bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical properties and microstructure of A356 alloy reinforced AlN/MWCNT/graphite/Al composites fabricated by stir casting
Authors: Logesh K , Hariharasakthisudhan P , Arul Marcel Moshi A , Rajan B Surya , K Sathickbasha 
Published: November 2019

Abstract
In this experimental research work, the metal matrix composites of A356 alloy were prepared by reinforcing different shaped particles Aluminium Nitride (AlN), Multi-Walled Carbon Nano Tube (MWCNT) and graphite (Gr). The main objective of this research work was to investigate the influence of different shaped reinforcement in the microstructure and mechanical behaviour of composites. The reinforcements (AlN & MWCNT) were added as 0.5, 0.75, 1 and 2 vol% and the graphite was maintained in 0.5 vol%. The composites were fabricated using stir casting followed by ultrasonic vibration treatment. The tensile, compression and Brinell hardness test were carried out by following ASTM standards. The characterization of reinforcements, castings and fractured surfaces was performed using Optical Microscope (OM) and Scanning Electron Microscope (SEM). The mechanical tests and characterization results revealed that there was a significant influence of morphology of reinforcements on mechanical properties of the materials. Particle strengthening and grain refinement strengthening were found to be operative in the composites. The SEM micrograph of fractured surface of composites with MWCNT exhibited the crack bridging effect as strengthening mechanism apart from particle strengthening. The porosity and cluster of reinforcements were observed in the composites with MWCNT more than 1 vol% of and AlN 0.75 vol%.
Blue and green emission from Ho3+ doped zinc titanate phosphor thin films by sol-gel
Authors: Elhadi Suliman Eltayeb , Lu Yadong , Liu Chao 
Published: November 2019

Abstract
Zinc titanate ZnTiO3 phosphor thin films doped with 1, 2, and 3 mol% of Ho3+ ions were fabricated using sol-gel method a combined with dip-coating technique on silica glass substrate and subsequent thermal annealing in the range of 600–900 °C. Effects of annealing temperature and Ho3+ ions concentration on the structure and optical properties of these phosphor thin films were investigated using x-ray diffraction (XRD), scanning electron microscopy (SEM), UV-visible transmittance spectroscopy, excitation, and emission spectroscopy. Results revealed that ZnTiO3 nanocrystals were formed upon 600 °C annealing temperature. At 900 °C polycrystalline films including ZnO and TiO2 anatase phase were observed. The average diameter of nanocrystals showed temperature dependence and was varied in the range-over 15–48 nm which was revealed by SEM images with cracks free. The EDS showed homogenous distribution of Ho3+ ions in the thin film specimens. It was found that Ho3+ ions incorporated into the nanocrystals. As a result, the room temperature luminescence color emission of the synthesized phosphor thin film specimens can be tuned from blue to green by switching the excitation wavelength from 360 nm to 430 nm. The achieved result makes these phosphor thin films promising for several applications such as optoelectronics and light-emitting.
Topological current for transverse electrical and thermal conductivity in thermoelectric effect
Authors: Shi Xuguang 
Published: November 2019

Abstract
Thermoelectric efficiency of the traditional thermoelectric material is low, which restricts the large scale applications. Recently, the developing of the topological insulator provides a new opportunity to get high thermoelectric efficiency material. There are two effects in topological insulator: anomalous Hall and Nernst effect, which have contribution to the transport properties. Because of anomalous Hall and Nernst effect the electrical thermal conductivity have transverse parts, which affect the Seebeck coefficient. However, the transverse parts can be expressed by Berry curvature. By using of φ-mapping topological theory, the Berry curvature is studied and we find there is topological vortex in the momentum space. The Bloch wave function is zero at the topological vortex. Finally, the relationships between the topological vortex and the transverse electrical and thermal conductivity is given and how the topology affects the Seebeck coefficient is researched in detail.
Mortality and HSP Genes Expression in the Endoparasitoid Cotesia chilonis (Hymenoptera: Braconidae) After Cold Acclimation at Different Temperatures
Authors: Song Jie , Cao Shuang-Shuang , Lu Ming-Xing , Du Yu-Zhou 
Published: November 2019

Abstract
Cotesia chilonis (Munakata) is an endoparasitoid wasp of Chilo suppressalis Walker (Lepidoptera: Pyralidea) larvae. Little is known regarding the tolerance of C. chilonis after cold acclimation at different temperatures. In this study, we investigated mortality and the molecular basis of temperature tolerance in C. chilonis reared under normal conditions (27°C) and after cold acclimation at 4°C for 5 d. We evaluated the relative expression of five genes encoding heat shock proteins (HSPs) in C. chilonis by RT-qPCR after cold acclimation and exposure to temperature stress. The results demonstrated that cold acclimation could significantly enhance the survival of C. chilonis adults under high temperatures, and expression of the five C. chilonis HSP genes had distinctly different expression patterns in response to temperatures. Cchsp40 and Cchsp90 had similar expression pattern that upregulated significantly at −12 and 39°C. Cchsp70 could be induced by high and low temperatures, whereas Cchsp60 and Cchsc70 showed no significant difference in expression when exposed to thermal stress. This study provides important biological information that may help extend the shelf life of C. chilonis, which is an important consideration in the use of this wasp as a biological control agent.
The Plastic Surgery Social Media Influencer: Ethical Considerations and a Literature Review
Authors: Gupta Nisha , Dorfman Robert , Saadat Sean , Roostaeian Jason 
Published: November 2019

Abstract

Background
Social media use has become a relevant tool in plastic surgery. These platforms are utilized for many reasons, such as business promotion. Although beneficial, social media can cause ethical dilemmas if used incorrectly.

Objectives
A review of the literature revealed what is understood about the implications of social media in regards to sponsorship/promotion. This paper aimed to create the foundation surrounding this topic and help facilitate future discussions on this new ethical dilemma.

Methods
A MEDLINE search with a custom publication date range and a review of the literature was conducted on June 15, 2019.

Results
The search yielded 139 articles and abstracts. After review, 26 publications were chosen for analysis. Articles were taken from the following journals: Plastic and Reconstructive Surgery (n = 12), Aesthetic Surgery Journal (n = 8), PRS Global Open (n = 2), Annals of Plastic Surgery (n = 1), BMJ (n = 1), AMA Journal of Ethics (n = 1), and Facial Plastic Surgery (n = 1). The 4 principles of medical ethics were analyzed in respect to promotion and sponsorship in plastic surgery.

Conclusions
Social media is a novel platform that is becoming increasingly utilized in plastic surgery. Although its impact can be beneficial, it is not well understood in the context of social media sponsorship and promotion. To date, no peer-reviewed articles specifically discuss these limitations. It is critical that all plastic surgeons be cognizant of both the positive and negative aspects of social media before integrating it into their professional lives.
Human body-fluid proteome: quantitative profiling and computational prediction
Authors: Huang Lan , Shao Dan , Wang Yan , Cui Xueteng , Li Yufei , Chen Qian , Cui Juan 
Published: November 2019

AbstractEmpowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein–protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
SCOT: Rethinking the classification of secondary structure elements
Authors: Brinkjost Tobias , Ehrt Christiane , Koch Oliver , Mutzel Petra 
Published: November 2019

Abstract

Motivation
Secondary structure classification is one of the most important issues in structure-based analyses due to its impact on secondary structure prediction, structural alignment and protein visualization. There are still open challenges concerning helix and sheet assignments which are currently not addressed by a single multi-purpose software.

Results
We introduce SCOT (Secondary structure Classification On Turns) as a novel secondary structure element assignment software which supports the assignment of turns, right-handed α-, 310- and π-helices, left-handed α- and 310-helices, 2.27- and polyproline II helices, β-sheets and kinks. We demonstrate that the introduction of helix Purity values enables a clear differentiation between helix classes. SCOT’s unique strengths are highlighted by comparing it to six state-of-the-art methods (DSSP, STRIDE, ASSP, SEGNO, DISICL and SHAFT). The assignment approaches were compared concerning geometric consistency, protein structure quality and flexibility dependency and their impact on secondary structure element-based structural alignments. We show that only SCOT’s combination of hydrogen bonds, geometric criteria and dihedral angles enables robust assignments independent of the structure quality and flexibility. We demonstrate that this combination and the elaborate kink detection lead to SCOT’s clear superiority for protein alignments. As the resulting helices and strands are provided in a PDB conform output format, they can immediately be used for structure alignment algorithms. Taken together, the application of our new method and the straight-forward visualization using the accompanying PyMOL scripts enable the comprehensive analysis of regular backbone geometries in proteins.

Availability and implementation
https://this-group.rocks

Supplementary information
Supplementary data are available at Bioinformatics online.
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
Authors: Aramaki Takuya , Blanc-Mathieu Romain , Endo Hisashi , Ohkubo Koichi , Kanehisa Minoru , Goto Susumu , Ogata Hiroyuki 
Published: November 2019

Abstract

Summary
KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction.

Availability and implementation
KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/).

Supplementary information
Supplementary data are available at Bioinformatics online.
Absence of TRIM32 Leads to Reduced GABAergic Interneuron Generation and Autism-like Behaviors in Mice via Suppressing mTOR Signaling
Authors: Zhu Jian-Wei , Zou Ming-Ming , Li Yi-Fei , Chen Wen-Jin , Liu Ji-Chuan , Chen Hong , Fang Li-Pao , Zhang Yan , Wang Zhao-Tao , Chen Ji-Bo , Huang Wenhui , Li Shen , Jia Wei-Qiang , Wang Qin-Qin , Zhen Xue-Chu , Liu Chun-Feng , Li Shao , Xiao Zhi-Cheng , Xu Guo-Qiang , Schwamborn Jens C , Schachner Melitta , Ma Quan-Hong , Xu Ru-Xiang 
Published: November 2019

AbstractMammalian target of rapamycin (mTOR) signaling plays essential roles in brain development. Hyperactive mTOR is an essential pathological mechanism in autism spectrum disorder (ASD). Here, we show that tripartite motif protein 32 (TRIM32), as a maintainer of mTOR activity through promoting the proteasomal degradation of G protein signaling protein 10 (RGS10), regulates the proliferation of medial/lateral ganglionic eminence (M/LGE) progenitors. Deficiency of TRIM32 results in an impaired generation of GABAergic interneurons and autism-like behaviors in mice, concomitant with an elevated autophagy, which can be rescued by treatment embryonically with 3BDO, an mTOR activator. Transplantation of M/LGE progenitors or treatment postnatally with clonazepam, an agonist of the GABAA receptor, rescues the hyperexcitability and the autistic behaviors of TRIM32−/− mice, indicating a causal contribution of GABAergic disinhibition. Thus, the present study suggests a novel mechanism for ASD etiology in that TRIM32 deficiency-caused hypoactive mTOR, which is linked to an elevated autophagy, leads to autism-like behaviors via impairing generation of GABAergic interneurons. TRIM32−/− mouse is a novel autism model mouse.
Mesophotic.org: a repository for scientific information on mesophotic ecosystems
Authors: Bongaerts Pim , Perez-Rosales Gonzalo , Radice Veronica Z , Eyal Gal , Gori Andrea , Gress Erika , Hammerman Nicholas M , Hernandez-Agreda Alejandra , Laverick Jack , Muir Paul , Pinheiro Hudson , Pyle Richard L , Rocha Luiz , Turner Joseph A , Booker Ryan 
Published: November 2019

Abstract
Mesophotic coral ecosystems (MCEs) and temperate mesophotic ecosystems (TMEs) occur at depths of roughly 30–150 m depth and are characterized by the presence of photosynthetic organisms despite reduced light availability. Exploration of these ecosystems dates back several decades, but our knowledge remained extremely limited until about a decade ago, when a renewed interest resulted in the establishment of a rapidly growing research community. Here, we present the ‘mesophotic.org’ database, a comprehensive and curated repository of scientific literature on mesophotic ecosystems. Through both manually curated and automatically extracted metadata, the repository facilitates rapid retrieval of available information about particular topics (e.g. taxa or geographic regions), exploration of spatial/temporal trends in research and identification of knowledge gaps. The repository can be queried to comprehensively obtain available data to address large-scale questions and guide future research directions. Overall, the ‘mesophotic.org’ repository provides an independent and open-source platform for the ever-growing research community working on MCEs and TMEs to collate and expedite our understanding of the occurrence, composition and functioning of these ecosystems.
Database URL: http://mesophotic.org/
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
Authors: Singh Abhijeet , Müller Bettina , Fuxelius Hans-Henrik , Schnürer Anna 
Published: November 2019

AbstractAcetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.
Left atrial strain: a multi-modality, multi-vendor comparison study
Authors: Pathan Faraz , Zainal Abidin Hafisyatul Aiza , Vo Quang Ha , Zhou Hui , D’Angelo Tommaso , Elen Elen , Negishi Kazuaki , Puntmann Valentina O , Marwick Thomas H , Nagel Eike 
Published: November 2019

Abstract

Aims
Left atrial (LA) strain is a prognostic biomarker with utility across a spectrum of acute and chronic cardiovascular pathologies. There are limited data on intervendor differences and no data on intermodality differences for LA strain. We sought to compare the intervendor and intermodality differences between transthoracic echocardiography (TTE) and cardiac magnetic resonance (CMR) derived LA strain. We hypothesized that various components of atrial strain would show good intervendor and intermodality correlation but that there would be systematic differences between vendors and modalities.

Methods and results
We evaluated 54 subjects (43 patients with a clinical indication for CMR and 11 healthy volunteers) in a study comparing TTE- and CMR-derived LA reservoir strain (ƐR), conduit strain (ƐCD), and contractile strain (ƐCT). The LA strain components were evaluated using four dedicated types of post-processing software. We evaluated the correlation and systematic bias between modalities and within each modality. Intervendor and intermodality correlation was: ƐR [intraclass correlation coefficient (ICC 0.64–0.90)], ƐCD (ICC 0.62–0.89), and ƐCT (ICC 0.58–0.77). There was evidence of systematic bias between vendors and modalities with mean differences ranging from (3.1–12.2%) for ƐR, ƐCD (1.6–8.6%), and ƐCT (0.3–3.6%). Reproducibility analysis revealed intraobserver coefficient of variance (COV) of 6.5–14.6% and interobserver COV of 9.9–18.7%.

Conclusion
Vendor derived ƐR, ƐCD, and ƐCT demonstrates modest to excellent intervendor and intermodality correlation depending on strain component examined. There are systematic differences in measurements depending on modality and vendor. These differences may be addressed by future studies, which, examine calibration of LA geometry/higher frame rate imaging, semi-quantitative approaches, and improvements in reproducibility.
Gut Microbiota: From the Forgotten Organ to a Potential Key Player in the Pathology of Alzheimer’s Disease
Authors: Seo Dong-Oh , Holtzman David M 
Published: November 2019

Abstract
More than 300 years ago, Antony van Leewenhoeck first described observing single-celled microorganisms, which he termed “animalcules,” examining his saliva under a microscope. Although the idea of the coexistence of microorganisms in our body is not new, we have only recently been able to investigate their ecological relationship to our body, with the development of high-throughput molecular techniques. The diverse microorganism communities residing in our guts are established and maintained by complex interactions among microorganisms and their host. Notably, their alteration has been implicated in influencing various diseases including neurological diseases. Alzheimer’s disease (AD) is the most common cause of dementia characterized by a progressive decline in memory and thinking severe enough to interfere with daily life. Despite the great progress in linking genetic risk factors with AD pathogenesis, treatments targeted at AD pathology and its modifiers have not yet resulted in a disease-modifying therapy. There is mounting evidence that the gut microbiota interacts with AD pathogenesis by disrupting neuroinflammation and metabolic homeostasis—the gut microbiota has gone from being the forgotten organ to a potential key player in the AD pathology.
Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
Authors: Strijk Joeri S , Hinsinger Damien D , Zhang Fengping , Cao Kunfang 
Published: November 2019

Abstract

Background
The wheel tree (Trochodendron aralioides) is one of only 2 species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate that this represents an evolutionary reversal for the group. Trochodendron aralioides is widespread in cultivation and popular for use in gardens and parks.

Findings
We assembled the T. aralioides genome using a total of 679.56 Gb of clean reads that were generated using both Pacific Biosciences and Illumina short-reads in combination with 10XGenomics and Hi-C data. Nineteen scaffolds corresponding to 19 chromosomes were assembled to a final size of 1.614 Gb with a scaffold N50 of 73.37 Mb in addition to 1,534 contigs. Repeat sequences accounted for 64.226% of the genome, and 35,328 protein-coding genes with an average of 5.09 exons per gene were annotated using de novo, RNA-sequencing, and homology-based approaches. According to a phylogenetic analysis of protein-coding genes, T. aralioides diverged in a basal position relative to core eudicots, ~121.8–125.8 million years ago.

Conclusions
Trochodendron aralioides is the first chromosome-scale genome assembled in the order Trochodendrales. It represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. This genome will support further studies of wood morphology and floral evolution, and will be an essential resource for understanding rapid changes that took place at the base of the Eudicot tree. Finally, it can further genome-assisted improvement for cultivation and conservation efforts of the wheel tree.