bluuebunny/crossref_metadata_2025_split huggingface dataset:
The spectrum of MALT lymphoma at different sites: biological and therapeutic relevance
Authors: Zucca Emanuele , Bertoni Francesco 
Published: March 2016

AbstractExtranodal marginal zone (MZ) B-cell lymphomas of the mucosa-associated lymphoid tissue (MALT) arise from lymphoid populations that are induced by chronic inflammation in extranodal sites. The best evidence of an etiopathogenetic link is provided by the association between Helicobacter pylori–positive gastritis and gastric MALT lymphoma. Indeed, successful eradication of this microorganism with antibiotics can be followed by gastric MALT lymphoma regression in most cases. Other microbial agents have been implicated in the pathogenesis of MZ lymphoma arising at different sites. Apart from gastric MALT lymphoma, antibiotic therapies have been adequately tested only in ocular adnexal MALT lymphomas where upfront doxycycline may be a reasonable and effective initial treatment of patients with Chlamydophila psittaci–positive lymphoma before considering more aggressive strategies. In all other instances, antibiotic treatment of nongastric lymphomas remains investigational. Indeed, there is no clear consensus for the treatment of patients with gastric MALT lymphoma requiring further treatment beyond H pylori eradication or with extensive disease. Both radiotherapy and systemic treatments with chemotherapy and anti-CD20 antibodies are efficacious and thus the experience of individual centers and each patient’s preferences in terms of adverse effects are important parameters in the decision process.
Maximal aerobic capacity in ageing subjects: actual measurementsversuspredicted values
Authors: Pistea Cristina , Lonsdorfer Evelyne , Doutreleau Stéphane , Oswald Monique , Enache Irina , Charloux Anne 
Published: March 2016

We evaluated the impact of selection of reference values on the categorisation of measured maximal oxygen consumption (V′O2peak) as “normal” or “abnormal” in an ageing population.We compared measuredV′O2peakwith predicted values and the lower limit of normal (LLN) calculated with five equations. 99 (58 males and 41 females) disease-free subjects aged ≥70 years completed an incremental maximal exercise test on a cycle ergometer.MeanV′O2peakwas 1.88 L·min−1in men and 1.26 L·min−1in women.V′O2peakranged from 89% to 108% of predicted in men, and from 88% to 164% of predicted in women, depending on the reference equation used. The proportion of subjects below the LLN ranged from 5% to 14% in men and 0–22% in women, depending on the reference equation. The LLN was lacking in one study, and was unsuitable for women in another. Most LLNs ranged between 53% and 73% of predicted. Therefore, choosing an 80% cut-off leads to overestimation of the proportion of “abnormal” subjects.To conclude, the proportion of subjects aged ≥70 years with a “low”V′O2peakdiffers markedly according to the chosen reference equations. In clinical practice, it is still relevant to test a sample of healthy volunteers and select the reference equations that better characterise this sample.
Artificial stone dust-induced functional and inflammatory abnormalities in exposed workers monitored quantitatively by biometrics
Authors: Ophir Noa , Shai Amir Bar , Alkalay Yifat , Israeli Shani , Korenstein Rafi , Kramer Mordechai R. , Fireman Elizabeth 
Published: March 2016

The manufacture of kitchen and bath countertops in Israel is based mainly on artificial stone that contains 93% silica as natural quartz, and ∼3500 workers are involved in cutting and processing it. Artificial stone produces high concentrations of silica dust. Exposure to crystalline silica may cause silicosis, an irreversible lung disease. Our aim was to screen exposed workers by quantitative biometric monitoring of functional and inflammatory parameters.68 exposed artificial stone workers were compared to 48 nonexposed individuals (controls). Exposed workers filled in questionnaires, and all participants underwent pulmonary function tests and induced sputum analyses. Silica was quantitated by a Niton XL3 X-ray fluorescence spectrometer.Pulmonary function test results of exposed workers were significantly lower and induced sputa showed significantly higher neutrophilic inflammation compared to controls; both processes were slowed down by the use of protective measures in the workplace. Particle size distribution in induced sputum samples of exposed workers was similar to that of artificial stone dust, which contained aluminium, zirconium and titanium in addition to silica.In conclusion, the quantitation of biometric parameters is useful for monitoring workers exposed to artificial stone in order to avoid deterioration over time.
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction
Authors: Öztürk Hakime , Ozkirimli Elif , Özgür Arzucan 
Published: March 2016

Abstract
Background
Molecular structures can be represented as strings of special characters using SMILES. Since each molecule is represented as a string, the similarity between compounds can be computed using SMILES-based string similarity functions. Most previous studies on drug-target interaction prediction use 2D-based compound similarity kernels such as SIMCOMP. To the best of our knowledge, using SMILES-based similarity functions, which are computationally more efficient than the 2D-based kernels, has not been investigated for this task before.

Results
In this study, we adapt and evaluate various SMILES-based similarity methods for drug-target interaction prediction. In addition, inspired by the vector space model of Information Retrieval we propose cosine similarity based SMILES kernels that make use of the Term Frequency (TF) and Term Frequency-Inverse Document Frequency (TF-IDF) weighting approaches. We also investigate generating composite kernels by combining our best SMILES-based similarity functions with the SIMCOMP kernel. With this study, we provided a comparison of 13 different ligand similarity functions, each of which utilizes the SMILES string of molecule representation. Additionally, TF and TF-IDF based cosine similarity kernels are proposed.

Conclusion
The more efficient SMILES-based similarity functions performed similarly to the more complex 2D-based SIMCOMP kernel in terms of AUC-ROC scores. The TF-IDF based cosine similarity obtained a better AUC-PR score than the SIMCOMP kernel on the GPCR benchmark data set. The composite kernel of TF-IDF based cosine similarity and SIMCOMP achieved the best AUC-PR scores for all data sets.
On the comparison of regulatory sequences with multiple resolution Entropic Profiles
Authors: Comin Matteo , Antonello Morris 
Published: March 2016

Abstract
Background
Enhancers are stretches of DNA (100–1000 bp) that play a major role in development gene expression, evolution and disease. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (CRMs). Although the binding of transcription factors is sequence-specific, the identification of functionally similar enhancers is very difficult and it cannot be carried out with traditional alignment-based techniques.

Results
The use of fast similarity measures, like alignment-free measures, to detect related regulatory sequences is crucial to understand functional correlation between two enhancers. In this paper we study the use of alignment-free measures for the classification of CRMs. However, alignment-free measures are generally tied to a fixed resolution k. Here we propose an alignment-free statistic, called $EP^{*}_{2}$
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2

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, that is based on multiple resolution patterns derived from the Entropic Profiles (EPs). The Entropic Profile is a function of the genomic location that captures the importance of that region with respect to the whole genome. As a byproduct we provide a formula to compute the exact variance of variable length word counts, a result that can be of general interest also in other applications.

Conclusions
We evaluate several alignment-free statistics on simulated data and real mouse ChIP-seq sequences. The new statistic, $EP^{*}_{2}$
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2

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, is highly successful in discriminating functionally related enhancers and, in almost all experiments, it outperforms fixed-resolution methods. We implemented the new alignment-free measures, as well as traditional ones, in a software called EP-sim that is freely available: http://www.dei.unipd.it/~ciompin/main/EP-sim.html.
The impairment of small nerve fibers in severe sepsis and septic shock
Authors: Axer Hubertus , Grimm Alexander , Pausch Christine , Teschner Ulrike , Zinke Jan , Eisenach Sven , Beck Sindy , Guntinas-Lichius Orlando , Brunkhorst Frank M. , Witte Otto W. 
Published: March 2016

Abstract
Background
A decrease of small nerve fibers in skin biopsies during the course of critical illness has been demonstrated recently. However, the diagnostic use of skin biopsies in sepsis and its time course is not known.

Methods
Patients (n=32) with severe sepsis or septic shock were examined using skin biopsies, neurological examination, nerve conduction studies, and sympathetic skin response in the first week after onset of sepsis, 2 weeks and 4 months later and compared to gender- and age-matched healthy controls.

Results
Skin biopsies at the ankle and thigh revealed a significant decrease of intraepidermal nerve fiber density (IENFD) during the first week of sepsis and 2 weeks later. All patients developed critical illness polyneuropathy (CIP) according to electrophysiological criteria and 11 showed IENFD values lower than the 0.05 quantile. Four patients were biopsied after 4 months and still showed decreased IENFD. Results of nerve conduction studies and IENFD did considerably change over time. No differences for survival time between patients with IEFND lower and larger than 3.5 fibers/mm were found.

Conclusions
Skin biopsy is able to detect an impairment of small sensory nerve fibers early in the course of sepsis. However, it may not be suited as a prognostic parameter for survival.

Trial registration
German Clinical Trials Register, DRKS-ID: DRKS00000642, 12/17/2010
Transcranial direct current stimulation as a memory enhancer in patients with Alzheimer’s disease: a randomized, placebo-controlled trial
Authors: Bystad Martin , Grønli Ole , Rasmussen Ingrid Daae , Gundersen Nina , Nordvang Lene , Wang-Iversen Henrik , Aslaksen Per M. 
Published: March 2016

Abstract
Background
The purpose of this study was to assess the efficacy of transcranial direct current stimulation (tDCS) on verbal memory function in patients with Alzheimer’s disease.

Methods
We conducted a randomized, placebo-controlled clinical trial in which tDCS was applied in six 30-minute sessions for 10 days. tDCS was delivered to the left temporal cortex with 2-mA intensity. A total of 25 patients with Alzheimer’s disease were enrolled in the study. All of the patients were diagnosed according to National Institute of Neurological and Communicative Disorders and Stroke and Alzheimer’s Disease and Related Disorders Association criteria. Twelve patients received active stimulation, and thirteen patients received placebo stimulation. The primary outcome measure was the change in two parallel versions of the California Verbal Learning Test–Second Edition, a standardized neuropsychological memory test normalized by age and gender. The secondary outcome measures were the Mini Mental State Examination, clock-drawing test, and Trail Making Test A and B.

Results
Changes in the California Verbal Learning Test–Second Edition scores were not significantly different between the active and placebo stimulation groups for immediate recall (p = 0.270), delayed recall (p = 0.052), or recognition (p = 0.089). There were nonsignificant differences in score changes on the Mini Mental State Examination (p = 0.799), clock-drawing test (p = 0.378), and Trail Making Test A (p = 0.288) and B (p = 0.093). Adverse effects were not observed.

Conclusions
Compared with placebo stimulation, active tDCS stimulation in this clinical trial did not significantly improve verbal memory function in Alzheimer’s disease. This study differs from previous studies in terms of the stimulation protocol, trial design, and application of standardized neuropsychological memory assessment.

Trial registration
ClinicalTrials.gov identifier NCT02518412. Registered on 10 August 2015.
Aging, inflammation, stem cells, and bone healing
Authors: Gibon Emmanuel , Lu Laura , Goodman Stuart B. 
Published: March 2016

AbstractComplex interactions among cells of the monocyte-macrophage-osteoclast lineage and the mesenchymal stem cell-osteoblast lineage play a major role in the pathophysiology of bone healing. Whereas the former lineage directs inflammatory events and bone resorption, the latter represents a source of cells for bone regeneration and immune modulation. Both of these lineages are affected by increasing age, which is associated with higher baseline levels of inflammatory mediators, and a significant reduction in osteogenic capabilities. Given the above, fracture healing, osteoporosis, and other related events in the elderly present numerous challenges, which potentially could be aided by new therapeutic approaches to modulate both inflammation and bone regeneration.
A projection method for approximating fixed points of quasinonexpansive mappings in Hadamard spaces
Authors: Huang Shuechin , Kimura Yasunori 
Published: March 2016

AbstractThis work is devoted to analyzing the feasibility study of a Moudafi viscosity projection method with a weak contraction for a finite family of quasinonexpansive mappings in a Hadamard space. To this end, we need to construct a countable family of nonexpansive mappings satisfying AKTT condition with a weak contraction by choosing an appropriate control sequence under certain conditions.
Micro-computed tomography scan and virtual histological slide data for the land planarian Obama otavioi (Platyhelminthes)
Authors: Carbayo Fernando , Lenihan Jennifer Winifred 
Published: March 2016

Abstract

Background:
We investigated whether images obtained through X-ray micro-computed tomography (μCT) can be used in conjunction with traditional methods for morphological studies of soft-bodied land planarians. μCT is non-invasive and provides true-to-scale three-dimensional imagery at high resolution. We compared μCT-based images of a recently described land planarian species of Obama otavioi (Platyhelminthes) with those obtained from light microphotography of histological sections, most of which were also digitized at high magnification.

Findings:
The specimens studied were collected in 2012. Subsequent μCT-based images of the stained body of a paratype show nearly all morphological features provided by traditional histology, with the exception of particularly minute structures, smaller than 5 μm, such as the sensory pits and single muscle fibers, which are best visible on traditional histological sections. Because the technique is non-destructive, the scanned specimen is preserved without damage. The raw and derivative μCT data and virtual histological sections are freely available in GigaDB.

Conclusions:
The μCT datasets of these stained soft-bodied organisms reveal images of external and internal structures that support previous taxonomic studies. This technique can be particularly important for non-destructively revealing internal details of whole museum specimens at a faster rate than histology alone. High-resolution virtual histological slides also allow further searches for new, previously unstudied morphological features. The use of X-ray equipment with higher resolution can enable smaller sensory organ and muscle fiber details to be seen. The image sets, μCT-based images and digitized histological slides can be disseminated without the constraints of specimen loans.
Can linear transportation infrastructure verges constitute a habitat and/or a corridor for biodiversity in temperate landscapes? A systematic review protocol
Authors: Jeusset Arzhvaël , Vargac Marianne , Bertheau Yves , Coulon Aurélie , Deniaud Nadine , Flamerie De Lachapelle Frédérique , Jaslier Emmanuel , Livoreil Barbara , Roy Véronique , Touroult Julien , Vanpeene Sylvie , Witté Isabelle , Sordello Romain 
Published: March 2016

Abstract
Background
The role of linear transportation infrastructures (roads, railways, oil and gas pipelines, power lines, rivers and canals) in fragmenting natural habitats has been demonstrated. Yet, the potential of habitat or corridor of their verges (road and railway embankments, strips of grass under power lines or above buried pipelines, or waterway banks) for biodiversity remains controversial. In a context of decreasing natural habitats, the potential of anthropogenic areas for contributing to wildlife conservation should be considered. Moreover, how linear transportation infrastructure verges should be managed in order to favor biodiversity is a crucial question. The present work describes the protocol of the first systematic synthesis of evidence of the potential of linear transportation infrastructure verges as habitat and/or corridor for biodiversity. Outcomes of the study will be useful for helping managers to improve their practices or for prioritizing actions of ecological restoration.

Methods
The subject population will include both flora and fauna of the temperate climate, either species or communities. Exposures to linear transportation infrastructure verges, interventions of verge management (mowing, pruning, etc.) and environmental disturbances (pollution, wildfires, etc.) will be included. Both temporal and spatial comparators will be considered. Relevant outcomes will include dispersal, species richness and abundance. The scientific literature on the topic of the review may turn out to be very heterogeneous. Various management types, biodiversity outcomes and study designs might be conceived. If any combination of these is covered by a sufficient number of studies, we will perform a meta-analysis. At the least, we will produce a systematic map and a narrative synthesis.
Parental Attitudes to Genetic Testing Differ by Ethnicity and Immigration in Childhood Nephrotic Syndrome: A Cross-Sectional Study
Authors: Borges Karlota , Vasilevska-Ristovska Jovanka , Hussain-Shamsy Neesha , Patel Viral , Banh Tonny , Hebert Diane , Pearl Rachel J. , Radhakrishnan Seetha , Piscione Tino D. , Licht Christoph P. B. , Langlois Valerie , Levin Leo , Strug Lisa , Parekh Rulan S. 
Published: March 2016

Background: Studies in the USA report differences in opinion among parents of different ethnic groups toward genetic testing for their child; however, there are no studies that address this issue in the diverse ethnic and immigrant population in Canada. Objective: This study aims to determine whether ethnicity and immigration status influences parental interest in clinical genetic testing for a potentially progressive kidney disease. Design: This is a cross-sectional study. Setting: Participants were recruited from the Greater Toronto Area, Canada. Participants: The study included 320 parents of children ages 1–18 years with nephrotic syndrome enrolled in the Insight into Nephrotic Syndrome: Investigating Genes, Health and Therapeutics (INSIGHT) observational cohort study. Measurements: Demographic, ethnicity, immigration, and child specific factors as well as interest in genetic testing were collected through self-reported questionnaires administered at baseline study visit. Methods: Logistic regression models were used to examine association of ethnicity and immigration status with interest in genetic testing. Results: The majority of parents (85 %) were interested in genetic testing for their child. South Asian and East/Southeast Asian parents had 74 and 76 % lower odds of agreeing to genetic testing when compared to Europeans (odds ratio (OR) 0.26, 95 % confidence interval (CI) 0.10–0.68; OR 0.24, 95 % CI 0.07–0.79, respectively) after controlling for age and sex of child, age and education level of parent, initial steroid resistance, and duration of time in Canada. Immigrants to Canada also had significantly lower odds (OR 0.29, 95 % CI 0.12–0.72) of agreeing to genetic testing after similar adjustment. Higher education level was not associated with greater interest in genetic testing (OR 1.24, 95 % CI 0.64–2.42). Limitations: Participants have already agreed to aggregate genetic testing for research purposes as part of enrolment in INSIGHT study. Conclusion: While majority of parents were interested in genetic testing for their child, immigrants, particularly South Asians and East/Southeast Asians, were more likely to decline genetic testing. Genetic counseling needs to be tailored to address specific concerns in these parental groups to maximize informed decision-making in the clinical setting. Trial registration: ClinicalTrials.gov , NCT01605266
The Canadian Experience Using the Expanded Criteria Donor Classification for Allocating Deceased Donor Kidneys for Transplantation
Authors: Young Ann , Dixon Stephanie N. , Knoll Greg A. , Garg Amit X. , Lok Charmaine E. , Lam Ngan N. , Kim S. Joseph 
Published: March 2016

Background: Although the outcomes of transplantation with expanded criteria donor (ECD) kidneys are inferior to non-ECD transplants in the USA, the impact of the ECD classification on Canadian kidney transplant recipients is not known. Objectives: The objective of the study was to assess the performance of the US-derived ECD classification among deceased donor kidney transplant recipients in a Canadian setting. Design: This study was a population-based cohort study. Setting: The study was conducted in all adult kidney transplant centers in the province of Ontario. Patients: The patients were incident-deceased donor kidney transplant recipients from January 1, 2005 to March 31, 2011. Measurements: Study subjects were identified through the Trillium Gift of Life Network and linked to healthcare databases in Ontario. ECD status was based on age, hypertension, kidney function, and stroke-related death. Outcomes of interest included graft loss, death, and delayed graft function. Methods: The Kaplan-Meier product limit method was used to graphically assess time to graft loss or death. Multivariable Cox proportional hazards models were used to assess graft loss or death as a function of ECD status. Multivariable logistic regression models were fitted for the outcome of delayed graft function. Results: Of 1422 deceased donor kidney transplants, 325 (23 %) were from ECDs. The median donor age was 63 vs. 42 years for ECD vs. non-ECD, respectively. The 5-year cumulative incidence of total graft loss was 29.2 % in ECD and 20.7 % in non-ECD kidney transplants. The relative hazards for total graft loss (HR 1.48 [95 % CI, 1.10; 2.00]) and death-censored graft loss (HR 1.80 [95 % CI, 1.19, 2.71]) were increased in ECD vs. non-ECD transplants. Increased relative risks were also observed for death and delayed graft function, albeit not statistically significant. Limitations: Although comprehensive in coverage and outcome ascertainment, the available details on covariate data may be limited in large healthcare databases. Conclusions: The ECD classification identifies kidneys at increased risk for graft loss in Canadian patients. The performance of more granular measures of donor risk (e.g., Kidney Donor Risk Index) and its impact on organ allocation/utilization in Canadian patients requires further study.