bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical efficacy of a traditional Japanese (kampo) medicine for burning mouth syndrome
Authors: Sakata Ken‐ichiro , Yamazaki Yutaka , Ohga Noritaka , Sato Jun , Asaka Takuya , Yoshikawa Kazuhito , Nakazawa Seitaro , Sato Chiharu , Nakamura Yusuke , Kitagawa Yoshimasa 
Published: April 2016

AbstractAimAt Hokkaido University Hospital, selective serotonin re‐uptake inhibitors (SSRI) or serotonin and norepinephrine re‐uptake inhibitors (SNRI) are the first‐line medications for burning mouth syndrome (BMS). Occasionally, when standard SSRI/SNRI are deemed inappropriate because of certain side‐effects, treatment incompatibility, age concerns, or doctor discretion, a kampo medicine called rikkosan can be used. The purpose of this study was to evaluate the effectiveness of rikkosan for BMS.MethodsThis retrospective study included 48 patients (four men, 44 women; mean age, 70 years) who were diagnosed with BMS in the present department between 2006 and 2014. Only patients who received rikkosan (7.5 g/day) for >4 weeks were included. Patients who were taking other medicines for BMS were excluded. Pain was assessed using a visual analog scale.ResultsImprovement was seen in 54% of patients (26/48).ConclusionRikkosan is an effective alternative treatment for BMS.
Recent progresses in incorporating human land–water management into global land surface models toward their integration into Earth system models
Authors: Pokhrel Yadu N. , Hanasaki Naota , Wada Yoshihide , Kim Hyungjun 
Published: April 2016

The global water cycle has been profoundly affected by human land–water management. As the changes in the water cycle on land can affect the functioning of a wide range of biophysical and biogeochemical processes of the Earth system, it is essential to represent human land–water management in Earth system models (ESMs). During the recent past, noteworthy progress has been made in large‐scale modeling of human impacts on the water cycle but sufficient advancements have not yet been made in integrating the newly developed schemes intoESMs. This study reviews the progresses made in incorporating human factors in large‐scale hydrological models and their integration intoESMs. The study focuses primarily on the recent advancements and existing challenges in incorporating human impacts in global land surface models (LSMs) as a way forward to the development ofESMswith humans as integral components, but a brief review of global hydrological models (GHMs) is also provided. The study begins with the general overview of human impacts on the water cycle. Then, the algorithms currently employed to represent irrigation, reservoir operation, and groundwater pumping are discussed. Next, methodological deficiencies in current modeling approaches and existing challenges are identified. Furthermore, light is shed on the sources of uncertainties associated with model parameterizations, grid resolution, and datasets used for forcing and validation. Finally, representing human land–water management inLSMsis highlighted as an important research direction toward developing integrated models usingESMframeworks for the holistic study of human–water interactions within the Earths system.WIREs Water2016, 3:548–574. doi: 10.1002/wat2.1150This article is categorized under:Engineering Water > Planning WaterScience of Water > Water and Environmental Change
Using nanobiotechnology to increase the prevalence of epigenotyping assays in precision medicine
Authors: Heimer Brandon W. , Tam Brooke E. , Minkovsky Alissa , Sikes Hadley D. 
Published: April 2016

Epigenetic silencing of genes that are important for DNA repair, cell cycle control, apoptosis, and cellular interactions with the extracellular matrix has been causally linked to several subtypes of cancer. Translating this knowledge of the implications of promoter methylation to wide and routine use in clinical pathology laboratories has been more challenging than the case of genetic analyses because epigenetic modifications do not change the underlying sequence of the affected nucleic acid, rendering polymerase chain reaction analysis alone uninformative. Two epigenotyping assays that detect promoter methylation are currently standard of care in treatment of two distinct tumor types in only a few top hospitals across the United States. Both rely on a harsh chemical step that degrades over 90% of tumor DNA samples, which are often available in limited quantities, and imparts the potential for false‐negative or false‐positive results if the reaction conditions are not exactly correct. Using nanotechnology and biotechnology to devise practical new analysis techniques that avoid the drawbacks of current techniques represents a powerful approach that is likely to significantly increase the clinical use of this class of biomarkers in the coming years. WIREs Nanomed Nanobiotechnol 2017, 9:e1407. doi: 10.1002/wnan.1407This article is categorized under:

Diagnostic Tools > Biosensing
Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease
Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts
Authors: Jakobi Tobias , Czaja-Hasse Lisa F. , Reinhardt Richard , Dieterich Christoph 
Published: April 2016

Abstract
For several decades, cardiovascular disease has been the leading cause of death throughout all countries. There is a strong genetic component to many disease subtypes (e.g., cardiomyopathy) and we are just beginning to understand the relevant genetic factors. Several studies have related RNA splicing to cardiovascular disease and circular RNAs (circRNAs) are an emerging player. circRNAs, which originate through back-splicing events from primary transcripts, are resistant to exonucleases and typically not polyadenylated. Initial functional studies show clear phenotypic outcomes for selected circRNAs. We provide, for the first time, a comprehensive catalogue of RNase R-resistant circRNA species for the adult murine heart. This work combines state-of-the-art circle sequencing with our novel DCC software to explore the circRNA landscape of heart tissue. Overall, we identified 575 circRNA species that pass a beta-binomial test for enrichment (false discovery rate of 1%) in the exonuclease-treated sequencing sample. Several circRNAs can be directly attributed to host genes that have been previously described as associated with cardiovascular disease. Further studies of these candidate circRNAs may reveal disease-relevant properties or functions of specific circRNAs.
Up-Regulation of Long Non-Coding RNA TUG1 in Hibernating Thirteen-Lined Ground Squirrels
Authors: Frigault Jacques J. , Lang-Ouellette Daneck , Morin Pier Jr. 
Published: April 2016

Abstract
Mammalian hibernation is associated with multiple physiological, biochemical, and molecular changes that allow animals to endure colder temperatures. We hypothesize that long non-coding RNAs (lncRNAs), a group of non-coding transcripts with diverse functions, are differentially expressed during hibernation. In this study, expression levels of lncRNAsH19 and TUG1 were assessed via qRT-PCR in liver, heart, and skeletal muscle tissues of the hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus). TUG1 transcript levels were significantly elevated 1.94-fold in skeletal muscle of hibernating animals when compared with euthermic animals. Furthermore, transcript levels of HSF2 also increased 2.44-fold in the skeletal muscle in hibernating animals. HSF2 encodes a transcription factor that can be negatively regulated by TUG1 levels and that influences heat shock protein expression. Thus, these observations support the differential expression of the TUG1–HSF2 axis during hibernation. To our knowledge, this study provides the first evidence for differential expression of lncRNAs in torpid ground squirrels, adding lncRNAs as another group of transcripts modulated in this mammalian species during hibernation.
Comparison of low frequency repetitive transcranial magnetic stimulation parameters on motor cortex excitability in normal subjects
Authors: Schrader Lara , Sadeghinejad Sima , Sadeghinejad Jalleh , Kazanchyan Movses , Koski Lisa , Stern John , Wu Allan , Iacoboni Marco , Nuwer Marc 
Published: April 2016

Abstract
Background/objectives Optimal low frequency repetitive transcranial magnetic stimulation (LF-rTMS) parameters for treating epilepsy and other brain disorders are unknown. To address this question, a systematic study of the effects of LF-rTMS frequency and intensity on cortical excitability was performed.
Methods Using a four-period crossover design, subjects were scheduled for four LF-rTMS sessions that were at least four weeks apart. LF-rTMS was delivered as 900 pulses directed at primary motor cortex using four protocols: 0.5 Hz at 90% resting motor threshold (RMT), 0.5 Hz at 110% RMT, 1 Hz at 90% RMT, and 1 Hz at 110% RMT. Motor evoked potential (MEP) amplitude, resting motor threshold (RMT), and cortical silent period (CSP) were measured before, immediately after, and 60 min after LF-rTMS. Each of the four protocols was analyzed separately to compare baseline measurements to those after LF-rTMS.
Results None of the four LF-rTMS protocols produced a trend or significant change in MEP amplitude, RMT, or CSP.
Conclusion The lack of significant effect from the four LF-rTMS protocols indicates that none produced evidence for alteration of cortical excitability. The direct comparison of four LF-rTMS protocols is distinct to this investigation, as most similar studies were exploratory and studied only one or two protocols. The negative result relates only to the methods used in this investigation and does not indicate that LF-rTMS does not alter cortical excitability with other parameters. These results may be useful when designing additional investigations into the effect of LF-rTMS on epilepsy, other disorders, and cortical excitability.
Variability of the pubic arch architecture and its influence on the minimal levator hiatus area
Authors: Rostaminia Ghazaleh , Machiorlatti Michael , Shobeiri S. Abbas , Quiroz Lieschen H. 
Published: April 2016

AbstractObjectiveTo investigate the association between the minimal levator hiatus (MLH) area at rest with its surrounding soft‐tissue and bony structures in nulliparous asymptomatic women with a normal levator ani muscle.MethodsA subanalysis was undertaken of a prospective study of the appearance of the levator ani in asymptomatic nulliparous women conducted between September 2010 and September 2011. The subanalysis included women with a normal levator ani muscle. Three‐dimensional ultrasonography volumes were used to obtain pelvic floor measurements.ResultsThe analysis included 56 women with mean age of 43.0 ± 13.4 years. The mean MLH area was 13.1 ± 1.8 cm2 (range 9.0–17.3). The pubic arch angle had no influence on the MLH area (Pearson correlation coefficient r = 0.13). Height and pubic arch length were positively correlated with the MLH area (r = 0.26 [P = 0.52] and r = 0.50 [P < 0.001], respectively).ConclusionThe MLH size of nulliparous women varied widely and was positively correlated with the height and pubic arch length of the women. Therefore, caution is warranted when interpreting the MLH area as an indicator of a levator ani defect or a predictor of pelvic organ prolapse without taking a woman's pelvic bone characteristics into account.
There is an agreement between constipation referred and that documented by objective criteria?
Authors: Neto Isaac José Felippe Corrêa , Maneira Ana Luiza Chaves , Teixeira Noelle Breda , Vettorato Beatriz Doine , de Oliveira Mariana Campello , Menezes Tatielle Alves Trivelato , Robles Laercio 
Published: April 2016

Abstract
Introduction Chronic constipation is the most common digestive complaint at the doctor's office, with high prevalence in the population. However, many patients – and even those physicians not so familiar with pelvic floor disorders–define and consider constipation based on intestinal functionality and stool consistency. But symptoms of incomplete defecation, digital maneuvers, abdominal discomfort, and straining should not be overlooked.
Objectives To investigate the correlation between constipation referred and documented through objective criteria in patients admitted on a daytime-nursing ward basis at the Hospital Santa Marcelina, São Paulo.
Methodology This is a prospective study of a random sample of patients admitted on a daytime-ward hospitalization basis at Santa Marcelina Hospital to perform minor surgical procedures not related to functional disorders of the gastrointestinal tract in the period from September 2014 to June 2015; the only exclusion criterion was “not agreed to participate in the interview conducted by students of medicine at Santa Marcelina Medical School”.
Results 102 patients were randomly analyzed in the period considered (51% female) with a mean overall age of 48.6 (19–82) years. Constipation has been reported spontaneously by 17.6% of participants and denied by 82.4%. With the implementation of the Cleveland Clinic's criteria for the diagnosis of constipation, the compliance with the referred symptomatology was 88.9%; the same value was found with the use of the Rome III criteria (Kappa = 0.665). In addition, a higher incidence of constipation was observed in female patients (p = 0.002).
Conclusion A higher incidence of constipation was observed in female participants, with no statistical difference with respect to age. Furthermore, a substantial agreement was found between constipation referred and constipation documented through objective criteria.
Bioinformatics microarray analysis and identification of gene expression profiles associated with cirrhotic liver
Authors: Chan Kun‐Ming , Wu Tsung‐Han , Wu Ting‐Jung , Chou Hong‐Shiue , Yu Ming‐Chin , Lee Wei‐Chen 
Published: April 2016

AbstractCirrhosis is the endpoint of liver fibrosis that is accompanied by limited regeneration capacity and complications and is the ultimate cause of death in many patients. Despite this, few studies have thoroughly looked at the gene expression profiles in the cirrhotic liver. Hence, this study aims to identify the genes that were differentially expressed in the cirrhotic liver and to explore the putative related signaling pathway and interaction networks. The gene expression profiles of cirrhotic livers and noncirrhotic livers were examined and compared using microarray gene analysis. Proteins encoded by the differentially expressed genes were analyzed for functional clustering and signaling pathway involvement using MetaCore bioinformatics analyses. The Gene Ontology analysis as well as the Kyoto encyclopedia of Genes and Genomes pathway analysis were also performed. A total of 213 significant genes were differentially expressed at more than a two‐fold change in cirrhotic livers as compared to noncirrhotic livers. Of these, 105 upregulated genes and 63 downregulated genes were validated through MetaCore bioinformatics analyses. The signaling pathways and major functions of proteins encoded by these differentially expressed genes were further analyzed; results showed that the cirrhotic liver has a unique gene expression pattern related to inflammatory reaction, immune response, and cell growth, and is potentially cancer related. Our findings suggest that the microarray analysis may provide clues to the molecular mechanisms of liver cirrhosis for future experimental studies. However, further exploration of areas regarding therapeutic strategy might be possible to support metabolic activity, decrease inflammation, or enhance regeneration for liver cirrhosis.
EssC: domain structures inform on the elusive translocation channel in the Type VII secretion system
Authors: Zoltner Martin , Ng Wui M.A.V. , Money Jillian J. , Fyfe Paul K. , Kneuper Holger , Palmer Tracy , Hunter William N. 
Published: April 2016

The membrane-bound protein EssC is an integral component of the bacterial Type VII secretion system (T7SS), which is a determinant of virulence in important Gram-positive pathogens. The protein is predicted to consist of an intracellular repeat of forkhead-associated (FHA) domains at the N-terminus, two transmembrane helices and three P-loop-containing ATPase-type domains, D1–D3, forming the C-terminal intracellular segment. We present crystal structures of the N-terminal FHA domains (EssC-N) and a C-terminal fragment EssC-C from Geobacillus thermodenitrificans, encompassing two of the ATPase-type modules, D2 and D3. Module D2 binds ATP with high affinity whereas D3 does not. The EssC-N and EssC-C constructs are monomeric in solution, but the full-length recombinant protein, with a molecular mass of approximately 169 kDa, forms a multimer of approximately 1 MDa. The observation of protomer contacts in the crystal structure of EssC-C together with similarity to the DNA translocase FtsK, suggests a model for a hexameric EssC assembly. Such an observation potentially identifies the key, and to date elusive, component of pore formation required for secretion by this recently discovered secretion system. The juxtaposition of the FHA domains suggests potential for interacting with other components of the secretion system. The structural data were used to guide an analysis of which domains are required for the T7SS machine to function in pathogenic Staphylococcus aureus. The extreme C-terminal ATPase domain appears to be essential for EssC activity as a key part of the T7SS, whereas D2 and FHA domains are required for the production of a stable and functional protein.
Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution
Authors: Alves Gelio , Yu Yi-Kuo 
Published: April 2016

AbstractMotivation : There is a growing trend for biomedical researchers to extract evidence and draw conclusions from mass spectrometry based proteomics experiments, the cornerstone of which is peptide identification. Inaccurate assignments of peptide identification confidence thus may have far-reaching and adverse consequences. Although some peptide identification methods report accurate statistics, they have been limited to certain types of scoring function. The extreme value statistics based method, while more general in the scoring functions it allows, demands accurate parameter estimates and requires, at least in its original design, excessive computational resources. Improving the parameter estimate accuracy and reducing the computational cost for this method has two advantages: it provides another feasible route to accurate significance assessment, and it could provide reliable statistics for scoring functions yet to be developed.Results : We have formulated and implemented an efficient algorithm for calculating the extreme value statistics for peptide identification applicable to various scoring functions, bypassing the need for searching large random databases.Availability and Implementation : The source code, implemented in C ++ on a linux system, is available for download at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/RAId/RAId_Linux_64BitContact: yyu@ncbi.nlm.nih.govSupplementary information: Supplementary data are available at Bioinformatics online.
Myoepithelioma of Soft Tissues
Authors: Domingo-Musibay Evidio , Oliveira Andre M. , Okuno Scott H. , Petersen Ivy A. , Rose Peter S. , Robinson Steven I. 
Published: April 2016

Background:Myoepithelioma of the soft tissues is a rare entity and little is known about how best to manage locally recurrent and high-grade disease. Here, we retrospectively examined outcomes of surgery, chemotherapy, and radiation therapy (RT) for treatment of low-grade and high-grade myoepithelioma of soft tissues.Methods:We reviewed 20 cases of myoepithelioma of soft tissues seen at Mayo Clinic between 1994 and 2014. The effect of histologic grade and therapies received on relapse and survival were assessed.Results:We identified 13 patients with low-grade disease and 7 patients with high-grade disease. We found that low-grade disease was frequently effectively managed with surgical resection alone, whereas high-grade disease frequently metastasized and was often fatal. The 5-year event-free survival was 88% (confidence interval, 46%-98%) for low-grade disease versus 36% (confidence interval, 7%-75%;P=0.04) for high-grade disease. The relapse rate in low-grade disease was 29% at 5 years versus 64% (P=0.04) in high-grade disease. No significant responses to chemotherapy were noted, however, excellent responses to perioperative RT were seen.Conclusions:Surgery continues as the primary modality of treatment for myoepithelioma of soft tissues. Our study did not show a clear benefit of chemotherapy in the metastatic disease setting, but supports the use of perioperative RT in the management of high-grade disease; further investigation is warranted.
Graded Cycling Test Combined With the Talk Test Is Responsive in Cardiac Rehabilitation
Authors: Nielsen Susanne Grøn , Vinther Anders 
Published: April 2016

PURPOSE:
To evaluate clinical assessment outcome of cardiac rehabilitation, a simple and reliable submaximal exercise test, not based on heart rate, is warranted. The Talk Test (TT) has been found to correlate well with the ventilatory threshold, and excellent reliability was observed for TT combined with the Graded Cycling Test (GCT-TT) in cardiac patients. The purpose was to investigate responsiveness of GCT-TT in cardiac rehabilitation patients.

METHODS:
Patients (n = 93) referred to 8 weeks of cardiac rehabilitation were included. Pre- and posttests were performed using GCT-TT. Mean test changes in watts (W) were compared with the standard error of measurement (SEM95) for groups and the smallest real difference (SRD) for individuals. Minimal clinically important difference was assessed by comparing patient perceived changes in physical fitness with the test changes.

RESULTS:
A statistically significant improvement of GCT-TT was observed; 18.1 ± 21.1 W (mean ± SD) (P < .001). This was close to the previously observed SEM95 of 18.3 W. Thirty-six percent of the patients exceeded SRD (2 test stages). The subgroup with a perceived “major change” improved 28.8 ± 20.7 W compared with the groups reporting “some” (P < .001) and “no or minor” change (P = .002). A change of 30 W (equivalent to 2 stages ≈ 1 metabolic equivalent task [MET]) in the present test protocol is suggested as the minimal clinically important difference.

CONCLUSIONS:
GCT-TT was responsive to changes of power output for these patients, and these changes were generally in agreement with patient perceived changes in physical fitness.