesized as filler for a high dielectric elastomer.
Influence of reduced graphene oxide on flow behaviour, glass transition temperature and secondary crystallinity of plasticized poly(vinyl chloride)
Authors: Akhina H. , Ramya Koduvayur A. , Gopinathan Nair M. R. , Saiter-Fourcin Allisson , Garda Marie-Rose , Deshpande Abhijit P. , Kalarikkal Nandakumar , Thomas Sabu
Published: August 2020

Understanding the rheological behaviour of thermoplastic nanocomposites is important to obtain a concrete knowledge of their processability.
Activating intramolecular singlet exciton fission by altering π-bridge flexibility in perylene diimide trimers for organic solar cells
Authors: Carlotti Benedetta , Madu Ifeanyi K. , Kim Hyungjun , Cai Zhengxu. , Jiang Hanjie , Muthike Angelar K. , Yu Luping , Zimmerman Paul M. , Goodson Theodore
Published: August 2020

We show via time resolved spectroscopy that triplet formation proceeds via intersystem crossing in a rigid-bridged perylene diimide trimer and via efficient and fast intramolecular singlet exciton fission in the analogous flexible-bridged trimer.
Targeted and direct intracellular delivery of native DNAzymes enables highly specific gene silencing
Authors: Li Xia , Yang Fang , Zhou Wenjiao , Yuan Ruo , Xiang Yun
Published: August 2020

The stimuli-responsive and constrained aptamer/DNAzyme catenane nanostructure enables the targeted delivery of native DNAzymes for highly specific gene silencing.
Phase transitions on non-uniformly curved surfaces: coupling between phase and location
Authors: Law Jack O. , Dean Jacob M. , Miller Mark A. , Kusumaatmaja Halim
Published: August 2020

The stable phases of matter for attractive colloids on non-uniformly curved surfaces are coupled to their location, and their phase transitions are accompanied by wholesale migration of matter to different parts of the surface.
Tuning the selective permeability of polydisperse polymer networks
Authors: Kim Won Kyu , Chudoba Richard , Milster Sebastian , Roa Rafael , Kanduč Matej , Dzubiella Joachim
Published: August 2020

We study the permeability and selectivity (‘permselectivity’) of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations.
The impact of oxygen evolution and cation migration on the cycling stability of a Li-rich Li[Li0.2Mn0.6Ni0.1Co0.1]O2 positive electrode
Authors: Redel Katarzyna , Kulka Andrzej , Walczak Katarzyna , Plewa Anna , Borca Camelia N. , Molenda Janina
Published: August 2020

Comprehensive analysis of the oxygen and 3d metal redox reaction in electrochemical processes clarifies the extraordinary behavior of a Li[Li0.2Mn0.6Ni0.1Co0.1]O2 cathode.
Selective CO2-to-formate electrochemical conversion with core–shell structured Cu2O/Cu@C composites immobilized on nitrogen-doped graphene sheets
Authors: Li Da , Liu Tongtong , Huang Linlin , Wu Jing , Li Jiannan , Zhen Liang , Feng Yujie
Published: August 2020

Synergistic effects between the Cu2O/Cu sites and N-doped graphene result in higher selectivity and stability during CO2-to-formate conversion.
Oxygen defect chemistry for the reversible transformation of titanates for sizeable potassium storage
Authors: Lao Cheng-Yen , Yu Qiyao , Hu Jun , Li Neng , Divitini Giorgio , Kim Hyun-Kyung , Wang Wei (Alex) , Liu Yingjun , Chen Xingzhu , Kumar R. Vasant
Published: August 2020

An oxygen-deficient loose-layered titanate (K(TiO1.875)4OH (LL-KTO)) is prepared to push the kinetic boundary and approached the thermodynamic limit for potassium-ion batteries.
Advancements in the development on new liquid embolic agents for use in therapeutic embolisation
Authors: Lord Jasmine , Britton Hugh , Spain Sebastian G. , Lewis Andrew L.
Published: August 2020

This review covers the current state-of-the-art in the development of liquid embolics for therapeutic embolisation.
High throughput profiling drug response and apoptosis of single polar cells
Authors: Wu Xixi , Chen Shuangshuang , Lu Qinghua
Published: August 2020

The drug response of single polar cells was evaluated via single cell trapping on anisotropic microwells for tumor heterogeneity.
Elucidating charge transport mechanisms in cellulose-stabilized graphene inks
Authors: de Moraes Ana C. M. , Obrzut Jan , Sangwan Vinod K. , Downing Julia R. , Chaney Lindsay E. , Patel Dinesh K. , Elmquist Randolph E. , Hersam Mark C.
Published: August 2020

Thin-films derived from solution-processed graphene inks that use ethyl cellulose as a polymer stabilizer show mixed metallic-semiconducting charge transport with high charge carrier mobility.
Enhanced hydrolytic and electrical stability of eco-friendly processed polyimide gate dielectrics for organic transistors
Authors: Jeong Yuri , Park Hyunjin , So Yujin , Mun Hyun Jung , Shin Tae Joo , Park No Kyun , Kim Jinsoo , Yoo Sungmi , Won Jong Chan , Kim Yun Ho
Published: August 2020

Aromatic polyimides based on BPDA–pPDA incorporated with DMIZ exhibit a significant enhancement in hydrolytic stability and allow eco-friendly fabrication.
ALG2 Influences T cell apoptosis by regulating FASLG intracellular transportation
Authors: Ji Wangsheng , Xin Yang , Zhang Lianfei , Liu Xinqi
Published: August 2020

In the immune system, T lymphocytes undergo rapid clonal expansion upon pathogen infection. Following pathogen clearance, most of proliferated T cells will be eliminated by the apoptosis pathway to keep the balance of immune cells. FASLG, by interacting with its cognate receptor FAS, plays a major role in controlling the T cell death. FASLG is a type II transmembrane protein, with its C-terminal extracellular domain responsible for interacting with FAS. The N-terminal cytosolic region, despite short and intrinsically disordered, plays critical roles on the protein stability and transportation. The correct localization, either on the plasma membrane or secreted with exosome, or shed into the extracellular region after protease cleavage, has a great impact on the proper function of FASLG. Following synthesis, FASLG is transported by intracellular vesicle transportation system to the final destination. In this report, ALG2, a molecule identified in the T cell apoptosis and shown to be involved in vesicle trafficking previously, was found to interact with FASLG and regulate FASLG transportation. Therefore, we identified a new regulating factor for FASLG function within T cells and also revealed a new pathway for ALG2 involvement in T cell apoptosis.