bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic competition for noise reduction shaped evolutionary landscape of mir-4673
Authors: Farahani Ramin M. , Rezaei-Lotfi Saba , Hunter Neil 
Published: May 2020

AbstractThe genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalised on the recent evolutionary trajectory of hominin-specific miRNA-4673, encoded in intron 4 of notch-1, to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression. Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localise a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism. In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalise on non-random distribution of genomic cis-signatures.
Information gain modulates brain activity evoked by reading
Authors: Kangassalo Lauri , Spapé Michiel , Ravaja Niklas , Ruotsalo Tuukka 
Published: May 2020

AbstractThe human brain processes language to optimise efficient communication. Studies have shown extensive evidence that the brain’s response to language is affected both by lower-level features, such as word-length and frequency, and syntactic and semantic violations within sentences. However, our understanding on cognitive processes at discourse level remains limited: How does the relationship between words and the wider topic one is reading about affect language processing? We propose an information theoretic model to explain cognitive resourcing. In a study in which participants read sentences from Wikipedia entries, we show information gain, an information theoretic measure that quantifies the specificity of a word given its topic context, modulates word-synchronised brain activity in the EEG. Words with high information gain amplified a slow positive shift in the event related potential. To show that the effect persists for individual and unseen brain responses, we furthermore show that a classifier trained on EEG data can successfully predict information gain from previously unseen EEG. The findings suggest that biological information processing seeks to maximise performance subject to constraints on information capacity.
Anomalous magneto-transport properties of bilayer phosphorene
Authors: Wu Jhao-Ying , Su Wu-Pei , Gumbs Godfrey 
Published: May 2020

AbstractThe magneto-transport properties of phosphorene are investigated by employing the generalized tight-binding model to calculate the energy bands. For bilayer phosphorene, a composite magnetic and electric field is shown to induce a feature-rich Landau level (LL) spectrum which includes two subgroups of low-lying LLs. The two subgroups possess distinct features in level spacings, quantum numbers, as well as field dependencies. These together lead to anomalous quantum Hall (QH) conductivities which include a well-shape, staircase and composite quantum structures with steps having varying heights and widths. The Fermi energy-magnetic field-Hall conductivity (EF−Bz−σxy) and Fermi energy-electric field-Hall conductivity (EF−Ez−σxy) phase diagrams clearly exhibit oscillatory behaviors and cross-over from integer to half-integer QH effect. The predicted results should be verifiable by magneto-transport measurements in a dual-gated system.
The Intersection between Spliff Usage, Tobacco Smoking, and Having the First Joint after Waking
Authors: Kumar Navin , Puljević Cheneal , Ferris Jason , Winstock Adam , Barratt Monica J. 
Published: May 2020

AbstractCannabis users who are also tobacco smokers are more likely to exhibit cannabis dependence and psychosocial problems. However, there has been minimal research around various cannabis and tobacco mixing (spliff usage) behaviours and likeliness to smoke the first joint within an hour of waking, known colloquially as wake and bake. The time of first joint and spliff usage may be related as they are associated with the intersection of tobacco and cannabis use. Compared to non-morning cannabis users, morning users reported significantly more cannabis-related problems. Through a survey of US cannabis users, we test the association between various cannabis and spliff use behaviours and likeliness to smoke the first joint within an hour of waking. Compared to those who smoked tobacco and did not use spliffs, the following spliff use behaviour groups were less likely to have their first joint within 60 minutes after waking: those who smoked tobacco and used spliffs (95%CI: 0.605–0.988); those who never smoked tobacco and did not use spliffs (95%CI: 0.489–0.892); those who never smoked tobacco and used spliffs (95%CI:0.022–0.915). We provided possible explanations for our results and suggested further research to better understand findings, important given expanding US cannabis markets.
Population mobility induced phase separation in SIS epidemic and social dynamics
Authors: Harding Nathan , Spinney Richard E. , Prokopenko Mikhail 
Published: May 2020

AbstractUnderstanding the impact of behavior dependent mobility in the spread of epidemics and social disorders is an outstanding problem in computational epidemiology. We present a modelling approach for the study of mobility that adapts dynamically according to individual state, epidemic/social-contagion state and network topology in accordance with limited data and/or common behavioral models. We demonstrate that even for simple compartmental network processes, our approach leads to complex spatial patterns of infection in the endemic state dependent on individual behavior. Specifically, we characterize the resulting phenomena in terms of phase separation, highlighting phase transitions between distinct spatial states and determining the systems’ phase diagram. The existence of such phases implies that small changes in the populations’ perceptions could lead to drastic changes in the spatial extent and morphology of the epidemic/social phenomena.
Soil organic matter stoichiometry as indicator for peatland degradation
Authors: Leifeld Jens , Klein Kristy , Wüst-Galley Chloé 
Published: May 2020

AbstractPeatlands accumulate organic matter (OM) under anaerobic conditions. After drainage for forestry or agriculture, microbial respiration and peat oxidation induce OM losses and change the stoichiometry of the remaining organic material. Here, we (i) evaluate whether land use (cropland CL, grassland GL, forest FL, natural peatland NL) is associated with different peat stoichiometry, (ii) study how peat stoichiometry changes with OM content and (iii) infer the fate of nitrogen upon soil degradation. Organic C and soil N were measured for 1310 samples from 48 sites in Switzerland, and H and O for 1165. The soil OM content and C/N ratio were most sensitive to land use and are hence best suited as indicators for peatland degradation. OM contents (CL < GL < FL < NL), H/C, O/C, C/N ratios, and OM oxidation states were significantly different between land use types in top- and subsoils. With decreasing bulk OM content, C was relatively depleted while H and particularly N were higher. The data suggest very high N mobilization rates from strongly decomposed peat in agricultural topsoil. A comparison to peat C and N from mostly intact peatlands of the Northern hemisphere reveals that agriculture and, to a lesser extent, forestry induce a progressed state of soil degradation.
Different exercise training modalities produce similar endothelial function improvements in individuals with prehypertension or hypertension: a randomized clinical trial
Authors: Pedralli Marinei L. , Marschner Rafael A. , Kollet Daniel P. , Neto Salvador G. , Eibel Bruna , Tanaka Hirofumi , Lehnen Alexandre M. 
Published: May 2020

AbstractEndothelial dysfunction is a characteristic of systemic arterial hypertension (SAH) and an early marker of atherosclerosis. Aerobic exercise training (AT) improves endothelial function. However, the effects of resistance training (RT) and combined training (CT) on endothelial function remain controversial in individuals with SAH. We determined the effects of AT, RT, and CT on endothelial function and systolic (SBP)/diastolic blood pressure (DBP) in individuals with prehypertension or hypertension. Forty-two participants (54 ± 11 y, resting SBP/DBP 137 ± 9/86 ± 6 mmHg) were randomly allocated into AT (n = 14, 40 min of cycling, 50–75% heart rate reserve), RT (n = 14, 6 resistance exercises, 4 × 12 repetitions, 60% maximum strength) and CT (n = 14, 2 × 12 repetitions of RT + 20 min of AT). All participants performed a 40-minute exercise session twice a week for 8 weeks. Endothelial function was evaluated by brachial artery flow-mediated dilation (FMD). Blood pressure was evaluated through ambulatory monitoring for 24 hours. After 8 weeks of exercise training, blood pressure was reduced in all 3 groups: −5.1 mmHg in SBP (95%CI –10.1, 0.0; p = 0.003) in AT; −4.0 mmHg in SBP (95%CI −7.8, −0.5; p = 0.027) in RT; and −3.2 mmHg in DBP (95%CI −7.9, 1.5; p = 0.001) in CT. All 3 exercise training modalities produced similar improvements in FMD: + 3.2% (95%CI 1.7, 4.6) (p < 0.001) in AT; + 4.0% (95%CI 2.1, 5.7) (p < 0.001) in RT; and +6.8% (95%CI 2.6, 11.1) (p = 0.006) in CT. In conclusion, different exercise training modalities were similarly effective in improving endothelial function but impacts on ambulatory blood pressure appear to be variable in individuals with prehypertension or hypertension.
Relationships of virus titers and transmission rates among sympatric and allopatric virus isolates and thrips vectors support local adaptation
Authors: Linak Jessica A. , Jacobson Alana L. , Sit Tim L. , Kennedy George G. 
Published: May 2020

AbstractPlant viruses rely on insect vectors for transmission among plant hosts, but many of the specifics of virus-vector interactions are not fully understood. Thrips tabaci, which transmits Tomato spotted wilt virus (TSWV) in a persistent and propagative manner, varies greatly in its ability to transmit different isolates of TSWV. Similarly, TSWV isolates are transmitted at different efficiencies by different populations of T. tabaci. This study characterizes differences in virus titers in the vector among TSWV isolate-T. tabaci isoline pairings in relation to differences in transmission rates, and demonstrates that although transmission rates were higher for sympatric than allopatric TSWV isolate-T. tabaci isoline pairings, virus titers in the thrips vector were significantly lower in the sympatric pairings. Results further demonstrate that TSWV titers in the vector were unrelated to virus titers in the leaf tissue from which they acquired the virus and provide evidence for the importance of specific vector-virus interactions and local adaptation in determining transmission efficiency of TSWV by T. tabaci.
Effect of Ki-67 Expression Levels and Histological Grade on Breast Cancer Early Relapse in Patients with Different Immunohistochemical-based Subtypes
Authors: Liang Qin , Ma Ding , Gao Run-Fang , Yu Ke-Da 
Published: May 2020

AbstractThis retrospective analysis evaluated the interaction between Ki-67 and histological grade and their prognostic role in different breast cancer subtypes. In total, 2,573 breast cancer patients underwent surgery, and their histological grade and Ki-67 values were evaluated by breast pathologists. The median Ki-67 index was 15%, which was used as the cut-off for low/high Ki-67 expression. Recurrence-free survival (RFS) was calculated and compared, and the results indicated that Ki-67 expression was significantly associated with histological grade in all breast cancer patients (p < 0.001) and in each immunohistochemical (IHC)-based subtype (p < 0.001). Both high Ki-67 expression and grade 3 tumours were independent predictors of inferior RFS in all patients, especially in those with luminal-like tumours (p < 0.05). Ki-67 was an independent prognostic factor for RFS in grade 1, 2 patients with luminal-like tumours (adjusted hazard ratio [HR] = 1.92, 95% confidence interval [CI]: 1.22-3.03, p = 0.005), but not in the other subtypes. Similarly, histological grade predicted shorter RFS in patients with low Ki-67 expression who had luminal-like tumours (adjusted HR = 2.12, 95% CI: 1.13-3.99, p = 0.02) but not in the other subtypes. Conversely, Ki-67 showed no prognostic value for patients with grade 3 tumours and vice versa.
Structural Basis for PPARα Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives
Authors: Yoshida Takuya , Oki Hiroya , Doi Michihiro , Fukuda Syohei , Yuzuriha Tomohiro , Tabata Ryotaro , Ishimoto Kenji , Kawahara Kazuki , Ohkubo Tadayasu , Miyachi Hiroyuki , Doi Takefumi , Tachibana Keisuke 
Published: May 2020

AbstractSmall-molecule agonism of peroxisome proliferator-activated receptor α (PPARα), a ligand-activated transcriptional factor involved in regulating fatty acid metabolism, is an important approach for treating dyslipidemia. Here, we determined the structures of the ligand-binding domain (LBD) of PPARα in complex with 1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid derivatives, which were recently identified as PPARα-selective activators with markedly different structures from those of the well-known PPARα agonists fibrates. The crystal structures of the complexes showed that they form a canonical hydrogen-bond network involving helix 12 in the LBD, which is thought to be essential for PPARα activation, as also observed for fibrates. However, the phenyl side chain of the compounds occupies a small cavity between Ile272 and Ile354, which is rarely accessed by fibrates. This unique feature may be essential for subtype selectivity and combine with the well-characterized binding mode of fibrates to improve activity. These findings demonstrate the advantage of using 1H-pyrazolo-[3,4-b]pyridine as a skeleton of PPARα agonists and provide insight into the design of molecules for treating dyslipidemia.
Roles of PI3K pan-inhibitors and PI3K-δ inhibitors in allergic lung inflammation: a systematic review and meta-analysis
Authors: Kim Jong Seung , Jeong Jae Seok , Kwon Sam Hyun , Kim So Ri , Lee Yong Chul 
Published: May 2020

AbstractMeta-analysis can be applied to study the effectiveness of the summary estimates for experimental papers, producing objective and unbiased results. We investigated the effects of phosphoinositide-3-kinase (PI3K) on the inflammatory profile in allergic mouse models, which are currently under development in signal transduction materials. PubMed, EMBASE and Web of Science databases were searched for relevant literature using the search terms “ PI3K inhibitor” and “allergy” or “asthma”. Cochrane Review Manager and R were used for handling continuous variables. The primary outcomes of the inflammatory profile were divided into cell counts and inflammatory cytokines. We used a random effects model to draw a forest plot. Through the database search and subsequent selection, 17 articles were identified. Regarding the cell counts, both the PI3K pan-inhibitors and PI3K-δ inhibitors effectively reduced the total cell counts, eosinophils, neutrophils and lymphocytes. In contrast to PI3K-δ inhibitors, PI3K pan-inhibitors effectively reduced macrophages. Regarding the inflammatory cytokines, PI3K pan-inhibitors and PI3K-δ inhibitors effectively reduced total IgE, IL-4, IL-5, IL-13, TNF-α, IL-1β, VEGF and had no effect on IL-6. Compared to the PI3K pan-inhibitors, which block all pathways, selective PI3K-δ inhibitors are expected to be relatively less toxic. Regarding the efficacy, PI3K-δ inhibitors have at least the same or better efficacy than PI3K pan-inhibitors in effector cells and inflammatory mediators.
Crystal-like order and defects in metazoan epithelia with spherical geometry
Authors: Roshal Daria S. , Azzag Karim , Le Goff Emilie , Rochal Sergei B. , Baghdiguian Stephen 
Published: May 2020

AbstractSince Robert Hooke studied cork cell patterns in 1665, scientists have been puzzled by why cells form such ordered structures. The laws underlying this type of organization are universal, and we study them comparing the living and non-living two-dimensional systems self-organizing at the spherical surface. Such-type physical systems often possess trigonal order with specific elongated defects, scars and pleats, where the 5-valence and 7-valence vertices alternate. In spite of the fact that the same physical and topological rules are involved in the structural organization of biological systems, such topological defects were never reported in epithelia. We have discovered them in the follicular spherical epithelium of ascidians that are emerging models in developmental biology. Surprisingly, the considered defects appear in the epithelium even when the number of cells in it is significantly less than the previously known threshold value. We explain this result by differences in the cell sizes and check our hypothesis considering the self-assembly of different random size particles on the spherical surface. Scars, pleats and other complex defects found in ascidian samples can play an unexpected and decisive role in the permanent renewal and reorganization of epithelia, which forms or lines many tissues and organs in metazoans.
The transcutaneous electromyography recording method for intraoperative neuromonitoring of recurrent laryngeal nerve during minimally invasive parathyroidectomy
Authors: Li Peng , Liang Qing-Zhuang , Wang Dong-Lai , Han Bin , Yi Xin , Wei Wei , Chiang Feng-Yu 
Published: May 2020

AbstractIntraoperative neuromonitoring (IONM) facilitates recurrent laryngeal nerve (RLN) protection in thyroid and parathyroid surgeries. This study aimed to investigate a novel transcutaneous electromyography (EMG) recording method for IONM of the RLN during minimally invasive parathyroidectomy (MIP). Twenty patients with primary hyperparathyroidism undergoing MIP were enrolled. Two paired needle electrodes were percutaneously inserted into the bilateral laminas of thyroid cartilage for monitoring the vagus nerve and RLN. A standardized IONM procedure (V1-R1-R2-V2 signals) was strictly followed, and the RLN was routinely located and mapped. Pre- and postoperative laryngofiberoscopy was performed to confirm vocal cord function. The proposed technique was successfully used in all patients, and typical EMG signals were effectively detected. No significant change in EMG signals before and after tumor resection was noted, and a normal vocal cord movement was ensured in all patients with postoperative laryngofiberoscopy. IONM helped localize the position of the RLN and facilitated the safe resection of the parathyroid tumor during MIP. The novel transcutaneous EMG recording method proposed in this study was feasible, convenient, reliable, and inexpensive.
Motion-picture recording of ultrafast behavior of polarized light incident at Brewster’s angle
Authors: Sasaki Mika , Matsunaka Atsushi , Inoue Tomoyoshi , Nishio Kenzo , Awatsuji Yasuhiro 
Published: May 2020

AbstractObserving light propagation plays an important role in clarifying ultrafast phenomena occurring on femtosecond to picosecond time scales. In particular, observing the ultrafast behavior of polarized light is useful for various fields. We have developed a technique based on Polarization Light-in-Flight Holography, which can record light propagation as a motion picture that can provide information about the polarization direction. Here we demonstrate motion-picture recording of a phenomenon, which is characteristic of polarized light, by using the proposed technique. As a phenomenon, we adopted the behavior of a light pulse incident at Brewster’s angle. We succeeded in recording the light reflection of specific polarized light by the proposed optical setup. The method of recording the motion-picture, reconstruction procedure, and the quantitative evaluation of the results are demonstrated.
Structural and mechanical remodeling of the cytoskeleton maintains tensional homeostasis in 3D microtissues under acute dynamic stretch
Authors: Walker Matthew , Rizzuto Pauline , Godin Michel , Pelling Andrew E. 
Published: May 2020

AbstractWhen stretched, cells cultured on 2D substrates share a universal softening and fluidization response that arises from poorly understood remodeling of well-conserved cytoskeletal elements. It is known, however, that the structure and distribution of the cytoskeleton is profoundly influenced by the dimensionality of a cell’s environment. Therefore, in this study we aimed to determine whether cells cultured in a 3D matrix share this softening behavior and to link it to cytoskeletal remodeling. To achieve this, we developed a high-throughput approach to measure the dynamic mechanical properties of cells and allow for sub-cellular imaging within physiologically relevant 3D microtissues. We found that fibroblast, smooth muscle and skeletal muscle microtissues strain softened but did not fluidize, and upon loading cessation, they regained their initial mechanical properties. Furthermore, microtissue prestress decreased with the strain amplitude to maintain a constant mean tension. This adaptation under an auxotonic condition resulted in lengthening. A filamentous actin cytoskeleton was required, and responses were mirrored by changes to actin remodeling rates and visual evidence of stretch-induced actin depolymerization. Our new approach for assessing cell mechanics has linked behaviors seen in 2D cultures to a 3D matrix, and connected remodeling of the cytoskeleton to homeostatic mechanical regulation of tissues.
Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease
Authors: Li Meng , Liu Sixiang , Wang Mingying , Hu Hongwei , Yin Jianwen , Liu Chuanfa , Huang Yongkun 
Published: May 2020

AbstractNeonatal cholestasis disease (NCD) is a complex and easily mis-diagnosed condition. We analyzed microbiota community structure in feces and measured short-chain fatty acids, bile acids (BAs) and liver function of 12 healthy, 13 NCD, and 13 treated infants after diagnosis. Based on 16S rRNA gene amplicon sequencing and gas-chromatographic-mass-spectrometric analysis of secondary BAs, we identified microbial genera and metabolites that associate with abnormal bile secretion. Streptococcus gallolyticus and Parabacteroides distasonis, and Lactobacillus gasseri had higher relative abundance in healthy and NCD infants respectively. Compared to NCD patients, healthy infants had higher LCA, CDCA and GCDCA fecal concentrations. The three microbial species and three secondary bile acids were selected as potential non-invasive combined biomarkers to diagnose NCD. We propose that microbiota-metabolite combined biomarkers could be used for diagnosis of NCD, and this may contribute to improved early clinical diagnosis of NCD in the future.