bluuebunny/crossref_metadata_2025_split huggingface dataset:
Different environmental variables predict body and brain size evolution in Homo
Authors: Will Manuel , Krapp Mario , Stock Jay T. , Manica Andrea 
Published: July 2021

AbstractIncreasing body and brain size constitutes a key macro-evolutionary pattern in the hominin lineage, yet the mechanisms behind these changes remain debated. Hypothesized drivers include environmental, demographic, social, dietary, and technological factors. Here we test the influence of environmental factors on the evolution of body and brain size in the genusHomoover the last one million years using a large fossil dataset combined with global paleoclimatic reconstructions and formalized hypotheses tested in a quantitative statistical framework. We identify temperature as a major predictor of body size variation withinHomo, in accordance with Bergmann’s rule. In contrast, net primary productivity of environments and long-term variability in precipitation correlate with brain size but explain low amounts of the observed variation. These associations are likely due to an indirect environmental influence on cognitive abilities and extinction probabilities. Most environmental factors that we test do not correspond with body and brain size evolution, pointing towards complex scenarios which underlie the evolution of key biological characteristics in laterHomo.
Chemical heterogeneity enhances hydrogen resistance in high-strength steels
Authors: Sun Binhan , Lu Wenjun , Gault Baptiste , Ding Ran , Makineni Surendra Kumar , Wan Di , Wu Chun-Hung , Chen Hao , Ponge Dirk , Raabe Dierk 
Published: July 2021

AbstractThe antagonism between strength and resistance to hydrogen embrittlement in metallic materials is an intrinsic obstacle to the design of lightweight yet reliable structural components operated in hydrogen-containing environments. Economical and scalable microstructural solutions to this challenge must be found. Here, we introduce a counterintuitive strategy to exploit the typically undesired chemical heterogeneity within the material’s microstructure that enables local enhancement of crack resistance and local hydrogen trapping. We use this approach in a manganese-containing high-strength steel and produce a high dispersion of manganese-rich zones within the microstructure. These solute-rich buffer regions allow for local micro-tuning of the phase stability, arresting hydrogen-induced microcracks and thus interrupting the percolation of hydrogen-assisted damage. This results in a superior hydrogen embrittlement resistance (better by a factor of two) without sacrificing the material’s strength and ductility. The strategy of exploiting chemical heterogeneities, rather than avoiding them, broadens the horizon for microstructure engineering via advanced thermomechanical processing.
Stability analysis of the coexistence equilibrium of a balanced metapopulation model
Authors: Rao Shodhan , Muyinda Nathan , De Baets Bernard 
Published: July 2021

AbstractWe analyze the stability of a unique coexistence equilibrium point of a system of ordinary differential equations (ODE system) modelling the dynamics of a metapopulation, more specifically, a set of local populations inhabiting discrete habitat patches that are connected to one another through dispersal or migration. We assume that the inter-patch migrations are detailed balanced and that the patches are identical with intra-patch dynamics governed by a mean-field ODE system with a coexistence equilibrium. By making use of an appropriate Lyapunov function coupled with LaSalle’s invariance principle, we are able to show that the coexistence equilibrium point within each patch is locally asymptotically stable if the inter-patch dispersal network is heterogeneous, whereas it is neutrally stable in the case of a homogeneous network. These results provide a mathematical proof confirming the existing numerical simulations and broaden the range of networks for which they are valid.
MEMS enabled miniaturized light-sheet microscopy with all optical control
Authors: Bakas Spyridon , Uttamchandani Deepak , Toshiyoshi Hiroshi , Bauer Ralf 
Published: July 2021

AbstractWe have designed and implemented a compact, cost-efficient miniaturised light-sheet microscopy system based on optical microelectromechanical systems scanners and tunable lenses. The system occupies a footprint of 20 × 28 × 13 cm3 and combines off-the-shelf optics and optomechanics with 3D-printed structural and optical elements, and an economically costed objective lens, excitation laser and camera. All-optical volume scanning enables imaging of 435 × 232 × 60 µm3 volumes with 0.25 vps (volumes per second) and minimum lateral and axial resolution of 1.0 µm and 3.8 µm respectively. An open-top geometry allows imaging of samples on flat bottomed holders, allowing integration with microfluidic devices, multi-well plates and slide mounted samples, with applications envisaged in biomedical research and pre-clinical settings.
Implications of Tamarkoz on stress, emotion, spirituality and heart rate
Authors: Bahadorani Nasim , Lee Jerry W. , Martin Leslie R. 
Published: July 2021

AbstractPerceived stress among university students is a prevalent health issue directly correlated with poor academic performance, poor sleep quality, hopelessness, compromised physical and mental health, high risk of substance abuse, and suicidal ideation. Tamarkoz, a Sufi meditation, may reduce the impact of stressors to prevent illness among students. Tamarkoz is the art of self-knowledge through concentration and meditation. It is a method of concentration that can be applied to any task. The method is said to discipline the mind, body, and emotions to avoid unintended distractions. Therefore, it can be used in daily life activities, such as studying, eating, driving, de-stressing or in Sufism, seeking self-knowledge. This study was an 18-week quasi-experimental design with pre-intervention, post-intervention and follow-up assessments in the experimental group, a wait-list control, and a third group that utilized the campus health center’s stress management resources. Participants, university students, had no prior exposure to Tamarkoz, and there were no statistically significant differences among groups on baseline measurements. Using a generalized linear mixed model, significant increases in positive emotions and daily spiritual experiences, and reductions in perceived stress and heart rate were found in the experimental group compared to the other two groups. Tamarkoz seems to show some advantages over the usual stress management resources offered by a student health center.Trial registration: ClinicalTrials.gov Protocol Registration Date: (03/04/2018); ClinicalTrials.gov ID: NCT03489148.
Multi-volume hemacytometer
Authors: Thunyaporn Ravangnam , Doh Il , Lee Dong Woo 
Published: July 2021

AbstractCell counting has become an essential method for monitoring the viability and proliferation of cells. A hemacytometer is the standard device used to measure cell numbers in most laboratories which are typically automated to increase throughput. The principle of both manual and automated hemacytometers is to calculate cell numbers with a fixed volume within a set measurement range (105 ~ 106 cells/ml). If the cell concentration of the unknown sample is outside the range of the hemacytometer, the sample must be prepared again by increasing or decreasing the cell concentration. We have developed a new hemacytometer that has a multi-volume chamber with 4 different depths containing different volumes (0.1, 0.2, 0.4, 0.8 µl respectively). A multi-volume hemacytometer can measure cell concentration with a maximum of 106 cells/ml to a minimum of 5 × 103 cells/ml. Compared to a typical hemacytometer with a fixed volume of 0.1 µl, the minimum measurable cell concentration of 5 × 103 cells/ml on the multi-volume hemacytometer is twenty times lower. Additionally, the Multi-Volume Cell Counting model (cell concentration calculation with the slope value of cell number in multi-chambers) showed a wide measurement range (5 × 103 ~ 1 × 106 cells/ml) while reducing total cell counting numbers by 62.5% compared to a large volume (0.8 µl-chamber) hemacytometer.
Spatiotemporal sensitivity of mesoderm specification to FGFR signalling in the Drosophila embryo
Authors: Yadav V. , Tolwinski N. , Saunders T. E. 
Published: July 2021

AbstractDevelopment of the Drosophila embryonic mesoderm is controlled through both internal and external inputs to the mesoderm. One such factor is Heartless (Htl), a Fibroblast Growth Factor Receptor (FGFR) expressed in the mesoderm. Although Htl has been extensively studied, the dynamics of its action are poorly understood after the initial phases of mesoderm formation and spreading. To begin to address this challenge, we have developed an optogenetic version of the FGFR Heartless in Drosophila (Opto-htl). Opto-htl enables us to activate the FGFR pathway in selective spatial (~ 35 μm section from one of the lateral sides of the embryo) and temporal domains (ranging from 40 min to 14 h) during embryogenesis. Importantly, the effects can be tuned by the intensity of light-activation, making this approach significantly more flexible than other genetic approaches. We performed controlled perturbations to the FGFR pathway to define the contribution of Htl signalling to the formation of the developing embryonic heart and somatic muscles. We find a direct correlation between Htl signalling dosage and number of Tinman-positive heart cells specified. Opto-htl activation favours the specification of Tinman positive cardioblasts and eliminates Eve-positive DA1 muscles. This effect is seen to increase progressively with increasing light intensity. Therefore, fine tuning of phenotypic responses to varied Htl signalling dosage can be achieved more conveniently than with other genetic approaches. Overall, Opto-htl is a powerful new tool for dissecting the role of FGFR signalling during development.
Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma
Authors: He Huiling , Liyanarachchi Sandya , Li Wei , Comiskey Daniel F. , Yan Pearlly , Bundschuh Ralf , Turkoglu Altan M. , Brock Pamela , Ringel Matthew D. , de la Chapelle Albert 
Published: July 2021

AbstractPapillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. The molecular characteristics of histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed total RNA sequencing with fresh frozen thyroid tissues from a cohort of three categories of samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex or the presence of lymphocytic thyroiditis. Among the differentially expressed genes (DEGs) of NAT vs N, 256 coding genes and 5 noncoding genes have been reported as cancer genes involved in cell proliferation, apoptosis, and/or tumorigenesis. Bioinformatics analysis with Ingenuity Pathway Analysis software revealed that “Cancer, Organismal Injury and Abnormalities, Cellular Response to Therapeutics, and Cellular Movement” were major dysregulated pathways in the NAT tissues. This study provides improved insight into the complexity of gene expression changes in the thyroid glands of patients with PTC.
Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand
Authors: Luk-in Sirirat , Chatsuwan Tanittha , Kueakulpattana Naris , Rirerm Ubolrat , Wannigama Dhammika Leshan , Plongla Rongpong , Lawung Ratana , Pulsrikarn Chaiwat , Chantaroj Siriporn , Chaichana Pattharaporn , Saksaengsopa Nattida , Shanthachol Teerarat , Techapornroong Malee , Chayangsu Sunee , Kulwichit Wanla 
Published: July 2021

AbstractNontyphoidal Salmonella, an important zoonotic pathogen and a major cause of foodborne illnesses, could be a potential reservoir of plasmids harbouring mobile colistin resistance gene (mcr). This study reported, for the first time, a high rate of mcr-carrying Salmonella clinical isolates (3.3%, 24/724) in Thailand, associated with mcr-3 gene (3.0%, 22/724) in S. 4,[5],12:i:-(15.4%, 4/26), S. Typhimurium (8.8%, 5/57), and S. Choleraesuis (5.6%, 13/231). Remarkably, the increasing trends of colistin and extended-spectrum cephalosporin resistances have displayed a high agreement over the years, with a dramatic rise in the mcr-carrying Salmonella from 1.1% (6/563) during 2005–2007 to 11.2% (18/161) during 2014–2018 when CTX-M-55 became abundant. Clonal and plasmid analysis revealed that the self-transferable IncA/C and a novel hybrid IncA/C-FIIs MDR plasmids were the major vehicles to disseminate both mcr-3 and blaCTX-M55 genes among diverse Salmonella strains, from as early as 2007. To our knowledge the occurrence of mcr-3 and the co-existence of it with blaCTX-M-55 in S. Choleraesuis are reported here for the first time, leading to clinical concern over the treatment of the invasive salmonellosis. This study provides evidence of the potential reservoirs and vectors in the dissemination of the mcr and highlights the co-selection by colistin and/or cephalosporins.
Effects of brewing conditions on infusible fluoride levels in tea and herbal products and probabilistic health risk assessment
Authors: Pattaravisitsate Nattha , Phetrak Athit , Denpetkul Thammanitchpol , Kittipongvises Suthirat , Kuroda Keisuke 
Published: July 2021

AbstractExcessive ingestion of fluorides might adversely affect the health of humans. Hence, this study aimed to investigate the concentrations of infusible fluoride in five different types of tea and herbal products; additionally, the probabilistic health risks associated with the ingestion of fluoride in drinking tea and herbal products were estimated. The highest and lowest concentrations of infusible fluoride were detected in black and white tea, respectively. On average, the highest amount of infusible fluoride was extracted following a short brewing time of 5 min in the case of black tea (2.54 mg/L), herbal tea (0.40 mg/L), and white tea (0.21 mg/L). The level of infusible fluoride during brewing was inversely associated with the leaf size of the tea and herbal products. Furthermore, the type of water used influenced the release of infusible fluoride; purified water yielded lower amounts of infused fluoride. The findings of the probabilistic health risk assessment indicated that the consumption of black tea can increase the fluoride intake leading to chronic exposure. Thus, the health risk posed by fluoride intake from drinking tea needs to be evaluated in more details in the future. Appropriate measures for health risk mitigation need to be implemented to minimize the total body burden of fluorides in humans.
Screening of the HBx transactivation domain interacting proteins and the function of interactor Pin1 in HBV replication
Authors: Zhou Qiaoxia , Yan Libo , Xu Baofu , Wang Xue’er , Sun Xuehong , Han Ning , Tang Hong , Huang Feijun 
Published: July 2021

AbstractHepatitis B virus (HBV) X protein (HBx) has been determined to play a crucial role in the replication and transcription of HBV, and its biological functions mainly depend on the interaction with other host proteins. This study aims at screening the proteins that bind to the key functional domain of HBx by integrated proteomics. Proteins that specifically bind to the transactivation domain of HBx were selected by comparing interactors of full-length HBx and HBx-D5 truncation determined by glutathione-S-transferase (GST) pull-down assay combined with mass spectrometry (MS). The function of HBx interactor Pin1 in HBV replication was further investigated by in vitro experiments. In this study, a total of 189 proteins were identified from HepG2 cells that specifically bind to the transactivation domain of HBx by GST pull-down and subsequent MS. After gene ontology (GO) analysis, Pin1 was selected as the protein with the highest score in the largest cluster functioning in protein binding, and also classified into the cluster of proteins with the function of structural molecule activity, which is of great potential to be involved in HBV life cycle. The interaction between Pin1 and HBx has been further confirmed by Ni2+-NTA pulldown assay, co-immunoprecipitation, and immunofluorescence microscopy. HBsAg and HBeAg levels significantly decreased in Pin1 expression inhibited HepG2.2.15 cells. Besides, the inhibition of Pin1 expression in HepG2 cells impeded the restored replication of HBx-deficient HBV repaired by ectopic HBx expression. In conclusion, our study identified Pin1 as an interactor binds to the transactivation domain of HBx, and suggested the potential association between Pin1 and the function of HBx in HBV replication.
Easy and quick (EQ) sperm freezing method for urgent preservation of mouse strains
Authors: Mochida Keiji , Hasegawa Ayumi , Shikata Daiki , Itami Nobuhiko , Hada Masashi , Watanabe Naomi , Tomishima Toshiko , Ogura Atsuo 
Published: July 2021

AbstractCryopreservation of mouse spermatozoa is widely used for the efficient preservation and safe transport of valuable mouse strains. However, the current cryopreservation method requires special containers (plastic straws), undefined chemicals (e.g., skim milk), liquid nitrogen, and expertise when handling sperm suspensions. Here, we report an easy and quick (EQ) sperm freezing method. The main procedure consists of only one step: dissecting a single cauda epididymis in a microtube containing 20% raffinose solution, which is then stored in a −80 °C freezer. The frozen–thawed spermatozoa retain practical fertilization rates after 1 (51%) or even 3 months (25%) with the C57BL/6 J strain, the most sensitive strain for sperm freezing. More than half of the embryos thus obtained developed into offspring after embryo transfer. Importantly, spermatozoa stored at −80 °C can be transferred into liquid nitrogen for indefinite storage. As far as we know, our EQ method is the easiest and quickest method for mouse sperm freezing and should be applicable in all laboratories without expertise in sperm cryopreservation. This technique can help avoid the loss of irreplaceable strains because of closure of animal rooms in emergency situations such as unexpected microbiological contamination or social emergencies such as the COVID-19 threat.
Fuzzy rank-based fusion of CNN models using Gompertz function for screening COVID-19 CT-scans
Authors: Kundu Rohit , Basak Hritam , Singh Pawan Kumar , Ahmadian Ali , Ferrara Massimiliano , Sarkar Ram 
Published: July 2021

AbstractCOVID-19 has crippled the world’s healthcare systems, setting back the economy and taking the lives of several people. Although potential vaccines are being tested and supplied around the world, it will take a long time to reach every human being, more so with new variants of the virus emerging, enforcing a lockdown-like situation on parts of the world. Thus, there is a dire need for early and accurate detection of COVID-19 to prevent the spread of the disease, even more. The current gold-standard RT-PCR test is only 71% sensitive and is a laborious test to perform, leading to the incapability of conducting the population-wide screening. To this end, in this paper, we propose an automated COVID-19 detection system that uses CT-scan images of the lungs for classifying the same into COVID and Non-COVID cases. The proposed method applies an ensemble strategy that generates fuzzy ranks of the base classification models using the Gompertz function and fuses the decision scores of the base models adaptively to make the final predictions on the test cases. Three transfer learning-based convolutional neural network models are used, namely VGG-11, Wide ResNet-50-2, and Inception v3, to generate the decision scores to be fused by the proposed ensemble model. The framework has been evaluated on two publicly available chest CT scan datasets achieving state-of-the-art performance, justifying the reliability of the model. The relevant source codes related to the present work is available in: GitHub.
Low expression of miR-29a is associated with aggressive biology and worse survival in gastric cancer
Authors: Tokumaru Yoshihisa , Oshi Masanori , Huyser Michelle R. , Yan Li , Fukada Masahiro , Matsuhashi Nobuhisa , Futamura Manabu , Akao Yukihiro , Yoshida Kazuhiro , Takabe Kazuaki 
Published: July 2021

AbstractAdvanced gastric cancer (GC) is one of the most lethal cancer types, thus a better understanding of its biology in patients is urgently needed. MicroRNA (miR)-29a is a known tumor suppressive miR that is related to metastasis, but its clinical relevance in GC remains ambiguous. Here, using a large GC patient cohort we hypothesized that low expression of miR-29a in GC is associated with aggressive cancer biology and worse survival. We demonstrated that low miR-29a GC enriched cell proliferation, apoptosis, metastasis, and angiogenesis related gene sets, as well as the higher expression of related genes. Low miR-29a GC was associated with less anti-cancer immune cell infiltration as well as immune related scoring. Low miR-29a GC demonstrated a worse overall survival (OS) as well as disease specific survival (DSS) compared with high expressing miR-29a GC. Notably, low miR-29a expression was the only factor, other than residual tumor status, to be an independent prognostic biomarker of worse OS and DSS. In conclusion, low miR-29a GC was associated with aggressive cancer biology and worse OS as well as DSS. Additionally, low expression of miR-29a was an independent prognostic biomarker of OS and DSS in gastric cancer patients.
Yield estimation of the 2020 Beirut explosion using open access waveform and remote sensing data
Authors: Pilger Christoph , Gaebler Peter , Hupe Patrick , Kalia Andre C. , Schneider Felix M. , Steinberg Andreas , Sudhaus Henriette , Ceranna Lars 
Published: July 2021

AbstractWe report on a multi-technique analysis using publicly available data for investigating the huge, accidental explosion that struck the city of Beirut, Lebanon, on August 4, 2020. Its devastating shock wave led to thousands of injured with more than two hundred fatalities and caused immense damage to buildings and infrastructure. Our combined analysis of seismological, hydroacoustic, infrasonic and radar remote sensing data allows us to characterize the source as well as to estimate the explosive yield. The latter is determined within 0.13 to 2 kt TNT (kilotons of trinitrotoluene). This range is plausible given the reported 2.75 kt of ammonium nitrate as explosive source. As there are strict limitations for an on-site analysis of this catastrophic explosion, our presented approach based on data from open accessible global station networks and satellite missions is of high scientific and social relevance that furthermore is transferable to other explosions.