bluuebunny/crossref_metadata_2025_split huggingface dataset:
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data
Authors: Kaushik Aman Chandra , Mehmood Aamir , Dai Xiaofeng , Wei Dong-Qing 
Published: March 2020

AbstractMany molecular system biology approaches recognize various interactions and functional associations of proteins that occur in cellular processing. Further understanding of the characterization technique reveals noteworthy information. These types of known and predicted interactions, gained through multiple resources, are thought to be important for experimental data to satisfy comprehensive and quality needs. The current work proposes the “WeiBI (WeiBiologicalInteractions)” database that clarifies direct and indirect partnerships associated with biological interactions. This database contains information concerning protein’s functional partnerships and interactions along with their integration into a statistical model that can be computationally predicted for humans. This novel approach in WeiBI version 1.0 collects information using an improved algorithm by transferring interactions between more than 115570 entries, allowing statistical analysis with the automated background for the given inputs for functional enrichment. This approach also allows the input of an entity’s list from a database along with the visualization of subsets as an interaction network and successful performance of the enrichment analysis for a gene set. This wisely improved algorithm is user-friendly, and its accessibility and higher accuracy make it the best database for exploring interactions among genomes’ network and reflects the importance of this study. The proposed server “WeiBI” is accessible at http://weislab.com/WeiDOCK/?page=PKPD.
Decoding of Pain Perception using EEG Signals for a Real-Time Reflex System in Prostheses: A Case Study
Authors: Tayeb Zied , Bose Rohit , Dragomir Andrei , Osborn Luke E. , Thakor Nitish V. , Cheng Gordon 
Published: March 2020

AbstractIn recent times, we have witnessed a push towards restoring sensory perception to upper-limb amputees, which includes the whole spectrum from gentle touch to noxious stimuli. These are essential components for body protection as well as for restoring the sense of embodiment. Notwithstanding the considerable advances that have been made in designing suitable sensors and restoring tactile perceptions, pain perception dynamics and its decoding using effective bio-markers, are still not fully understood. Here, using electroencephalography (EEG) recordings, we identified and validated a spatio-temporal signature of brain activity during innocuous, moderately more intense, and noxious stimulation of an amputee’s phantom limb using transcutaneous nerve stimulation (TENS). Based on the spatio-temporal EEG features, we developed a system for detecting pain perception and reaction in the brain, which successfully classified three different stimulation conditions with a test accuracy of 94.66%, and we investigated the cortical activity in response to sensory stimuli in these conditions. Our findings suggest that the noxious stimulation activates the pre-motor cortex with the highest activation shown in the central cortex (Cz electrode) between 450 ms and 750 ms post-stimulation, whereas the highest activation for the moderately intense stimulation was found in the parietal lobe (P2, P4, and P6 electrodes). Further, we localized the cortical sources and observed early strong activation of the anterior cingulate cortex (ACC) corresponding to the noxious stimulus condition. Moreover, activation of the posterior cingulate cortex (PCC) was observed during the noxious sensation. Overall, although this is a single case study, this work presents a novel approach and a first attempt to analyze and classify neural activity when restoring sensory perception to amputees, which could chart a route ahead for designing a real-time pain reaction system in upper-limb prostheses.
3′-Sialyllactose prebiotics prevents skin inflammation via regulatory T cell differentiation in atopic dermatitis mouse models
Authors: Kang Li-Jung , Oh Eunjeong , Cho Chanmi , Kwon HoKeun , Lee Choong-Gu , Jeon Jimin , Lee Hyemi , Choi Sangil , Han Seong Jae , Nam Jiho , Song Chi-une , Jung Hyunho , Kim Hye Young , Park Eun-Jung , Choi Eun-Ju , Kim Jooyoung , Eyun Seong-il , Yang Siyoung 
Published: March 2020

Abstract3′-Sialyllactose (3′-SL), a natural prebiotic, maintains immune homeostasis and exerts anti-inflammatory and anti-arthritic effects. Although regulatory T cells (Tregs) prevent excessive inflammation and maintain immune tolerance, the effect of 3′-SL on Treg regulation is unclear. This study aimed to investigate the effect of 3′-SL on Treg responses in atopic dermatitis (AD) pathogenesis. Oral administration of 3′-SL reduced AD-like symptoms such as ear, epidermal, and dermal thickness in repeated topical application of house dust mites (HDM) and 2,4-dinitrochlorobenzene (DNCB). 3′-SL inhibited IgE, IL-1β, IL-6, and TNF-α secretion and markedly downregulated AD-related cytokines including IL-4, IL-5, IL-6, IL-13, IL-17, IFN-γ, TNF-α, and Tslp through regulation of NF-κB in ear tissue. Additionally, in vitro assessment of Treg differentiation revealed that 3′-SL directly induced TGF-β-mediated Treg differentiation. Furthermore, 3′-SL administration also ameliorated sensitization and elicitation of AD pathogenesis by suppressing mast cell infiltration and production of IgE and pro-inflammatory cytokines in mouse serum by mediating the Treg response. Furthermore, Bifidobacterium population was also increased by 3′-SL administration as prebiotics. Our data collectively show that 3′-SL has therapeutic effects against AD progression by inducing Treg differentiation, downregulating AD-related cytokines, and increasing the Bifidobacterium population.
Circadian rhythm impacts preclinical FDG-PET quantification in the brain, but not in xenograft tumors
Authors: Krueger Marcel A. , Calaminus Carsten , Schmitt Julia , Pichler Bernd J. 
Published: March 2020

AbstractThe inner clock of biological organisms plays a pivotal role and has strong effects on metabolic processes such as glucose consumption. Since the commonly used positron emission tomography (PET) tracer 18F-flourodeoxygucose (FDG) is a glucose analogue, it is not surprising that the FDG distribution in mice and humans has been shown to succumb to daily rhythms. In preclinical studies, the circadian rhythm of animals is often not considered, and studies are performed at different times of day. Only a few studies have analyzed the effect of the circadian rhythm on FDG uptake in mice, and none of these studies included human tumor xenografts. Therefore, it is not known how strongly a preclinical tumor study is influenced by the time of day. In this work, the effect of the circadian rhythm on FDG uptake in human tumor xenografts and other organs was analyzed. CD1 nu/nu mice were kept for three weeks under a 12 h light/12 h dark rhythm and then injected s.c. with PC3 or A431 tumor cells. When the tumors had reached an appropriate volume, FDG-PET scans were performed on different animal groups (n = 4–5) every 4 h over a time period from 8 A.M. to 8 P.M. Tracer uptake in the tumors and in other organs was determined based on the PET scans and biodistribution studies. The standardized uptake value and %injected dose/cc of the tumors remained constant over the whole observed time period, and no statistically significant differences were determined according to the PET analysis. In the brain, we found a small but statistically significant increase from noon to 4 P.M., which led to a decrease in the tumor-to-brain ratio. No evidence for an effect of the circadian rhythm on FDG uptake could be found in subcutaneous tumors, however, in brain studies the circadian rhythm needs to be considered.
The relationship of human tissue microRNAs with those from body fluids
Authors: Cui Chunmei , Cui Qinghua 
Published: March 2020

AbstractIt is known that many microRNAs (miRNAs) stably exist in various body fluids, however, the relationship of body fluids miRNAs (BF-miRNAs) with those from tissues (T-miRNAs) remains largely unclear but is important for understanding the potential of BF-miRNAs to be biomarkers of specific diseases. Here by analyzing miRNA expression data from 40 human healthy tissues and those from human body fluids, including plasma, serum, urine, bile, and feces, we revealed a positive correlation between BF-miRNAs and T-miRNAs. Moreover, plasma and serum have the most communication with pericardium, adipose, liver, and spleen. Urinary miRNAs show the highest correlation with kidney miRNAs. For fecal miRNAs, gastrointestinal tract (colon, ileum, jejunum, small intestine, stomach, proximal colon, duodenum, and distal colon) miRNAs show the strongest correlation. Moreover, miRNA set enrichment analysis revealed that highly expressed fecal miRNAs are mostly associated with gastric and colon cancers etc. Additionally, bile miRNAs from suspected cholangiocarcinoma patients show a positive correlation with the cholangiocarcinoma tumor tissue. Interestingly, the relationship of BF-miRNAs and T-miRNAs shows significant sex differences. Serum miRNAs showed higher correlation with T-miRNAs in males, whereas plasma miRNAs and urine miRNAs showed higher correlations with T-miRNAs in females. These findings together indicate a potential role of BF-miRNAs as biomarkers to monitor corresponding specific human diseases.
Characteristics of Hourly Extreme Precipitation along the Yangtze River Basin, China during Warm Season
Authors: Zhao Yong , Huang Anning , Kan Menyun , Dong Xinning , Yu Xiaojing , Wu Yang , Zhang Xindan , Cai Shuxin 
Published: March 2020

AbstractBased on the hourly gauge-satellite merged precipitation data with the spatial resolution of 0.1° × 0.1° during 2008–2016, the characteristics of extreme precipitation (EP) diurnal cycle along the Yangtze River Basin (YRB) and their regional and sub-seasonal differences during warm season have been indicated and revealed in this study. Results show that the EP amount (EPA) over most lower reaches of YRB exhibits two diurnal peaks with one in late afternoon and the other in morning, while the EPA over most eastern Tibetan Plateau (the Sichuan Basin and the northern Yunnan-Guizhou Plateau) generally peaks during late afternoon to midnight (midnight to early morning). The afternoon (morning) EPA diurnal peaks over the areas east to 110°E is mainly resulted from the short (long) duration EP events. However, both the short and long duration EP events lead to the nocturnal diurnal peaks and eastward propagating features of EPA over the regions west to110°E. The EP events over the Sichuan Basin generally begin at midnight and mostly peak around 03:00-04:00 Beijing time, and they start earlier and end later with the duration time increased. However, the EP events with short (long) duration over the lower reaches of YRB frequently start and peak in afternoon (early morning) and typically end at around 18:00 (07:00-08:00) Beijing time, and they start later (earlier) and end later with the duration time increased. Meanwhile, the EP frequency (EPF) diurnal cycles over the lower reaches of YRB exhibit obvious sub-seasonal differences in warm season, which show only a morning peak in the pre-Meiyu period, two comparable peaks with one in afternoon and the other in morning during the Meiyu period, and a predominant afternoon peak and a secondary morning peak in the post-Meiyu period, respectively. While the EPF over Sichuan Basin characterized by only one dominant early morning peak during all periods of the warm season exhibits much smaller sub-seasonal differences in the diurnal phase relative to that over the lower reaches of YRB.
Dual use of electronic and conventional cigarettes is associated with higher cardiovascular risk factors in Korean men
Authors: Kim Choon-Young , Paek Yu-Jin , Seo Hong Gwan , Cheong Yoo Seock , Lee Cheol Min , Park Sang Min , Park Da Won , Lee Kiheon 
Published: March 2020

AbstractMost smokers who use electronic cigarettes (e-cigarettes) to stop smoking simultaneously use conventional cigarettes (dual users). We aimed to compare the prevalence of cardiovascular risk factors among dual users, cigarette-only smokers, and never smokers in Korean men. We used data acquired from Korean National Health and Nutrition Examination Survey (2013–2017) pertaining to 7,505 male participants aged 19 years or older. About 85% of e-cigarette users were dual users. Dual users had greater nicotine dependence and higher urinary cotinine levels than cigarette-only smokers. Dual users had more psychosocial and behavioural risk factors, including perceived high stress, depressive mood, high daily intake of energy, and obesity, than never smokers and cigarette-only smokers. The prevalence of metabolic syndrome (MetS) was higher among dual users, and their multivariate-adjusted prevalence odds ratio for MetS was 2.79 (P < 0.001) compared with never smokers and 1.57 (P = 0.038) compared with cigarette-only smokers. Given that most e-cigarette users are dual users and dual users are more vulnerable to cardiovascular risk factors than cigarette-only smokers and never smokers, more active treatment for smoking cessation and intensive lifestyle interventions for dual users should be considered with priority.
Effects of prophylactic antibiotic-treatment on post-surgical recovery following intraperitoneal bio-logger implantation in rainbow trout
Authors: Hjelmstedt Per , Sundh Henrik , Brijs Jeroen , Ekström Andreas , Sundell Kristina Snuttan , Berg Charlotte , Sandblom Erik , Bowman Jennifer , Morgenroth Daniel , Gräns Albin 
Published: March 2020

AbstractBio-logging devices can provide unique insights on the life of freely moving animals. However, implanting these devices often requires invasive surgery that causes stress and physiological side-effects. While certain medications in connection to surgeries have therapeutic capacity, others may have aversive effects. Here, we hypothesized that the commonly prescribed prophylactic treatment with enrofloxacin would increase the physiological recovery rate and reduce the presence of systemic inflammation following the intraperitoneal implantation of a heart rate bio-logger in rainbow trout (Oncorhynchus mykiss). To assess post-surgical recovery, heart rate was recorded for 21 days in trout with or without enrofloxacin treatment. Contrary to our hypothesis, treated trout exhibited a prolonged recovery time and elevated resting heart rates during the first week of post-surgical recovery compared to untreated trout. In addition, an upregulated mRNA expression of TNFα in treated trout indicate a possible inflammatory response 21 days post-surgery. Interestingly, the experience level of the surgeon was observed to have a long-lasting impact on heart rate. In conclusion, our study showed no favorable effects of enrofloxacin treatment. Our findings highlight the importance of adequate post-surgical recovery times and surgical training with regards to improving the welfare of experimental animals and reliability of research outcomes.
Conjugation with carbon nanotubes improves the performance of mesoporous silicon as Li-ion battery anode
Authors: Ikonen Timo , Kalidas Nathiya , Lahtinen Katja , Isoniemi Tommi , Toppari J. Jussi , Vázquez Ester , Herrero-Chamorro M. Antonia , Fierro José Luis G. , Kallio Tanja , Lehto Vesa-Pekka 
Published: March 2020

AbstractCarbon nanotubes can be utilized in several ways to enhance the performance of silicon-based anodes. In the present work, thermally carbonized mesoporous silicon (TCPSi) microparticles and single-walled carbon nanotubes (CNTs) are conjugated to create a hybrid material that performs as the Li-ion battery anode better than the physical mixture of TCPSi and CNTs. It is found out that the way the conjugation is done has an essential role in the performance of the anode. The conjugation should be made between negatively charged TCPSi and positively charged CNTs. Based on the electrochemical experiments it is concluded that the positive charges, i.e., excess amine groups of the hybrid material interfere with the diffusion of the lithium cations and thus they should be removed from the anode. Through the saturation of the excess positive amine groups on the CNTs with succinic anhydride, the performance of the hybrid material is even further enhanced.
Occurrence and pathogenicity of Corinectria spp. – an emerging canker disease of Abies sibirica in Central Siberia
Authors: Pavlov Igor N. , Vasaitis Rimvydas , Litovka Yulia A. , Stenlid Jan , Jankovsky Libor , Timofeev Anton A. , Menkis Audrius 
Published: March 2020

AbstractDuring recent years, a new disease of Siberian fir (A. sibirica) emerged in Central Siberia, exhibiting symptoms of stem/branch deformation, cambium necrosis, and dieback of branches and twigs, the causal agent remaining unknown. The aim was to identify agent of the disease and to investigate its pathogenicity toA. sibiricaand Norway spruce (Picea abies). Symptomatic tissues of fir were subjected to pure culture isolation of anticipated pathogen(s). Obtained isolates were subjected to molecular identification, phylogenetic analyses, and pathogenicity tests withA. sibiricasaplings, and seeds and seedlings ofA. sibiricaandP. abies. The study demonstrated that, (i) most commonly isolated fungus from canker wounds ofA. sibiricaexhibitedAcremonium-like anamorphs; (ii) phylogeny demonstrated that investigated fungi belong to genusCorinectria, but are genetically well separated from other worldwide knownCorinectriaspp.; (iii) one species of isolated fungi has the capacity to cause the disease and killA. sibiricasaplings and seedlings, but also seedlings ofP. abies. Guidelines for future research were defined in order to generate needed information on species description, its origin and ecology, and estimation of potential risks upon the eventual invasion of the pathogen to new geographic areas, in particular of Europe.
The Association of Pregnancy-induced Hypertension with Bronchopulmonary Dysplasia – A Retrospective Study Based on the Korean Neonatal Network database
Authors: Shin Seung Hyun , Shin Seung Han , Kim Seh Hyun , Kim Yoo-Jin , Cho Hannah , Kim Ee-Kyung , Kim Han-Suk 
Published: March 2020

AbstractThe prevalence of pregnancy-induced hypertension (PIH) and preeclampsia (PE) are 5–10% and 2–4%, respectively. PIH might affect angiogenesis in preterm neonates, but its association with bronchopulmonary dysplasia (BPD) remains controversial. This study evaluated the association between PIH and BPD in very low-birth weight infants. We retrospectively analysed the maternal, perinatal, and neonatal data of preterm infants born before 30 weeks of gestation, selected from the nationwide registry of very low-birth weight infants, between January 2013 and December 2014. As a result, 1,624 infants without maternal PIH (gestational age: 27.3 ± 1.8 weeks) and 203 infants with maternal PIH (28.0 ± 1.4 weeks, p < 0.001) were included. Birth weight was higher in the non-PIH group, compared with the PIH group (1027.4 ± 250.2 vs. 876.4 ± 261.5 g, p < 0.001). Multivariate logistic regression showed that PIH was associated with BPD (adjusted OR 1.474, 95% confidence interval 1.025–2.121), after adjusting for confounders, including small-for-gestation age (SGA). The result of present study is consistent with the current concept of BPD as an early form of pulmonary vascular disease, for both PIH and BPD are attributed by abnormal vascular formation.
Temporal contrast effects in human speech perception are immune to selective attention
Authors: Bosker Hans Rutger , Sjerps Matthias J. , Reinisch Eva 
Published: March 2020

AbstractTwo fundamental properties of perception are selective attention and perceptual contrast, but how these two processes interact remains unknown. Does an attended stimulus history exert a larger contrastive influence on the perception of a following target than unattended stimuli? Dutch listeners categorized target sounds with a reduced prefix “ge-” marking tense (e.g., ambiguous between gegaan-gaan “gone-go”). In ‘single talker’ Experiments 1–2, participants perceived the reduced syllable (reporting gegaan) when the target was heard after a fast sentence, but not after a slow sentence (reporting gaan). In ‘selective attention’ Experiments 3–5, participants listened to two simultaneous sentences from two different talkers, followed by the same target sounds, with instructions to attend only one of the two talkers. Critically, the speech rates of attended and unattended talkers were found to equally influence target perception – even when participants could watch the attended talker speak. In fact, participants’ target perception in ‘selective attention’ Experiments 3–5 did not differ from participants who were explicitly instructed to divide their attention equally across the two talkers (Experiment 6). This suggests that contrast effects of speech rate are immune to selective attention, largely operating prior to attentional stream segregation in the auditory processing hierarchy.
VHS, US3 and UL13 viral tegument proteins are required for Herpes Simplex Virus-Induced modification of protein kinase R
Authors: Pennisi Rosamaria , Musarra-Pizzo Maria , Lei Zhixiang , Zhou Grace Guoying , Sciortino Maria Teresa 
Published: March 2020

AbstractTo replicate, spread and persist in the host environment, viruses have evolved several immunological escape mechanisms via the action of specific viral proteins. The model “host shut off” adopted by virion host shut off (VHS) protein of Herpes simplex type 1 (HSV-1) represents an immune evasion mechanism which affects the best-characterized component of the innate immunological response, protein kinase R (PKR). However, up to now, the real mechanism employed by VHS to control PKR is still unknown. In this paper, we implement and extend our previous findings reporting that wild-type HSV-1 is able to control PKR, whereas a VHS mutant virus (R2621) clearly induces an accumulation of phosphorylated PKR in several cell types in a VHS-RNase activity-dependent manner. Furthermore, we demonstrate for the first time a new PKR-regulatory mechanism based on the involvement of Us3 and UL13 tegument viral proteins. The combined approach of transfection and infection assay was useful to discover the new role of both viral proteins in the immunological escape and demonstrate that Us3 and UL13 control the accumulation of the phosphorylated form (ph-PKR). Lastly, since protein kinases are tightly regulated by phosphorylation events and, at the same time, phosphorylate other proteins by inducing post-translational modifications, the interplay between Us3 and VHS during HSV-1 infection has been investigated. Interestingly, we found that VHS protein accumulates at higher molecular weight following Us3 transfection, suggesting an Us3-mediated phosphorylation of VHS. These findings reveal a new intriguing interplay between viral proteins during HSV-1 infection involved in the regulation of the PKR-mediated immune response.