bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro neuraotropic growth of cholangiocarcinoma: an experimental study
Authors: Wang Yu-Xue , Liu Wei , Tan Xin-Yu , Tang Hui-Huan 
Published: October 2013

Summary Objective Perineural invasion of cholangiocarcinoma happens in the early stage of the disease but is often not recognized until its later stages. Research about the behaviour and mechanism of perineural invasion by cholangiocarcinoma is urgently needed for a useful new model. The aim of this work is to establish a novel model to address the problem. Design Neural cells and cholangiocarcinoma cells were co-cultured to mimic the neurotropic invasion of cholangiocarcinoma. Setting Human embryonic stem cells were induced to form neural cells by glial cell-derived neurotropic factor and retinoic acid; neural cells and cholangiocarcinoma cells were co-cultured in Transwell chamber. Participants Human embryonic stem cells and cholangiocarcinoma cells were applied. Main outcome measures Paired t-test was used to compare the counts of penetrating cholangiocarcinoma cells in co-culture and control group. Results Formation of neurospheres and neural-like cells were observed following induction at 24 and 48 h, respectively; synapses were viewed to protrude from neural-like cell bodies after incubation for 96 h. Forty-eight hours after incubation, immunocytochemical staining of the cells showed that synaptophysin and glial fibrillary acidic protein were expressed in the neuron-like cells and gliocytes-like cells, respectively. The cholangiocarcinoma cells that had penetrated through the Matrigel/polyethylene terephthalate membrane from the upper chamber to the lower chamber of the Transwell in the co-culture group were significantly more numerous than those in the control group (68 ± 8.3/field versus 46 ± 5.7/field, P < 0.05). Conclusion The novel model is a valuable tool to study the perineural invasion of cholangiocarcinoma.
How distressing is it to participate in medical research? A calibration study using an everyday events questionnaire
Authors: Petrie Keith J , Faasse Kate , Notman Tracey Anne , O'Carroll Ronan 
Published: October 2013

Objectives To investigate how distressing participating in medical research is perceived to be, compared to everyday events. Design Anonymous questionnaire. Setting Scotland and New Zealand. Participants One hundred members of the Scottish general public, 94 University of Auckland students, 22 New Zealand Ministry of Health ethics committee members. Main outcome measures Distress ratings made on a 0–10 scale for everyday events and common medical research procedures. Results Both general population and student samples generally rated the distress caused by participating in various medical research procedures as low or very low. Most research procedures were rated less than the distress caused by not being able to find a car park at a supermarket. In contrast, the ethics committee members rated the distress caused by most of the medical research procedures at a significantly higher level than the ratings of the student and general population samples. Ethics committee members overestimated the distress caused by interview or questionnaire assessments ( M = 203.31%, SE = 11.42, 95% CI [179.79, 226.83]) more than medical testing for research ( M = 158.06%, SE = 12.33, 95% CI [132.66, 183.46], p = 0.04) and everyday events ( M = 133.10%, SE = 7.80, 95% CI [117.03, 149.16], p < 0.001). Conclusions Common medical research procedures are not rated as particularly distressing by the general public, and ethics committees may be adopting an over-protective role when evaluating research applications that involve the use of questionnaire or survey methodology.
Preoperative Thyroid Dysfunction Predicts 30-Day Postoperative Complications in Elderly Patients With Hip Fracture
Authors: Ling Xi Wern , Howe Tet Sen , Koh Joyce Suang Bee , Wong Merng Koon , Ng Alvin Choong Meng 
Published: October 2013

Objectives: To investigate the relationship between thyroid function and short-term outcomes in elderly patients undergoing surgery for hip fracture. Methods: Patients aged >60 years admitted from July 2009 to June 2010 who underwent surgical fixation of low-energy hip fracture, excluding those with pathological or periprosthetic fracture, were enrolled in a retrospective observational cohort study. Patients were classified as having biochemically overt or subclinical hyperthyroidism or hypothyroidism, normal thyroid function, or nonclassifiable state based on preoperative thyroid-stimulating hormone and free thyroxine values. Outcome data were collected from hospital records. Biochemical thyroid dysfunction was not systematically treated. Outcomes measured were length of stay (LOS), 30-day postoperative complications, readmissions, and mortality. Results: A total of 254 patients were analyzed; 64 (25.2%) were male and mean age was 77.8 years. There were 128 (50.4%) patients with euthyroid, 68 (26.8%) nonclassifiable, 13 (5.1%) overtly hyperthyroid, 20 (7.9%) subclinically hyperthyroid, 4 (1.6%) overtly hypothyroid, and 21 (8.3%) subclinically hypothyroid. The 30-day postoperative complication rate was 38% (96 patients). The most common complication was urinary tract infection (12.6%), followed by cardiac events (8.3%) and delirium (5.5%). Patients with overt hyperthyroidism had an increased risk of complications in multivariate analysis (odds ratio 3.75, 95% confidence interval 1.10-12.84). Complications in this group were similar to those in the overall cohort. Thyroid function did not predict LOS, readmissions, or mortality. Conclusion: Older patients frequently develop complications following surgery for hip fractures. This risk appears to be increased by preoperative biochemically overt hyperthyroidism. Further study is warranted to confirm this finding and to determine whether preoperative treatment improves outcomes.
Genetic structure of Trypanosoma cruziin Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach
Authors: Ramírez Juan David , Tapia-Calle Gabriela , Guhl Felipe 
Published: September 2013

Abstract

Background
Chagas disease is a systemic pathology caused by Trypanosoma cruzi. This parasite reveals remarkable genetic variability, evinced in six Discrete Typing Units (DTUs) named from T. cruzi I to T. cruzi VI (TcI to TcVI). Recently newly identified genotypes have emerged such as TcBat in Brazil, Colombia and Panama associated to anthropogenic bats. The genotype with the broadest geographical distribution is TcI, which has recently been associated to severe cardiomyopathies in Argentina and Colombia. Therefore, new studies unraveling the genetic structure and natural history of this DTU must be pursued.

Results
We conducted a spatial and temporal analysis on 50 biological clones of T. cruzi I (TcI) isolated from humans with different clinical phenotypes, triatomine bugs and mammal reservoirs across three endemic regions for Chagas disease in Colombia. These clones were submitted to a nuclear Multilocus Sequence Typing (nMLST) analysis in order to elucidate its genetic diversity and clustering. After analyzing 13 nuclear housekeeping genes and obtaining a 5821 bp length alignment, we detected two robust genotypes within TcI henceforth named TcIDOM (associated to human infections) and a second cluster associated to peridomestic and sylvatic populations. Additionaly, we detected putative events of recombination and an intriguing lack of linkage disequilibrium.

Conclusions
These findings reinforce the emergence of an enigmatic domestic T. cruzi genotype (TcIDOM), and demonstrates the high frequency of recombination at nuclear level across natural populations of T. cruzi. Therefore, the need to pursue studies focused on the diferential virulence profiles of TcI strains. The biological and epidemiological implications of these findings are herein discussed.
Investigating silent strokes in hypertensives: a magnetic resonance imaging study (ISSYS): rationale and protocol design
Authors: Riba-Llena Iolanda , Jarca Carmen Ioana , Mundet Xavier , Tovar Jose L , Orfila Francesc , López-Rueda Antonio , Nafría Cristina , Fernández Jose L , Castañé Xavier , Domingo Mar , Álvarez-Sabín José , Fernández-Cortiñas Inés , Maisterra Olga , Montaner Joan , Delgado Pilar 
Published: October 2013

Abstract

Background
Silent brain infarcts are detected by neuroimaging in up to 20% of asymptomatic patients based on population studies. They are five times more frequent than stroke in general population, and increase significantly both with advancing age and hypertension. Moreover, they are independently associated with the risk of future stroke and cognitive decline.
Despite these numbers and the clinical consequences of silent brain infarcts, their prevalence in Mediterranean populations is not well known and their role as predictors of future cerebrovascular and cardiovascular events in hypertensive remains to be determined.
ISSYS (Investigating Silent Strokes in Hypertensives: a magnetic resonance imaging study) is an observational cross-sectional and longitudinal study aimed to: 1- determine the prevalence of silent cerebrovascular infarcts in a large cohort of 1000 hypertensives and to study their associated factors and 2-to study their relationship with the risk of future stroke and cognitive decline.

Methods/Design
Cohort study in a randomly selected sample of 1000 participants, hypertensive aged 50 to 70 years old, with no history of previous stroke or dementia.
On baseline all participants will undergo a brain MRI to determine the presence of brain infarcts and other cerebrovascular lesions (brain microbleeds, white matter changes and enlarged perivascular spaces) and will be also tested to determine other than brain organ damage (heart-left ventricular hypertrophy, kidney-urine albumin to creatinine ratio, vessels-pulse wave velocity, ankle brachial index), in order to establish the contribution of other subclinical conditions to the risk of further vascular events. Several sub-studies assessing the role of 24 hour ambulatory BP monitoring and plasma or genetic biomarkers will be performed.
Follow-up will last for at least 3 years, to assess the rate of further stroke/transient ischemic attack, other cardiovascular events and cognitive decline, and their predictors.

Discussion
Improving the knowledge on the frequency and determinants of these lesions in our setting might help in the future to optimize treatments or establish new preventive strategies to minimize clinical and socioeconomic consequences of stroke and cognitive decline.
Brain-Derived Neurotrophic Factor Enhances the Excitability of Small-Diameter Trigeminal Ganglion Neurons Projecting to the Trigeminal Nucleus Interpolaris/Caudalis Transition Zone following Masseter Muscle Inflammation
Authors: Takeda Mamoru , Takahashi Masayuki , Kitagawa Junichi , Kanazawa Takuya , Nasu Masanori , Matsumoto Shigeji 
Published: September 2013

Background The trigeminal subnuclei interpolaris/caudalis transition zones (Vi/Vc) play an important role in orofacial deep pain, however, the role of primary afferent projections to the Vi/Vc remains to be determined. This study investigated the functional significance of hyperalgesia to the brain-derived neurotrophic factor (BDNF)-tyrosine kinase B (trkB) signaling system in trigeminal ganglion (TRG) neurons projecting to the Vi/Vc transition zone following masseter muscle (MM) inflammation. Results The escape threshold from mechanical stimulation applied to skin above the inflamed MM was significantly lower than in naïve rats. Fluorogold (FG) labeling was used to identify the TRG neurons innervating the MM, while microbeads (MB) were used to label neurons projecting to the Vi/Vc region. FG/MB-labeled TRG neurons were immunoreactive (IR) for BDNF and trkB. The mean number of BDNF/trkB-IR small/medium-diameter TRG neurons was significantly higher in inflamed rats than in naïve rats. In whole-cell current-clamp experiments, the majority of dissociated small-diameter TRG neurons showed a depolarization response to BDNF that was associated with spike discharge, and the concentration of BDNF that evoked a depolarizing response was significantly lower in the inflamed rats. In addition, the relative number of BDNF-induced spikes during current injection was significantly higher in inflamed rats. The BDNF-induced changes in TRG neuron excitability was abolished by tyrosine kinase inhibitor, K252a. Conclusion The present study provided evidence that BDNF enhances the excitability of the small-diameter TRG neurons projecting onto the Vi/Vc following MM inflammation. These findings suggest that ganglionic BDNF-trkB signaling is a therapeutic target for the treatment of trigeminal inflammatory hyperalgesia.
Jaccard index based similarity measure to compare transcription factor binding site models
Authors: Vorontsov Ilya E , Kulakovskiy Ivan V , Makeev Vsevolod J 
Published: September 2013

Abstract

Background
Positional weight matrix (PWM) remains the most popular for quantification of transcription factor (TF) binding. PWM supplied with a score threshold defines a set of putative transcription factor binding sites (TFBS), thus providing a TFBS model.
TF binding DNA fragments obtained by different experimental methods usually give similar but not identical PWMs. This is also common for different TFs from the same structural family. Thus it is often necessary to measure the similarity between PWMs. The popular tools compare PWMs directly using matrix elements. Yet, for log-odds PWMs, negative elements do not contribute to the scores of highly scoring TFBS and thus may be different without affecting the sets of the best recognized binding sites. Moreover, the two TFBS sets recognized by a given pair of PWMs can be more or less different depending on the score thresholds.

Results
We propose a practical approach for comparing two TFBS models, each consisting of a PWM and the respective scoring threshold. The proposed measure is a variant of the Jaccard index between two TFBS sets. The measure defines a metric space for TFBS models of all finite lengths. The algorithm can compare TFBS models constructed using substantially different approaches, like PWMs with raw positional counts and log-odds. We present the efficient software implementation: MACRO-APE (MAtrix CompaRisOn by Approximate P-value Estimation).

Conclusions
MACRO-APE can be effectively used to compute the Jaccard index based similarity for two TFBS models. A two-pass scanning algorithm is presented to scan a given collection of PWMs for PWMs similar to a given query.

Availability and implementation
MACRO-APE is implemented in ruby 1.9; software including source code and a manual is freely available at http://autosome.ru/macroape/ and in supplementary materials.
The role of PD-1 and PD-L1 in T-cell immune suppression in patients with hematological malignancies
Authors: Shi Li , Chen Shaohua , Yang Lijian , Li Yangqiu 
Published: September 2013

Abstract
T-cell activation and dysfunction relies on direct and modulated receptors. Based on their functional outcome, co-signaling molecules can be divided as co-stimulators and co-inhibitors, which positively and negatively control the priming, growth, differentiation and functional maturation of a T-cell response. We are beginning to understand the power of co-inhibitors in the context of lymphocyte homeostasis and the pathogenesis of leukemia, which involves several newly described co-inhibitory pathways, including the programmed death-1 (PD-1) and PD-1 ligand (PD-L1) pathway. The aim of this review is to summarize the PD-1 and PD-L1 biological functions and their alterative expression in hematological malignancies. The role of PD-1 and PD-L1 in T-cell immune suppression and the potential for immunotherapy via blocking PD-1 and PD-L1 in hematological malignancies are also reviewed.
Leaf swallowing and parasitic infection of the Chinese lesser civet Viverricula indica in northeastern Taiwan
Authors: Su Hsiu-hui , Su Ying-chen , Huffman Michael A 
Published: September 2013

Abstract

Background
Ingestion of plant parts purportedly for their non-nutritive and/or bioactive properties has been widely reported across the animal kingdom. Many of these examples are viewed as behavioral strategies to maintain health by controlling the level of parasite infections. One such behavior is leaf swallowing, the folding and swallowing of whole leaves without chewing. Void of any nutritional benefit, defecation of the whole leaves is associated with the physical expulsion of intestinal parasites. Fecal samples of the Chinese lesser civet Viverricula indica were collected along a fixed transect line monthly for 17 months in the Fushan Experimental Forest, northeastern Taiwan. We inspected samples for the occurrence of undigested leaves and parasite worms to test the possible antiparasitic function of the behavior in this species.

Results
Of the collected feces, 14.3% contained whole, folded, undigested leaves of grass. The co-occurrence of undigested grass and Toxocara paradoxura worms in the feces was statistically significant. Adult worms of T. paradoxura were trapped inside the fecal-grass mass or on the surface of leaves in these samples. Increases in the T. paradoxura prevalence and infection intensity were associated with a higher presence of whole leaves in the feces.

Conclusions
Reported for the first time in the context of self-medication for civet species, we propose that swallowing grass may facilitate expulsion of adult worms of T. paradoxura, which resembles behaviors widely reported in African great apes, bears, and geese.
Individual differences in the physiological effects of forest therapy based on Type A and Type B behavior patterns
Authors: Song Chorong , Ikei Harumi , Lee Juyoung , Park Bum-Jin , Kagawa Takahide , Miyazaki Yoshifumi 
Published: October 2013

Abstract

Background
In recent years, the physiological relaxation effects of natural environments have been widely exploited, and although individual differences in the effects of forest therapy are known, assessment methods have not been clearly established. This study used a classification based on Type A and Type B behavior patterns to explain individual differences in physiological responses to forest environments.

Methods
We performed physiological experiments in 44 forest and urban (controls) areas. In total, 485 male university students (age, 21.8 ± 1.6 years) participated in the study. The subjects were asked to visit forest or urban environments randomly and observe each landscape for 15 min. The subjects’ pulse rates and blood pressures were tested to evaluate their physiological responses. The Kwansei Gakuin daily life questionnaire was used to identify Type A and Type B behavior patterns in subjects.

Results
The pulse rate was significantly lower in the Type B group after exposure to forest areas than after exposure to urban areas, whereas no significant difference was observed in the Type A group. In addition, the pulse rate was significantly lower in the low scoring subjects in the Type B group, which was consistent with changes in their diastolic blood pressure.

Conclusions
These results suggest that individual differences in pulse rate and blood pressure in response to forest environments can be explained by Type A and Type B behavior patterns.
An in vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
Authors: Edlund Anna , Yang Youngik , Hall Adam P , Guo Lihong , Lux Renate , He Xuesong , Nelson Karen E , Nealson Kenneth H , Yooseph Shibu , Shi Wenyuan , McLean Jeffrey S 
Published: October 2013

Abstract

Background
Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level.

Results
Comparative metagenomic analyses confirmed a high similarity of metabolic potential in biofilms to recently available oral metagenomes from healthy subjects as part of the Human Microbiome Project. A time-series metagenomic analysis of the taxonomic community composition in biofilms revealed that the proportions of major species at 3 hours of growth are maintained during 48 hours of biofilm development. By employing deep pyrosequencing of the 16S rRNA gene to investigate this biofilm model with regards to bacterial taxonomic diversity, we show a high reproducibility of the taxonomic carriage and proportions between: 1) individual biofilm samples; 2) biofilm batches grown at different dates; 3) DNA extraction techniques and 4) research laboratories.

Conclusions
Our study demonstrates that we now have the capability to grow stable oral microbial in vitro biofilms containing more than one hundred operational taxonomic units (OTU) which represent 60-80% of the original inoculum OTU richness. Previously uncultivated Human Oral Taxa (HOT) were identified in the biofilms and contributed to approximately one-third of the totally captured 16S rRNA gene diversity. To our knowledge, this represents the highest oral bacterial diversity reported for an in vitro model system so far. This robust model will help investigate currently uncultivated species and the known virulence properties for many oral pathogens not solely restricted to pure culture systems, but within multi-species biofilms.
Light-driven Bending of Polymer Films in Which Salicylidenephenylethylamine Crystals are Aligned Magnetically
Authors: Koshima Hideko , Matsudomi Masafumi , Uemura Yutaro , Kimura Fumiko , Kimura Tsunehisa 
Published: October 2013

Abstract
Silicone polymer films in which plate-like chiral and achiral crystals of salicylidenephenylethylamines were aligned by a magnetic field were prepared. The polymer films exhibited reversible photomechanical bending upon alternate irradiation with UV and visible light.
Integration Process Of Slovakia Into The European Monetary Union In Perspective Of Selected Macro-Economic Theories During The Current Economic Crisis
Authors: Kotuliè Rastislav 
Published: October 2013

Each national economy anticipates mostly positive effects after joining the Euro. Positive expectations are logical, since every new country admitted to the EU pledges to join the Monetary Union and till the admission has the status of a member state with a temporal exemption for the joining of the Euro. According to the macro­economic results, there is usually an illusion present that the membership in the Eurozone itself absorbs the progress of the global recession. On the other hand, in favor of the membership in the Eurozone speaks the fact that all countries admitted had to rigidly fulfill the Maastricht Convergence Criteria leading to the medium­term guarantee of a healthy and long­term sustainable economy.