bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divergent viral presentation among human tumors and adjacent normal tissues
Authors: Cao Song , Wendl Michael C. , Wyczalkowski Matthew A. , Wylie Kristine , Ye Kai , Jayasinghe Reyka , Xie Mingchao , Wu Song , Niu Beifang , Grubb Robert , Johnson Kimberly J. , Gay Hiram , Chen Ken , Rader Janet S. , Dipersio John F. , Chen Feng , Ding Li 
Published: June 2016

AbstractWe applied a newly developed bioinformatics system called VirusScan to investigate the viral basis of 6,813 human tumors and 559 adjacent normal samples across 23 cancer types and identified 505 virus positive samples with distinctive, organ system- and cancer type-specific distributions. We found that herpes viruses (e.g., subtypes HHV4, HHV5 and HHV6) that are highly prevalent across cancers of the digestive tract showed significantly higher abundances in tumor versus adjacent normal samples, supporting their association with these cancers. We also found three HPV16-positive samples in brain lower grade glioma (LGG). Further, recurrent HBV integration at the KMT2B locus is present in three liver tumors, but absent in their matched adjacent normal samples, indicating that viral integration induced host driver genetic alterations are required on top of viral oncogene expression for initiation and progression of liver hepatocellular carcinoma. Notably, viral integrations were found in many genes, including novel recurrent HPV integrations at PTPN13 in cervical cancer. Finally, we observed a set of HHV4 and HBV variants strongly associated with ethnic groups, likely due to viral sequence evolution under environmental influences. These findings provide important new insights into viral roles of tumor initiation and progression and potential new therapeutic targets.
Biogas generation in anaerobic wastewater treatment under tetracycline antibiotic pressure
Authors: Lu Meiqing , Niu Xiaojun , Liu Wei , Zhang Jun , Wang Jie , Yang Jia , Wang Wenqi , Yang Zhiquan 
Published: June 2016

AbstractThe effect of tetracycline (TC) antibiotic on biogas generation in anaerobic wastewater treatment was studied. A lab-scale Anaerobic Baffled Reactor (ABR) with three compartments was used. The reactor was operated with synthetic wastewater in the absence of TC and in the presence of 250 μg/L TC for 90 days, respectively. The removal rate of TC, volatile fatty acids (VFAs), biogas compositions (hydrogen (H2), methane (CH4), carbon dioxide (CO2)), and total biogas production in each compartment were monitored in the two operational conditions. Results showed that the removal rate of TC was 14.97–67.97% in the reactor. The presence of TC had a large negative effect on CH4 and CO2 generation, but appeared to have a positive effect on H2 production and VFAs accumulation. This response indicated that the methanogenesis process was sensitive to TC presence, but the acidogenesis process was insensitive. This suggested that the presence of TC had less influence on the degradation of organic matter but had a strong influence on biogas generation. Additionally, the decrease of CH4 and CO2 generation and the increase of H2 and VFAs accumulation suggest a promising strategy to help alleviate global warming and improve resource recovery in an environmentally friendly approach.
Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters
Authors: Bao Weichen , Mi Zhihui , Xu Haiyan , Zheng Yi , Kwok Lai Yu , Zhang Heping , Zhang Wenyi 
Published: June 2016

AbstractThe present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.
Resonance Raman Probes for Organelle-Specific Labeling in Live Cells
Authors: Kuzmin Andrey N. , Pliss Artem , Lim Chang-Keun , Heo Jeongyun , Kim Sehoon , Rzhevskii Alexander , Gu Bobo , Yong Ken-Tye , Wen Shuangchun , Prasad Paras N. 
Published: June 2016

AbstractRaman microspectroscopy provides for high-resolution non-invasive molecular analysis of biological samples and has a breakthrough potential for dissection of cellular molecular composition at a single organelle level. However, the potential of Raman microspectroscopy can be fully realized only when novel types of molecular probes distinguishable in the Raman spectroscopy modality are developed for labeling of specific cellular domains to guide spectrochemical spatial imaging. Here we report on the design of a next generation Raman probe, based on BlackBerry Quencher 650 compound, which provides unprecedentedly high signal intensity through the Resonance Raman (RR) enhancement mechanism. Remarkably, RR enhancement occurs with low-toxic red light, which is close to maximum transparency in the biological optical window. The utility of proposed RR probes was validated for targeting lysosomes in live cultured cells, which enabled identification and subsequent monitoring of dynamic changes in this organelle by Raman imaging.
Identification of a 5-Methylcytosine Site that may Regulate C/EBPβ Binding and Determine Tissue-Specific Expression of the BPI Gene in Piglets
Authors: Sun Li , Wang Jing , Yin Xuemei , Sun Shouyong , Zi Chen , Zhu Guoqiang , Wu Shenglong , Bao Wenbin 
Published: June 2016

AbstractBactericidal/permeability-increasing protein (BPI) plays an important role in innate immune defense in mammals. A previous study showed that BPI gene expression correlates to gram-negative bacteria resistance. However, this gene showed tissue-specific expression in piglets and strongly expressed only in the digestive tract. To investigate the mechanisms governing the tissue-specificity, bisulfite sequencing PCR and next generation sequencing were used for high accuracy methylation quantitation of CpG islands of BPI gene upstream in 11 different tissues from weaned Yorkshire piglets. Additionally, qPCR was used to examine mRNA levels of BPI gene as well as transcription factor. We additionally analyzed transcriptional regulation by studying key 5-methylcytosine sites and transcription factors. Results showed that BPI mRNA levels significantly correlated with the overall methylation as well as methylation at mC-15 which was non-CpG site, no significant correlation could be found between the BPI and transcription factor mRNA levels, EMSA test showed that C/EBPβ could interact with BPI wild-type promoter DNA, but not methylated DNA. So we confirmed that methylation of mC-15 residue could inhibit the ability of C/EBPβ binding to the BPI promoter and affect the expression, and this mechanism probably plays a role in the tissue specificity of BPI gene expression in weaned piglets.
Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China
Authors: Fei Xufeng , Christakos George , Lou Zhaohan , Ren Yanjun , Liu Qingmin , Wu Jiaping 
Published: June 2016

AbstractThyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008–2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008–2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy.
Unified selective sorting approach to analyse multi-electrode extracellular data
Authors: Veerabhadrappa R. , Lim C. P. , Nguyen T. T. , Berk M. , Tye S. J. , Monaghan P. , Nahavandi S. , Bhatti A. 
Published: June 2016

AbstractExtracellular data analysis has become a quintessential method for understanding the neurophysiological responses to stimuli. This demands stringent techniques owing to the complicated nature of the recording environment. In this paper, we highlight the challenges in extracellular multi-electrode recording and data analysis as well as the limitations pertaining to some of the currently employed methodologies. To address some of the challenges, we present a unified algorithm in the form of selective sorting. Selective sorting is modelled around hypothesized generative model, which addresses the natural phenomena of spikes triggered by an intricate neuronal population. The algorithm incorporates Cepstrum of Bispectrum, ad hoc clustering algorithms, wavelet transforms, least square and correlation concepts which strategically tailors a sequence to characterize and form distinctive clusters. Additionally, we demonstrate the influence of noise modelled wavelets to sort overlapping spikes. The algorithm is evaluated using both raw and synthesized data sets with different levels of complexity and the performances are tabulated for comparison using widely accepted qualitative and quantitative indicators.
The odor of a plant metabolite affects life history traits in dietary restricted adult olive flies
Authors: Gerofotis Christos D. , Ioannou Charalampos S. , Nakas Christos T. , Papadopoulos Nikos T. 
Published: June 2016

AbstractFood quality shapes life history traits either directly or through response of individuals to additional environmental factors, such as chemical cues. Plant extracts used as food additives modulate key life history traits; however little is known regarding such effects for olfactory chemical cues. Exploiting an interesting experimental system that involves the olive fly (Bactrocera oleae) and the plant metabolite α-pinene we asked whether exposure of adults to this compound modulates adult longevity and female reproduction in similar manner in a stressful – dietary (protein) restricted (DR) and in a relaxed- full diet (FD) feeding environment. Accordingly, we exposed males and females to the aroma of α-pinene and measured lifespan and age-specific fecundity in the above two dietary contexts. Our results demonstrate that exposure to α-pinene increased longevity in males and fecundity in females only under dietary restricted conditions. In relaxed food conditions, females exposed to α-pinene shifted high egg-laying towards younger ages compared to non-exposed ones. This is the first report demonstrating that a plant compound affects key life history traits of adult olive flies through olfaction. These effects are sex-specific and more pronounced in dietary restricted adults. Possible underlying mechanisms and the ecological significance are discussed.
Self-Propelled Hovercraft Based on Cold Leidenfrost Phenomenon
Authors: Shi Meng , Ji Xing , Feng Shangsheng , Yang Qingzhen , Lu Tian Jian , Xu Feng 
Published: June 2016

AbstractThe Leidenfrost phenomenon of liquid droplets levitating and dancing when placed upon a hot plate due to propulsion of evaporative vapor has been extended to many self-propelled circumstances. However, such self-propelled Leidenfrost devices commonly need a high temperature for evaporation and a structured solid substrate for directional movements. Here we observed a “cold Leidenfrost phenomenon” when placing a dry ice device on the surface of room temperature water, based on which we developed a controllable self-propelled dry ice hovercraft. Due to the sublimated vapor, the hovercraft could float on water and move in a programmable manner through designed structures. As demonstrations, we showed that the hovercraft could be used as a cargo ship or a petroleum contamination collector without consuming external power. This phenomenon enables a novel way to utilize programmable self-propelled devices on top of room temperature water, holding great potential for applications in energy, chemical engineering and biology.
Effective-mass model and magneto-optical properties in hybrid perovskites
Authors: Yu Z. G. 
Published: June 2016

AbstractHybrid inorganic-organic perovskites have proven to be a revolutionary material for low-cost photovoltaic applications. They also exhibit many other interesting properties, including giant Rashba splitting, large-radius Wannier excitons and novel magneto-optical effects. Understanding these properties as well as the detailed mechanism of photovoltaics requires a reliable and accessible electronic structure, on which models of transport, excitonic and magneto-optical properties can be efficiently developed. Here we construct an effective-mass model for the hybrid perovskites based on the group theory, experiment and first-principles calculations. Using this model, we relate the Rashba splitting with the inversion-asymmetry parameter in the tetragonal perovskites, evaluate anisotropic g-factors for both conduction and valence bands and elucidate the magnetic-field effect on photoluminescence and its dependence on the intensity of photoexcitation. The diamagnetic effect of exciton is calculated for an arbitrarily strong magnetic field. The pronounced excitonic peak emerged at intermediate magnetic fields in cyclotron resonance is assigned to the 3D±2 states, whose splitting can be used to estimate the difference in the effective masses of electron and hole.
Bacillus cereus strain S2 shows high nematicidal activity against Meloidogyne incognita by producing sphingosine
Authors: Gao Huijuan , Qi Gaofu , Yin Rong , Zhang Hongchun , Li Chenggang , Zhao Xiuyun 
Published: June 2016

AbstractPlant-parasitic nematodes cause serious crop losses worldwidely. This study intended to discover the antagonistic mechanism of Bacillus cereus strain S2 against Meloidogyne incognita. Treatment with B. cereus strain S2 resulted in a mortality of 77.89% to Caenorhabditis elegans (a model organism) and 90.96% to M. incognita. In pot experiment, control efficiency of B. cereus S2 culture or supernatants were 81.36% and 67.42% towards M. incognita, respectively. In field experiment, control efficiency was 58.97% towards M. incognita. Nematicidal substances were isolated from culture supernatant of B. cereus S2 by polarity gradient extraction, silica gel column chromatography and HPLC. Two nematicidal compounds were identified as C16 sphingosine and phytosphingosine by LC-MS. The median lethal concentration of sphingosine was determined as 0.64 μg/ml. Sphingosine could obviously inhibit reproduction of C. elegans, with an inhibition rate of 42.72% for 24 h. After treatment with sphingosine, ROS was induced in intestinal tract, and genital area disappeared in nematode. Furthermore, B. cereus S2 could induce systemic resistance in tomato, and enhance activity of defense-related enzymes for biocontrol of M. incognita. This study demonstrates the nematicidal activity of B. cereus and its product sphingosine, as well provides a possibility for biocontrol of M. incognita.
Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera
Authors: Li Qin-Qin , Zhou Song-Dong , Huang De-Qing , He Xing-Jin , Wei Xian-Qin 
Published: June 2016

AbstractA primary aim of historical biogeography is to identify the causal factors or processes that have shaped the composition and distribution of biotas over time. Another is to infer the evolution of geographic ranges of species and clades in a phylogenetic context. To this end, historical biogeography addresses important questions such as: Where were ancestors distributed? Where did lineages originate? Which processes cause geographic ranges to evolve through time? Allium subgenus Anguinum comprises approximately twelve taxa with a disjunct distribution in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Although both the systematic position and the geographical limits of Anguinum have been identified, to date no molecular systematic study has been performed utilizing a comprehensive sampling of these species. With an emphasis on the Anguinum eastern Asian geographical group, the goals of the present study were: (i) to infer species-level phylogenetic relationships within Anguinum , (ii) to assess molecular divergence and estimated the times of the major splits in Anguinum and (iii) to trace the biogeographic history of the subgenus. Four DNA sequences (ITS, matK , trnH-psbA , rps16 ) were used to reconstruct the phylogeny of Allium subgen. Anguinum . RbcL sequences were used to estimate divergences time for Allium , and sequences of ITS were used to estimate the divergence times for Anguinum and its main lineages and to provide implications for the evolutionary history of the subgenus. Phylogenetic analyses for all Allium corroborate that Anguinum is monophyletic and indicate that Anguinum is composed of two sister groups: one with a Eurasian–American distribution, and the other restricted to eastern Asia. In the eastern Asian geographical group, incongruence between gene trees and morphology-based taxonomies was recovered as was incongruence between data from plastid and nuclear sequences. This incongruence is likely due to the combined effects of a recent radiation, incomplete lineage sorting, and hybridization/introgression. Divergence time estimates suggest that the crown group of Anguinum originated during the late Miocene (ca. 7.16 Mya) and then diverged and dispersed. Biogeographic analyses using statistical dispersal–vicariance analysis (S-DIVA) and a likelihood method support an eastern Asia origin of Anguinum . It is inferred that in the late Pliocene/Early Pleistocene, with cooling climates and the uplift of the Himalayas and Hengduan Mountains, the ancestor of the eastern Asian alliance clade underwent a very recent radiation.
The defensive role of foliar endophytic fungi for a South American tree
Authors: González-Teuber Marcia 
Published: June 2016

Abstract
Fungal endophytes colonize living internal plant tissues without causing any visible symptoms of disease. Endophytic fungi associated with healthy leaves may play an important role in the protection of hosts against herbivores and pathogens. In this study, the diversity of foliar endophytic fungi (FEF) of the southern temperate tree Embothrium coccineum (Proteaceae), as well as their role in plant protection in nature was determined. Fungal endophytes were isolated from 40 asymptomatic leaves by the culture method for molecular identification of the 18S rRNA gene. A relationship between FEF frequency and plant protection was evaluated in juveniles of E. coccineum . Fungal endophyte frequency was estimated using real-time PCR analyses to determine endophyte DNA content per plant. A total of 178 fungal isolates were identified, with sequence data revealing 34 different operational taxonomic units (OTUs). A few common taxa dominated the fungal endophyte community, whereas most taxa qualified as rare. A significant positive correlation between plant protection (evaluated in terms of percentage of leaf damage) and FEF frequency was found. Furthermore, in vitro confrontation assays indicated that FEF were able to inhibit the growth of fungal pathogens. The data showed a relatively high diversity of fungal endophytes associated with leaves of E. coccineum , and suggest a positive relationship between fungal endophyte frequencies in leaves and host protection in nature.
Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination
Authors: Kim Junho , Maeng Ju Heon , Lim Jae Seok , Son Hyeonju , Lee Junehawk , Lee Jeong Ho , Kim Sangwoo 
Published: June 2016

Abstract
Motivation: Advances in sequencing technologies have remarkably lowered the detection limit of somatic variants to a low frequency. However, calling mutations at this range is still confounded by many factors including environmental contamination. Vector contamination is a continuously occurring issue and is especially problematic since vector inserts are hardly distinguishable from the sample sequences. Such inserts, which may harbor polymorphisms and engineered functional mutations, can result in calling false variants at corresponding sites. Numerous vector-screening methods have been developed, but none could handle contamination from inserts because they are focusing on vector backbone sequences alone.
Results: We developed a novel method—Vecuum—that identifies vector-originated reads and resultant false variants. Since vector inserts are generally constructed from intron-less cDNAs, Vecuum identifies vector-originated reads by inspecting the clipping patterns at exon junctions. False variant calls are further detected based on the biased distribution of mutant alleles to vector-originated reads. Tests on simulated and spike-in experimental data validated that Vecuum could detect 93% of vector contaminants and could remove up to 87% of variant-like false calls with 100% precision. Application to public sequence datasets demonstrated the utility of Vecuum in detecting false variants resulting from various types of external contamination.
Availability and Implementation: Java-based implementation of the method is available at http://vecuum.sourceforge.net/
Contact: swkim@yuhs.ac
Supplementary information: Supplementary data are available at Bioinformatics online.