bluuebunny/crossref_metadata_2025_split huggingface dataset:
cudaMap: a GPU accelerated program for gene expression connectivity mapping
Authors: McArt Darragh G , Bankhead Peter , Dunne Philip D , Salto-Tellez Manuel , Hamilton Peter , Zhang Shu-Dong 
Published: October 2013

Abstract

Background
Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take > 2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping.

Results
cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance.

Conclusion
Emerging ‘omics’ technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap.
Experimental hybridization and backcrossing reveal forces of reproductive isolation in Microbotryum
Authors: Büker Britta , Petit Elsa , Begerow Dominik , Hood Michael E 
Published: October 2013

Abstract

Background
Hybridization and reproductive isolation are central to the origin and maintenance of species, and especially for sympatric species, gene flow is often inhibited through barriers that depend upon mating compatibility factors. The anther-smut fungi (genus Microbotryum) serve as models for speciation in the face of sympatry, and previous studies have tested for but not detected assortative mating. In addition, post-mating barriers are indicated by reduced fitness of hybrids, but sources of those barriers (i.e. ecological maladaptation or genetic incompatibilities) have not yet been detected. Here, backcrossing experiments, specifically controlling for the fungal species origins of the mating compatibility factors, were used to investigate reproductive isolation in the recently-derived species Microbotryum lychnidis-dioicae and Microbotryum silenes-dioicae.

Results
Assortative mating was detected during backcrossing and was manifested by the preferential conjugation of the hybrid-produced gametes with non-hybrid gametes containing mating compatibility factors from the same parental species. Patterns of post-mating performance supported either a level of extrinsic isolation mechanism, where backcross progeny with a higher proportion of the pathogen genome adapted to the particular host environment were favored, or an infection advantage attributed to greater genetic contribution to the hybrid from the M. lychnidis-dioicae genome.

Conclusion
The use of controlled backcrossing experiments reveals significant species-specific mating type effects on conjugations between recently-derived sister species, which are likely to play important roles in both maintaining species separation and the nature of hybrids lineages that emerge in sympatry between Microbotryum species.
Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.)
Authors: Huang You-Jun , Liu Li-Li , Huang Jian-Qin , Wang Zheng-Jia , Chen Fang-Fang , Zhang Qi-Xiang , Zheng Bing-Song , Chen Ming 
Published: October 2013

Abstract

Background
Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis.

Results
Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better.

Conclusions
Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC’ model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.
Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods
Authors: Kamoun Choumouss , Payen Thibaut , Hua-Van Aurélie , Filée Jonathan 
Published: October 2013

Abstract

Background
Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based method using profile HMM searches.

Results
In this study, we have developed three different work flows dedicated to ISs and MITEs detection: the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats; the third one use 28 in-house transposase alignment profiles with HMM search methods. We have compared the respective performances of each method using a reference dataset of 30 archaeal and 30 bacterial genomes in addition to simulated and real metagenomes. Compared to a BLAST-based method using ISFinder as library, de novo methods significantly improve ISs and MITEs detection. For example, in the 30 archaeal genomes, we discovered 30 new elements (+20%) in addition to the 141 multi-copies elements already detected by the BLAST approach. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs has even doubled with the discovery of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of short reads data (<300 bp) for which both techniques seem equally limited, profile HMM searches considerably ameliorate the detection of transposase encoding genes (up to +50%) generating low level of false positives compare to BLAST-based methods.

Conclusion
Compared to classical BLAST-based methods, the sensitivity of de nov o and profile HMM methods developed in this study allow a better and more reliable detection of transposons in prokaryotic genomes and metagenomes. We believed that future studies implying ISs and MITEs identification in genomic data should combine at least one de novo and one library-based method, with optimal results obtained by running the two de novo methods in addition to a library-based search. For metagenomic data, profile HMM search should be favored, a BLAST-based step is only useful to the final annotation into groups and families.
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Authors: Vidal Elena A , Moyano Tomás C , Krouk Gabriel , Katari Manpreet S , Tanurdzic Milos , McCombie W Richard , Coruzzi Gloria M , Gutiérrez Rodrigo A 
Published: October 2013

Abstract

Background
Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out.

Results
In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A + enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3.

Conclusions
Sequencing of small RNAs and mRNAs uncovered new genes, and enabled us to develop new hypotheses for nitrate regulation and coordination of carbon and nitrogen metabolism.
The role and prognostic value of apoptosis in colorectal carcinoma
Authors: Alcaide Julia , Funez Rafael , Rueda Antonio , Perez-Ruiz Elisabeth , Pereda Teresa , Rodrigo Isabel , Coveñas Rafael , Muñoz Miguel , Redondo Maximino 
Published: October 2013

Abstract

Background
Alterations to apoptosis are a common occurrence in human tumours. The aim of our study was to determine the influence of apoptotic variations on the carcinogenesis and prognosis of colorectal carcinomas (CRCs).

Methods
A TUNEL assay was performed on archival material from 103 colorectal carcinomas, 26 adenomas and 20 samples of normal epithelia.

Results
The number of apoptotic cells was higher in CRCs (1.09 ± 0.13) than in adenomas (0.38 ± 0.23, p = 0.059) and normal epithelium (0.06 ± 0.04, p = 0.001). In addition, the apoptotic index (AI) was greater in metastatic disease (stage IV) than in other stages (p = 0.017). No relationship was found between apoptotic rates and age, gender or tumour grade. However, patients with tumours that showed higher AI values had a significantly lower disease-free survival (DFS) and overall survival (OS) than those with tumours that had lower AIs (p = 0.020 and p = 0.027). In a multivariate Cox proportional hazards model, AI remained a significant independent predictor of survival.

Conclusions
We conclude that disregulated apoptosis is an important event during CRC development and progression. Higher AIs are associated with more aggressive tumours and a poorer prognosis for patients with CRC.
MiRNA-497 regulates cell growth and invasion by targeting cyclin E1 in breast cancer
Authors: Luo Qifeng , Li Xiaoyu , Gao Yan , Long Yin , Chen Lei , Huang Yixiang , Fang Lin 
Published: October 2013

Abstract

Background
MicroRNAs are a class of endogenous single strand non-coding RNAs that are involved in many important physiological and pathological processes. The purpose of this study was to examine the expression levels of miR-497 in human breast cancer and its function in MDA-MB-231 breast cancer cells.

Methods
Quantitative polymerase chain reaction was used to measure the expression levels of miR-497 in 40 breast cancer specimens and adjacent normal breast tissues. MTT assays, colony formation assays, wound healing assays, transwell assays and cell cycle assays were used to explore the potential function of miR-497 in MDA-MB-231 breast cancer cells. Dual-luciferase reporter assays were performed to analyze the regulation of putative target of miR-497, and western blot assays were used to validate the dual-luciferase results.

Results
The expression of miR-497 in breast cancer specimens was lower than adjacent normal tissues (P < 0.05). Overexpression of miR-497 inhibited cellular growth, suppressed cellular migration and invasion, and caused a G1 arrest. Dual-luciferase reporter assays showed that miR-497 binds the 3′-untranslated region (3′-UTR) of cyclin E1, suggesting that cyclin E1 is a direct target of miR-497. Western blot assays confirmed that overexpression of miR-497 reduced cyclin E1 protein levels.

Conclusions
MiR-497 may act as a tumor suppressor gene in breast cancer. Inhibited cellular growth, suppressed cellular migration and invasion, and G1 cell cycle arrest were observed upon overexpression of miR-497 in cells, possibly by targeting cyclin E1. These results indicate miR-497 could be considered a therapeutic target for the development of treatment for breast cancer.
Risk factors associated with slide positivity among febrile patients in a conflict zone of north-eastern Myanmar along the China-Myanmar border
Authors: Li Nana , Parker Daniel M , Yang Zhaoqing , Fan Qi , Zhou Guofa , Ai Guoping , Duan Jianhua , Lee Ming-chieh , Yan Guiyun , Matthews Stephen A , Cui Liwang , Wang Ying 
Published: October 2013

Abstract

Background
Malaria within the Greater Mekong sub-region is extremely heterogeneous. While China and Thailand have been relatively successful in controlling malaria, Myanmar continues to see high prevalence. Coupled with the recent emergence of artemisinin-resistant malaria along the Thai-Myanmar border, this makes Myanmar an important focus of malaria within the overall region. However, accurate epidemiological data from Myanmar have been lacking, in part because of ongoing and emerging conflicts between the government and various ethnic groups. Here the results are reported from a risk analysis of malaria slide positivity in a conflict zone along the China-Myanmar border.

Methods
Surveys were conducted in 13 clinics and hospitals around Laiza City, Myanmar between April 2011 and October 2012. Demographic, occupational and educational information, as well as malaria infection history, were collected. Logistic models were used to assess risk factors for slide positivity.

Results
Age patterns in Plasmodium vivax infections were younger than those with Plasmodium falciparum. Furthermore, males were more likely than females to have falciparum infections. Patients who reported having been infected with malaria during the previous year were much more likely to have a current vivax infection. During the second year of the study, falciparum infections among soldiers increased signficiantly.

Conclusions
These results fill some knowledge gaps with regard to risk factors associated with malaria slide positivity in this conflict region of north-eastern Myanmar. Since epidemiological studies in this region have been rare or non-existent, studies such as the current are crucial for understanding the dynamic nature of malaria in this extremely heterogeneous epidemiological landscape.
Nitric oxide synthase mediates PC12 differentiation induced by the surface topography of nanostructured TiO2
Authors: Tamplenizza Margherita , Lenardi Cristina , Maffioli Elisa , Nonnis Simona , Negri Armando , Forti Stefania , Sogne Elisa , De Astis Silvia , Matteoli Michela , Schulte Carsten , Milani Paolo , Tedeschi Gabriella 
Published: October 2013

Abstract

Background
Substrate nanoscale topography influences cell proliferation and differentiation through mechanisms that are at present poorly understood. In particular the molecular mechanism through which cells 'sense’ and adapt to the substrate and activate specific intracellular signals, influencing cells survival and behavior, remains to be clarified.

Results
To characterize these processes at the molecular level we studied the differentiation of PC12 cells on nanostructured TiO2 films obtained by supersonic cluster beam deposition.
Our findings indicate that, in PC12 cells grown without Nerve Growth Factor (NGF), the roughness of nanostructured TiO2 triggers neuritogenesis by activating the expression of nitric oxide synthase (NOS) and the phospho-extracellular signal-regulated kinase 1/2 (pERK1/2) signaling. Differentiation is associated with an increase in protein nitration as observed in PC12 cells grown on flat surfaces in the presence of NGF. We demonstrate that cell differentiation and protein nitration induced by topography are not specific for PC12 cells but can be regarded as generalized effects produced by the substrate on different neuronal-like cell types, as shown by growing the human neuroblastoma SH-SY5Y cell line on nanostructured TiO2.

Conclusion
Our data provide the evidence that the nitric oxide (NO) signal cascade is involved in the differentiation process induced by nanotopography, adding new information on the mechanism and proteins involved in the neuritogenesis triggered by the surface properties.
Expression of VPAC1 in a murine model of allergic asthma
Authors: Lauenstein Hans D , Quarcoo David , Welte Tobias , Braun Armin , Groneberg David A 
Published: October 2013

Abstract
Vasoactive intestinal polypeptide (VIP) is a putative neurotransmitter of the inhibitory non-adrenergic non-cholinergic nervous system and influences the mammalian airway function in various ways. Hence known for bronchodilatory, immunomodulatory and mucus secretion modulating effects by interacting with the VIP receptors VPAC1 and VPAC2, it is discussed to be a promising target for pharmaceutical intervention in common diseases such as COPD and bronchial asthma. Here we examined the expression and transcriptional regulation of VPAC1 in the lungs of allergic mice using an ovalbumin (OVA) -induced model of allergic asthma. Mice were sensitized to OVA and challenged with an OVA aerosol. In parallel a control group was sham sensitized with saline. VPAC1 expression was examined using RT-PCR and real time-PCR studies were performed to quantify gene transcription. VPAC1 mRNA expression was detected in all samples of OVA-sensitized and challenged animals and control tissues. Further realtime analysis did not show significant differences at the transcriptional level.
Although the present studies did not indicate a major transcriptional regulation of VPAC1 in states of allergic airway inflammation, immunomodulatory effects of VPAC1 might still be present due to regulations at the translational level.
Follicle-stimulating hormone-secreting pituitary adenoma manifesting as recurrent ovarian cysts in a young woman – latent risk of unidentified ovarian hyperstimulation: a case report
Authors: Kawaguchi Tomohiro , Ogawa Yoshikazu , Ito Kenji , Watanabe Mika , Tominaga Teiji 
Published: October 2013

Abstract

Background
Ovarian hyperstimulation caused by follicle-stimulating hormone-secreting gonadotroph cell adenoma is a rare, with a few reported cases, but almost certainly unnoticed cases occur because of the absence of detailed examinations. We retrospectively reviewed 200 patients treated for gonadotroph cell adenoma in our institute and identified 26 women of reproductive age. Two of these 26 patients had a history of ovarian cysts. One patient was considered to have had typical ovarian hyperstimulation, successfully treated by transsphenoidal surgery. The other patient initially underwent transsphenoidal surgery because of visual disturbance, but endocrinological examinations suggested possible relationships with previous ovarian hyperstimulation. We present the former case and discuss the latent risk of failure to identify this entity.

Case presentation
A 36-year-old woman with a sellar tumor was referred to our hospital with suspected ovarian hyperstimulation. She had a history of repeated surgery for ovarian cysts. Serum follicle-stimulating hormone and estradiol levels were within the normal ranges, and only the luteinizing hormone level was suppressed significantly. Transsphenoidal surgery achieved gross total tumor removal, and the histological diagnosis was follicle-stimulating hormone-secreting gonadotroph cell adenoma. The serum follicle-stimulating hormone, luteinizing hormone, and estradiol levels returned to the normal ranges postoperatively, and the ovarian cysts subsequently decreased in size without particular interventions.

Conclusion
Ovarian hyperstimulation could regress after resolving the causes of high follicle-stimulating hormone level, so avoiding unnecessary ovary surgery. Detailed endocrinological examination including estradiol evaluation with pituitary imaging is quite important in women of reproductive age to establish the correct diagnosis.
Physiological relaxation induced by horticultural activity: transplanting work using flowering plants
Authors: Lee Min-sun , Park Bum-jin , Lee Juyoung , Park Kun-tae , Ku Ja-hyeong , Lee Jun-woo , Oh Kyung-ok , Miyazaki Yoshifumi 
Published: October 2013

AbstractBackgroundDespite increasing attention and a growing volume of research data, little physiological evidence is available on the benefits of horticultural activity and the different effects on individuals. Therefore, the aim of the present study was to investigate the physiological effects of horticultural activity and to examine how differences in personality alter these effects.ResultsThe effects of transplanting real flowers (horticultural activity) and handling artificial flowers (control activity) on human physiological activity were compared. On the first day, eight participants engaged in horticultural activity and another eight in the control activity. On the second day, participants switched roles. Participants’ physiological conditions during each activity were assessed by measuring the heart rate and heart rate variability (HRV). Psychological responses, which were measured using a semantic differential rating scale, showed that the horticultural activity promoted comfortable, soothed, and natural feelings, compared to the control activity. Analysis of physiological responses using two-way repeated measures analysis of variance (ANOVA) revealed that sympathetic nervous activity significantly decreased in the late time period (11 to 15 minutes) of horticultural activity only in the type A group.ConclusionsThis study supports the fact that the horticultural activity can enhance psychological and physiological relaxation effects, although these physiological effects can differ among individuals with different personalities.