bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmonella enterica changes Macrosteles quadrilineatus feeding behaviors resulting in altered S. enterica distribution on leaves and increased populations
Authors: Harrod Victoria L. , Groves Russell L. , Guillemette Ellie G. , Barak Jeri D. 
Published: May 2022

AbstractHemipteran insects are ubiquitous inhabitants of the phyllosphere. Changes in microbial phyllosphere communities have recently been demonstrated following infestation by Macrosteles quadrilineatus (Aster Leafhopper). Although epiphytic Salmonella enterica populations naturally decline in the phyllosphere of plants, M. quadrilineatus infestation facilitated the growth of the bacterial pathogen populations. Here, we demonstrate that cellular damage by insect stylet penetration results in a localized beneficial niche on the leaf surface, leading to enhanced S. enterica populations. We measured S. enterica populations and colonization patterns on plants infested with Hemipterans with distinct feeding behaviors. M. quadrilineatus infestation resulted in higher solute leakage and significantly greater bacterial populations than plants absent of insects. Following immigration via contaminated irrigation water, the highest populations of S. enterica are naturally found on the tips of tomato leaflets. We discovered M. quadrilineatus feeding preference altered the natural distribution of S. enterica populations, and that the presence of S. enterica altered the distribution of probing attempts. These findings elucidate how cellular damage resulting from insect feeding drives changes in bacterial colonization of the phyllosphere.
The electro-oxidation of primary alcohols via a coral-shaped cobalt metal–organic framework modified graphite electrode in neutral media
Authors: Khakyzadeh Vahid , Sediqi Salbin 
Published: May 2022

AbstractThe electro-oxidation of alcohols into corresponding aldehydes achieved enormous attention. However, numerous challenges remain in exploring catalytic systems with high conversion efficiency and selectivity. Considering the worldwide attention toward metal–organic frameworks (MOFs) as outstanding crystalline porous materials, many chemists have been encouraged to use them in organic transformations. In this study, a novel coral-shaped cobalt organic framework was grown onto the surface of a functionalized graphite electrode (Co-MOF/C) to fabricate an efficient modified electrode in the electro-oxidation alcohols. The modified Co-MOF/C electrode showed high stability, large surface area, rich pores, and good conductivity as a desirable water-stable working electrode for selective oxidation of alcohols into aldehydes in good to excellent yields under a diffusion-controlled process.
Differences in interaction lead to the formation of different types of insulin amyloid
Authors: Mori Wakako , Kawakami Ryosuke , Niko Yosuke , Haruta Tomohiro , Imamura Takeshi , Shiraki Kentaro , Zako Tamotsu 
Published: May 2022

AbstractInsulin balls, localized insulin amyloids formed at the site of repeated insulin injections in patients with diabetes, cause poor glycemic control and cytotoxicity. Our previous study has shown that insulin forms two types of amyloids; toxic amyloid formed from the intact insulin ((i)-amyloid) and less-toxic amyloid formed in the presence of the reducing reagent TCEP ((r)-amyloid), suggesting insulin amyloid polymorphism. However, the differences in the formation mechanism and cytotoxicity expression are still unclear. Herein, we demonstrate that the liquid droplets, which are stabilized by electrostatic interactions, appear only in the process of toxic (i)-amyloid formation, but not in the less-toxic (r)-amyloid formation process. The effect of various additives such as arginine, 1,6-hexanediol, and salts on amyloid formation was also examined to investigate interactions that are important for amyloid formation. Our results indicate that the maturation processes of these two amyloids were significantly different, whereas the nucleation by hydrophobic interactions was similar. These results also suggest the difference in the formation mechanism of two different insulin amyloids is attributed to the difference in the intermolecular interactions and could be correlated with the cytotoxicity.
Synthesis of palaeoecological data from the Polish Lowlands suggests heterogeneous patterns of old-growth forest loss after the Migration Period
Authors: Czerwiński Sambor , Marcisz Katarzyna , Wacnik Agnieszka , Lamentowicz Mariusz 
Published: May 2022

AbstractHuman impact on Central European forests dates back thousands of years. In this study we reanalyzed 36 published pollen data sets with robust chronologies from Polish Lowlands to determine the patterns of large-scale forest decline after the Migration Period (fourth to sixth century CE). The study revealed substantial heterogeneity in the old-growth forest decline patterns. Using new high-resolution studies, we could better understand the timing of this transition related to increasing economic development. After the Migration Period, forest expansion continued until the seventh to ninth centuries cal. CE, when the dawn of Slavic culture resulted in large-scale forest decline, especially in north-western and north-central Poland. Later, forest decline was recorded mainly in north-eastern Poland and was related to Prussian settlements, including activities associated with the Teutonic Order, as well as with new settlements from the fourteenth century. The composite picture shows a varied spatio-temporal forest loss and transition towards the present-day, human activity dominated landscapes. However, some sites, such as in north-eastern Poland, are characterized by a less abrupt critical transition. The pristine nature of the oak-hornbeam forest had already been destroyed in Early Medieval times (eighth to ninth centuries cal. CE) and the potential for recovery was largely lost. Our study has confirmed previous assumptions that the decline of hornbeam across the Polish Lowlands may be an early indicator of local settlement processes, preceding severe forest loss, and establishment of permanent agriculture.
Spatial distribution and risk assessments due to the microplastics pollution in sediments of Karnaphuli River Estuary, Bangladesh
Authors: Rakib Md. Refat Jahan , Hossain M. Belal , Kumar Rakesh , Ullah Md. Akram , Al Nahian Sultan , Rima Nazmun Naher , Choudhury Tasrina Rabia , Liba Samia Islam , Yu Jimmy , Khandaker Mayeen Uddin , Sulieman Abdelmoneim , Sayed Mohamed Mahmoud 
Published: May 2022

AbstractMicroplastics (MPs) have become an emerging global pollutant due to their widespread dispersion and potential threats to marine ecosystems. However, studies on MPs in estuarine and coastal ecosystems of Bangladesh are very limited. Here, we conducted the first study on abundance, distribution, characteristics, and risk assessment of microplastics in the sediment of Karnaphuli River estuary, Bangladesh. Microplastic particles were extracted from sediments of 30 stations along the estuary by density separation and then enumerated and characterized using a stereomicroscope and Fourier Transform Infrared (FT-IR) spectroscopy. In the collected sediment of the Karnaphuli River estuary, the number of MPs varied from 22.29 to 59.5 items kg−1 of dry weight. The mean abundance was higher in the downstream and left banks of the estuary, whereas the predominant shape, colour, and size of MPs were films (35%), and white (19%), and 1–5 mm (30.38%), respectively. Major polymer types were polyethylene terephthalate, polystyrene, polyethylene, cellulose, and nylon. MPs were found to pose risks (low to high) in the sediment of the estuary, with the highest risk occurring at one station near a sewage outlet, according to the results of risk analyses using the pollution risk index, polymer risk index (H), contamination factors, and pollution load index (PLI). The single value index, PLI, clearly demonstrated that all sampling sites were considerably polluted with microplastics (PLI > 1). H values showed toxic polymers, even in lower proportions, possess higher polymeric hazard scores and vice versa. This investigation uncovered new insights on the status of MPs in the sediments of the Karnaphuli River estuary, laying the groundwork for future research and control of microplastic pollution and management.
The effect of intermittent pneumatic compression on deep-vein thrombosis and ventilation-free days in critically ill patients with heart failure
Authors: Al-Dorzi Hasan M. , Al-Dawood Abdulaziz , Al-Hameed Fahad M. , Burns Karen E. A. , Mehta Sangeeta , Jose Jesna , Alsolamy Sami , Abdukahil Sheryl Ann I. , Afesh Lara Y. , Alshahrani Mohammed S. , Mandourah Yasser , Almekhlafi Ghaleb A. , Almaani Mohammed , Al Bshabshe Ali , Finfer Simon , Arshad Zia , Khalid Imran , Mehta Yatin , Gaur Atul , Hawa Hassan , Buscher Hergen , Lababidi Hani , Al Aithan Abdulsalam , Arabi Yaseen M. 
Published: May 2022

AbstractThere are contradictory data regarding the effect of intermittent pneumatic compression (IPC) on the incidence of deep-vein thrombosis (DVT) and heart failure (HF) decompensation in critically ill patients. This study evaluated the effect of adjunctive use of IPC on the rate of incident DVT and ventilation-free days among critically ill patients with HF. In this pre-specified secondary analysis of the PREVENT trial (N = 2003), we compared the effect of adjunctive IPC added to pharmacologic thromboprophylaxis (IPC group), with pharmacologic thromboprophylaxis alone (control group) in critically ill patients with HF. The presence of HF was determined by the treating teams according to local practices. Patients were stratified according to preserved (≥ 40%) versus reduced (< 40%) left ventricular ejection fraction, and by the New York Heart Association (NYHA) classification. The primary outcome was incident proximal lower-limb DVT, determined with twice weekly venous Doppler ultrasonography. As a co-primary outcome, we evaluated ventilation-free days as a surrogate for clinically important HF decompensation. Among 275 patients with HF, 18 (6.5%) patients had prevalent proximal lower-limb DVT (detected on trial day 1 to 3). Of 257 patients with no prevalent DVT, 11/125 (8.8%) patients in the IPC group developed incident proximal lower-limb DVT compared to 6/132 (4.5%) patients in the control group (relative risk, 1.94; 95% confidence interval, 0.74–5.08,p = 0.17). There was no significant difference in ventilator-free days between the IPC and control groups (median 21 days versus 25 days respectively,p = 0.17). The incidence of DVT with IPC versus control was not different across NYHA classes (pvalue for interaction = 0.18), nor across patients with reduced and preserved ejection fraction (pvalue for interaction = 0.15). Ventilator-free days with IPC versus control were also not different across NYHA classes nor across patients with reduced or preserved ejection fraction. In conclsuion, the use of adjunctive IPC compared with control was associated with similar rate of incident proximal lower-limb DVT and ventilator-free days in critically ill patients with HF.Trial registration: The PREVENT trial is registered at ClinicalTrials.gov, ID: NCT02040103 (registered on 3 November 2013,https://clinicaltrials.gov/ct2/show/study/NCT02040103) and Current controlled trials, ID: ISRCTN44653506 (registered on 30 October 2013).
Baseline serum Krebs von den Lungen-6 as a biomarker for the disease progression in idiopathic pulmonary fibrosis
Authors: Chung Chiwook , Kim Jiwon , Cho Hyo Sin , Kim Ho Cheol 
Published: May 2022

AbstractDisease progression (DP) is an important parameter for the prognosis of idiopathic pulmonary fibrosis (IPF). This study aimed to evaluate the baseline serum biomarkers for predicting the DP in IPF. Seventy-four patients who were diagnosed with IPF and had their serum Krebs von den Lungen-6 (KL-6) and monocyte count, which might be associated with prognosis of IPF, checked more than twice were included. KL-6 ≥ 1000 U/mL and monocyte ≥ 600/μL were arbitrarily set as the cut-off values for DP. The DP was defined as a 10% reduction in forced vital capacity, a 15% reduction in diffusing capacity of the lung for carbon monoxide relative to the baseline, or disease-related mortality. Of the 74 patients, 18 (24.3%) were defined as having DP. The baseline KL-6 level was significantly increased in the DP group compared to the stable disease group (median, 1228.0 U/mL vs. 605.5 U/mL, P = 0.019). Multivariate Cox analyses demonstrated that a high KL-6 level (KL-6 ≥ 1000 U/mL; hazard ratio, 2.761 or 2.845; P = 0.040 or 0.045) was independently associated with DP in each model. The baseline serum KL-6 level might be a useful biomarker for DP in IPF.
Origin of an antifreeze protein gene in response to Cenozoic climate change
Authors: Graham Laurie A. , Gauthier Sherry Y. , Davies Peter L. 
Published: May 2022

AbstractAntifreeze proteins (AFPs) inhibit ice growth within fish and protect them from freezing in icy seawater. Alanine-rich, alpha-helical AFPs (type I) have independently (convergently) evolved in four branches of fishes, one of which is a subsection of the righteye flounders. The origin of this gene family has been elucidated by sequencing two loci from a starry flounder, Platichthys stellatus, collected off Vancouver Island, British Columbia. The first locus had two alleles that demonstrated the plasticity of the AFP gene family, one encoding 33 AFPs and the other allele only four. In the closely related Pacific halibut, this locus encodes multiple Gig2 (antiviral) proteins, but in the starry flounder, the Gig2 genes were found at a second locus due to a lineage-specific duplication event. An ancestral Gig2 gave rise to a 3-kDa “skin” AFP isoform, encoding three Ala-rich 11-a.a. repeats, that is expressed in skin and other peripheral tissues. Subsequent gene duplications, followed by internal duplications of the 11 a.a. repeat and the gain of a signal sequence, gave rise to circulating AFP isoforms. One of these, the “hyperactive” 32-kDa Maxi likely underwent a contraction to a shorter 3.3-kDa “liver” isoform. Present day starry flounders found in Pacific Rim coastal waters from California to Alaska show a positive correlation between latitude and AFP gene dosage, with the shorter allele being more prevalent at lower latitudes. This study conclusively demonstrates that the flounder AFP arose from the Gig2 gene, so it is evolutionarily unrelated to the three other classes of type I AFPs from non-flounders. Additionally, this gene arose and underwent amplification coincident with the onset of ocean cooling during the Cenozoic ice ages.
Apparent regional differences in the spectrum of BARD1 pathogenic variants in Spanish population and importance of copy number variants
Authors: Benito-Sánchez B. , Barroso A. , Fernández V. , Mercadillo F. , Núñez-Torres R. , Pita G. , Pombo L. , Morales-Chamorro R. , Cano-Cano J. M. , Urioste M. , González-Neira A. , Osorio A. 
Published: May 2022

AbstractOnly up to 25% of the cases in which there is a familial aggregation of breast and/or ovarian cancer are explained by germline mutations in the well-known BRCA1 and BRCA2 high-risk genes. Recently, the BRCA1-associated ring domain (BARD1), that partners BRCA1 in DNA repair, has been confirmed as a moderate-risk breast cancer susceptibility gene. Taking advantage of next-generation sequencing techniques, and with the purpose of defining the whole spectrum of possible pathogenic variants (PVs) in this gene, here we have performed a comprehensive mutational analysis of BARD1 in a cohort of 1946 Spanish patients who fulfilled criteria to be tested for germline pathogenic mutations in BRCA1 and BRCA2. We identified 22 different rare germline variants, being 5 of them clearly pathogenic or likely pathogenic large deletions, which account for 0.26% of the patients tested. Our results show that the prevalence and spectrum of mutations in the BARD1 gene might vary between different regions of Spain and expose the relevance to test for copy number variations.
A lightweight deep learning model for automatic segmentation and analysis of ophthalmic images
Authors: Sharma Parmanand , Ninomiya Takahiro , Omodaka Kazuko , Takahashi Naoki , Miya Takehiro , Himori Noriko , Okatani Takayuki , Nakazawa Toru 
Published: May 2022

AbstractDetection, diagnosis, and treatment of ophthalmic diseases depend on extraction of information (features and/or their dimensions) from the images. Deep learning (DL) model are crucial for the automation of it. Here, we report on the development of a lightweight DL model, which can precisely segment/detect the required features automatically. The model utilizes dimensionality reduction of image to extract important features, and channel contraction to allow only the required high-level features necessary for reconstruction of segmented feature image. Performance of present model in detection of glaucoma from optical coherence tomography angiography (OCTA) images of retina is high (area under the receiver-operator characteristic curve AUC ~ 0.81). Bland–Altman analysis gave exceptionally low bias (~ 0.00185), and high Pearson’s correlation coefficient (p = 0.9969) between the parameters determined from manual and DL based segmentation. On the same dataset, bias is an order of magnitude higher (~ 0.0694, p = 0.8534) for commercial software. Present model is 10 times lighter than Unet (popular for biomedical image segmentation) and have a better segmentation accuracy and model training reproducibility (based on the analysis of 3670 OCTA images). High dice similarity coefficient (D) for variety of ophthalmic images suggested it’s wider scope in precise segmentation of images even from other fields. Our concept of channel narrowing is not only important for the segmentation problems, but it can also reduce number of parameters significantly in object classification models. Enhanced disease diagnostic accuracy can be achieved for the resource limited devices (such as mobile phone, Nvidia’s Jetson, Raspberry pi) used in self-monitoring, and tele-screening (memory size of trained model ~ 35 MB).
Irregular shape as an independent predictor of prognosis in patients with primary intracerebral hemorrhage
Authors: Liu Chunyang , Zhang Haopeng , Wang Lixiang , Jiang Qiuyi , Lu Enzhou , Yuan Chao , Liang Yanchao , Sun Zhenying , Xiang Huan , Xu Xun , Sun Jingxian , Fu Bo , Zhao Boxian , Zhang Daming , Chen Xin , Wang Ning , Wang Lu , Yang Guang 
Published: May 2022

AbstractThe utility of noncontrast computed tomography markers in the prognosis of spontaneous intracerebral hemorrhage has been studied. This study aimed to investigate the predictive value of the computed tomography (CT) irregularity shape for poor functional outcomes in patients with spontaneous intracerebral hemorrhage. We retrospectively reviewed all 782 patients with intracranial hemorrhage in our stroke emergency center from January 2018 to September 2019. Laboratory examination and CT examination were performed within 24 h of admission. After three months, the patient's functional outcome was assessed using the modified Rankin Scale. Multinomial logistic regression analyses were applied to identify independent predictors of functional outcome in patients with intracerebral hemorrhage. Out of the 627 patients included in this study, those with irregular shapes on CT imaging had a higher proportion of poor outcomes and mortality 90 days after discharge (P < 0.001). Irregular shapes were found to be significant independent predictors of poor outcome and mortality on multiple logistic regression analysis. In addition, the increase in plasma D-dimer was associated with the occurrence of irregular shapes (P = 0.0387). Patients with irregular shapes showed worse functional outcomes after intracerebral hemorrhage. The elevated expression level of plasma D-dimers may be directly related to the formation of irregular shapes.
Spin-orbit coupling effects on transport properties of electronic Lieb lattice in the presence of magnetic field
Authors: Sadeghi Elham , Rezania Hamed 
Published: May 2022

AbstractIn this paper, the transport properties of a two-dimensional Lieb lattice that is a line-centered square lattice are investigated in the presence of magnetic field and spin-orbit coupling. Specially, we address the temperature dependence of electrical and thermal conductivities as well as Seebeck coefficient due to spin-orbit interaction. We have exploited Green’s function approach in order to study thermoelectric and transport properties of Lieb lattice in the context of Kane–Mele model Hamiltonian. The results for Seebeck coefficient show the sign of thermopower is positive in the presence of spin-orbit coupling. Also the temperature dependence of transport properties indicates that the increase of spin-orbit coupling leads to decrease thermal conductivity however the decrease of gap parameter causes the reduction of thermal conductivity. There is a peak in temperature dependence of thermal conductivity for all values of magnetic fields and spin-orbit coupling strengths. Both electrical and thermal conductivities increase with increasing the temperature at low amounts of temperature due to the increasing of transition rate of charge carriers and excitation of them to the conduction bands. Also we have studied the temperature dependence of Seebeck coefficient of Lieb monolayer due to both spin orbit coupling and magnetic field factors in details.
No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy
Authors: Lubośny Marek , Śmietanka Beata , Arculeo Marco , Burzyński Artur 
Published: May 2022

AbstractTwo genetically different mitochondrial haplogroups ofBrachidontes pharaonis(p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes ofBrachidontes pharaonismussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.
Selection of RNA-based evaluation methods for tumor microenvironment by comparing with histochemical and flow cytometric analyses in gastric cancer
Authors: Saito Noriyuki , Sato Yasuyoshi , Abe Hiroyuki , Wada Ikuo , Kobayashi Yukari , Nagaoka Koji , Kushihara Yoshihiro , Ushiku Tetsuo , Seto Yasuyuki , Kakimi Kazuhiro 
Published: May 2022

AbstractUnderstanding the tumor microenvironment (TME) and anti-tumor immune responses in gastric cancer are required for precision immune-oncology. Taking advantage of next-generation sequencing technology, the feasibility and reliability of transcriptome-based TME analysis were investigated. TME of 30 surgically resected gastric cancer tissues was analyzed by RNA-Seq, immunohistochemistry (IHC) and flow cytometry (FCM). RNA-Seq of bulk gastric cancer tissues was computationally analyzed to evaluate TME. Computationally analyzed immune cell composition was validated by comparison with cell densities established by IHC and FCM from the same tumor tissue. Immune cell infiltration and cellular function were also validated with IHC and FCM. Cell proliferation and cell death in the tumor as assessed by RNA-Seq and IHC were compared. Computational tools and gene set analysis for quantifying CD8+ T cells, regulatory T cells and B cells, T cell infiltration and functional status, and cell proliferation and cell death status yielded an excellent correlation with IHC and FCM data. Using these validated transcriptome-based analyses, the immunological status of gastric cancer could be classified into immune-rich and immune-poor subtypes. Transcriptome-based TME analysis is feasible and is valuable for further understanding the immunological status of gastric cancer.