bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a colorectal cancer diagnostic model and dietary risk assessment through gut microbiome analysis
Authors: Yang Jinho , McDowell Andrea , Kim Eun Kyoung , Seo Hochan , Lee Won Hee , Moon Chang-Mo , Kym Sung-Min , Lee Dong Ho , Park Young Soo , Jee Young-Koo , Kim Yoon-Keun 
Published: October 2019

AbstractColorectal cancer (CRC) is the third most common form of cancer and poses a critical public health threat due to the global spread of westernized diets high in meat, cholesterol, and fat. Although the link between diet and colorectal cancer has been well established, the mediating role of the gut microbiota remains elusive. In this study, we sought to elucidate the connection between the gut microbiota, diet, and CRC through metagenomic analysis of bacteria isolated from the stool of CRC (n = 89) and healthy (n = 161) subjects. This analysis yielded a dozen genera that were significantly altered in CRC patients, including increased Bacteroides, Fusobacterium, Dorea, and Porphyromonas prevalence and diminished Pseudomonas, Prevotella, Acinetobacter, and Catenibacterium carriage. Based on these altered genera, we developed two novel CRC diagnostic models through stepwise selection and a simplified model using two increased and two decreased genera. As both models yielded strong AUC values above 0.8, the simplified model was applied to assess diet-based CRC risk in mice. Mice fed a westernized high-fat diet (HFD) showed greater CRC risk than mice fed a regular chow diet. Furthermore, we found that nonglutinous rice, glutinous rice, and sorghum consumption reduced CRC risk in HFD-fed mice. Collectively, these findings support the critical mediating role of the gut microbiota in diet-induced CRC risk as well as the potential of dietary grain intake to reduce microbiota-associated CRC risk. Further study is required to validate the diagnostic prediction models developed in this study as well as the preventive potential of grain consumption to reduce CRC risk.
Lrrc7 mutant mice model developmental emotional dysregulation that can be alleviated by mGluR5 allosteric modulation
Authors: Chong Chi Ho , Li Qi , Mak Priscilla Hoi Shan , Ng Cypress Chun Pong , Leung Eva Hin Wa , Tan Vicky Huiqi , Chan Anthony Kin Wang , McAlonan Grainne , Chan Siu Yuen 
Published: October 2019

AbstractLRRC7 has been identified as a candidate gene for severe childhood emotional dysregulation. Direct experimental evidence for a role of LRRC7 in the disease is needed, as is a better understanding of its impact on neuronal structure and signaling, and hence potential treatment targets. Here, we generated and analyzed an Lrrc7 mutant mouse line. Consistent with a critical role of LRRC7 in emotional regulation, mutant mice had inappropriate juvenile aggressive behavior and significant anxiety-like behavior and social dysfunction in adulthood. The pivotal role of mGluR5 signaling was demonstrated by rescue of behavioral defects with augmentation of mGluR5 receptor activity by 3-Cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (CDPPB). Intra-peritoneal injection of CDPPB alleviated abnormal juvenile behavior, as well as anxiety-like behavior and hypersociability at adulthood. Furthermore, mutant primary neurons had impaired neurite outgrowth which was rescued by CDPPB treatment. In conclusion, Lrrc7 mutant mice provide a valuable tool to model childhood emotional dysregulation and persistent mental health comorbidities. Moreover, our data highlight an important role of LRRC7 in mGluR5 signaling, which is a potential new treatment target for anxiety and social dysfunction.
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos
Authors: Erceg Jelena , AlHaj Abed Jumana , Goloborodko Anton , Lajoie Bryan R. , Fudenberg Geoffrey , Abdennur Nezar , Imakaev Maxim , McCole Ruth B. , Nguyen Son C. , Saylor Wren , Joyce Eric F. , Senaratne T. Niroshini , Hannan Mohammed A. , Nir Guy , Dekker Job , Mirny Leonid A. , Wu C.-ting 
Published: October 2019

AbstractGenome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.
Zinc-doped Prussian blue enhances photothermal clearance of Staphylococcus aureus and promotes tissue repair in infected wounds
Authors: Li Jun , Liu Xiangmei , Tan Lei , Cui Zhenduo , Yang Xianjin , Liang Yanqin , Li Zhaoyang , Zhu Shengli , Zheng Yufeng , Yeung Kelvin Wai Kwok , Wang Xianbao , Wu Shuilin 
Published: October 2019

AbstractThe application of photothermal therapy to treat bacterial infections remains a challenge, as the high temperatures required for bacterial elimination can damage healthy tissues. Here, we develop an exogenous antibacterial agent consisting of zinc-doped Prussian blue (ZnPB) that kills methicillin-resistant Staphylococcus aureus in vitro and in a rat model of cutaneous wound infection. Local heat triggered by the photothermal effect accelerates the release and penetration of ions into the bacteria, resulting in alteration of intracellular metabolic pathways and bacterial killing without systemic toxicity. ZnPB treatment leads to the upregulation of genes involved in tissue remodeling, promotes collagen deposition and enhances wound repair. The efficient photothermal conversion of ZnPB allows the use of relatively few doses and low laser flux, making the platform a potential alternative to current antibiotic therapies against bacterial wound infections.
Fusion dynamics of cubosome nanocarriers with model cell membranes
Authors: Dyett Brendan P. , Yu Haitao , Strachan Jamie , Drummond Calum J. , Conn Charlotte E. 
Published: October 2019

AbstractDrug delivery with nanocarriers relies on the interaction of individual nanocarriers with the cell surface. For lipid-based NCs, this interaction uniquely involves a process of membrane fusion between the lipid bilayer that makes up the NC and the cell membrane. Cubosomes have emerged as promising fusogenic NCs, however their individual interactions had not yet been directly observed due to difficulties in achieving adequate resolution or disentangling multiple interactions with common characterization techniques. Moreover, many studies on these interactions have been performed under static conditions which may not mimic the actual transport of NCs. Herein we have observed fusion of lipid cubosome NCs with lipid bilayers under flow. Total internal reflection microscopy has allowed visualisation of the fusion event which was sensitive to the lipid compositions and rationalized by lipid diffusion. The fusion event in supported lipid bilayers has been compared with those in cells, revealing a distinct similarity in kinetics.
New protein-DNA complexes in archaea: a small monomeric protein induces a sharp V-turn DNA structure
Authors: Loth Karine , Largillière Justine , Coste Franck , Culard Françoise , Landon Céline , Castaing Bertrand , Delmas Agnès F. , Paquet Françoise 
Published: October 2019

AbstractMC1, a monomeric nucleoid-associated protein (NAP), is structurally unrelated to other DNA-binding proteins. The protein participates in the genome organization of several Euryarchaea species through an atypical compaction mechanism. It is also involved in DNA transcription and cellular division through unknown mechanisms. We determined the 3D solution structure of a new DNA-protein complex formed by MC1 and a strongly distorted 15 base pairs DNA. While the protein just needs to adapt its conformation slightly, the DNA undergoes a dramatic curvature (the first two bend angles of 55° and 70°, respectively) and an impressive torsional stress (dihedral angle of 106°) due to several kinks upon binding of MC1 to its concave side. Thus, it adopts a V-turn structure. For longer DNAs, MC1 stabilizes multiple V-turn conformations in a flexible and dynamic manner. The existence of such V-turn conformations of the MC1-DNA complexes leads us to propose two binding modes of the protein, as a bender (primary binding mode) and as a wrapper (secondary binding mode). Moreover, it opens up new opportunities for studying and understanding the repair, replication and transcription molecular machineries of Archaea.
Niobium-titanium (Nb-Ti) superconducting joints for persistent-mode operation
Authors: Patel Dipak , Kim Su-Hun , Qiu Wenbin , Maeda Minoru , Matsumoto Akiyoshi , Nishijima Gen , Kumakura Hiroaki , Choi Seyong , Kim Jung Ho 
Published: October 2019

AbstractSuperconducting joints are essential for persistent-mode operation in a superconducting magnet system to produce an ultra-stable magnetic field. Herein, we report rationally designed niobium-titanium (Nb-Ti) superconducting joints and their evaluation results in detail. For practical applications, superconducting joints were fabricated by using a solder matrix replacement method with two types of lead-bismuth (Pb-Bi) solder, including Pb42Bi58 as a new composition. All the joints attained a critical current of >200 A below 1.43 T at 4.2 K. Our optimized superconducting joining method was tested in a closed-loop coil, obtaining a total circuit resistance of 3.25 × 10−14 Ω at 4.2 K in self-field. Finally, persistent-mode operation was demonstrated in an Nb-Ti solenoid coil with a persistent-current switch. This work will pave the way to developing high-performance Nb-Ti superconducting joints for practical applications.
Nonlinearity- and dispersion- less integrated optical time magnifier based on a high-Q SiN microring resonator
Authors: Misra Arijit , Preußler Stefan , Zhou Linjie , Schneider Thomas 
Published: October 2019

AbstractThe ability to measure optical signals with fast dynamics is of significant interest in many application fields. Usually, single-shot measurements of non-periodic signals can be enabled by time magnification methods. Like an optical lens in the spatial domain, a time magnifier, or a time lens, stretches a signal in the time domain. This stretched signal can then be further processed with low bandwidth photonics and electronics. For a robust and cost-effective measurement device, integrated solutions would be especially advantageous. Conventional time lenses require dispersion and nonlinear optical effects. Integration of a strong dispersion and nonlinearities is not straightforward on a silicon photonics platform and they might lead to signal distortions. Here we present a time magnifier based on an integrated silicon nitride microring resonator and frequency-time coherence optical sampling, which requires neither a dispersion, nor a nonlinearity. Sampling of signals with up to 100 GHz bandwidth with a stretching factor of more than 100 is achieved using low bandwidth measurement equipment. Nevertheless, with already demonstrated integrated 100 GHz modulators, the method enables the measurement of signals with bandwidths of up to 400 GHz. Since amplitude and phase can be sampled, a combination with the spectrum slicing method might enable integrated, cost-effective, small-footprint analog-to-digital converters, and measurement devices for the characterization of single irregular optical signals with fast dynamics and bandwidths in the THz range.
A novel miRNA-4484 is up-regulated on microarray and associated with increased MMP-21 expression in serum of systemic sclerosis patients
Authors: Rusek Marta , Michalska-Jakubus Małgorzata , Kowal Małgorzata , Bełtowski Jerzy , Krasowska Dorota 
Published: October 2019

AbstractSystemic sclerosis (SSc) is a complex, heterogeneous connective tissue disease, characterized by fibrosis and ECM deposition in skin and internal organs, autoimmunity, and changes in the microvasculature. Profiling of circulating miRNAs in serum has been found to be changed in pathological states, creating new possibilities for molecular diagnostics as blood-based biomarkers. This study was designed to identify miRNAs that are differentially expressed in SSc and might be potentially contributing to the disease etiopathogenesis or be used for diagnostic purposes. Thus, we compared the expression pattern of multiple miRNAs in serum of 10 SSc patients to 6 healthy controls using microarray analysis, and RT-qPCR to confirm the obtained results. In addition, bioinformatics analysis was performed to explore miRNAs target genes and the signaling pathways that may be potentially involved in SSc pathogenesis. Our study shows a different expression of 15 miRNAs in SSc patients. We identified that miR-4484, located on chromosome 10q26.2, was an 18-fold up-regulated in SSc patients compared to a control group. Bioinformatics analysis of the miR-4484 target genes and the signaling pathways showed that it might be potentially involved in the TGF-β signaling pathway, ECM-receptor interaction, and metalloproteinases expression. Based on the chromosomal location, the most interesting target gene of miR-4484 may be MMP-21. We found that the expression of MMP-21 significantly increased in SSc patients compared to healthy subjects (P < 0.05). Our results suggest that miR-4484, and MMP-21 might be novel serum biomarkers that may correspond to pathological fibrosis in SSc, but it needs to be validated in further studies.
Signal flow control of complex signaling networks
Authors: Lee Daewon , Cho Kwang-Hyun 
Published: October 2019

AbstractComplex disease such as cancer is often caused by genetic mutations that eventually alter the signal flow in the intra-cellular signaling network and result in different cell fate. Therefore, it is crucial to identify control targets that can most effectively block such unwanted signal flow. For this purpose, systems biological analysis provides a useful framework, but mathematical modeling of complicated signaling networks requires massive time-series measurements of signaling protein activity levels for accurate estimation of kinetic parameter values or regulatory logics. Here, we present a novel method, called SFC (Signal Flow Control), for identifying control targets without the information of kinetic parameter values or regulatory logics. Our method requires only the structural information of a signaling network and is based on the topological estimation of signal flow through the network. SFC will be particularly useful for a large-scale signaling network to which parameter estimation or inference of regulatory logics is no longer applicable in practice. The identified control targets have significant implication in drug development as they can be putative drug targets.
Whale counting in satellite and aerial images with deep learning
Authors: Guirado Emilio , Tabik Siham , Rivas Marga L. , Alcaraz-Segura Domingo , Herrera Francisco 
Published: October 2019

AbstractDespite their interest and threat status, the number of whales in world’s oceans remains highly uncertain. Whales detection is normally carried out from costly sighting surveys, acoustic surveys or through high-resolution images. Since deep convolutional neural networks (CNNs) are achieving great performance in several computer vision tasks, here we propose a robust and generalizable CNN-based system for automatically detecting and counting whales in satellite and aerial images based on open data and tools. In particular, we designed a two-step whale counting approach, where the first CNN finds the input images with whale presence, and the second CNN locates and counts each whale in those images. A test of the system on Google Earth images in ten global whale-watching hotspots achieved a performance (F1-measure) of 81% in detecting and 94% in counting whales. Combining these two steps increased accuracy by 36% compared to a baseline detection model alone. Applying this cost-effective method worldwide could contribute to the assessment of whale populations to guide conservation actions. Free and global access to high-resolution imagery for conservation purposes would boost this process.
Anti-aphrodisiac pheromone, a renewable signal in adult butterflies
Authors: Mozuraitis Raimondas , Murtazina Rushana , Zurita Javier , Pei Yuxin , Ilag Leopold , Wiklund Christer , Karlson Anna Karin Borg 
Published: October 2019

AbstractThe male butterfly Pieris napi produces the anti-aphrodisiac pheromone methyl salicylate (MeS) and transfers it to the female during mating. After mating she releases MeS, when courted by conspecific males, which decreases her attractiveness and the duration of male harassment, thus increasing her time available for egg-laying. In previous studies we have shown that males produced MeS from the amino acid L-phenylalanine (L-Phe) acquired during larval stage. In this study we show that adult males of P. napi can utilize L-Phe and aromatic flower volatiles as building blocks for production of anti-aphrodisiac pheromone and transfer it to females during mating. We demonstrate this by feeding butterflies with stable isotope labelled molecules mixed in sugar solutions, and, to mimic the natural conditions, we fed male butterflies with floral nectar of Bunias orientalis plants treated with labelled L-Phe. The volatiles from butterflies and plants were collected and identified by solid phase micro extraction, gas chromatography and mass spectrometry techniques. Since P. napi is polygamous, males would gain from restoring the titre of MeS after mating and the use of aromatic precursors for production of MeS could be considered as an advantageous trait which could enable butterflies to relocate L-Phe for other needs.
Long-term Outcomes Following Lumbar Microendoscopic Diskectomy and Microendoscopic Decompression: Minimum 10-year Follow-up Evaluation Performed Using a Patient-based Outcome Measure
Authors: Aihara Takato , Endo Kenji , Suzuki Hidekazu , Sawaji Yasunobu , Urushibara Makoto , Matsuoka Yuji , Takamatsu Taichiro , Murata Kazuma , Kusakabe Takuya , Maekawa Asato , Ouchi Juntaro 
Published: October 2019

Abstract
Study Design Retrospective study of prospectively collected outcome data.
Background No studies have evaluated the long-term outcomes following microendoscopic diskectomy for lumbar disk herniation (MEDH) and microendoscopic decompression for lumbar spinal stenosis (MEDS) using the Japanese Orthopaedic Association Back Pain Evaluation Questionnaire (JOABPEQ).
Objective To assess the minimum 10-year outcomes following MEDH and MEDS.
Patients and Methods Seventy-six patients were classified into three groups: disk herniation (DH) group (33 patients underwent MEDH); spinal stenosis (SS) group (23 patients underwent MEDS); and degenerative spondylolisthesis (DS) group (20 DS patients underwent MEDS). The follow-up rate was 50.3% (76/151). The results were statistically compared using Scheffé's F test for differences among the DH, SS, and DS groups. The paired t test was used to compare the preoperative and postoperative visual analog scale (VAS) scores. The degrees of improvement (DOIs) on JOABPEQ and the intensities of improvement (IOIs) on VAS at the first follow-up evaluation (FFE) (mean: 12 months after the operation) and at the most recent follow-up evaluation (MRFE) (mean: 126 months) of the DH group were statistically compared by the paired t test. DOIs and IOIs at MRFE of the SS group (mean: 126 months) and DS group (mean: 125 months) were statistically compared by the unpaired t test. A p value < 0.05 was considered statistically significant.
Results Statistical comparisons of the DOIs in all five functional scores and IOIs in low back pain (LBP), leg pain, and leg numbness showed no significant differences among the DH, SS, and DS groups. The effectiveness rates of pain-related disorders, gait disturbance, and social life disturbance in JOABPEQ were almost equally high in all three groups. Significant decreases in LBP, leg pain, and numbness, as measured with VAS, were noted at MRFE in all three groups. No significant differences were observed between FFE and MRFE concerning the DOIs and IOIs of the DH group, and between the SS and DS groups concerning the DOIs and IOIs at MRFE.
Conclusion Clinical 1-year outcomes of MEDH were thought to be maintained for  > 10 years, and MEDS leads to the same clinical long-term outcomes with DS as without DS. Moreover, MEDH and MEDS were almost equally effective for  > 10 years not only in improving LBP, leg pain, and numbness but also especially in improving pain-related disorders, gait disturbance, and social life disturbance by detailed quality-of-life assessment using JOABPEQ.
Pancreatic Incidentalomas: Review and Current Management Recommendations
Authors: Sureka Binit , Varshney Vaibhav 
Published: October 2019

AbstractThere has been significant increase in the detection of incidental pancreatic lesions due to widespread use of cross-sectional imaging like computed tomography and magnetic resonance imaging supplemented with improvements in imaging resolution. Hence, accurate diagnosis (benign, borderline, or malignant lesion) and adequate follow-up is advised for these incidentally detected pancreatic lesions. In this article, we would review the various pancreatic parenchymal (cystic or solid) and ductal lesions (congenital or pathological), discuss the algorithmic approach in management of incidental pancreatic lesions, and highlight the key imaging features for accurate diagnosis.