bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hidden endoscopic burden of Roux-en-Y gastric bypass surgery
Authors: Steed Helen , Golar Harjeet , Manjunath Srikantaiah 
Published: December 2012

Background and aimsComplication rates of Roux-en-Y gastric bypass (RYGB) vary from centre to centre, but anastomotic stricture is the commonest, and is managed in the majority by endoscopic pneumatic dilatation. The aim of this study was to assess the endoscopic burden of RYGB surgery.Patients and methodsAll patients undergoing RYGB surgery over a 29-month period were included and were followed-up retrospectively and prospectively for a minimum of 180 days to monitor for endoscopic procedures performed in relation to the RYGB at Walsall Manor Hospital, UK. Five hundred and fifty-three patients underwent RYGB surgery during the study period.ResultsOne hundred and thirteen patients had 147 endoscopic procedures, including 65 pneumatic dilatations, at a cost to the NHS of £58 077 over a 29-month study period, with an average cost of £2003 a month. or £105 per RYGB operation performed. The anastomotic stricture rate for the group was 11.39%. The complication rate for dilatation of anastomotic strictures was 0%.ConclusionsRYGB anastomotic strictures can be safely managed by dilatation. If bariatric surgery is performed locally, then endoscopy departments must expect to factor in, not only the burden of dealing with actual complications, but also the burden of investigating for potential complications.
Effects of spatial scale and choice of statistical model (linear versus tree-based) on determining species–habitat relationships
Authors: Sharma Sapna , Legendre Pierre , Boisclair Daniel , Gauthier Stéphane 
Published: December 2012

The choice of spatial scale and modelling technique used to capture species–habitat relationships needs to be considered when ascertaining environmental determinants of habitat quality for species and communities. Fish densities and environmental data were collected at three Laurentian lakes using underwater surveys by four snorkelers collecting fine spatial data acquired through geographic positioning systems. At both fine (20 m) and broad (100 m) spatial scales, tree-based approaches, which incorporated both linear and nonlinear relationships, explained more variation than their linear counterparts. At the finest spatial scale considered (20 m), local environmental conditions, such as habitat structure and heterogeneity, were important determinants of fish habitat selection. At the broadest spatial scale considered (100 m), fish tended to select habitat based on both local environmental features and riparian development. Moran’s eigenvector maps further revealed that fish–habitat associations were operating at broader spatial scales than the predefined analytical units, which can be partially attributed to the spatial structure of environmental conditions acting at spatial scales greater than 100 m. This study highlights the importance of evaluating statistical approaches at different spatial scales to identify key determinants of habitat quality for species, ultimately to assess the effects of perturbations on ecosystems.
DATA PRIVACY: DEFINITIONS AND TECHNIQUES
Authors: DE CAPITANI DI VIMERCATI SABRINA , FORESTI SARA , LIVRAGA GIOVANNI , SAMARATI PIERANGELA 
Published: December 2012

The proper protection of data privacy is a complex task that requires a careful analysis of what actually has to be kept private. Several definitions of privacy have been proposed over the years, from traditional syntactic privacy definitions, which capture the protection degree enjoyed by data respondents with a numerical value, to more recent semantic privacy definitions, which take into consideration the mechanism chosen for releasing the data. In this paper, we illustrate the evolution of the definitions of privacy, and we survey some data protection techniques devised for enforcing such definitions. We also illustrate some well-known application scenarios in which the discussed data protection techniques have been successfully used, and present some open issues.
Pressure–Diameter Relationship in Human Coronary Arteries
Authors: Muller Olivier , Pyxaras Stylianos A. , Trana Catalina , Mangiacapra Fabio , Barbato Emanuele , Wijns William , Taylor Charles A. , De Bruyne Bernard 
Published: December 2012

Background—
To quantify the changes in arterial dimensions after the acute changes in pressure associated with percutaneous coronary intervention (PCI).

Methods and Results—

Forty-eight patients with one angiographically moderate-to-severe stenosis were included in the study. The pressure proximal and distal to the stenosis and the arterial diameter proximal and distal to the stenosis were measured at baseline, after intracoronary nitrates, and after stent PCI. In addition, in 8 patients distal pressure and coronary diameter were assessed while graded, controlled stenoses were created in the stented segment by progressive inflation of a balloon catheter. The mean diameter of the proximal coronary segment was 2.75±0.08 mm, 2.92±0.08 mm (+7.4%), and 3.10±0.07 mm (+14.7%) at baseline, after nitrates and after PCI, respectively (
P
<0.001). The mean diameter of the distal coronary segment was 2.07±0.09 mm, 2.23±0.09 mm (+9.7%), and 2.5±0.07 mm (+28.4%) at baseline, after nitrates and after PCI, respectively (
P
<0.001). The increase in distal diameter correlated significantly with the increase in distal pressure after PCI (
r
2
=0.57;
P
<0.001). When graded stenoses were created, a decrease in diameter of 18±4% was observed with a pressure drop of 43±5 mm Hg.

Conclusions—
The diameter of coronary arteries markedly varies with their distending pressure. After re-establishment of a normal distending pressure by stenting of severe coronary stenoses, a proportional increase in vessel diameter is observed. This should be taken into account when choosing the stent diameter and is an argument to discourage direct stenting.
Selecting Antiplatelet Therapy at the Time of Percutaneous Intervention for an Acute Coronary Syndrome
Authors: Salisbury Adam C. , Wang Kaijun , Cohen David J. , Li Yan , Jones Philip G. , Spertus John A. 
Published: December 2012

Background—
On average, acute coronary syndrome patients treated with prasugrel experience fewer ischemic complications, but more bleeding, than those receiving clopidogrel. However, heterogeneity in treatment effects can alter the likelihood of benefits and risks of an individual patient. We developed predictive models of the benefits (reduced ischemic events) and risks (increased bleeding) to support targeting prasugrel to those who benefit most from treatment.

Methods and Results—
Using 12 579 patients from Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition With Prasugrel–Thrombolysis in Myocardial Infarction 38 (TRITON-TIMI 38), we fit risk models for ischemic events (cardiovascular death, spontaneous myocardial infarction, stroke) and bleeding (TIMI major/minor) over a 14.8-month follow-up and then calculated each patient’s predicted risk for major ischemia and bleeding with both prasugrel and clopidogrel. We found substantial heterogeneity of the treatment effect of prasugrel (mean absolute reduction in the ischemia risk with prasugrel=1.5±3.0%, ranging from an 8.4% increased risk to a 31.2% reduction in risk for ischemia compared with clopidogrel). The mean absolute increase in the bleeding risk with prasugrel versus clopidogrel was 1.3±1.4% and ranged from a 7.9% lower risk to an 11.2% higher risk with prasugrel. The ratio of the difference in predicted ischemia risk/difference in predicted bleeding risk between prasugrel and clopidogrel was calculated for each patient to identify the proportion likely to benefit from prasugrel. Considering both ischemia and bleeding risk, a large proportion of TRITON participants (42%) were predicted to experience net benefit with prasugrel, a rate that increased if patients more strongly preferred avoiding ischemic events than bleeding.

Conclusions—
The expected benefits and risks of prasugrel versus clopidogrel depend highly on patient characteristics. The use of risk models could support individualized thienopyridine selection to maximize the benefits and safety of these drugs.
Inactive Period of Western North Pacific Tropical Cyclone Activity in 1998–2011
Authors: Liu Kin Sik , Chan Johnny C. L. 
Published: December 2012

Abstract
Tropical cyclone (TC) activity over the western North Pacific (WNP) exhibits a significant interdecadal variation during 1960–2011, with two distinct active and inactive periods each. This study examines changes in TC activity and atmospheric conditions in the recent inactive period (1998–2011). The overall TC activity shows a significant decrease, which is partly related to the decadal variation of TC genesis frequency in the southeastern part of the WNP and the downward trend of TC genesis frequency in the main development region.
The investigation on the factors responsible for the low TC activity mainly focuses on the effect of vertical wind shear and subtropical high on multidecadal time scales. A vertical wind shear index, defined as the mean magnitude of the difference of the 200- and 850-hPa horizontal zonal winds (10°–17.5°N, 150°E–180°) averaged between June and October, is highly correlated with the annual TC number and shows a significant interdecadal variation. Positive anomalies of vertical wind shear are generally found in the eastern part of the tropical WNP during this inactive period. A subtropical high area index, calculated as the area enclosed by the 5880-gpm line of the June–October 500-hPa geopotential height (0°–40°N, 100°E–180°), shows a significant upward trend. A high correlation is also found between this index and the annual TC number, and a stronger-than-normal subtropical high is generally observed during this inactive period. The strong vertical wind shear and strong subtropical high observed during 1998–2011 together apparently lead to unfavorable atmospheric conditions for TC genesis and hence the low TC activity during the period.
Self consistency grouping: a stringent clustering method
Authors: Kim Bong-Hyun , Chitturi Bhadrachalam , Grishin Nick V 
Published: December 2012

Abstract

Background
Numerous types of clustering like single linkage and K-means have been widely studied and applied to a variety of scientific problems. However, the existing methods are not readily applicable for the problems that demand high stringency.

Methods
Our method, self consistency grouping, i.e. SCG, yields clusters whose members are closer in rank to each other than to any member outside the cluster. We do not define a distance metric; we use the best known distance metric and presume that it measures the correct distance. SCG does not impose any restriction on the size or the number of the clusters that it finds. The boundaries of clusters are determined by the inconsistencies in the ranks. In addition to the direct implementation that finds the complete structure of the (sub)clusters we implemented two faster versions. The fastest version is guaranteed to find only the clusters that are not subclusters of any other clusters and the other version yields the same output as the direct implementation but does so more efficiently.

Results
Our tests have demonstrated that SCG yields very few false positives. This was accomplished by introducing errors in the distance measurement. Clustering of protein domain representatives by structural similarity showed that SCG could recover homologous groups with high precision.

Conclusions
SCG has potential for finding biological relationships under stringent conditions.
Inference of gene regulatory subnetworks from time course gene expression data
Authors: Liang Xi-Jun , Xia Zhonghang , Zhang Li-Wei , Wu Fang-Xiang 
Published: December 2012

Abstract

Background
Identifying gene regulatory network (GRN) from time course gene expression data has attracted more and more attentions. Due to the computational complexity, most approaches for GRN reconstruction are limited on a small number of genes and low connectivity of the underlying networks. These approaches can only identify a single network for a given set of genes. However, for a large-scale gene network, there might exist multiple potential sub-networks, in which genes are only functionally related to others in the sub-networks.

Results
We propose the network and community identification (NCI) method for identifying multiple subnetworks from gene expression data by incorporating community structure information into GRN inference. The proposed algorithm iteratively solves two optimization problems, and can promisingly be applied to large-scale GRNs. Furthermore, we present the efficient Block PCA method for searching communities in GRNs.

Conclusions
The NCI method is effective in identifying multiple subnetworks in a large-scale GRN. With the splitting algorithm, the Block PCA method shows a promosing attempt for exploring communities in a large-scale GRN.
A systematic model of the LC-MS proteomics pipeline
Authors: Sun Youting , Braga-Neto Ulisses , Dougherty Edward R 
Published: December 2012

Abstract

Motivation
Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view.

Results
In this work, we investigate this problem by putting together the different modules in a typical proteomics work flow, in order to capture and analyze key factors that impact the number of identified peptides and quantified proteins, protein quantification error, differential expression results, and classification performance. The proposed proteomics pipeline model can be used to optimize the work flow as well as to pinpoint critical bottlenecks worth investing time and resources into for improving performance. Using the model-based approach proposed here, one can study systematically the critical problem of proteomic biomarker discovery, by means of simulation using ground-truthed synthetic MS data.
Minocycline reduces reactive gliosis in the rat model of hydrocephalus
Authors: Xu Hao , Tan Guowei , Zhang Shaolin , Zhu Hongwei , Liu Feng , Huang Caiquan , Zhang Feifei , Wang Zhanxiang 
Published: December 2012

Abstract

Background
Reactive gliosis had been implicated in injury and recovery patterns associated with hydrocephalus. Our aim is to determine the efficacy of minocycline, an antibiotic known for its anti-inflammatory properties, to reduce reactive gliosis and inhibit the development of hydrocephalus.

Results
The ventricular dilatation were evaluated by MRI at 1-week post drugs treated, while GFAP and Iba-1were detected by RT-PCR, Immunohistochemistry and Western blot. The expression of GFAP and Iba-1 was significantly higher in hydrocephalic group compared with saline control group (p < 0.05). Minocycline treatment of hydrocephalic animals reduced the expression of GFAP and Iba-1 significantly (p < 0.05). Likewise, the severity of ventricular dilatation is lower in minocycline treated hydrocephalic animals compared with the no minocycline group (p < 0.05).

Conclusion
Minocycline treatment is effective in reducing the gliosis and delaying the development of hydrocephalus with prospective to be the auxiliary therapeutic method of hydrocephalus.
MC1R variants predisposing to concomitant primary cutaneous melanoma in a monozygotic twin pair
Authors: Pellegrini Cristina , Fargnoli Maria Concetta , Suppa Mariano , Peris Ketty 
Published: December 2012

AbstractBackgroundConcomitant primary cutaneous melanoma in monozygotic twins has been reported in only two pairs but in neither of them genetic analysis was performed. Two high-penetrance susceptibility genes,CDKN2AandCDK4and one low-penetrance gene,MC1R,are well-defined genetic risk factors for melanoma.MITFhas been recently identified as a novel intermediate risk melanoma-predisposing gene.Case presentationWe describe the extraordinary occurrence of a primary cutaneous invasive melanoma in two 44-year-old identical, female twins, on the same body site within 30 days of each other and report for the first time the genetic analysis of melanoma susceptibility genes in both twins. Data on characteristics of the twins were collected through a standardized questionnaire and skin examination. Exons 1α, 1β, 2 and 3 ofCDKN2A, exon 2 ofCDK4, the entire open reading frame ofMC1Rand the recently describedMITFc.952 G > A (p.Glu318Lys) variant were investigated by direct sequencing. Sequencing analysis of the high-penetrance susceptibility genes showed no changes inCDKN2Aand in exon 2 of theCDK4gene. Both patients were heterozygous for the sameCDKN2AUTR c.*29C > G variant. Interestingly, the same two heterozygous variants of theMC1Rwere identified in both twins: the c.451C > T (p.Arg151Cys) and the c.456C > A (p.Tyr152*) variants. Neither patient showed the c.952 G > A (p.Glu318Lys) substitution in theMITFgene.ConclusionsIdentification of two high-riskMC1Rvariants in our identical twins in the absence ofCDKN2AandCDK4mutations highlights the contribution of low penetrance genes, such asMC1R, in melanoma susceptibility.
MRI findings are often missed in the diagnosis of Creutzfeldt-Jakob disease
Authors: Carswell Christopher , Thompson Andrew , Lukic Ana , Stevens John , Rudge Peter , Mead Simon , Collinge John , Hyare Harpreet 
Published: December 2012

Abstract

Background
Establishing a confident clinical diagnosis before an advanced stage of illness can be difficult in Creutzfeldt-Jakob disease (CJD) but unlike common causes of dementia, prion diseases can often be diagnosed by identifying characteristic MRI signal changes. However, it is not known how often CJD-associated MRI changes are identified at the initial imaging report, whether the most sensitive sequences are used, and what impact MRI-diagnosis has on prompt referral to clinical trial-like studies.

Methods
We reviewed the MRI scans of 103 patients with CJD referred to the National Prion Clinic since 2007 and reviewed the presence of CJD-associated changes, compared these findings with the formal report from the referring centre and reviewed the types of sequence performed.

Results
In sCJD we found CJD-associated MRI changes in 83 of 91 cases (91% sensitivity). However, the referring centres documented CJD-associated MRI changes in 43 of the sCJD cases (47% sensitivity). The most common region not documented by referring centres was the cortex (23 of 68 sCJD cases), but there was a statistically significant discrepancy in all regions (p<0.0001). Patients in whom MRI abnormalities were missed by the referring hospital were more advanced at the time of recruitment to a clinical trial-like study (p=0.03).

Conclusions
CJD-associated MRI changes are often not documented on the formal investigation report at the referring centre. This is important as delay makes enrolment to clinical trials futile because of highly advanced disease. If a diagnosis of CJD is suspected, even if the initial imaging is reported as normal, a specialist MRI review either by an experienced neuroradiologist or by a prion disease specialist unit could facilitate earlier diagnosis.
Patient-tailored modulation of the immune system may revolutionize future lung cancer treatment
Authors: Heuvers Marlies E , Aerts Joachim G , Cornelissen Robin , Groen Harry , Hoogsteden Henk C , Hegmans Joost P 
Published: December 2012

AbstractCancer research has devoted most of its energy over the past decades on unraveling the control mechanisms within tumor cells that govern its behavior. From this we know that the onset of cancer is the result of cumulative genetic mutations and epigenetic alterations in tumor cells leading to an unregulated cell cycle, unlimited replicative potential and the possibility for tissue invasion and metastasis. Until recently it was often thought that tumors are more or less undetected or tolerated by the patient’s immune system causing the neoplastic cells to divide and spread without resistance. However, it is without any doubt that the tumor environment contains a wide variety of recruited host immune cells. These tumor infiltrating immune cells influence anti-tumor responses in opposing ways and emerges as a critical regulator of tumor growth. Here we provide a summary of the relevant immunological cell types and their complex and dynamic roles within an established tumor microenvironment. For this, we focus on both the systemic compartment as well as the local presence within the tumor microenvironment of late-stage non-small cell lung cancer (NSCLC), admitting that this multifaceted cellular composition will be different from earlier stages of the disease, between NSCLC patients. Understanding the paradoxical role that the immune system plays in cancer and increasing options for their modulation may alter the odds in favor of a more effective anti-tumor immune response. We predict that the future standard of care of lung cancer will involve patient-tailor-made combination therapies that associate (traditional) chemotherapeutic drugs and biologicals with immune modulating agents and in this way complement the therapeutic armamentarium for this disease.
Idiopathic pleuroparenchymal fibroelastosis: consideration of a clinicopathological entity in a series of Japanese patients
Authors: Kusagaya Hideki , Nakamura Yutaro , Kono Masato , Kaida Yusuke , Kuroishi Shigeki , Enomoto Noriyuki , Fujisawa Tomoyuki , Koshimizu Naoki , Yokomura Koshi , Inui Naoki , Suda Takafumi , Colby Thomas V , Chida Kingo 
Published: December 2012

Abstract

Background
Idiopathic pleuroparenchymal fibroelastosis (IPPFE) is a recently reported group of disorders characterized by fibrotic thickening of the pleural and subpleural parenchyma predominantly in the upper lobes. We report five Japanese cases fulfilling the criteria of IPPFE and address whether it should be considered a separate clinicopathologic entity. And this study was an attempt to identify features in common between IPPFE and previously described idiopathic upper lobe fibrosis (IPUF), allowing IPPFE to be considered as a distinct entity in our Japanese series.

Methods
Five consecutive cases of idiopathic interstitial lung disease confirmed as IPPFE by surgical lung biopsy were studied.

Results
There were four males and one female, aged 70±2.76 yr. No associated disorder or presumed cause was found in any case. Lung function tests found a restrictive ventilatory defect (4/5) and/or impairment of DLco (4/5). Chest X-ray showed marked apical pleural thickening in all cases. Computed tomography of the chest in all cases mainly showed intense pleural thickening and volume loss associated with evidence of fibrosis, predominantly in the upper lobes. In all cases in this study, markedly thickened visceral pleura and prominent subpleural fibrosis characterized by both elastic tissue and dense collagen were clearly shown. All cases were alive at the last follow-up, 17.6±13.59 months after diagnosis; however, all had deteriorated both clinically and radiologically.

Conclusions
IPPFE deserves to be defined as a separate, original clinicopathologic entity owing to its uniformity and IPPFE has some features in common with previously described idiopathic upper lobe fibrosis (IPUF). Our limited experience with a cohort of 5 subjects suggests that IPPFE can be rapidly progressive.