bluuebunny/crossref_metadata_2025 huggingface dataset:
Prototype Application of Online Mental - Health Screening Design Among Junior and High School Through Strength and Difficulties Measure
Authors: Sirait E , Utomo B , Siregar K
Published: July 2020

Mental disorders are a major cause of disability and death throughout the world every year. Indonesia has low mental health and is mostly experienced by adolescents. Indeed, recognizing the signs and symptoms of stress in adolescents early is a preventive measure before the condition worsens and causes many losses. Mental health service programs have so far been limited, both in schools and in health care centres. Facing such conditions, this study proposes a mobile application model that can be an early detection tool for adolescent mental health and information sharing between adolescents and teachers or health workers. The screening results will be followed up by the health service if a problem is found. This research builds a prototype of the mobile application to the modelling stage. The model is produced from the system requirements analysis, the model presented here is in the form of; Context Diagram, Entity Relational Diagram (ERD), Relational Diagram Table (TRD), Flow Chart and User Interface Design. Early mental health detection uses the Strength and Difficulties Questionnaire (SDQ). Data collection is done by interview, observation and study of literature. This information system can be used by primary health care and implemented in schools, making it easier for adolescent mental health screening.
Study of Crack Connections in Materials Composite Based on Polymer
Authors: Tjahjanti P H , Firdaus R , Iswanto  , Ahnan M F
Published: July 2020

The main problem in composite materials based on polymer arises when receiving dynamic loads resulting in initial cracks that continue to propagate. When crack on the metal, it can be connected by welding. Also, when a crack on concrete can be reconnected by grouting. While when crack in composite materials based on polymer, there is no special way to deal with cracks so far. The purpose of this research is to reconnect the composite materials based on polymer which has cracked and do the impact test (ASTM D6110-04 standard) is carried out to determine the impact strength and the amount of energy to break, tensile strength test, and observe the structure using Scanning Electron Microscopy (SEM). The highest of impact strength and the amount of energy to break, and tensile strength in sample A is 50% resin + 1% catalyst + 19% calcium carbonate + 25% fine fiber + 5% roving fiber, with an impact strength value of 23.89 Joules / mm2 and a large amount of energy to break 130.67 Joules, and value of tensile strength is 7.22 kgf/mm2. While observed microstructure by using SEM shows the crack that happened is brittle.
Computational algorithm PAOR for time-fractional diffusion equations
Authors: Sunarto A , Sulaiman J
Published: July 2020

We deal with the application of an unconditionally implicit finite difference approximation equation of the one-dimensional linear time fractional diffusion equations (TFDE’s) via the Caputo’s time fractional derivative. Based on this implicit approximation equation, the corresponding linear system can be generated in which its coefficient matrix is large scale and sparse. To speed up the convergence rate in solving the linear system iteratively, we construct the corresponding preconditioned linear system. Then we formulate and implement the Preconditioned AOR (PAOR) iterative method for solving the generated linear system. One example of the problem is presented to illustrate the effectiveness of PAOR method. The numerical results of this study show that the proposed iterative method is superior to PSOR and PGS, GS iterative method.
Validating The Fully Raster-Based Suitability Model for Sea Cucumber (Holothuria scabra)
Authors: Sulistyo Bambang , Purnama Dewi , Anggraini Maya , Listyaningrum Noviyanti
Published: July 2020

This research aimed at validating the fully raster-based suitability modelling for sea cucumber (Holothuria scabra) that has been created for the waters of Kiowa Bay, Enggano Island, Bengkulu. To validate the model, eighty-four sea cucumbers were cultivated on two different suitability classes. The field test phase includes setting the cultivation cages; measurement of sea cucumber weight; measurement of water quality parameter; and substrate analysis. Sea cucumbers were put into 2 cultivation cages (Cage 1: highly suitable, and Cage 2: less suitable), and for each cage, it was divided into 3 sub-cages. Before weighing, the sea cucumber was taken out from the water and then put into a tray layered with tissue, and left for 30 seconds. Measurements were conducted at the beginning of the study (t0) and then carried out every three weeks until t3. The data analysis includes the Specific Growth Rate; Daily Growth Rate; Absolute Growth; and Survival Rate. The results showed that the Specific Growth Rate; Daily Growth Rate; Absolute Growth; and Survival Rate at Cage 1 (ie 0.5%; 0.88 gram; 62.28 gram; and 85.71%) better than the same parameters at Cage 2 (ie 0.34%; 0.64 gram; 45.33 grams; and 69.05%). These results indicate that the raster-based data for sea cucumber suitability model has advantages over the sea cucumber suitability model analyzed using vector-based data.
Simplified fuzzy logic and arduino-based controller for maximum power tracking in solar panel
Authors: Suherman  , Fajri Mufrihul , Harahap Raja
Published: July 2020

Maximum power tracking for solar panel has been explored since long time ago for increasing solar panel output. Various methods have been implemented from combinational based algorithm to intelligent system, including the use of fuzzy logic. This paper demonstrates the implementation of fuzzy logic on the arduino microcontroller system. A maximum power tracking prototype is developed, and experimental assessments are conducted. Arduino uno is used for the microcontroller, small scale mechanic is developed driven by two electric motors, and 13V solar cell is used as the object. The assessments show that fuzzy logic algorithm is successfully implemented in arduino, the solar panel output is enhanced up to x% and the solar panel efficiency is up to x%.
Physical, mechanical and morphological properties of laminated bamboo hybrid composite: a potential raw material for furniture manufacturing
Authors: Siti Suhaily S , Islam Md Nazrul , Asniza M , Rizal Samsul , Abdul Khalil H P S
Published: July 2020

Laminated hybrid composites were prepared by incorporating dry bamboo strips and oil palm trunk veneer (OPTV) to form five-layer laminated composites. Two different species of bamboo were used including Dendrocalamus asper and Gigantochloa levis to explore their potential for furniture manufacturing. Influence of the bamboo species along with the different arrangements of lamination on the physical, mechanical and morphology properties of the hybrid laminated composites were investigated via scanning electron microscope (SEM), density, water absorption (WA), thickness swelling (TS) as well as impact and hardness strength test. Morphological study showed that filling up of surface cavity by adhesive improved the bonding strength between the surfaces of the bamboo strips and OPTV in the laminated hybrid composites. Additionally, different layer arrangements affected the mechanical properties, i.e., perpendicular arrangement exhibited higher strength compared to the parallel arrangement for both hardness and impact strength. The species of bamboo did not show significant impact on the density for different layer arrangements. Thus, test results clearly indicated that bamboo strips and OPTV hybrid composites could be used as an alternative to wood-based composites for furniture manufacturing.
Study of burning rate characteristics of propellants containing Al–Mg alloy nanopowder
Authors: C Mohammed Iqbal , L Santhosh Kumar , Chakravarthy S R , Jayaganthan R , Sarathi R , A Srinivasan
Published: July 2020

Nanopowder of Al–Mg alloy was synthesized using the method of electrical explosion of thin wires of hypo-eutectic Al–Mg alloy. Thin wires of hypo-eutectic Al–Mg alloy were cut by electrical discharge machining and exploded electrically. The nanopowder obtained is examined using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) for studying the morphology of the particles. TEM and SEM images substantiate the spherical structure of the nanoparticles and the diameter of particles ranges from 20 nm to 95 nm. Solid propellants were prepared by adding the alloy nanopowder as an energetic additive element with bimodal ammonium perchlorate (AP) and Hydroxyl Terminated Polybutadiene (HTPB) propellant formulations. Burning rates of the propellant with nano Al–Mg alloy powder are compared with micro aluminised propellants and propellants with micro Al–Mg powder with the same composition. Mean burn rate of 22.03 mm s−1 was obtained at a pressure level of 9 MPa with nano Al–Mg powder and 20.4 mm s−1 with micro Al–Mg powder compared to mean burning rate of 10.03 mm s−1 at 8 MPa pressure for aluminised propellants. The improved mean burn rate of propellants containing Al–Mg alloy nanoparticles could be accounted for the reduction in the size of the alloy particle and selective melting of eutectic phases along with magnesium. In the process, it gives heat feedback to the high-temperature reaction zone, which results in augmenting further reaction of metal particles.
Ternary alloyed HgCdTe nanocrystals for short-wave and mid-wave infrared region optoelectronic applications
Authors: Balakrishnan Janani , Sreeshma D , Siddesh B M , Jagtap Amardeep , Abhale Atul , Rao KSR Koteswara
Published: July 2020

Semiconductor quantum dots (QDs) are emerging as the forefront alternative for the conventional imaging technology, particularly in infrared region from near infrared (0.75–1.4 μm) to long-wave infrared (8–14 μm) region. A handful of materials are explored for mid infrared imaging QDs and they are all invariably binary semiconductor compounds. Ternary alloyed quantum dots in many previous cases have shown properties that are unique and better than parent binary compounds. In this work, we have synthesized ternary alloyed HgCdTe quantum dots and studied their photophysical properties. Previously studied ternary alloyed HgCdTe CQDs absorb and emit in regions limited upto near-infrared region. We have tuned the excitonic absorption of HgCdTe QDs in the range of 2.2–5 μm, where addition of cadmium clearly showed blueshift in excitonic peak as compared to that of HgTe QDs. Structural properties are studied by TEM, XRD & XPS techniques. Electrical behaviour is studied by measuring I-V, I-V-T curves. Photodetectors are fabricated in photoconductive geometry showing promising photo-response under visible (532 nm) and NIR (810 nm, 1550 nm) excitation. Responsivity of the devices is in the order of 1 mA W−1 at 1 V bias and show good linearity over irradiance range of 0.025 and 2.5 W cm−2. These results pave the way for development of next generation cost-effective short-wave and mid-wave infrared region optoelectronic devices based on narrow bandgap HgCdTe nanocrystals.
Effect of constant high-voltage electric field on wheat seed germination
Authors: Krivov S A , Lazukin A V , Serdyukov Y A , Gundareva S V , Romanov G A
Published: July 2020

In this work an effect of the 10-min pre-sowing treatment by the constant electric field with the 3 kV cm−1 electric field strength on the soft spring wheat seed germination is studied at various positions of the seeds in a plane-parallel electrode system. The effects of the electric field direction and contact conditions of the seeds with a plane aluminum electrode (no contact, when the seeds lie on the isolating plate; contact with the positive or negative high-voltage or grounded electrode) are compared. The treatment response is estimated by the morphological characteristics of 3-day seedlings—germination, the shoot length and the length of individual roots. At all modes, the treatment does not change seed germination. At each considered variant of seed location, the electric field effect did not reduce the average length of the root system and the shoot length below the ones at the control variant. The significant increase of morphological characteristics is achieved at the seed contact with the high voltage electrode.
Development of a novel CdTe/ZnS/ZnTe heterojunction thin-film solar cells: a numerical approach
Authors: Ahmed Sheikh Rashel Al , Ferdous Jannatul , Mian Md Suruz
Published: July 2020

A novel heterojunction structure of cadmium telluride (CdTe)/zinc sulfide (ZnS)/zinc telluride (ZnTe) for thin-film solar cell (TFSC) applications was investigated numerically by Solar Cell Capacitance Simulator in One Dimension (SCAPS-1D). We made a comparative study on the performance of single-layer of Si/CdTe and multi-layers of Si/CdTe/ZnS/ZnTe structures. The optimum values for the thicknesses of CdTe absorber, ZnS, and ZnTe layers in the cell were found to be 2500, 40, and 80 nm, respectively. In the present work, the conversion efficiency (η) of 21.38% was obtained with open-circuit voltage, V
oc = 1.01 V, short-circuit current density, J
sc = 29.32 mA cm−2, and fill-factor, FF = 72.06% in case of multi-layer structure with antireflection coatings (ARCs). The simulation results suggest that the ARC layers presented in this study would be effective to fabricate the high-efficiency solar cells.
Literature and Other White-Man Tricks: Borges and Jarmusch Imagine the Frontier
Authors: Montero Gonzalo
Published: July 2020

In this article, I analyze the representation of the Frontier in the short story ‘El Sur’ by the Argentine Jorge Luis Borges and the movie Dead Man by American director Jim Jarmusch. Going beyond explicit plot similarities, I argue that Jarmusch’s movie carries out an implicit form of adaptation of Borges’s literary text. Both works not only narrate the violent encounter of urban subjects with an unknown and threatening space, but also underscore how the ‘civilized’ subjectivity experiences a crisis that challenges foundational cultural assumptions. Due to its relevance in the process of nation formation, the Frontier served as a source for symbolic discourses, literary representations, and cultural imaginaries. In the case of Argentina and the United States, specific artistic genres fictionalized the life on the Frontier. Stylistically, both Borges and Jarmusch use tropes and narrative devices from these seemingly outdated genres—gauchesca literature and Western movies—but the use of these devices is highly experimental and installs a much more complex depiction of the symbolic space of the Frontier, thus challenging hegemonic accounts of processes of territorial expansion and racial superiority.
Integrated omics analysis reveals the alteration of gut microbe–metabolites in obese adults
Authors: Li Rong , Huang Xue , Liang Xiao , Su Min , Lai Keng Po , Chen Jian
Published: July 2020

Obesity, a risk to health, is a global problem in modern society. The prevalence of obesity was approximately 13% among world’s adult population. Recently, several reports suggested that the interference of gut microbiota composition and function is associated with metabolic disorders, including obesity. Gut microbiota produce a board range of metabolites involved in energy and glucose homeostasis, leading to the alteration in host metabolism. However, systematic evaluation of the relationship between gut microbiota, gut metabolite and host metabolite profiles in obese adults is still lacking. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut–host metabolite profiles in six normal and obese adults of Chinese origin, respectively. Following the functional and pathway analysis, we aimed to understand the possible impact of gut microbiota on the host metabolites via the change in gut metabolites. The result showed that the change in gut microbiota may result in the modulation of gut metabolites contributing to glycolysis, tricarboxylic acid cycle and homolactic fermentation. Furthermore, integrated metabolomic analysis demonstrated a possible positive correlation of dysregulated metabolites in the gut and host, including l-phenylalanine, l-tyrosine, uric acid, kynurenic acid, cholesterol sulfate and glucosamine, which were reported to contribute to metabolic disorders such as obesity and diabetes. The findings of this study provide the possible association between gut microbiota–metabolites and host metabolism in obese adults. The identified metabolite changes could serve as biomarkers for the evaluation of obesity and metabolic disorders.
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
Authors: Piro Vitor C , Dadi Temesgen H , Seiler Enrico , Reinert Knut , Renard Bernhard Y
Published: July 2020

Motivation

The exponential growth of assembled genome sequences greatly benefits metagenomics studies. However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates. Indexing the current RefSeq can take days and hundreds of GB of memory on large servers. Few methods address these issues thus far, and even though many can theoretically handle large amounts of references, time/memory requirements are prohibitive in practice. As a result, many studies that require sequence classification use often outdated and almost never truly up-to-date indices.

Results

Motivated by those limitations, we created ganon, a k-mer-based read classification tool that uses Interleaved Bloom Filters in conjunction with a taxonomic clustering and a k-mer counting/filtering scheme. Ganon provides an efficient method for indexing references, keeping them updated. It requires <55 min to index the complete RefSeq of bacteria, archaea, fungi and viruses. The tool can further keep these indices up-to-date in a fraction of the time necessary to create them. Ganon makes it possible to query against very large reference sets and therefore it classifies significantly more reads and identifies more species than similar methods. When classifying a high-complexity CAMI challenge dataset against complete genomes from RefSeq, ganon shows strongly increased precision with equal or better sensitivity compared with state-of-the-art tools. With the same dataset against the complete RefSeq, ganon improved the F1-score by 65% at the genus level. It supports taxonomy- and assembly-level classification, multiple indices and hierarchical classification.

Availability and implementation

The software is open-source and available at: https://gitlab.com/rki_bioinformatics/ganon.

Supplementary information

Supplementary data are available at Bioinformatics online.
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens
Authors: Hasegawa Takanori , Hayashi Shuto , Shimizu Eigo , Mizuno Shinichi , Niida Atsushi , Yamaguchi Rui , Miyano Satoru , Nakagawa Hidewaki , Imoto Seiya
Published: July 2020

It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants. Beyond the existing applications, Neoantimon is capable of attaching and reflecting several additional information, e.g. wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information and combinations of mutations to filter out infeasible peptides as neoantigen.

Availability and implementation

The R package is available at http://github/hase62/Neoantimon.
Right Posterior Insula and Putamen Volume Mediate the Effect of Oxytocin Receptor Polygenic Risk for Autism Spectrum Disorders on Reward Dependence in Healthy Adults
Authors: Wang Junping , Zhang Peng , Li Wei , Wen Qin , Liu Feng , Xu Jiayuan , Xu Qiang , Zhu Dan , Ye Zhaoxiang , Yu Chunshui
Published: July 2020

Much evidence indicates the influence of the oxytocin receptor (OXTR) gene on autism spectrum disorders (ASDs), a set of disorders characterized by a range of deficits in prosocial behaviors, which are closely related to the personality trait of reward dependence (RD). However, we do not know the effect of the OXTR polygenic risk score for ASDs (OXTR-PRSASDs) on RD and its underlying neuroanatomical substrate. Here, we aimed to investigate associations among the OXTR-PRSASDs, gray matter volume (GMV), and RD in two independent datasets of healthy young adults (n = 450 and 540). We found that the individuals with higher OXTR-PRSASDs had lower RD and significantly smaller GMV in the right posterior insula and putamen. The GMV of this region showed a positive correlation with RD and a mediation effect on the association between OXTR-PRSASDs and RD. Moreover, the correlation map between OXTR-PRSASDs and GMV showed spatial correlation with OXTR gene expression. All results were highly consistent between the two datasets. These findings highlight a possible neural pathway by which the common variants in the OXTR gene associated with ASDs may jointly impact the GMV of the right posterior insula and putamen and further affect the personality trait of RD.
Spatiotemporal Characteristics of the COVID-19 Epidemic in the United States
Authors: Wang Yun , Liu Ying , Struthers James , Lian Min
Published: July 2020

Background

A range of near-real-time online/mobile mapping dashboards and applications have been used to track the coronavirus disease 2019 (COVID-19) pandemic worldwide; however, small area-based spatiotemporal patterns of COVID-19 in the United States remain unknown.

Methods

We obtained county-based counts of COVID-19 cases confirmed in the United States from 22 January to 13 May 2020 (N = 1 386 050). We characterized the dynamics of the COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis.

Results

Along with the national plateau reached in early April, COVID-19 incidence significantly decreased in the Northeast (estimated weekly percentage change [EWPC]: −16.6%) but continued increasing in the Midwest, South, and West (EWPCs: 13.2%, 5.6%, and 5.7%, respectively). Higher risks of clustering and incidence of COVID-19 were consistently observed in metropolitan versus rural counties, counties closest to core airports, the most populous counties, and counties with the highest proportion of racial/ethnic minorities. However, geographic differences in incidence have shrunk since early April, driven by a significant decrease in the incidence in these counties (EWPC range: −2.0%, −4.2%) and a consistent increase in other areas (EWPC range: 1.5–20.3%).

Conclusions

To substantially decrease the nationwide incidence of COVID-19, strict social-distancing measures should be continuously implemented, especially in geographic areas with increasing risks, including rural areas. Spatiotemporal characteristics and trends of COVID-19 should be considered in decision making on the timeline of re-opening for states and localities.
The Role of Remdesivir in South Africa: Preventing COVID-19 Deaths Through Increasing Intensive Care Unit Capacity
Authors: Nichols Brooke E , Jamieson Lise , Zhang Sabrina R C , Rao Gabriella A , Silal Sheetal , Pulliam Juliet R C , Sanne Ian , Meyer-Rath Gesine
Published: July 2020

Countries such as South Africa have limited intensive care unit (ICU) capacity to handle the expected number of patients with COVID-19 requiring ICU care. Remdesivir can prevent deaths in countries such as South Africa by decreasing the number of days people spend in ICU, therefore freeing up ICU bed capacity.
On providing systematized access to consolidated principles, guidelines and patterns for usable security research and development†
Authors: Gorski Peter L , von Zezschwitz Emanuel , Lo Iacono Luigi , Smith Matthew
Published: July 2020

We present a systematization of usable security principles, guidelines and patterns to facilitate the transfer of existing knowledge to researchers and practitioners. Based on a literature review, we extracted 23 principles, 11 guidelines and 47 patterns for usable security and identified their interconnection. The results indicate that current research tends to focus on only a subset of important principles. The fact that some principles are not yet addressed by any design patterns suggests that further work on refining these patterns is needed. We developed an online repository, which stores the harmonized principles, guidelines and patterns. The tool enables users to search for relevant guidance and explore it in an interactive and programmatic manner. We argue that both the insights presented in this article and the web-based repository will be highly valuable for students to get a good overview, practitioners to implement usable security and researchers to identify areas of future research.
Evidence against a geographic gradient of Alzheimer's disease and the hygiene hypothesis
Authors: Lathe J Constance , Lathe Richard
Published: July 2020

A significant positive correlation was previously reported (Fox et al.Evol Med Public Health 2013; 2013:173–86) between hygiene and the global prevalence of Alzheimer's disease (AD) based on World Health Organization (2004) data. These data have now been updated by the Global Burden of Disease (GBD; 2016) dataset that takes into account under-registration and other potential confounds. We therefore addressed whether the association between hygiene and AD is maintained in light of these more recent data. We report a significant positive correlation between GBD AD prevalence rates and parasite burden, and a negative association with hygiene. These newer data argue that hygiene is not a risk factor for AD, and instead suggest that parasite burden may increase AD risk.

Lay summary: It was previously hypothesized that hygeine might be a risk factor for the development of Alzheimer disease (AD), based on a global gradient of dementia. Newer data that correct global AD rates for under-reporting now demonstrate that parasite burden is positively correlated with AD.
Viewing Cortical Collecting Duct Function Through Phenotype-guided Single-Tubule Proteomics
Authors: Himmerkus Nina , Svendsen Samuel L , Quintanova Catarina , Bleich Markus , Von Schwerdtner Otto , Benzing Thomas , Welling Paul A , Leipziger Jens , Rinschen Markus M
Published: July 2020

The revolution of the omics technologies has enabled profiling of the molecules of any sample. However, the heterogeneity of the kidney with highly specialized nephron segments like the cortical collecting duct (CCD) poses a challenge regarding integration of omics data and functional analysis. We examined function and proteome from the same single CCDs of C57Bl6 mice by investigating them in a double-barreled perfusion system before targeted mass spectrometry. Transepithelial voltage (Vte), transepithelial resistance, as well as amiloride-sensitive voltage (ΔVteamil) were recorded. CCDs were of 400–600 µm of length, showed lumen negative Vte between −8.5 and −32.5 mV and an equivalent short circuit current I’sc between 54 and 192 µA/cm2. On a single-tubule proteome level, intercalated cell (IC) markers strongly correlated with other intercalated cell markers and negatively with principal cell markers. Integration of proteome data with phenotype data revealed that tubular length correlated with actin and Na+-K+-ATPase expression. ΔVte(amil) reflected the expression level of the β-subunit of the epithelial sodium channel. Intriguingly, ΔVte(amil) correlated inversely with the water channel AQP2 and the negative regulator protein NEDD4L (NEDD4-2). In pendrin knockout (KO) mice, the CCD proteome was accompanied by strong downregulation of other IC markers like CLCNKB, BSND (Barttin), and VAA (vH+-ATPase), a configuration that may contribute to the salt-losing phenotype of Pendred syndrome. Proteins normally coexpressed with pendrin were decreased in pendrin KO CCDs. In conclusion, we show that functional proteomics on a single nephron segment scale allows function–proteome correlations, and may potentially help predicting function from omics data.
The Relationship Between Intermuscular Fat and Physical Performance Is Moderated by Muscle Area in Older Adults
Authors: Farsijani Samaneh , Santanasto Adam J , Miljkovic Iva , Boudreau Robert M , Goodpaster Bret H , Kritchevsky Stephen B , Newman Anne B
Published: July 2020

Background

Age-related deposition of fat in skeletal muscle is associated with functional limitations. Skeletal muscle fat may be present in people with preserved muscle mass or accompanied by muscle wasting. However, it is not clear if the association between muscle fat deposition and physical performance is moderated by muscle mass.

Objective

To determine whether the association between midthigh intermuscular fat and physical performance is moderated by muscle area.

Methods

We performed a cross-sectional analysis of the Health, Aging, and, Body Composition (ABC) study data collected in 2002–2003 (n = 1897, women: 52.2%). Midthigh muscle cross-sectional area (by computed tomography) and physical performance measures were compared across quartiles of intermuscular fat absolute area. Moderation analysis was performed to determine the conditional effect of intermuscular fat on physical performance as a function of muscle area. Conditional effects were evaluated at three levels of muscle area (mean and ± 1 standard deviation [SD]; 213.2 ± 53.2 cm2).

Results

Simple slope analysis showed that the negative association between intermuscular fat area (cm2) and leg strength (N·m) was of greater magnitude (beta coefficient [b], 95% confidence interval [CI] = −0.288 [−0.427, −0.148]) in participants with greater muscle area (ie, 1 SD above the mean) compared to those with lower muscle area (ie, at mean [b = −0.12 {−0.248, 0.008}] or 1 SD below the mean [b = 0.048 {−0.122, 0.217}]). Similarly, the negative association of intermuscular fat with 400-m walk speed (m/s) and chair stand (seconds) was greater in those with higher muscle areas (p < .001) compared to those with lower muscle areas.

Conclusions

The association between higher intermuscular fat area and impaired physical function in aging is moderated by muscle area.
A rock-physics model to determine the pore microstructure of cracked porous rocks
Authors: Zhang Lin , Ba Jing , Carcione José M
Published: July 2020

Determining rock microstructure remains challenging, since a proper rock-physics model is needed to establish the relation between pore microstructure and elastic and transport properties. We present a model to estimate pore microstructure based on porosity, ultrasonic velocities and permeability, assuming that the microstructure consists on randomly oriented stiff equant pores and penny-shaped cracks. The stiff pore and crack porosity varying with differential pressure is estimated from the measured total porosity on the basis of a dual porosity model. The aspect ratio of pores and cracks and the crack density as a function of differential pressure are obtained from dry-rock P- and S-wave velocities, by using a differential effective medium model. These results are used to invert the pore radius from the matrix permeability by using a circular pore model. Above a crack density of 0.13, the crack radius can be estimated from permeability, and below that threshold, the radius is estimated from P-wave velocities, taking into account the wave dispersion induced by local fluid flow between pores and cracks. The approach is applied to experimental data for dry and saturated Fontainebleau sandstone and Chelmsford Granite.
Distribution and diversity of glycocin biosynthesis gene clusters beyond Firmicutes
Authors: Singh Vaidhvi , Rao Alka
Published: July 2020

Glycocins are the ribosomally synthesized glycosylated bacteriocins discovered and characterized in Firmicutes, only. These peptides have antimicrobial activity against several pathogenic bacteria, including Streptococcus pyogenes , methicillin-resistant Staphylococcus aureus and food-spoilage bacteria Listeria monocytogenes. Glycocins exhibit immunostimulatory properties and make a promising source of new antibiotics and food preservatives akin to Nisin. Biochemical studies of Sublancin, Glycocin F, Pallidocin and ASM1 prove that the nested disulfide-bonds are essential for their bioactivities. Using in silico approach of genome mining coupled with manual curation, here we identify 220 new putative glycocin biosynthesis gene clusters (PGBCs) spread across 153 bacterial species belonging to seven different bacterial phyla. Based on gene composition, we have grouped these PGBCs into five distinct conserved cluster Types I–V. All experimentally identified glycocins belong to Type I PGBCs. From protein sequence based phylograms, tanglegrams, global similarity heat-maps and cumulative mutual information analysis, it appears that glycocins may have originated from closely related bacteriocins, whereas recruitment of cognate glycosyltransferases (GTs) might be an independent event. Analysis further suggests that GTs may have coevolved with glycocins in cluster-specific manner to define distinctive donor specificities of GTs or to contribute to glycocin diversity across these clusters. We further identify 162 hitherto unreported PGBCs wherein the corresponding product glycocins have three or less than three cysteines. Secondary structure predictions suggest that these putative glycocins may not form di-nested disulfide-bonds. Therefore, production of such glycocins in heterologous host Escherichia coli is feasible and may provide novel antimicrobial spectrum and or mechanism of action for varied applications.
Skewed allelic expression on X chromosome associated with aberrant expression of XIST on systemic lupus erythematosus lymphocytes
Authors: Zhang Yanfeng , Li Xinrui , Gibson Andrew , Edberg Jeffrey , Kimberly Robert P , Absher Devin M
Published: July 2020

A common feature of autoimmune diseases, including systemic lupus erythematosus (SLE), is an increased prevalence in women. However, the molecular basis for sex disparity in SLE remains poorly understood. To examine the role of X-linked transcription in SLE adaptive immune cells, we performed RNA-seq in T cell and B cell subsets from either healthy donors or patients with SLE. Analyses of allelic expression (AE) profiles identified a pattern of increased allelic imbalance across the entire X chromosome in SLE lymphocytes. X-linked genes exhibiting AE in SLE had an extensive overlap with genes known to escape X chromosome inactivation (XCI). XIST RNA was overexpressed in SLE patients. Differential XIST expression correlated with AE profiles more positively at X-linked genes than the genome-wide background. Analysis of three independent RNA-seq data verified the XIST-associated skewed AE on X chromosome in SLE. Integrative analyses of DNA methylation profiles showed an increased variability of DNA methylation levels at these AE-related X-linked genes. In cultured lymphoblastic cells, knockdown of XIST specifically altered allelic imbalance patterns between X chromosomes. Our study provides genetic evidence that upregulation of XIST accompanied with more skewed allelic expression on X chromosome is associated with the pathogenesis of SLE and may provide mechanistic insights into the increased incidence of SLE in females.
The emerging field of polygenic risk scores and perspective for use in clinical care
Authors: Yanes Tatiane , McInerney-Leo Aideen M , Law Matthew H , Cummings Shelly
Published: July 2020

Genetic testing is used widely for diagnostic, carrier and predictive testing in monogenic diseases. Until recently, there were no genetic testing options available for multifactorial complex diseases like heart disease, diabetes and cancer. Genome-wide association studies (GWAS) have been invaluable in identifying single-nucleotide polymorphisms (SNPs) associated with increased or decreased risk for hundreds of complex disorders. For a given disease, SNPs can be combined to generate a cumulative estimation of risk known as a polygenic risk score (PRS). After years of research, PRSs are increasingly used in clinical settings. In this article, we will review the literature on how both genome-wide and restricted PRSs are developed and the relative merit of each. The validation and evaluation of PRSs will also be discussed, including the recognition that PRS validity is intrinsically linked to the methodological and analytical approach of the foundation GWAS together with the ethnic characteristics of that cohort. Specifically, population differences may affect imputation accuracy, risk magnitude and direction. Even as PRSs are being introduced into clinical practice, there is a push to combine them with clinical and demographic risk factors to develop a holistic disease risk. The existing evidence regarding the clinical utility of PRSs is considered across four different domains: informing population screening programs, guiding therapeutic interventions, refining risk for families at high risk, and facilitating diagnosis and predicting prognostic outcomes. The evidence for clinical utility in relation to five well-studied disorders is summarized. The potential ethical, legal and social implications are also highlighted.
Pharmacogenomics for immunotherapy and immune-related cardiotoxicity
Authors: Castrillon Jessica A , Eng Charis , Cheng Feixiong
Published: July 2020

Immune checkpoint blockade (ICB) has become a standard of care in a subset of solid tumors. Although cancer survivorship has extended, rates of durable response of ICB remain poor; furthermore, cardiac adverse effects are emerging, which impact several mechanical aspects of the heart. Cardio-oncology programs implement a clinical assessment to curtail cardiovascular disease progression but are limited to the current clinical parameters used in cardiology. Pharmacogenomics provides the potential to unveil heritable and somatic genetic variations for guiding precision immunotherapy treatment to reduce the risk of immune-related cardiotoxicity. A better understanding of pharmacogenomics will optimize the current treatment selection and dosing of immunotherapy. Here, we summarize the recent pharmacogenomics studies in immunotherapy responsiveness and its related cardiotoxicity and highlight how patient genetics and epigenetics can facilitate researchers and clinicians in designing new approaches for precision immunotherapy. We highlight and discuss how single-cell technologies, human-induced pluripotent stem cells and systems pharmacogenomics accelerate future studies of precision cardio-oncology.
Retrovirus reactivation in CHMP2BIntron5 models of frontotemporal dementia
Authors: Fort-Aznar Laura , Ugbode Chris , Sweeney Sean T
Published: July 2020

Frontotemporal dementia (FTD) is the second most prevalent form of pre-senile dementia after Alzheimer’s disease. Amyotrophic lateral sclerosis (ALS) can overlap genetically, pathologically and clinically with FTD indicating the two conditions are ends of a spectrum and may share common pathological mechanisms. FTD–ALS causing mutations are known to be involved in endosomal trafficking and RNA regulation. Using an unbiased genome-wide genetic screen to identify mutations affecting an FTD–ALS-related phenotype in Drosophila caused by CHMP2BIntron5 expression, we have uncovered repressors of retrovirus (RV) activity as modifiers of CHMP2BIntron5 toxicity. We report that neuronal expression of CHMP2BIntron5 causes an increase in the activity of the endogenous Drosophila RV, gypsy, in the nervous system. Genetically blocking Drosophila gypsy activation and pharmacologically inhibiting viral reverse transcriptase activity prevents degenerative phenotypes observed in fly and rat neurons. These findings directly link endosomal dysfunction to RV de-repression in an FTD–ALS model without TDP-43 pathology. These observations may contribute an understanding to previous discoveries of RV activation in ALS affected patients.
Degree of Rational Maps and Specialization
Authors: Cid-Ruiz Yairon , Simis Aron
Published: July 2020

One considers the behavior of the degree of a rational map under specialization of the coefficients of the defining linear system. The method rests on the classical idea of Kronecker as applied to the context of projective schemes and their specializations. For the theory to work, one is led to develop the details of rational maps and their graphs when the ground ring of coefficients is a Noetherian domain.
User reactions to COVID-19 screening chatbots from reputable providers
Authors: Dennis Alan R , Kim Antino , Rahimi Mohammad , Ayabakan Sezgin
Published: July 2020

Objectives

The objective was to understand how people respond to coronavirus disease 2019 (COVID-19) screening chatbots.

Materials and Methods

We conducted an online experiment with 371 participants who viewed a COVID-19 screening session between a hotline agent (chatbot or human) and a user with mild or severe symptoms.

Results

The primary factor driving user response to screening hotlines (human or chatbot) is perceptions of the agent’s ability. When ability is the same, users view chatbots no differently or more positively than human agents. The primary factor driving perceptions of ability is the user’s trust in the hotline provider, with a slight negative bias against chatbots’ ability. Asian individuals perceived higher ability and benevolence than did White individuals.

Conclusions

Ensuring that COVID-19 screening chatbots provide high-quality service is critical but not sufficient for widespread adoption. The key is to emphasize the chatbot’s ability and assure users that it delivers the same quality as human agents.
Validation of the Free Fatty Acid Test Kit for the Measurement of the Free Fatty Acid Content of Vegetable Oils, Fish Oils, Animal Fats (Tallows), Meat and Fish Meals, and Potato Chips and Grain-Based Snack Products: AOAC Performance Tested MethodSM 052004
Authors: Gordon I Virginia C , Rainey Christopher C , Studmire Willainia C
Published: July 2020

Background

The Official American Oil Chemists’ Society (AOCS) Ca 5a-40 method for the determination of free fatty acids is based on titration of an ethanolic solution and requires a large volume of organic solvents, large sample aliquots, and up to 18 hours extraction time for some samples. The SafTest Free Fatty Acid Test Kit is a rapid method designed to measure the free fatty acid content of vegetable oils; fish oil; animal fats (tallows); meat meal and fish meal products; and crackers, chips, and other processed grain-based snack products using micro-analytical and membrane separation principles.

Objective

The study objective was to validate the SafTest Free Fatty Acid Test in one internal study, two contracted studies, and an independent laboratory study studies.

Method

Recovery, limit of quantitation, selectivity, robustness, stability, and consistency of the SafTest Free Fatty Acid Test were evaluated.

Results

Recoveries from control solutions ranged from 97 to 106%. Repeatability (RSDr) from method developer matrix studies ranged from 1.1 to 8.1%. Biases, expressed as a percentage recovery from AOCS Ca 5a-40, averaged 96.5% for olive oils, 94.0% for animal fats, and 103.9% for meat meals. Results observed in the independent laboratory study were similar.

Conclusions

The SafTest Free Fatty Acid Test can measure free fatty acid levels in oils, fats, meal, and snack matrices with accuracy and precision comparable to AOCS Ca 5a-40.

Highlights

The SafTest Free Fatty Acid Test Kit has the advantage of using reagent volumes, instrumental analysis, and easy-to-use, standardized procedures with rapid detection times for the determination of free fatty acids.
Protection of Detainees from Sexual Violence under International Humanitarian Law
Authors: Bradley Samantha Frances
Published: July 2020

This article addresses the question of whether current frameworks under international humanitarian law offer adequate protection to persons detained for reasons relating to armed conflict from crimes of sexual violence. Sexual violence against detainees is a persistent issue in both international and non-international armed conflicts. Sexual violence against male detainees is also a widespread issue, with men and boys constituting the bulk of persons detained in conflict, and also facing unique barriers in reporting abuses. An evaluation of current legal frameworks under the Geneva Conventions of 1949 and the Additional Protocols of 1977 identifies key fault-lines in the law, including a widespread statutory characterisation of sexual violence as a crime principally committed against women. Case law demonstrates a resultant tendency to conceptualise sexual abuse of male detainees as torture, rather than sexual violence. Additionally, state interpretations of the law reflect this absence of gender neutrality. Compliance mechanisms are furthermore held back by the lack of clarity and specificity of prohibitions on sexual violence against detainees in international and non-international armed conflicts. Ultimately, options for strengthening the law in this area are subject to the political will of states and carry the risk of winding back existing standards of protection. The development of a non-binding but standard-setting instrument devised with the support of states and specifically prohibiting the issue of sexual violence against detainees in gender- neutral and comprehensive terms may ultimately be the most effective means of strengthening existing legal frameworks.
Outcome of tantalum rod insertion in the treatment of osteonecrosis of the femoral head with minimum follow-up of 1 year: a meta-analysis and systematic review
Authors: Onggo James Randolph , Nambiar Mithun , Onggo Jason Derry , Tay Guan , Singh Parminder J , Babazadeh Sina
Published: July 2020

Osteonecrosis of the femoral head (ONFH) is a debilitating disease that can cause deformity and collapse of the femoral head, thus leading to the development of degenerative joint disease that can incapacitate the patient with pain and reduction in hip mobility. This study aims to determine the safety and efficacy of tantalum rod insertion in the treatment of ONFH with a minimum follow-up period of 1 year. A multi-database search was performed according to Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Data from studies assessing the clinical and radiological outcomes as well as complications of tantalum rod insertion in the treatment of ONFH with a minimum follow-up period of 1 year were extracted and analyzed. Ten studies were included in this meta-analysis, consisting of 550 hips. There was a statistically significant increase in HHS (MD = 30.35, 95% CI: 20.60–40.10, P < 0.001) at final follow-up versus pre-operative scores. The weighted pooled proportion (PP) of radiographic progression of ONFH was 0.221 (95% CI: 0.148–0.316), while that of progression into femoral head collapse was 0.102 (95% CI: 0.062–0.162). Conversion to total hip arthroplasty (THA) had a PP of 0.158 (95% CI: 0.107–0.227) with a mean weighted period of 32.4 months (95% CI: 24.9–39.9 months). Subgroup analysis of conversion to THA when tantalum rods were used in conjunction with bone grafting (PP = 0.150, 95% CI: 0.092–0.235) showed a marginal risk reduction than when compared with subgroup analysis of tantalum rods being used alone (PP = 0.154, 95% CI: 0.078–0.282). Tantalum rod is a safe alternative option to the current joint-preserving procedures available in the treatment of ONFH. However, more studies are needed to investigate and identify the most appropriate patients who would benefit most and the synergistic effect brought on by the use of complementary biological augmentation of bone grafting or stem cells with tantalum rods.