bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary history of the extant amphioxus lineage with shallow-branching diversification
Authors: Igawa Takeshi , Nozawa Masafumi , Suzuki Daichi G. , Reimer James D. , Morov Arseniy R. , Wang Yiquan , Henmi Yasuhisa , Yasui Kinya 
Published: April 2017

AbstractAmphioxus or lancelets have been regarded as a key animal in understanding the origin of vertebrates. However, the evolutionary history within this lineage remains unexplored. As the amphioxus lineage has likely been separated from other chordates for a very long time and displays a marked left-right asymmetry, its evolutionary history is potentially helpful in better understanding chordate and vertebrate origins. We studied the phylogenetic relationships within the extant amphioxus lineage based on mitochondrial genomes incorporating newAsymmetronandEpigonichthyspopulations, and based on previously reported nuclear transcriptomes. The resulting tree patterns are consistent, showing theAsymmetronclade diverging first, followed by theEpigonichthysandBranchiostomaclades splitting. Divergence time estimates based on nuclear transcriptomes with vertebrate calibrations support a shallow diversification of the extant amphioxus lineage in the Tertiary. These estimates fit well with the closure of seaways between oceans by continental drift, ocean currents, and present geographical distributions, and suggest a long cryptic history from the origin of amphioxus to its most recent diversification. Deduced character polarities based on phylogenetic analyses suggest that the common ancestor of the extant amphioxus existed in a tiny epibenthic state with larva-like appearance of extant amphioxus, likely with ciliate epidermis.
Physical Links: defining and detecting inter-chain entanglement
Authors: Caraglio Michele , Micheletti Cristian , Orlandini Enzo 
Published: April 2017

AbstractFluctuating filaments, from densely-packed biopolymers to defect lines in structured fluids, are prone to become interlaced and form intricate architectures. Understanding the ensuing mechanical and relaxation properties depends critically on being able to capture such entanglement in quantitative terms. So far, this has been an elusive challenge. Here we introduce the first general characterization of non-ephemeral forms of entanglement in linear curves by introducing novel descriptors that extend topological measures of linking from close to open curves. We thus establish the concept of physical links. This general method is applied to diverse contexts: equilibrated ring polymers, mechanically-stretched links and concentrated solutions of linear chains. The abundance, complexity and space distribution of their physical links gives access to a whole new layer of understanding of such systems and open new perspectives for others, such as reconnection events and topological simplification in dissipative fields and defect lines.
Nanoscale Membrane Domain Formation Driven by Cholesterol
Authors: Javanainen Matti , Martinez-Seara Hector , Vattulainen Ilpo 
Published: April 2017

AbstractBiological membranes generate specific functions through compartmentalized regions such as cholesterol-enriched membrane nanodomains that host selected proteins. Despite the biological significance of nanodomains, details on their structure remain elusive. They cannot be observed via microscopic experimental techniques due to their small size, yet there is also a lack of atomistic simulation models able to describe spontaneous nanodomain formation in sufficiently simple but biologically relevant complex membranes. Here we use atomistic simulations to consider a binary mixture of saturated dipalmitoylphosphatidylcholine and cholesterol — the “minimal standard” for nanodomain formation. The simulations reveal how cholesterol drives the formation of fluid cholesterol-rich nanodomains hosting hexagonally packed cholesterol-poor lipid nanoclusters, both of which show registration between the membrane leaflets. The complex nanodomain substructure forms when cholesterol positions itself in the domain boundary region. Here cholesterol can also readily flip–flop across the membrane. Most importantly, replacing cholesterol with a sterol characterized by a less asymmetric ring region impairs the emergence of nanodomains. The model considered explains a plethora of controversial experimental results and provides an excellent basis for further computational studies on nanodomains. Furthermore, the results highlight the role of cholesterol as a key player in the modulation of nanodomains for membrane protein function.
Chlamydia trachomatis neither exerts deleterious effects on spermatozoa nor impairs male fertility
Authors: Puerta Suarez Jenniffer , Sanchez Leonardo R. , Salazar Florencia C. , Saka Hector A. , Molina Rosa , Tissera Andrea , Rivero Virginia E. , Cardona Maya Walter D. , Motrich Ruben D. 
Published: April 2017

AbstractChlamydia trachomatis is the most prevalent sexually transmitted bacterial infection. However, whether Chlamydia trachomatis has a negative impact on sperm quality and male fertility is still controversial. Herein, we report the effects on sperm quality of the in vitro exposure of spermatozoa to Chlamydia trachomatis, and also the effects of male genital infection on male fertility using an animal model. Human and mouse sperm were obtained from healthy donors and cauda epididimys from C57BL/6 mice, respectively. Highly motile human or mouse spermatozoa were in vitro exposed to C. trachomatis (serovar E or LGV) or C. muridarum, respectively. Then, sperm quality parameters were analyzed. Moreover, male fertility of Chlamydia muridarum infected male C57BL/6 mice was assessed. Human or murine sperm in vitro exposed to increasing bacterial concentrations or soluble factors from C. trachomatis or C. muridarum, respectively, did not show differences in sperm motility and viability, apoptosis, mitochondrial membrane potential, DNA fragmentation, ROS production and lipid peroxidation levels, when compared with control sperm (p > 0.05). Moreover, no differences in fertility parameters (potency, fecundity, fertility index, pre- and post-implantation loss) were observed between control and infected males. In conclusion, our results indicate that Chlamydia spp. neither directly exerts deleterious effects on spermatozoa nor impairs male fertility.
Leukemia and Risk of Venous Thromboembolism: A Meta-analysis and Systematic Review of 144 Studies Comprising 162,126 Patients
Authors: Wu Ying-Ying , Tang Liang , Wang Ming-Huan 
Published: April 2017

AbstractVenous thromboembolism (VTE) has significant clinical implications in leukemia patients. However, the actual frequency of this complication remains unknown. We performed a systematic review and meta-analysis to better estimate the frequency of this complication and to assess the risk factors that contribute to its occurrence. We searched several databases, including PubMed, Embase, and Web of Science, and assessed study quality using the Newcastle–Ottawa scale. The pooled frequency of VTE in leukemia patients was calculated. A total of 144 studies met the eligibility criteria. The incidence rate (IR) of VTE from 72 prospective studies comprising 9,061 patients was 5% (95%CI: 4–6%). The incidence rate (IR) of VTE in ALL, CLL, total-AML, and CML population was 5% (95%CI: 4–6%), 3% (95%CI: 2–5%), 6% (95%CI: 4–8%) and 13% (95%CI: 1–36%). The incidence of VTE was markedly decreased among ALL patients who received anticoagulation treatment (IR: 1%, 95%CI: 0–6%) or concentrates therapy (IR: 3%, 95%CI: 0–9%). The overall incidence of VTE in the leukemia population was high, particularly in transplant recipients, who had the highest risk (IR: 8%, 95% CI: 4–13%). Prophylactic approaches could significantly decrease the occurrence of VTE events.
MicroRNA-30a Regulation of Epithelial-Mesenchymal Transition in Diabetic Cataracts Through Targeting SNAI1
Authors: Zhang Lu , Wang Ye , Li Wenfeng , Tsonis Panagiotis A. , Li Zhiyuan , Xie Lixin , Huang Yusen 
Published: April 2017

AbstractEpithelial-mesenchymal transition (EMT) is a highly conserved and fundamental process in development, fibrosis, and metastasis. During the process, epithelial cells lose their morphology and transcriptional program, and transdifferentiate to mesenchymal cells. It has been reported that lens epithelial cells undergo EMT during cataract formation, and regulation of microRNAs on genes is associated with lens development. However, the molecular mechanisms of this regulation in diabetic cataract still need to be investigated. In the present study, the expression of E-cadherin was downregulated, while the expression of alpha-SMA and vimentin was upregulated in diabetic cataract tissues and the in vitro model, suggesting the involvement of EMT in diabetic cataract formation. Results of miRNA profiling demonstrated that miR-30a was markedly downregulated in diabetic cataract tissues. Overexpression of miR-30a-5p decreased SNAI1, a known modulator of EMT, and the expression of vimentin and alpha-SMA in our diabetic cataract model in vitro. It is concluded that EMT is involved in human diabetic cataract, and upregulation of miR-30a can repress EMT through its targeting of SNAI1 in lens epithelial cells, which make miR-30a a novel target of therapeutic intervention for human diabetic cataract.
The upper limit of the in-plane spin splitting of Gaussian beam reflected from a glass-air interface
Authors: Zhu Wenguo , Yu Jianhui , Guan Heyuan , Lu Huihui , Tang Jieyuan , Zhang Jun , Luo Yunhan , Chen Zhe 
Published: April 2017

AbstractOptical spin splitting has a promising prospect in quantum information and precision metrology. Since it is typically small, many efforts have been devoted to its enhancement. However, the upper limit of optical spin splitting remains uninvestigated. Here, we investigate systematically the in-plane spin splitting of a Gaussian beam reflected from a glass-air interface and find that the spin splitting can be enhanced in three different incident angular ranges: around the Brewster angle, slightly smaller than and larger than the critical angle for total reflection. Within the first angular range, the reflected beam can undergo giant spin splitting but suffers from low energy reflectivity. In the second range, however, a large spin splitting and high energy reflectivity can be achieved simultaneously. The spin splitting becomes asymmetrical within the last angular range, and the displacement of one spin component can be up to half of incident beam waist w0/2. Of all the incident angles, the spin splitting reaches its maximum at Brewster angle. This maximum splitting increases with the refractive index of the “glass” prism, eventually approaching an upper limit of w0. These findings provide a deeper insight into the optical spin splitting phenomena and thereby facilitate the development of spin-based applications.
Metabolic Syndrome Modulates Association between Endothelial Lipase and Lipid/Lipoprotein Plasma Levels in Acute Heart Failure Patients
Authors: Potočnjak Ines , Trbušić Matias , Terešak Sanda Dokoza , Radulović Bojana , Pregartner Gudrun , Berghold Andrea , Tiran Beate , Marsche Gunther , Degoricija Vesna , Frank Saša 
Published: April 2017

AbstractWe hypothesised that the established association of endothelial lipase (EL) plasma levels with atherogenic lipid profile is altered in acute heart failure (AHF) and additionally affected by overlapping metabolic syndrome (MetS). We examined the association of EL plasma levels and lipid/lipoprotein plasma levels in AHF patients without and with overlapping MetS. The study was performed as a single-centre, observational study on 152 AHF patients, out of which 85 had overlapping MetS. In the no-MetS group, EL plasma levels were significantly positively correlated with plasma levels of atherogenic lipids/lipoproteins, including total cholesterol, low-density lipoprotein (LDL)-cholesterol, total LDL particles and triglycerides, but also with plasma levels of antiatherogenic high-density lipoprotein (HDL)-cholesterol, total HDL particles and small HDL particles. In the MetS group, EL plasma levels were positively correlated with triglyceride and small LDL-particle levels, and significantly negatively correlated with plasma levels of large HDL particles as well as with LDL- and HDL-particle size, respectively. EL- and lipid/lipoprotein- plasma levels were different in the no-MetS patients, compared to MetS patients. The association of EL with atherogenic lipid profile is altered in AHF and additionally modified by MetS, which strongly modulates EL- and lipid/lipoprotein-plasma levels in AHF.
First, you need a Gestalt: An interaction of bottom-up and top-down streams during the perception of the ambiguously rotating human walker
Authors: Pastukhov Alexander 
Published: April 2017

AbstractOur visual system combines sensory evidence with prior knowledge to produce a representation of an outside world. Here, we explored the limits of the feedforward computation using an ambiguously rotating human biological motion. Specifically, we investigated whether an overall rotation, which was added to all the displays used in the study, would be perceived when the point-light walker was presented upside-down, a condition that typically obliterates perception of a human Gestalt. We report that inversion of the point-light walker or the absence of an identifiable Gestalt abolished the perception of an overall rotation. Perception of rotation was restored if the human walker Gestalt could be identified (an upright walker), if observers were informed about the nature of the motion display, or if observers expected to see the rotation of an unknown dynamic object. This implies that a mathematically more complex human motion was accounted for before the remaining motion components could be used to infer an overall rotation. Our results indicate that the perceptual inference does not proceed in a hierarchical manner with the simpler components being identified first. Instead, prior knowledge acts as a starting point for the decomposition of an even relatively simple combination of two motions.
Epidemiology of 45,616 suspect cases of Hand, Foot and Mouth Disease in Chongqing, China, 2011–2015
Authors: Tao Jian , He Xiao-yan , Shi Yu , Zhu Guohun , Liu Shan , Zhang Zhenzhen , Tang Shi , Zhang Rong , Peng Bin , Liu Zhidai , Tan Junjie , Chen Qian , Wang Xingbin , Bao Liming , Zou Lin , Zhang Penghui 
Published: April 2017

AbstractEpidemiology and etiology of hand, foot, and mouth disease (HFMD) based on large sample size or evaluation of detection for more enterovirus serotypes are not well investigated in Chongqing of China. 45,616 suspect HFMD patients were prospectively enrolled among whom 21,615 were laboratory confirmed HFMD cases over a 5-year period (January 2011 to December 2015). Their epidemiological, clinical, and laboratory data were extracted and stratified by month, age, sex, disease severity, and enterovirus serotype. Subsequently 292 non-EV-A71/CV-A16 HFMD confirmed cases were randomly selected in three consecutive outbreaks to detect CV-A6 and CV-A10, using RT-PCR. Results showed that the HFMD epidemic peaked in early summer and autumn. The median age of onset was 2.45 years with a male-to-female ratio of 1.54:1, and with children under 5 years of age accounting for 92.54% of all confirmed cases. EV-A71 and CV-A16 infection accounted for only 36.05% (7793/21615) of total confirmed cases while EV-A71 accounted for 59.64% (232/389) of severe cases. Importantly, the proportion of EV-A71 infection generally increased with age which showed rapid growth in severe cases. CV-A6 and CV-A10 were tested positive in Chongqing, but CV-A6 had greater positive rates of 62.33% while CV-A10 had 4.79% in non-EV-A71/CV-A16 HFMD confirmed cases.
Running exercise strengthens the intervertebral disc
Authors: Belavý Daniel L. , Quittner Matthew J. , Ridgers Nicola , Ling Yuan , Connell David , Rantalainen Timo 
Published: April 2017

AbstractThere is currently no evidence that the intervertebral discs (IVDs) can respond positively to exercise in humans. Some authors have argued that IVD metabolism in humans is too slow to respond anabolically to exercise within the human lifespan. Here we show that chronic running exercise in men and women is associated with better IVD composition (hydration and proteoglycan content) and with IVD hypertrophy. Via quantitative assessment of physical activity we further find that accelerations at fast walking and slow running (2 m/s), but not high-impact tasks, lower intensity walking or static positions, correlated to positive IVD characteristics. These findings represent the first evidence in humans that exercise can be beneficial for the IVD and provide support for the notion that specific exercise protocols may improve IVD material properties in the spine. We anticipate that our findings will be a starting point to better define exercise protocols and physical activity profiles for IVD anabolism in humans.
Accurate and effective multidrug-resistant Mycobacterium tuberculosis detection method using gap-filling ligation coupled with high-resolution capillary electrophoresis-based single strand conformation polymorphism
Authors: Choi Woong , Lee Jongseok , Cho Eunjin , Jung Gyoo Yeol 
Published: April 2017

AbstractTuberculosis (TB) has severely threatened public health via emerging multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains. For effective TB treatment, rapid, accurate, and multiplex detection of drug resistance is extremely important. However, conventional methods for TB diagnosis are time consuming and have a limited effect on treatment. Nucleic acid-based molecular detection methods have been developed as an effective MDR/XDR-TB diagnosis technology. Among the nucleic acid-based methods, ligation-dependent methods are attractive as MDR/XDR-MTB detection technologies, but multiplex analysis is limited by the detection method. Although an electrophoresis-based method is considered for multiple target detection because it is free from the errors pertaining to hybridization-based systems, the procedure of multiplex analysis is quite complicated owing to the DNA size-based separation system. In this study, we report an accurate, rapid, and simple multiple MDR/XDR-MTB detection technology using gap-filling ligation reaction coupled with high-resolution capillary electrophoresis-based single-strand conformation polymorphism. Using this system, rapid and accurate MDR/XDR-MTB detection is feasible via similar length probes without the complicated step of probe design. We found that this method could accurately and effectively detect highly polymorphic regions in specific codons associated with drug resistance.
Differential Control of Asexual Development and Sterigmatocystin Biosynthesis by a Novel Regulator in Aspergillus nidulans
Authors: Kim Yong Jin , Yu Yeong Man , Maeng Pil Jae 
Published: April 2017

AbstractThe filamentous fungus Aspergillus nidulans primarily reproduces by forming asexual spores called conidia and produces the mycotoxin sterigmatocystin (ST), the penultimate precursor of aflatoxins. It has been known that asexual development and ST production are tightly co-regulated by various regulatory inputs. Here, we report that the novel regulator AslA with a C2H2 domain oppositely regulates development and ST biosynthesis. Nullifying aslA resulted in defective conidiation and reduced expression of brlA encoding a key activator of asexual development, which indicates that AslA functions as an upstream activator of brlA expression. aslA deletion additionally caused enhanced ST production and expression of aflR encoding a transcriptional activator for ST biosynthetic genes, suggesting that AslA functions as an upstream negative regulator of aflR. Cellular and molecular studies showed that AslA has a trans-activation domain and is localized in the nuclei of vegetative and developing cells but not in spores, indicating that AslA is likely a transcription factor. Introduction of the aslA homologs from distantly-related aspergilli complemented the defects caused by aslA null mutation in A. nidulans, implying a functional conservancy of AslA. We propose that AslA is a novel regulator that may act at the split control point of the developmental and metabolic pathways.
Distorted Immunodominance by Linker Sequences or other Epitopes from a Second Protein Antigen During Antigen-Processing
Authors: Kim AeRyon , Boronina Tatiana N. , Cole Robert N. , Darrah Erika , Sadegh-Nasseri Scheherazade 
Published: April 2017

AbstractThe immune system focuses on and responds to very few representative immunodominant epitopes from pathogenic insults. However, due to the complexity of the antigen processing, understanding the parameters that lead to immunodominance has proved difficult. In an attempt to uncover the determinants of immunodominance among several dominant epitopes, we utilized a cell free antigen processing system and allowed the system to identify the hierarchies among potential determinants. We then tested the resultsin vivo; in mice and in human. We report here, that immunodominance of known sequences in a given protein can change if two or more proteins are being processed and presented simultaneously. Surprisingly, we find that new spacer/tag sequences commonly added to proteins for purification purposes can distort the capture of the physiological immunodominant epitopes. We warn against adding tags and spacers to candidate vaccines, or recommend cleaving it off before using for vaccination.
Sea-level proxies in Holocene raised beach ridge deposits (Greenland) revealed by ground-penetrating radar
Authors: Nielsen Lars , Bendixen Mette , Kroon Aart , Hede Mikkel Ulfeldt , Clemmensen Lars B. , Weβling Ronny , Elberling Bo 
Published: April 2017

AbstractIdentification of sea-level proxies is important for reconstruction of past sea-level variation. Methods for reconstructing Holocene relative sea-level curves are crucial for quantification of the impact of Greenland ice thickness variation on global sea level and vertical land movement. Arctic beach ridges constitute important potential archives of sea-level variation. However, their surface morphology may have undergone modification since deposition due to freezing/thawing processes and erosion, and their morphology may therefore not be trustworthy for sea-level reconstruction. Therefore, geophysical imaging is used to examine the internal structures of the beach ridges and to define a sea-level proxy unaffected by surface processes. The GPR reflections from study sites in West and South Greenland show deposition of beachface deposits and upper shoreface deposits; the contact between steeply dipping beachface reflections and less-dipping shoreface reflections is used as sea-level proxy. Numerous points are identified along GPR transects facilitating reconstruction of relative sea-level variation of hitherto unprecedented resolution. Erosional events and deformation caused by freezing/thawing processes are clearly delineated. The approach constitutes a solid base for reconstruction of relative sea-level curves affected by a well-defined vertical land movement history since the studied beach ridge systems represent long time intervals and only relatively small spatial extents.