bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global pentapeptide statistics are far away from expected distributions
Authors: Poznański Jarosław , Topiński Jan , Muszewska Anna , Dębski Konrad J. , Hoffman-Sommer Marta , Pawłowski Krzysztof , Grynberg Marcin 
Published: October 2018

AbstractThe relationships between polypeptide composition, sequence, structure and function have been puzzling biologists ever since first protein sequences were determined. Here, we study the statistics of occurrence of all possible pentapeptide sequences in known proteins. To compensate for the non-uniform distribution of individual amino acid residues in protein sequences, we investigate separately all possible permutations of every given amino acid composition. For the majority of permutation groups we find that pentapeptide occurrences deviate strongly from the expected binomial distributions, and that the observed distributions are also characterized by high numbers of outlier sequences. An analysis of identified outliers shows they often contain known motifs and rare amino acids, suggesting that they represent important functional elements. We further compare the pentapeptide composition of regions known to correspond to protein domains with that of non-domain regions. We find that a substantial number of pentapeptides is clearly strongly favored in protein domains. Finally, we show that over-represented pentapeptides are significantly related to known functional motifs and to predicted ancient structural peptides.
Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission
Authors: Muth Doreen , Corman Victor Max , Roth Hanna , Binger Tabea , Dijkman Ronald , Gottula Lina Theresa , Gloza-Rausch Florian , Balboni Andrea , Battilani Mara , Rihtarič Danijela , Toplak Ivan , Ameneiros Ramón Seage , Pfeifer Alexander , Thiel Volker , Drexler Jan Felix , Müller Marcel Alexander , Drosten Christian 
Published: October 2018

AbstractA 29 nucleotide deletion in open reading frame 8 (ORF8) is the most obvious genetic change in severe acute respiratory syndrome coronavirus (SARS-CoV) during its emergence in humans. In spite of intense study, it remains unclear whether the deletion actually reflects adaptation to humans. Here we engineered full, partially deleted (−29 nt), and fully deleted ORF8 into a SARS-CoV infectious cDNA clone, strain Frankfurt-1. Replication of the resulting viruses was compared in primate cell cultures as well as Rhinolophus bat cells made permissive for SARS-CoV replication by lentiviral transduction of the human angiotensin-converting enzyme 2 receptor. Cells from cotton rat, goat, and sheep provided control scenarios that represent host systems in which SARS-CoV is neither endemic nor epidemic. Independent of the cell system, the truncation of ORF8 (29 nt deletion) decreased replication up to 23-fold. The effect was independent of the type I interferon response. The 29 nt deletion in SARS-CoV is a deleterious mutation acquired along the initial human-to-human transmission chain. The resulting loss of fitness may be due to a founder effect, which has rarely been documented in processes of viral emergence. These results have important implications for the retrospective assessment of the threat posed by SARS.
Insight into the draft whole-genome sequence of the dermatophyte Arthroderma vanbreuseghemii
Authors: Alshahni Mohamed Mahdi , Yamada Tsuyoshi , Yo Ayaka , Murayama Somay Y. , Kuroda Makoto , Hoshino Yasutaka , Ishikawa Jun , Watanabe Shinichi , Makimura Koichi 
Published: October 2018

AbstractNext-generation technologies have prompted efforts towards generating a large repertoire of whole-genome sequences. The dermatophyte Arthroderma vanbreuseghemii has been considered as a good model in which to conduct molecular biological studies on this fungal group. Despite the considerable repertoire of molecular tools developed for this fungus, the lack of genomic data has represented a major limitation, preventing effective implementation of those tools. Herein, the authors report the first draft whole-genome sequence of this dermatophytic species. The size of the draft genome was 23 Mb, exhibiting a GC content of 48.1%. Given the significance of secreted proteases in tissue invasion, a comparative analysis of genes encoding extracellular proteases was performed between A. vanbreuseghemii and other dermatophytes. Furthermore, genes that might be involved in DNA repair also were compared among dermatophytes. Moreover, the complete mitochondrial genome of A. vanbreuseghemii was obtained and shown to consist of 24,287 bp with a GC content of 24%. In conclusion, the availability of genomic data for A. vanbreuseghemii is expected to facilitate the implementation of the molecular tools established for this fungus, enhancing our understanding of the biology of dermatophytes.
Dendritic processing of spontaneous neuronal sequences for single-trial learning
Authors: Haga Tatsuya , Fukai Tomoki 
Published: October 2018

AbstractSpontaneous firing sequences are ubiquitous in cortical networks, but their roles in cellular and network-level computations remain unexplored. In the hippocampus, such sequences, conventionally called preplay, have been hypothesized to participate in learning and memory. Here, we present a computational model for encoding input sequence patterns into internal network states based on the propagation of preplay sequences in recurrent neuronal networks. The model instantiates two synaptic pathways in cortical neurons, one for proximal dendrite-somatic interactions to generate intrinsic preplay sequences and the other for distal dendritic processing of extrinsic signals. The core dendritic computation is the maximization of matching between patterned activities in the two compartments through nonlinear spike generation. The model performs robust single-trial learning with long-term stability and independence that are modulated by the plasticity of dendrite-targeted inhibition. Our results demonstrate that dendritic computation enables somatic spontaneous firing sequences to act as templates for rapid and stable memory formation.
Detection of the carbapenemase gene blaVIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands
Authors: Adelowo Olawale O. , Vollmers John , Mäusezahl Ines , Kaster Anne-Kristin , Müller Jochen A. 
Published: October 2018

AbstractThere are increasing concerns about possible dissemination of clinically relevant antibiotic resistance genes, including genes encoding for carbapenemases in the environment. However, little is known about environmental distribution of antibiotic resistance in Africa. In this study, four polluted urban wetlands in Nigeria were investigated as potential reservoirs of carbapenem-resistant bacteria (CRB). CRB were isolated from the wetlands, characterized by Blue-Carba test, MIC determinations and whole genome sequencing (WGS). Nine of 65 bacterial isolates identified as members of the Pseudomonas putida group (P. plecoglossicida and P. guariconensis, respectively) harboured the metallo-beta-lactamase gene blaVIM-5. WGS revealed the blaVIM-5 in three novel Tn402-like class 1 integron structures containing the cassette arrays aadB|blaVIM-5|blaPSE-1, aadB|blaVIM-5|aadB|blaPSE-1, and blaVIM-5|aadB|tnpA|blaPSE-1|smr2|tnpA, respectively. Strains carrying the aadB|blaVIM-5|blaPSE-1 cassette also carried an identical integron without blaVIM-5. In addition, the strains harboured another Tn402-like class 1 integron carrying bcr2, several multidrug resistance efflux pumps, and at least one of ampC, aph(3”)-lb, aph(6)-ld, tetB, tetC, tetG, floR, and macAB. This is the first report of a carbapenemase gene in bacteria from environmental sources in Nigeria and the first report of blaVIM-5 in environmental bacteria isolates. This result underscores the role of the Nigerian environment as reservoir of bacteria carrying clinically relevant antibiotic resistance genes.
Large-scale nanoporous metal-coated silica aerogels for high SERS effect improvement
Authors: Kim Changwook , Baek Seunghwa , Ryu Yunha , Kim Yeonhong , Shin Dongheok , Lee Chang-Won , Park Wounjhang , Urbas Augustine M. , Kang Gumin , Kim Kyoungsik 
Published: October 2018

AbstractWe investigate the optical properties and surface-enhanced Raman scattering (SERS) characteristics of metal-coated silica aerogels. Silica aerogels were fabricated by easily scalable sol-gel and supercritical drying processes. Metallic nanogaps were formed on the top surface of the nanoporous silica network by controlling the thickness of the metal layer. The optimized metallic nanogap structure enabled strong confinement of light inside the gaps, which is a suitable property for SERS effect. We experimentally evaluated the SERS enhancement factor with the use of benzenethiol as a probe molecule. The enhancement factor reached 7.9 × 107 when molecules were adsorbed on the surface of the 30 nm silver-coated aerogel. We also theoretically investigated the electric field distribution dependence on the structural geometry and substrate indices. On the basis of FDTD simulations, we concluded that the electric field was highly amplified in the vicinity of the target analyte owing to a combination of the aerogel’s ultralow refractive index and the high-density metallic nanogaps. The aerogel substrate with metallic nanogaps shows great potential for use as an inexpensive, highly sensitive SERS platform to detect environmental and biological target molecules.
Hydroxyurea Treated β-Thalassemia Children Demonstrate a Shift in Metabolism Towards Healthy Pattern
Authors: Iqbal Ayesha , Ansari Saqib Hussain , Parveen Sadia , Khan Ishtiaq Ahmad , Siddiqui Amna Jabbar , Musharraf Syed Ghulam 
Published: October 2018

AbstractAugmentation of fetal hemoglobin (HbF) production has been an enduring therapeutic objective in β-thalassemia patients for which hydroxyurea (HU) has largely been the drug of choice and the most cost-effective approach. A serum metabolomics study on 40 patients with β-thalassemia prior to and after administration of HU was done along with healthy controls. Treated patients were divided further into non-responders (NR), partial (PR) and good (GR) per their response. 25 metabolites that were altered before HU therapy at p ≤ 0.05 and fold change >2.0 in β-thalassemia patients; started reverting towards healthy group after HU treatment. A prediction model based on another set of 70 HU treated patients showed a good separation of GR from untreated β-thalassemia patients with an overall accuracy of 76.37%. Metabolic pathway analysis revealed that various important pathways that were disturbed in β-thalassemia were reverted after treatment with HU and among them linoleic acid pathway was most impactfully improved in HU treated patients which is a precursor of important signaling molecules. In conclusion, this study indicates that HU is a good treatment option for β-thalassemia patients because in addition to reducing blood transfusion burden it also ameliorates disease complications by shifting body metabolism towards normal.
Increase in resistance to anticancer drugs involves occludin in spheroid culture model of lung adenocarcinoma A549 cells
Authors: Eguchi Hiroaki , Akizuki Risa , Maruhashi Ryohei , Tsukimoto Mitsutoshi , Furuta Takumi , Matsunaga Toshiyuki , Endo Satoshi , Ikari Akira 
Published: October 2018

AbstractChemoresistance is a serious issue in the therapy of many cancers, but the molecular mechanism is little understood. The mRNA level of occludin (OCLN), a tight junctional protein, was increased in the cisplatin (CDDP), doxorubicin (DXR), 7-ethyl-10-hydroxy-camptothecin, or gemcitabine-resistant human lung adenocarcinoma A549 cells. Here, we investigated the regulatory mechanism and pathophysiological role of OCLN. OCLN was mainly localized at tight junctions in A549 and CDDP-resistant A549 (A549/CDDP) cells. The level of p-Akt in A549/CDDP cells was higher than that in A549 cells, and the mRNA and protein levels of OCLN were suppressed by a phosphoinositide 3-kinase (PI3K)/Akt pathway inhibitor, LY-294002, suggesting that a PI3K/Akt pathway is involved in the elevation of OCLN expression. The overexpression of OCLN in A549 cells decreased paracellular permeability to DXR. Cytotoxicity to CDDP was unaffected by OCLN-overexpression in 2D culture model. In 3D culture model, the spheroid size, hypoxic level, and cell viability were significantly elevated by CDDP resistance, but not by OCLN-overexpression. The accumulation inside the spheroids and toxicity of DXR were correlated with OCLN expression. Our data suggest that OCLN is not directly involved in the chemoresistance, but it enhances chemoresistance mediated by suppression of accumulation of anticancer drugs inside the spheroids.
Explaining Reading Comprehension in Children With Developmental Language Disorder: The Importance of Elaborative Inferencing
Authors: Gough Kenyon Sheila M. , Palikara Olympia , Lucas Rebecca M. 
Published: October 2018

Purpose
Reading comprehension is a key indicator of academic and psychosocial outcomes. Children with developmental language disorder (DLD) tend to find reading comprehension challenging. This study aimed to explore the literal and inferential (cohesive, elaborative, and lexical) comprehension of children with DLD, their typically developing (TD) peers, and, uniquely, a group of children with low language (LL) proficiency.

Method

Children aged 10–11 years with either typical development (
n
= 16), LL proficiency (
n
= 14), or DLD (
n
= 14) were recruited from 8 primary schools. They completed a battery of standardized language and literacy assessments. Responses to literal and inferential questions on the Wechsler Individual Achievement Test–Second UK Edition (Wechsler, 2005) were analyzed.

Results
A disproportionate difficulty in answering inferential relative to literal questions was found for the DLD group compared to the LL and TD groups. Children with DLD were significantly poorer at elaborative inferencing than both their peers with LL proficiency and TD peers, but there were no group differences in cohesive or lexical inferencing. There was a significant positive association between inferencing ability and vocabulary knowledge, single word reading accuracy, grammatical skill, and verbal working memory. The importance of single word reading accuracy was especially evident as a partial mediator of the relationship between vocabulary knowledge and inferencing ability.

Conclusions
These results indicate that interventions targeting the reading comprehension of children with DLD should focus on elaborative inferencing skill. There are also clinical implications as the development of new standardized assessments differentiating between inference types is called for.
Characteristics of Speech Rate in Children With Cerebral Palsy: A Longitudinal Study
Authors: Darling-White Meghan , Sakash Ashley , Hustad Katherine C. 
Published: October 2018

Purpose
The purpose of this longitudinal study was to examine the effect of time and sentence length on speech rate and its characteristics, articulation rate and pauses, within 2 groups of children with cerebral palsy (CP).

Method
Thirty-four children with CP, 18 with no speech motor involvement and 16 with speech motor involvement, produced sentences of varying lengths at 3 time points that were 1 year apart (mean age = 56 months at first time point). Dependent measures included speech rate, articulation rate, proportion of time spent pausing, and average number and duration of pauses.

Results
There were no significant effects of time. For children with no speech motor involvement, speech rate increased with longer sentences due to increased articulation rate. For children with speech motor involvement, speech rate did not change with sentence length due to significant increases in the proportion of time spent pausing and average number of pauses in longer sentences.

Conclusions
There were no significant age-related differences in speech rate in children with CP regardless of group membership. Sentence length differentially impacted speech rate and its characteristics in both groups of children with CP. This may be due to cognitive–linguistic and/or speech motor control factors.
High specific capacity Mg‐doping LiNi1/3Mn1/3Co1/3O2 cathode materials synthesised by a simple stepwise co‐precipitation method
Authors: Zhu Jiping , Yan Jiawei , Zhang Lei 
Published: October 2018

The layered LiNi1/3Co1/3Mn1/3−x Mgx O2 (x = 0, 0.01, 0.02, 0.03) were synthesised by a stepwise co‐precipitation method. The effects of Mg substitution on the crystal structure of the synthesised powder have been characterised by X‐ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectrometer (EDS) mapping. Their electrochemical properties were evaluated by charge/discharge and electrical impedance spectroscopy tests. The results of XRD, SEM and EDS mapping characterisation indicated that all the modified cathode materials with their Ni, Co and Mn components doped by magnesium without destroying the crystal structure. Electrochemical characterisation confirms that the materials have optimal cycling performance and the least capacity loss under the 2% Mg‐doping. The specific capacity of the LiNi1/3Co1/3Mn1/3−0.02Mg0.02O2 was 180 mAh g−1 at 0.1 C and 138 mAh g−1 at 8 C, which compares favourably to 175 mAh g−1 at 0.1 C and 121 mAh g−1 at 8 C for the LiNi1/3Co1/3Mn1/3O2. The LiNi1/3Co1/3Mn1/3−0.02Mg0.02O2 also exhibited the best electrochemical performance with capacity retention of 89.4% after 50 cycles at 0.2 C between 2.5 and 4.3 V.
Stable temperature characteristic of phosphate glass ceramic for white light‐emitting diode
Authors: Ren Xiaobin , Pei Manting , Ming Chengguo , Zhou Aihua , Ju Dandan , Song Feng 
Published: October 2018

Thulium, terbium, and manganese tridoped phosphate glass ceramic was prepared by high‐temperature melting method and heat annealing technology. The sample can emit strong white light under 355 nm excitation. The luminescence intensities and peak positions keep unchanged in the temperature range of 25–300°C. The phosphate glass ceramic material shows good property of thermal stability, which can be exploited for the phosphor of white‐light‐emitting diode.
Associations of the Force-velocity Profile with Isometric Strength and Neuromuscular Factors
Authors: Morales-Artacho Antonio , Ramos Amador , Pérez-Castilla Alejandro , Padial Paulino , Argüelles-Cienfuegos Javier , de la Fuente Blanca , Feriche Belen 
Published: October 2018

AbstractWe aimed to explore relationships between the force-velocity (FV) profile and the isometric muscle torque performance during a knee extension task. The FV profile (force-intercept [F0], velocity-intercept [V0], maximum power [Pmax], and FV slope) during the countermovement jump (CMJ) exercise and isometric maximum voluntary torque (MVIC) and explosive voluntary torque production were assessed in 43 participants. Electromyography (EMG) was recorded during the isometric assessments and resting muscle architecture measurements were also performed (quadriceps thickness, vastus lateralis pennation angle and fascicle length). Pearson’s correlation coefficients were computed to assess bivariate relationships between the FV profile, isometric torque, EMG activation and muscle architecture. F0 predictions from neuromuscular measurements were assessed through multiple linear regression. Associations of F0 and Pmax with isometric torque increased from explosive to MVIC torque (r≥0.47; P<0.05). Significant associations were found between muscle architecture and F0 and Pmax (r≥0.69; P<0.05), while V0 and FV slope were unrelated (r≤0.27; P>0.05). Quadriceps thickness and VL pennation angle explained ~62% of F0 variance. In conclusion, the knee extensors maximal isometric strength and their morphological architecture are strongly related to F0 estimated from a CMJ FV profile test.
Assessment of the OPS Code 8918 Multimodal Pain Therapy
Authors: Schwarze Martin , Hollo Dierk , Schiltenwolf Marcus 
Published: October 2018

ZusammenfassungInterdisziplinäre multimodale Schmerztherapie ist der Goldstandard in der Therapie chronischer Schmerzen. Aufgrund insgesamt steigender Fallzahlen steigt auch die Zahl an MDK-Prüfungen, die zu der Beurteilung primärer Fehlbelegung kommen. Hieraus resultieren eine Vielzahl sozialgerichtlicher Auseinandersetzungen, in denen medizinische Sachverständigengutachten angefordert werden. Unter Kenntnis der juristischen Normen und relevanten Leitlinien bzw. sonstigen Empfehlungen kann der Gutachter sich Schritt für Schritt dieser Thematik stellen. Beginnend steht hierbei die Auswertung der Patientenakte, gefolgt von der Prüfung der ärztlichen Indikationsstellung, der Therapiedurchführung und abschließend der Beantwortung der Beweisfragen. Ein an das Konzept von Schröter angelehntes Prüfschema kann diesen Vorgang weiter vereinfachen.
Men’s Participation and Performance in the Boston Marathon from 1897 to 2017
Authors: Knechtle Beat , Di Gangi Stefania , Rüst Christoph , Rosemann Thomas , Nikolaidis Pantelis 
Published: October 2018

AbstractThis study examined men’s participation and performance in the Boston Marathon. Data from all 368,940 official male finishers in the Boston Marathon from 1897 through 2017 were analyzed using different analyses and regression models for all runners, annual top hundred finishers, annual top ten finishers and annual winners. Effect of calendar year on race time was examined alone, in a uni-variable model, and together with country of origin and weather conditions (average air temperature and precipitation) in a multi-variable model. The mean race time of all finishers increased across calendar years, in line with the participation, but it decreased when we considered the annual winners, 10 and 100 fastest. Kenyans and Ethiopians were the fastest nationalities (p<0.001) when we considered all finishers and the annual top 100 fastest but not when the annual 10 fastest were considered. Air temperature≤8 °C improved (p<0.001) race times compared to air temperature>8°C. Precipitation (>0 mm) improved performance for the annual 100 fastest and annual 10 fastest (p=0.013–0.031) but not for all finishers. Our findings improved the knowledge about the evolution of male marathoners across calendar years, considering as main effects country of origin and particular weather conditions.