bluuebunny/crossref_metadata_2025_split huggingface dataset:
A structural comparison of lipopolysaccharide biosynthesis loci of Legionella pneumophila serogroup 1 strains
Authors: Petzold Markus , Thürmer Alexander , Menzel Susan , Mouton Johan W , Heuner Klaus , Lück Christian 
Published: September 2013

Abstract

Background
The lipopolysaccharide (LPS) is the major immuno-dominant antigen of all Legionella species including L. pneumophila. Its diversity is the basis for the classification of L. pneumophila into serogroups and monoclonal subgroups and is thought to be involved in strain specific virulence. The understanding of the genetic basis of the LPS-antigen is incomplete. Thus, we analyzed the genetic locus involved in LPS-biosynthesis of L. pneumophila serogroup 1 (Sg1) strains with the focus on strain specific gene composition.

Results
The LPS-biosynthesis loci of 14 L. pneumophila Sg1 strains comprise two distinct regions: A 15 kb region containing LPS-biosynthesis genes that can be found in all L. pneumophila strains and a Sg1-specific 18 kb region. The 15 kb region is highly conserved among Sg1 strains as reflected by high homologies of single ORFs and by a consistent ORF arrangement. In contrast, the Sg1 specific 18 kb region is variable and partially disrupted by phage related genes. We propose that the region spanning from ORF 6 to ORF 11 of the Sg1-specific region is likely involved in late LPS-modification. Due to the high variability of this small region and various combinations of single ORFs within this region a strain specific LPS-structure could be synthesized including modifications of legionaminic acid derivates.

Conclusions
Our data clearly demonstrate that the gene structure of the LPS-biosynthesis locus of L. pneumophila Sg1 strains show significant interstrain variability. These data can be used for further functional analysis of the LPS synthesis to understand pathogenesis and reactivity with monoclonal antibodies. Moreover, variable but strain specific regions can serve as basis for the development of novel genotyping assays.
A prospective cohort study of prognosis for newly diagnosed epilepsy in east China
Authors: Zhang Yanfang , Yu Nian , Su Lingying , Di Qing 
Published: September 2013

Abstract

Background
Limited data are available on the outcome of antiepileptic drug treatment response in patients of Chinese Han ethnicity with newly diagnosed epilepsy. We sought to explore the prognosis with antiepileptic drug treatment and to identify the predictors of poor drug control of seizures in these patients.

Methods
For at least 2 years, we prospectively followed up a cohort of patients with newly diagnosed epilepsy and analyzed the response to each antiepileptic drug. Cumulative risk for seizure relapse after initial remission achieved was estimated. The patients were divided into two groups (poor and good control) and compared for clinical characteristics.

Results
A total of 180 patients were included. Early remission was reached in 125 (69.44%) patients, 19 (10.56%) patients entered late remission, while 36 (20%) patients failed to achieve remission. The relapse rates were 19.5% at 2 years and 31.9% at 3 years of the follow-up. The response rates of the first throughout the fourth treatment regimens were 60.0%, 16.1%, 2.8%, and 0.6%, respectively. Multiple seizure types and changes in seizure type during treatment were significantly (p = 0.013 and 0.047, respectively) associated with a poor control.

Conclusions
The prognosis of the majority of patients with newly diagnosed epilepsy is good and the clinical pattern of epilepsy during treatment is complex. The chances of seizure control declines with each subsequent treatment regimen. The prognosis for patients with multiple seizure types and seizure type changes during treatment is unfavorable.
Estrogenic and mutagenic activities of Crotalaria pallida measured by recombinant yeast assay and Ames test
Authors: Boldrin Paula Karina , Resende Flávia Aparecida , Höhne Ana Paula Oliveira , de Camargo Mariana Santoro , Espanha Lívia Greghi , Nogueira Catarine Haidê , Melo Maria do Socorro F , Vilegas Wagner , Varanda Eliana Aparecida 
Published: September 2013

Abstract

Background

Crotalaria pallida Ailton is a plant belonging to the Fabaceae family, popularly known as “rattle or rattlesnake” and used in traditional medicine to treat swelling of the joints and as a vermifuge. Previous pharmacological studies have also reported anti-inflammatory, antimicrobial and antifungal activities. Nevertheless, scientific information regarding this species is scarce, and there are no reports related to its possible estrogenic and mutagenic effects. Thus, the purpose of the present study was to investigate the estrogenic potential of C. pallida leaves by means of the Recombinant Yeast Assay (RYA), seeking an alternative for estrogen replacement therapy during menopause; and to reflect on the safe use of natural products to assess the mutagenic activity of the crude extract from C. pallida leaves, the dichloromethane fraction and stigmasterol by means of the Ames test.

Methods
The recombinant yeast assay with the strain BY4741 of Saccharomyces cerevisiae, was performed with the ethanolic extract, dichloromethane fraction and stigmasterol isolated from the leaves of C. pallida. Mutagenic activity was evaluated by the Salmonella/microsome assay (Ames test), using the Salmonella typhimurium tester strains TA100, TA98, TA97 and TA102, with (+S9) and without (-S9) metabolization, by the preincubation method.

Results
All samples showed estrogenic activity, mainly stigmasterol. The ethanolic extract from C. pallida leaves showed mutagenic activity in the TA98 strain (-S9), whereas dichloromethane fraction and stigmasterol were found devoid of activity.

Conclusion
Considering the excellent estrogenic activity performed by stigmasterol in the RYA associated with the absence of mutagenic activity when evaluated by the Ames test, stigmasterol becomes a strong candidate to be used in hormone replacement therapy during menopause.
Current practices in library/informatics instruction in academic libraries serving medical schools in the western United States: a three-phase action research study
Authors: Eldredge Jonathan D , Heskett Karen M , Henner Terry , Tan Josephine P 
Published: September 2013

Abstract

Background
To conduct a systematic assessment of library and informatics training at accredited Western U.S. medical schools. To provide a structured description of core practices, detect trends through comparisons across institutions, and to identify innovative training approaches at the medical schools.

Methods
Action research study pursued through three phases. The first phase used inductive analysis on reported library and informatics skills training via publicly-facing websites at accredited medical schools and the academic health sciences libraries serving those medical schools. Phase Two consisted of a survey of the librarians who provide this training to undergraduate medical education students at the Western U.S. medical schools. The survey revealed gaps in forming a complete picture of current practices, thereby generating additional questions that were answered through the Phase Three in-depth interviews.

Results
Publicly-facing websites reviewed in Phase One offered uneven information about library and informatics training at Western U.S. medical schools. The Phase Two survey resulted in a 77% response rate. The survey produced a clearer picture of current practices of library and informatics training. The survey also determined the readiness of medical students to pass certain aspects of the United States Medical Licensure Exam. Most librarians interacted with medical school curricular leaders through either curricula committees or through individual contacts. Librarians averaged three (3) interventions for training within the four-year curricula with greatest emphasis upon the first and third years. Library/informatics training was integrated fully into the respective curricula in almost all cases. Most training involved active learning approaches, specifically within Problem-Based Learning or Evidence-Based Medicine contexts. The Phase Three interviews revealed that librarians are engaged with the medical schools' curricular leaders, they are respected for their knowledge and teaching skills, and that they need to continually adapt to changes in curricula.

Conclusions
This study offers a long overdue, systematic view of current practices of library/informatics training at Western U.S. medical schools. Medical educators, particularly curricular leaders, will find opportunities in this study's results for more productive collaborations with the librarians responsible for library and informatics training at their medical schools.
Medical practices display power law behaviors similar to spoken languages
Authors: Paladino Jonathan D , Crooke Philip S , Brackney Christopher R , Kaynar A Murat , Hotchkiss John R 
Published: September 2013

Abstract

Background
Medical care commonly involves the apprehension of complex patterns of patient derangements to which the practitioner responds with patterns of interventions, as opposed to single therapeutic maneuvers. This complexity renders the objective assessment of practice patterns using conventional statistical approaches difficult.

Methods
Combinatorial approaches drawn from symbolic dynamics are used to encode the observed patterns of patient derangement and associated practitioner response patterns as sequences of symbols. Concatenating each patient derangement symbol with the contemporaneous practitioner response symbol creates “words” encoding the simultaneous patient derangement and provider response patterns and yields an observed vocabulary with quantifiable statistical characteristics.

Results
A fundamental observation in many natural languages is the existence of a power law relationship between the rank order of word usage and the absolute frequency with which particular words are uttered. We show that population level patterns of patient derangement: practitioner intervention word usage in two entirely unrelated domains of medical care display power law relationships similar to those of natural languages, and that–in one of these domains–power law behavior at the population level reflects power law behavior at the level of individual practitioners.

Conclusions
Our results suggest that patterns of medical care can be approached using quantitative linguistic techniques, a finding that has implications for the assessment of expertise, machine learning identification of optimal practices, and construction of bedside decision support tools.
Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population
Authors: Huang Chi-Cheng , Tu Shih-Hsin , Lien Heng-Hui , Jeng Jaan-Yeh , Liu Jung-Sen , Huang Ching-Shui , Wu Yih-Yiing , Liu Chih-Yi , Lai Liang-Chuan , Chuang Eric Y 
Published: September 2013

Abstract

Background
Breast cancer is a heterogeneous disease in terms of transcriptional aberrations; moreover, microarray gene expression profiles had defined 5 molecular subtypes based on certain intrinsic genes. This study aimed to evaluate the prediction consistency of breast cancer molecular subtypes from 3 distinct intrinsic gene sets (Sørlie 500, Hu 306 and PAM50) as well as clinical presentations of each molecualr subtype in Han Chinese population.

Methods
In all, 169 breast cancer samples (44 from Taiwan and 125 from China) of Han Chinese population were gathered, and the gene expression features corresponding to 3 distinct intrinsic gene sets (Sørlie 500, Hu 306 and PAM50) were retrieved for molecular subtype prediction.

Results
For Sørlie 500 and Hu 306 intrinsic gene set, mean-centring of genes and distance-weighted discrimination (DWD) remarkably reduced the number of unclassified cases. Regarding pairwise agreement, the highest predictive consistency was found between Hu 306 and PAM50. In all, 150 and 126 samples were assigned into identical subtypes by both Hu 306 and PAM50 genes, under mean-centring and DWD. Luminal B tended to show a higher nuclear grade and have more HER2 over-expression status than luminal A did. No basal-like breast tumours were ER positive, and most HER2-enriched breast tumours showed HER2 over-expression, whereas, only two-thirds of ER negativity/HER2 over-expression tumros were predicted as HER2-enriched molecular subtype. For 44 Taiwanese breast cancers with survival data, a better prognosis of luminal A than luminal B subtype in ER-postive breast cancers and a better prognosis of basal-like than HER2-enriched subtype in ER-negative breast cancers was observed.

Conclusions
We suggest that the intrinsic signature Hu 306 or PAM50 be used for breast cancers in the Han Chinese population during molecular subtyping. For the prognostic value and decision making based on intrinsic subtypes, further prospective study with longer survival data is needed.
New differential fault analysis on PRESENT
Authors: Bagheri Nasour , Ebrahimpour Reza , Ghaedi Navid 
Published: September 2013

Abstract
In this paper, we present two differential fault analyses on PRESENT-80 which is a lightweight block cipher. The first attack is a basic attack which induces a fault on only one bit of intermediate states, and we can obtain the last subkey of the block cipher, given 48 faulty cipher texts on average. The second attack can retrieve the master key of the block cipher, given 18 faulty cipher texts on average. In the latter attack, we assume that we can induce faults on a single nibble of intermediate states. Given those faulty cipher texts, the computational complexity of attacks is negligible.
Diversity is maintained by seasonal variation in species abundance
Authors: Shimadzu Hideyasu , Dornelas Maria , Henderson Peter A , Magurran Anne E 
Published: September 2013

Abstract

Background
Some of the most marked temporal fluctuations in species abundances are linked to seasons. In theory, multispecies assemblages can persist if species use shared resources at different times, thereby minimizing interspecific competition. However, there is scant empirical evidence supporting these predictions and, to the best of our knowledge, seasonal variation has never been explored in the context of fluctuation-mediated coexistence.

Results
Using an exceptionally well-documented estuarine fish assemblage, sampled monthly for over 30 years, we show that temporal shifts in species abundances underpin species coexistence. Species fall into distinct seasonal groups, within which spatial resource use is more heterogeneous than would be expected by chance at those times when competition for food is most intense. We also detect seasonal variation in the richness and evenness of the community, again linked to shifts in resource availability.

Conclusions
These results reveal that spatiotemporal shifts in community composition minimize competitive interactions and help stabilize total abundance.
Evolution and heterogeneity of multiple serotypes of Dengue virus in Pakistan, 2006–2011
Authors: Koo Carmen , Nasir Amna , Hapuarachchi Hapuarachchige Chanditha , Lee Kim-Sung , Hasan Zahra , Ng Lee-Ching , Khan Erum 
Published: September 2013

Abstract

Background
Even though dengue has been recognized as one of the major public health threats in Pakistan, the understanding of its molecular epidemiology is still limited. The genotypic diversity of Dengue virus (DENV) serotypes involved in dengue outbreaks since 2005 in Pakistan is not well studied. Here, we investigated the origin, diversity, genetic relationships and geographic distribution of DENV to understand virus evolution during the recent expansion of dengue in Pakistan.

Methods
The study included 200 sera obtained from dengue-suspected patients from 2006 to 2011. DENV infection was confirmed in 94 (47%) sera by a polymerase chain reaction assay. These included 36 (38.3%) DENV-2, 57 DENV-3 (60.6%) and 1 DENV-4 (1.1%) cases. Sequences of 13 whole genomes (6 DENV-2, 6 DENV-3 and 1 DENV-4) and 49 envelope genes (26 DENV-2, 22 DENV-3 and 1 DENV-4) were analysed to determine the origin, phylogeny, diversity and selection pressure during virus evolution.

Results
DENV-2, DENV-3 and DENV-4 in Pakistan from 2006 to 2011 shared 98.5-99.6% nucleotide and 99.3-99.9% amino acid similarity with those circulated in the Indian subcontinent during the last decade. Nevertheless, Pakistan DENV-2 and DENV-3 strains formed distinct clades characterized by amino acid signatures of NS2A-I116T + NS5-K861R and NS3-K590R + NS5-S895L respectively. Each clade consisted of a heterogenous virus population that circulated in Southern (2006–2009) and Northern Pakistan (2011).

Conclusions
DENV-2, DENV-3 and DENV-4 that circulated during 2006–2011 are likely to have first introduced via the southern route of Pakistan. Both DENV-2 and DENV-3 have undergone in-situ evolution to generate heterogenous populations, possibly driven by sustained local DENV transmission during 2006–2011 periods. While both DENV-2 and DENV-3 continued to circulate in Southern Pakistan until 2009, DENV-2 has spread in a Northern direction to establish in Punjab Province, which experienced a massive dengue outbreak in 2011.
Misplaced links in the chain of survival due to an incorrect manual for the emergency call at public facilities
Authors: Takei Yutaka , Nishi Taiki , Takase Keiko , Kamikura Takahisa , Inaba Hideo 
Published: September 2013

Abstract

Background
The incidence of delayed emergency calls and the outcome of out-of-hospital cardiac arrest (OHCA) may differ among public facilities when emergency calls are placed by institutional staff. The purpose of this study was to identify the actions prescribed in the rules and/or manuals of public facilities and to clarify whether the incidence of delayed emergency call placement and the outcome of OHCA differ among these facilities.

Methods
We performed a questionnaire-based survey regarding emergency calls in public facilities in our community and analyzed our regional Utstein-based OHCA database.

Results
Our questionnaire survey disclosed that the most common actions prescribed in the manuals or rules applied in care facilities and educational institutions are to report the situation when a cardiac arrest occurs and to follow the directions of a custodian or supervisor. The international web search disclosed that these actions are rarely prescribed in medical emergency manuals in other countries. Most of these manuals simply say that staff should make an emergency call immediately upon detecting a serious illness or medical emergency. Analysis of the Utstein-based database from our community revealed that the time interval between collapse and emergency call placement is prolonged and the outcome of cardiac arrest poor in care facilities. A prompt emergency call and cardiopulmonary resuscitation (CPR) after arrest are associated with improved 1-year survival following OHCA. Contrary to accepted wisdom, staff who recognize a cardiac arrest may consult their supervisor and then continue CPR until they receive instructions from him or her.

Conclusions
Manuals or rules for making emergency calls in our public facilities may contain incorrect information, and emergency calls may be delayed owing to correctable human factors. Such manuals should be checked and revised.
Expression of non-protein-coding antisense RNAs in genomic regions related to autism spectrum disorders
Authors: Velmeshev Dmitry , Magistri Marco , Faghihi Mohammad Ali 
Published: September 2013

Abstract

Background
Autism spectrum disorders (ASD) manifest with neurodevelopmental phenotypes including communicative, social and behavioral impairments that affect as many as 1 in 88 children. The majority of autism cases have no known genetic cause, suggesting complex genetics of the disorder, but a few genes of large effect have been identified.

Methods
In order to identify novel ASD genetic correlates, we investigated non-protein coding RNAs (ncRNAs) which are abundantly transcribed from the human genome, enriched in the brain, and have been implicated in neurodevelopmental disorders. Using an algorithm that we developed, we examined a publicly available transcriptomics database, AceView, to identify the natural antisense transcripts (NATs) that overlap with known autism-related genes. We validated the presence and differential expression of NATs in different brain regions of ASD and control brains using qRT-PCR. Additionally, we investigated the subcellular localization of these transcripts in a neuronal cell line using RNA-sequencing (RNA-seq).

Results
We found noncoding antisense RNA transcripts at approximately 40% of loci previously implicated in ASD. We confirmed the expression of 10 antisense RNAs in different postmortem human brain tissues. The expression of five antisense transcripts was found to be region-specific, suggesting a role for these ncRNAs in the development and function of specific brain regions. Some antisense RNAs overlapping suspected ASD genes exhibited concordant expression relative to their sense protein-coding genes, while other sense-antisense pairs demonstrate a discordant relationship. Interestingly, the antisense RNA corresponding to the SYNGAP1 locus (SYNGAP1-AS) was found to be differentially expressed in brain regions of patients with ASD compared to control individuals. RNA-seq analysis of subcellular compartments from SH-SY5Y human neuroblastoma cells demonstrated that antisense RNAs to ASD candidate genes are predominantly expressed in the nucleoplasmic or chromatin compartments, implying their involvement in nuclear-associated processes.

Conclusions
Our data suggests that NATs are abundantly expressed from ASD-related loci and provide evidence for their roles in target gene regulation, neurodevelopment and autism pathogenesis. This class of RNA should therefore be considered in functional studies aimed at understanding genetic risk factors for ASD.
Sociomicrobiome of wood decay in a tropical rain forest: unraveling complexity
Authors: Santiago-Rodriguez Tasha M , Toranzos Gary A , Bayman Paul , Massey Steven E , Cano Raul J 
Published: September 2013

Abstract
Given that microbial interactions in nature are very complex, we propose that quorum-sensing, as well as quorum-quenching, phenazine and secondary metabolite production, resistance and toxin-antitoxin systems within a microbial community should all comprise the battery of processes involving the study of what we would define as the “sociomicrobiome”. In the present study the genes/molecules, subsystems and taxonomic breakup of the mentioned processes were identified in decaying tropical wood from the El Yunque rainforest in Puerto Rico, and soil using a shotgun metagenomic approach. The rapid decomposition of wood and litter in tropical regions suggests that processes in these settings are governed by unexplored microbes with the potential of being further studied and exploited for various purposes. Both ecosystems were characterized by the presence of specific genes/molecules, subsystems and microbes associated with the mentioned processes, although the average abundances for specific processes differed. Of the sociomicrobiomes studied, that from El Yunque was found to be the most complex. The approach considered in the present study could also be applied to study the sociomicrobiome of other ecosystems.