bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast functional annotation of metagenomic shotgun data by DNA alignment to a microbial gene catalog
Authors: Brown Stuart M. , Hao Yuhan , Chen Hao , Laungani Bobby P. , Ali Thahmina A. , Dong Changsu , Lijeron Carlos , Kim Baekdoo , Krampis Konstantinos , Pei Zhiheng 
Published: March 2017

AbstractBackgroundMetagenomic shotgun sequencing is becoming increasingly popular to study microbes associated with the human body and in environmental samples. A key goal of shotgun metagenomic sequencing is to identify gene functions and metabolic pathways that differ between samples or conditions. However, current methods to identify function in the large number of reads in a high-throughput sequence data file rely on the computationally intensive and low stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.ResultsWe have developed an alternative analysis approach for shotgun metagenomic sequence data utilizing Bowtie2 DNA-DNA alignment of the reads to a database of well annotated genes compiled from human microbiome data. This method is rapid, and provides high stringency matches (>90% DNA sequence identity) of shotgun metagenomics reads to genes with annotated functions. We demonstrate the use of this method with synthetic data, Human Microbiome Project shotgun metagenomic data sets, and data from a study of liver disease. Differentially abundant KEGG gene functions can be detected in these experiments.ConclusionsFunctional annotation of metagenomic shotgun sequence reads can be accomplished by rapid DNA-DNA matching to a custom database of microbial sequences using the Bowtie2 sequence alignment tool. This method can be used for a variety of microbiome studies and allows functional analysis which is otherwise computationally demanding. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.
Using mobile phones as acoustic sensors for high-throughput mosquito surveillance
Authors: Mukundarajan Haripriya , Hol Felix J H , Castillo Erica A , Newby Cooper , Prakash Manu 
Published: March 2017

AbstractThe direct monitoring of mosquito populations in field settings is a crucial input for shaping appropriate and timely control measures for mosquito-borne diseases. Here, we demonstrate that commercially available mobile phones are a powerful tool for acoustically mapping mosquito species distributions worldwide. We show that even low-cost mobile phones with very basic functionality are capable of sensitively acquiring acoustic data on species-specific mosquito wingbeat sounds, while simultaneously recording the time and location of the human-mosquito encounter. We survey a wide range of medically important mosquito species, to quantitatively demonstrate how acoustic recordings supported by spatio-temporal metadata enable rapid, non-invasive species identification. As proof-of-concept, we carry out field demonstrations where minimally-trained users map local mosquitoes using their personal phones. Thus, we establish a new paradigm for mosquito surveillance that takes advantage of the existing global mobile network infrastructure, to enable continuous and large-scale data acquisition in resource-constrained areas.
De novoBK channel mutation causes epilepsy by regulating voltage-dependent, but not calcium-dependent, activation
Authors: Li Xia , Poschmann Sibylle , Chen Qiuyun , Oundjian Nelly Jouayed , Snoeijen-Schouwenaars Francesca M. , Kamsteeg Erik-Jan , Willemsen Marjolein , Wang Qing Kenneth 
Published: March 2017

AbstractEpilepsy is one of the most common neurological diseases. Here we report the firstde novomutation in the BK channel (p.N995S) that causes epilepsy in two independent families. The p.N995S mutant channel showed a markedly increased macroscopic potassium current mediated by increases in both channel open probability and channel open dwell time. Mutation p.N995S affects the voltage-activation pathway of BK channel, but does not affect the calcium sensitivity. Paxilline blocks potassium currents from both WT and mutant BK channels. We also identified two variants of unknown significance, p.E656A and p.N1159S in epilepsy patients. However, they do not affect BK channel functions, therefore, are unlikely to be a cause of disease. These results expand the BK channelopathy to a more common disease of epilepsy, suggest that the BK channel is a drug target for treatment of epilepsy, and highlight the importance of functional studies in the era of precision medicine.
Pattern component modeling: A flexible approach for understanding the representational structure of brain activity patterns
Authors: Diedrichsen Jörn , Yokoi Atsushi , Arbuckle Spencer A. 
Published: March 2017

AbstractRepresentational models specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. Here we review pattern component modeling (PCM), a practical Bayesian approach for evaluating such models. Similar to encoding models, PCM evaluates the ability of models to predict novel brain activity patterns. In contrast to encoding models, however, the activity of individual voxels across conditions (activity profiles) are not directly fitted. Rather, PCM integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model. By using an analytical expression for the marginal likelihood, PCM allows the fitting of flexible representational models, in which the relative strength and form of the encoded features can be estimated from the data. We discuss here a number of different forms with which such flexible representational models can be specified, and how models of different complexity can be compared. We then provide a number of practical examples from our recent work in motor control, ranging from fixed models to more complex non-linear models of brain representations. The code for the fitting and cross-validation of representational models is provided in a open-source Matlab toolbox.
Alternative miRNAs: Human sequences misidentified as plant miRNAs in plant studies and in human plasma
Authors: Witwer Kenneth W. 
Published: March 2017

AbstractA recent study reported that “Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi” 1. Analysis of two human blood plasma sequencing datasets was said to provide evidence for uptake of plant miRNAs into human plasma. The results were also purportedly inconsistent with contamination 1. However, a review of these data suggests that they do not support dietary xenomiR uptake, but instead confirm previous findings that detection of rare plant miRNAs in mammalian sequencing datasets is artifactual. Only one putative plant miRNA (“peu-MIR2910) in this study mapped consistently above background, and this sequence is found in a human rRNA. Several other rarer but consistently mapped plant miRNAs also have 100% or near 100% matches to human transcripts or genomic sequences, and some do not map to plant genomes at all. These misidentified “alternative miRNAs”—including MIR2910 and MIR2911—emphasize the need for rigorous filtering strategies when assessing possible xenomiRNAs.
Comparison between the effect of 6 weeks of morning or evening aerobic exercise on appetite and anthropometric indices: a randomized controlled trial
Authors: Alizadeh Z. , Younespour S. , Rajabian Tabesh M. , Haghravan S. 
Published: March 2017

SummarySeveral studies have shown that exercise is directly related to creating negative energy balance and changes in appetite. However, few studies have examined the effect of exercise time during the day on these factors. The aim of the present study was to demonstrate the effect of 6 weeks of morning and evening aerobic exercise on appetite and anthropometric indices. A total of 48 overweight females were recruited to this clinical trial. By the time of exercise, they were divided into two groups (morning or evening) and performed 6 weeks of exercise with a target heart rate on the ventilatory threshold. Appetite change, calorie intake and anthropometric indices were assessed. Consistent changes in appetite scores were not found during the 6 weeks (P > 0.05). Calorie consumption of the morning group decreased significantly more than that of the evening group (P = 0.02) during the 6 weeks. In addition, significant changes in body weight, body mass index, abdominal skin fold thickness and abdominal circumference were seen in the morning group. It appears that moderate‐ to high‐intensity aerobic exercise in the morning could be considered a more effective programme than evening exercise on appetite control, calorie intake and weight loss in inactive overweight women. However, the limitations of the study, such as short‐term duration, should be noticed.
Influence of severe drought on the resistance of Pinus yunnanensis to a bark beetle‐associated fungus
Authors: Gao X. , Zhou X. , Wang H. , Kong X. , Zhang S. , Wang Z. , Wu W. , Zhang Z. , Lieutier F. 
Published: March 2017

SummaryResearch on tree response to pest attacks under drought and heat stress is crucial for predicting the effect of climate change on forest pests and tree health. In this work, we studied the influence of severe water stress on the resistance of Pinus yunnanensis to inoculations of Grosmannia yunnanensis, a pathogenic fungus associated with the aggressive bark beetle, Tomicus yunnanensis. Experiments were performed in two plots, one located at the top of a hill and the other at the foot of a hill, in Xiaojiu, Yunnan, China, from May to September 2010 and March to April 2012. Measurements of soil and needle water content and predawn needle water potentials confirmed that severe droughts occurred during these periods. Maximum water stress intensity even occurred in 2010 during the typical rainy season. Following low‐density inoculations, the reaction zone length and fungal growth were measured in the phloem. Sapwood blue staining and total sapwood occlusion were quantified following fungal mass inoculations. Our results suggest that severe water stress has a negative impact on a tree's resistance to G. yunnanensis. By comparing our results to previous work performed from 1997 to 1999 on the same tree species, and in the same locality under mild water stress, we concluded that drought had opposite effects on tree resistance above and below a certain threshold of predawn needle water potential. The threshold, corresponded to maximum efficiency for tree defence mechanisms, was visible in our results, and was estimated to be approximately ‐1.1 MPa to ‐1.2 MPa for P. yunnanensis under local conditions. We suggest that the existence of such a threshold of water stress intensity may be viable for any conifer undergoing biotic aggressions and, specifically, bark beetle attacks.
A new genus and two new species of Pygmephoridae (Acari: Heterostigmata) associated with Trinervitermes trinervoides (Isoptera: Termitidae) from South Africa
Authors: Khaustov Alexander , Hugo-Coetzee Elizabeth , Ermilov Sergey 
Published: March 2017

A new genus of pygmephorid mites, Micropygmephorus gen. nov. (Acari: Pygmephoroidea: Pygmephoridae), and two new species, M. pusillus sp. nov. and M. heterotrichus sp. nov. are described from nests of and phoretic on termites, Trinervitermes trinervoides (Sjöstedt, 1911) (Isoptera: Termitidae), from South Africa. The taxonomic position of the new genus is discussed.
Evaluation of blood metabolites reflects presence or absence of liver abscesses in beef cattle
Authors: Macdonald Alaina G C , Bourgon Stéphanie L , Palme Rupert , Miller Stephen P , Montanholi Yuri R 
Published: March 2017

Liver abscesses constitute a prominent concern regarding animal health and profitability of the beef industry. Our objective was to evaluate potential biliary and blood indicators of liver abscesses. Twenty‐nine beef bulls (initially averaging 356±70.5 kg and 253±30 days of age) were fed a high‐concentrate diet during a performance test of 112 days, during which blood was collected at nine time points spaced 0.5–13 days apart within 56 days before slaughter. At the abattoir, blood and bile were collected and livers were inspected for liver abscesses. Results indicated that liver abscesses are associated with elevated levels of plasma cortisol and aspartate aminotransferase, and decreased levels of albumin, cholesterol and testosterone over the period before slaughter. Based on the blood samples collected during exsanguination, the presence of liver abscesses was associated with lower concentrations of thyroxine, albumin, cholesterol and alkaline phosphatase, and is suggested to be associated with lower blood carbon dioxide (P=0.08) and lower biliary cortisol metabolites (P=0.07). Albumin and cholesterol are established indicators of hepatic function and are consistently related to the presence of liver abscesses. Identifying blood parameters that predict liver abscesses has practical implications for cattle husbandry and for ensuring food safety.
<b>Ecology of marine macro algal flora of Visakhapatnam coastal areas, Bay of Bengal, India</b>
Authors: Sowjanya I. Vishnupriya , Sekhar P. S. Raja 
Published: March 2017

An ecological study was conducted on species composition, vertical distribution and monthly variations of marine macro algae along the Visakhapatnam coast, Bay of Bengal, India between May 2013 and April 2014. A total of 48 species was recorded, 18 species belonging to phylum Chlorophyta, nine species to Phaeophyta and 21 species to Rhodophyta. The phylum Rhodophyta was the most dominant group with the highest number of species composition (44.0%) followed by Chlorophyta (37.0%) and Phaeophyta (19.0%). Monthly seaweed distribution data showed the dominance of Rhodophyta members (43.75%) during November to February, when compared to that of Chlorophyta and Phaeophyta members. In addition, the data also revealed that the months from June to August contributed favourable conditions for the growth of Chlorophyta members (29.16%) when compared to that of other months. The present study has recorded two new species (Ulva lactuca and Enteromorpha intestinalis). Thirty-five species once recorded are absent from the Visakhapatnam coast. These changes are attributed to the impact of marine water pollution and climate change.
<b>Status, abundance and habitat preference of butterflies (Insecta: Lepidoptera) in Chittagong University Campus, Chittagong, Bangladesh</b>
Authors: Haidar Ibrahim Khalil Al , Rahman M. Mizanur , Ahsan M. Farid , Islam M. Ariful 
Published: March 2017

A study was conducted on the butterflies of the Chittagong University Campus (CUC), Bangladesh between March 2014 and May 2015. A total of 142 species of butterflies belonging to 87 genera and six families (Hesperiidae, Papilionidae, Pieridae, Lycaenidae, Riodinidae and Nymphalidae) were recorded from the CUC during the study period. Family Nymphalidae comprised the highest number of species followed by Lycaenidae, Hesperiidae, Pieridae, Papilionidae and Riodinidae. The abundance of this species stated in terms of very common, common, uncommon, rare and very rare. The butterflies used different types of habitat (viz., grass land, crop land, open forest, scrub forest, dense forest and bamboo patch) and among all, scrub forests were the most preferred habitat. Mud puddling of 35 species were also observed. Five species of butterflies (Ampittia dioscorides, Matapa purpurascens, Polytremis eltola, Unkana ambasa and Ypthima ceylonica) were recorded for the first time in Bangladesh.
<b>An updated report on the distribution and conservation status of the endangered Cat’s Head Rockrose <I>Helianthemum caput-felis</I> (Magnoliopsida: Violales: Cistaceae) in Algeria</b>
Authors: Agulló Jonás C. , Juan Ana , Crespo Manuel B. , Alonso María Ángeles , Terrones Alejandro 
Published: March 2017

Helianthemum caput-felis is an Endangered plant species growing in the western Mediterranean basin. Its distribution is well known to the European and Moroccan regional populations, but no data from its distribution in Algeria have been reported since the middle 20th century. In this study, we provide an up-to-date report on the distribution of the species in Algeria. Fieldwork surveys in the classical locations were unsuccessful in finding the species, probably due to human habitat disturbances; however, a relict location was found in Ain-el-Kerma, near one of the historical known locations. As there is reduced distribution we point out the main causes that threaten the habitat of H. caput-felis according to IUCN threats classification scheme and we also propose to label it in the Algerian Red List as regionally Critically Endangered (CRreg B1ab(i,ii,iii, v)+2ab(i,ii,iii,v); C2a(i,ii); D).
<b>A first report of the presence of the Indian Wild Pig <I>Sus scrofa cristatus</I> from Kajinag Range, Kashmir, India</b>
Authors: Ahmad Riyaz , Suhail Intesar , Bhatnagar Yash Veer 
Published: March 2017

Eurasian wild pig Sus scrofa is a widely distributed terrestrial mammal. In India, wild pig occurs from peninsular to north India. In Jammu and Kashmir, wild pig was naturally distributed in Jammu region but is mostly introduced in the Kashmir valley and became common along the eastern foothills of Kashmir mountains with Dachigam NP holding the core population. But there have been no reports of its occurrence in northern foothills of Kashmir. We for the first time report the presence of wild pig in the Limber and Lacchipora Wildlife Sanctuaries of the Kajinag Range in northern Kashmir.
<b>Impact of vehicular traffic on vertebrate fauna in Horton plains and Yala national parks of Sri Lanka: some implications for conservation and management</b>
Authors: Karunarathna Suranjan , Ranwala Sudheera , Surasinghe Thilina , Madawala Majintha 
Published: March 2017

Impacts of roadkills are extensively documented in developed nations. Only a handful of studies on road mortality has emerged from developing nations where tourism and rural development have led to an expansion of transportation networks. To fill such gaps, we conducted a survey to document roadkills in and around two tourism-heavy national parks of Sri Lanka and identified factors that contribute to road mortality. Based on a questionnaire, we interviewed 68 local villagers, 56 local and 59 foreign visitors, and 57 safari drivers to document their opportunistic observations on roadkills, their awareness about roadkills, and to understand potential causes of roadkills. We found 47 roadkilled vertebrate species at both parks; among these, 19 are threatened and 20 are endemic. Our research revealed that herpetofauna were killed the most. We concluded that increased visitation, high-speed driving, lack of awareness, and poor law enforcement as the likely causes of roadkills at both parks. As mitigatory actions, we proposed posting speed limits, increasing awareness of the tourists and safari drivers, limiting vehicle access to the parks, seasonal or night-time access restrictions, and strict enforcement of the speed limits inside national parks.
<b>Macrofungi in two botanical gardens in southwestern India</b>
Authors: Pavithra Mundamoole , Sridhar Kandikere R. , Greeshma Ammatanda A. 
Published: March 2017

This study reports 11 species of macrofungi in the botanical garden and arboretum of Mangalore University. Frequent species include Clathrus delicatus, Entoloma serrulatum and Tetrapyrgos nigripes in the botanical garden, and Collybia aurea and T. nigripes in the arboretum. Five species are edible (Collybia aurea, Lepista sp., Russula adusta, R. atropurpurea and Termitomyces microcarpus), one is medicinal (T. microcarpus) and two are ectomycorrhizal (Russula adusta and R. atropurpurea) with critically endangered endemic tree species Vateria indica (Dipterocarpaceae). Some macrofungi grow on bark, woody litter and leaf litter, while others were found on typical lateritic soils with organic matter. Termitomyces microcarpus was common in the faecal pellets of termites in the botanical garden. Brief descriptions of species based on field and laboratory observations, along with their substrates and distribution, are given.
<b>A report on some butterflies (Lepidoptera) from Ladakh in Jammu & Kashmir and Lahaul in Himachal Pradesh, India</b>
Authors: Sondhi Sanjay , Valappil Balakrishnan , Sondhi Yash , Sondhi Anchal 
Published: March 2017

Forty-two (42) species of butterflies were recorded from a short survey of Ladakh and Lahaul in the inner Himalaya in Jammu & Kashmir and Himachal Pradesh. Here, we provide location and altitude records for these species, data on their abundance, photo-documentation of the life cycle of Pieris deota and P. brassicae as well as the first published record of a larval host plant for P. deota. Twelve (12) of these species are protected under Schedule II of the Indian Wildlife (Protection) Act, 1972.
Development and validation of a yoga module for Parkinson disease
Authors: Kakde Noopur , Metri Kashinath G. , Varambally Shivarama , Nagaratna Raghuram , Nagendra H.R. 
Published: March 2017

Abstract

Background
Parkinson’s disease (PD), a progressive neurodegenerative disease, affects motor and nonmotor functions, leading to severe debility and poor quality of life. Studies have reported the beneficial role of yoga in alleviating the symptoms of PD; however, a validated yoga module for PD is unavailable. This study developed and validated an integrated yoga module(IYM) for PD.

Methods
The IYM was prepared after a thorough review of classical yoga texts and previous findings. Twenty experienced yoga experts, who fulfilled the inclusion criteria, were selected validating the content of the IYM. A total of 28 practices were included in the IYM, and each practice was discussed and rated as (i) not essential, (ii) useful but not essential, and (iii) essential; the content validity ratio (CVR) was calculated using Lawshe’s formula.

Results
Data analysis revealed that of the 28 IYM practices, 21 exhibited significant content validity (cut-off value: 0.42, as calculated by applying Lawshe’s formula for the CVR).

Conclusions
The IYM is valid for PD, with good content validity. However, future studies must determine the feasibility and efficacy of the developed module.
A New Proposal for Ultra-Compact Polarization Independent Power Splitter Based on Photonic Crystal Structures
Authors: Razmi Hadi , Soroosh Mohammad , Kavian Yousef S. 
Published: March 2017

Abstract
Polarization dependency imposes great limitations for application of optical device in optical networks and systems. In this paper, we are going to design and propose a 1*2 all optical polarization independent power splitter based on photonic crystal structures. For designing such a device we should employ a fundamental photonic crystal structure which has joint photonic band gap. The obtained results show that at 1,560 nm wavelength the final structure has transmission efficiency equal to 45 % for outputs in both TE and TM modes.
Performance Analysis of Spectral Amplitude Coding Optical Code Division Multiple Access System using Modified Double Weight Codes with Adomian Decomposition Method
Authors: Rani Monika , Bhatti Harbax Singh , Singh Vikramjeet 
Published: March 2017

Abstract
In this manuscript, we have analyzed a Spectral Amplitude Coding-Optical Code Division Multiple Access (SAC-OCDMA) System. The system performance is enhanced by reducing the effect of Multiple Access Interference (MAI) using uniform Fiber Bragg Gratings (FBGs) encoders and decoders at central office and subscriber’s end. The results are verified through a mathematical model and Modified Double Weight (MDW) codes for the proposed system using Adomian Decomposition Method (ADM). Further, we have demonstrated SAC-OCDMA system for transmission of 40 Gbps data rate up to a distance of 80 km by increasing the number of FBGs. The proposed system has been analyzed in terms of distance, bit error rate (BER) and Quality Factor.