bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic Yield of 2 Strategies for Adult Celiac Disease Identification in Primary Care
Authors: Scoglio Riccardo , Trifirò Gianluca , Sandullo Antonino , Marangio Giovanni , D’Agate Cinzia , Costa Stefano , Pellegrino Salvatore , Alibrandi Angela , Aiello Andrea , Currò Giovanni , Cuzzupè Chiara , Comisi Fabrizio , Amato Salvatore , Conti Nibali Roberto , Oteri Sergio , Magazzu Giuseppe , Carroccio Antonio 
Published: December 2017

Goals:
To compare the diagnostic yield and cost-consequences of 2 strategies, screening regardless of symptoms versus case finding (CF), using a point-of-care test (POCT), for the detection of celiac disease (CD) in primary care, to bridge the diagnostic gap of CD in adults.

Materials and Methods:
All subjects under 75 years of age who consecutively went to their general practitioners’ offices were offered POCT for anti-transglutaminase immunoglobulin A antibodies. The POCT was performed on all subjects who agreed, and then a systematic search for symptoms or conditions associated with higher risk for CD was performed, immediately after the test but before knowing the test results. The 2 resulting groups were: (a) POCT positive and (b) symptomatic subject at CF. Subjects were defined as symptomatic at CF in the presence of 1 or more symptoms. All POCT-positive or symptomatic subjects at CF were referred to the CD Centers for confirmation of CD. Data on resource consumption were gathered from patients’ charts. Cost of examinations, and diagnostic and laboratory tests were estimated with regional outpatient tariffs (Sicily), and a price of €2.5 was used for each POCT.

Results:
Of a total of 2197 subjects who agreed to participate in the study, 36 (1.6%) and 671 (30.5%) were POCT positive and symptomatic at CF, respectively. The yield from the screening and CF was 5 new celiac patients. The total cost and mean cost for each new CD case were €7497.35 and €1499.47 for the POCT screening strategy, and €9855.14 and €1971.03 for the CF strategy, respectively. Assuming consecutive use of both strategies, performing POCT only in symptomatic subjects at CF, the calculated yield would be 4 new diagnoses with a total cost of €2345.84 and a mean cost of €586.46 for each newly diagnosed patient. Only 1 patient was celiac despite a negative POCT.

Conclusions:
Testing symptomatic subjects at CF only by POCT seems the most cost-effective strategy to bridge the diagnostic gap of adult CD in primary care.
Prevalence and drug treatment practices of inflammatory bowel diseases in Poland in the years 2012–2014: an analysis of nationwide databases
Authors: Holko Przemysław , Kawalec Paweł , Stawowczyk Ewa 
Published: December 2017

Background
Inflammatory bowel diseases (IBDs) such as ulcerative colitis (UC) and Crohn’s disease (CD) are chronic autoimmune disorders that constitute a major societal and economic burden for individual patients, their families and the society. The aim of this study was to assess the current prevalence and treatment patterns of IBD in Poland.

Patients and methods
We carried out a retrospective analysis of the nationwide databases of the National Health Fund for the years from 2012 to 2014 to obtain data on the prevalence and treatment patterns of IBD. Patients with IBD were identified according to the ICD-10 codes indicated in medical records and the type of medical resource utilized during the study. Pharmacotherapy for IBD by age group, sex and IBD types was presented.

Results
The prevalence of IBDs was 157/100 000 individuals, including 35 patients with CD per 100 000 individuals. The use of drugs differed by age and diagnosis (P<0.001). Biologics, steroids and immunosuppressants were used more often by patients with CD than those with UC (13.2 vs. 0.3%, 54.5 vs. 37.5%, and 44.8 vs. 15.1%, respectively). Aminosalicylates were used more often by patients with UC than those with CD. Biologics were used most often by the youngest patients (≤18 years) and seldom by patients aged 65 years or older (7.7 and 0.1%, respectively).

Conclusion
Our study showed a moderate prevalence of IBD in Poland. Treatment patterns depended on the patient’s age and IBD type. The use of biologics was higher among young patients with CD than among older patients with other IBDs. Although not recommended, aminosalicylates were still commonly used in patients with CD, even during biologic and/or immunosuppressive treatment.
Self-Reported Cognitive Biases Are Equally Present in Patients Diagnosed With Psychotic Versus Nonpsychotic Disorders
Authors: Bastiaens Tim , Claes Laurence , Smits Dirk , Vanwalleghem Dominique , De Hert Marc 
Published: December 2017

Abstract
We investigated the relation between subjective cognitive biases measured with the Dutch Davos Assessment of Cognitive Biases (DACOBS-NL) and (1) the presence of a psychotic versus nonpsychotic psychiatric disorder, (2) the current dose of antipsychotic medication and current psychotic symptoms, and (3) the Personality Inventory for the DSM-5 (PID-5) Psychoticism personality trait. Results showed that DACOBS-NL subjective cognitive biases (1) were equally present in patients diagnosed with nonpsychotic disorders compared with patients with a psychotic disorder, (2) could not be explained by the current dose of antipsychotic medication, nor by current psychotic symptoms, and (3) significantly correlated with all PID-5 Personality domains. Moreover, in predicting membership of the psychotic versus nonpsychotic psychiatric disorder group, the addition of the PID-5 domains in step 2 rendered the contribution of the DACOBS-NL subjective cognitive biases in step 1 nonsignificant. Further research is needed to clarify the interplay between cognitive biases and aberrant salience in the prediction of psychotic disorders.
Is There a Limit? A Risk Assessment Model of Liposuction and Lipoaspirate Volume on Complications in Abdominoplasty
Authors: Vieira Brittany L. , Chow Ian , Sinno Sammy , Dorfman Robert G. , Hanwright Philip , Gutowski Karol A. 
Published: December 2017

Background:
Combining liposuction and abdominoplasty is controversial because of concerns for increased complications and potential for vascular compromise of the abdominoplasty flap. Also, the lipoaspirate volume in abdominoplasty is regulated in some areas to as little as 500 ml when performed with abdominoplasty. This study measures abdominoplasty complication rates when performed with and without trunk liposuction, and evaluates the effect of lipoaspirate volume on complications.

Methods:
Abdominoplasty and liposuction of the trunk procedures were identified in the Tracking Operations and Outcomes for Plastic Surgeons database. Multivariate regression models determined the effect of liposuction with abdominoplasty on complications compared with abdominoplasty alone and determined the effect of liposuction volume on complications.

Results:
Eleven thousand one hundred ninety-one patients were identified: 9638 (86.1 percent) having abdominoplasty with truncal liposuction and 1553 (13.9 percent) having abdominoplasty alone. Overall complication rates were 10.5 percent and 13.0 percent, respectively. Combined liposuction and abdominoplasty was independently associated with a reduced risk of both overall complications (p = 0.046) and seroma (p = 0.030). Given existing laws limiting liposuction volume to 500 or 1000 ml in combination with abdominoplasty, each of these thresholds was evaluated, with no effect on complications. Surprisingly, increasing liposuction volume was not independently associated with an increased risk of any complication.

Conclusions:
When done by board-certified plastic surgeons, abdominoplasty with truncal liposuction is safe, with fewer complications than abdominoplasty alone. Regulations governing liposuction volumes in abdominoplasty are arbitrary and do not reflect valid thresholds for increased complications.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Objective Assessment of the Unilateral Cleft Lip Nasal Deformity Using Three-Dimensional Stereophotogrammetry: Severity and Outcome
Authors: Mercan Ezgi , Oestreich Makinna , Fisher David M. , Allori Alexander C. , Beals Stephen P. , Samson Thomas D. , Sitzman Thomas J. , Matic Damir B. , Siebold Babette S. , Tse Raymond W. 
Published: December 2017

Background:
Optimization of care to correct the unilateral cleft lip nasal deformity is hampered by lack of objective measures to quantify preoperative severity and outcome. The purpose of this study was to develop a consensus standard of nasal appearance using three-dimensional stereophotogrammetry; determine whether anthropometric measurements could be used to quantify severity and outcome; and determine whether preoperative severity predicts postoperative outcome.

Methods:
The authors collected facial three-dimensional images of 100 subjects in three groups: 45 infants before cleft lip repair; the same 45 infants after cleft lip repair; and 45 children aged 8 to 10 years with previous repairs. Five additional age-matched unaffected control subjects were included in each group. Seven expert surgeons ranked images in each group according to nasal appearance. The rank sum score was used as consensus standard. Anthropometric analysis was performed on each image and compared to the rank sum score. Preoperative rank and anthropometric measurements were compared to postoperative rank.

Results:
Interrater and intrarater reliability was excellent (intraclass correlation coefficient, >0.76; Pearson correlation, >0.75) on each of the three image sets. Columellar angle, nostril width ratio, and lateral lip height ratio were highly correlated with preoperative severity and moderately correlated with postoperative nasal appearance. Postoperative outcome was associated with preoperative severity (rank and anthropometric measurement).

Conclusions:
Consensus ranking of preoperative severity and postoperative outcome can be achieved on three-dimensional images. Preoperative severity predicts postoperative outcomes. Columellar angle, nostril width ratio, and lateral lip height ratio are objective measures that correlate with consensus ratings by surgeons at multiple ages.
The first seizure as an indicator of epilepsy
Authors: Kunze Albrecht , Reuber Markus 
Published: December 2017

Purpose of reviewOptimal treatment of a possible first seizure depends on the determination if the paroxysmal event was an epileptic seizure and was on an accurate assessment of the recurrence risk. This review summarizes evidence from the last 5 years addressing the following questions: Is it an epileptic seizure? Is it a first seizure? When does a first seizure indicate epilepsy?Recent findingsThe acts of taking and interpreting the history from patients and witnesses continue to be the most important tools in the diagnosis of first seizures. Assessment tools based on factual questions and the observation of patients’ conversational behaviour can contribute to the differentiation of patients with epileptic seizures from those who have experienced other types of transient loss of consciousness (TLOC). At present, only about 40% of patients are seen after their very first seizure. Tests have a limited role in the initial diagnosis of a seizure but help to determine the recurrence risk based on the cause. A remote symptomatic cause and detection of epileptiform discharges are associated with a recurrence risk of at least 60% and allow a diagnosis of epilepsy after a first seizure. The risk of recurrence after an acute symptomatic first seizure is well below 60%.SummaryExpert history-taking continues to be the most important tool in the diagnosis of a first seizure. Cause is the most important determinant of the recurrence risk. Unfortunately, there is currently no formula enabling a precise calculation of an individualized recurrence risk.
Semantic Feature Disturbance in Alzheimer Disease: Evidence from an Object Decision Task
Authors: Flanagan Kieran J. , Copland David A. , Chenery Helen J. , Byrne Gerard J. , Angwin Anthony J. 
Published: December 2017

Background and Objective:It is widely held that semantic disturbance in Alzheimer disease (AD) involves the loss of distinctive features but the relative sparing of nondistinctive features. Many previous studies of semantic feature disturbance have used cognitively challenging tasks with verbal stimuli that allow for potential cognitive confounds. Our objective was to use a task with lower memory demands to investigate distinctive feature disturbance in AD.Methods:We used an object decision task to compare the processing of distinctive and nondistinctive semantic features in people with AD and age-matched controls. The task included six conditions based on the relationship between each prime and target object. We tested the processing of distinctive and nondistinctive features by selectively altering distinctive and nondistinctive semantic features between prime and target pairs.Results:Performance accuracy was significantly lower for participants with AD than for age-matched controls when distinctive features were manipulated, but no difference was found when nondistinctive features were manipulated.Conclusions:Our results provide evidence of semantic content disturbance in AD in the context of a task with low cognitive demands.
AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A
Authors: Davies Alexandra K. , Itzhak Daniel N. , Edgar James R. , Archuleta Tara L. , Hirst Jennifer , Jackson Lauren P. , Robinson Margaret S. , Borner Georg H. H. 
Published: December 2017

AbstractAdaptor protein 4 (AP-4) is an ancient membrane trafficking complex, whose function has largely remained elusive. In humans, AP-4 deficiency causes a severe neurological disorder of unknown aetiology. We apply unbiased proteomic methods, including ‘Dynamic Organellar Maps’, to find proteins whose subcellular localisation depends on AP-4. We identify three transmembrane cargo proteins, ATG9A, SERINC1 and SERINC3, and two AP-4 accessory proteins, RUSC1 and RUSC2. We demonstrate that AP-4 deficiency causes missorting of ATG9A in diverse cell types, including patient-derived cells, as well as dysregulation of autophagy. RUSC2 facilitates the transport of AP-4-derived, ATG9A-positive vesicles from the TGN to the cell periphery. These vesicles cluster in close association with autophagosomes, suggesting they are the “ATG9A reservoir” required for autophagosome biogenesis. Our study uncovers ATG9A trafficking as a ubiquitous function of the AP-4 pathway. Furthermore, it provides a potential molecular pathomechanism of AP-4 deficiency, through dysregulated spatial control of autophagy.
Measures of time series coupling based on generalized weighted multiple regression
Authors: Pascual-Marqui Roberto D. , Biscay Rolando J. , Bosch-Bayard Jorge , Faber Pascal , Kinoshita Toshihiko , Kochi Kieko , Milz Patricia , Nishida Keiichiro , Yoshimura Masafumi 
Published: December 2017

1.AbstractThe sharing and the transmission of information between cortical brain regions is carried out by mechanisms that are still not fully understood. A deeper understanding should shed light on how consciousness and cognition are implemented in the brain. Research activity in this field has recently been focusing on the discovery of non-conventional coupling mechanisms, such as all forms of cross-frequency couplings between diverse combinations of amplitudes and phases, applied to measured or estimated cortical signals of electric neuronal activity. However, all coupling measures that involve phase computation have poor statistical properties. In this work, the conventional estimators for the well-known phase-phase (phase synchronization or locking), phase-amplitude, and phaseamplitude-amplitude couplings are generalized by means of the weighted multiple regression model. The choice of appropriate weights produces estimators that bypass the need for computing the complex-valued phase. In addition, a new coupling, denoted as the inhibitory coupling (InhCo), is introduced and defined as the dependence of one complex-valued variable on the inverse and on the conjugate inverse of another complex-valued variable. A weighted version denoted as wInhCo is also introduced, bypassing the need for computing the inverse of a complex variable, which has very poor statistical properties. The importance of this form of inhibitory coupling is that it may capture well- known processes, such as the observed inverse alpha/gamma relation within the same cortical region, or the inverse alpha/alpha relation between distant cortical regions.
Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library
Authors: Mitov Venelin , Stadler Tanja 
Published: December 2017

AbstractPhylogenetic comparative models (PCMs) have been used to study macroevolutionary patterns, to characterize adaptive phenotypic landscapes, to quantify rates of evolution, to measure the heritability of traits, and to test various evolutionary hypotheses. A major obstacle to applying these models has been the complexity of evaluating their likelihood function. Recent works have shown that for many PCMs, the likelihood can be obtained in time proportional to the size of the tree based on post-order tree traversal, also known as pruning. Despite this progress, inferring complex multi-trait PCMs on large trees remains a time-intensive task. Here, we study parallelizing the pruning algorithm as a generic technique for speeding-up PCM-inference.We implement several parallel traversal algorithms in the form of a generic C++ library for Serial and Parallel LIneage Traversal of Trees (SPLITT). Based on SPLITT, we provide examples of parallel likelihood evaluation for several popular PCMs, ranging from a single-trait Brownian motion model to complex multi-trait Ornstein-Uhlenbeck and mixed Gaussian phylogenetic models.Using the phylogenetic Ornstein-Uhlenbeck mixed model (POUMM) as a showcase, we run benchmarks on up to 24 CPU cores, reporting up to an order of magnitude parallel speed-up on simulated balanced and unbalanced trees of up to 100,000 tips with up to 16 traits. Noticing that the parallel speed-up depends on multiple factors, the SPLITT library is capable to automatically select the fastest traversal strategy for a given hardware, tree-topology, and data. Combining SPLITT likelihood calculation with adaptive Metropolis sampling on real data, we show that the time for Bayesian POUMM inference on a tree of 10,000 tips can be reduced from several days to minutes.We conclude that parallel pruning effectively accelerates the likelihood calculation and, thus, the statistical inference of Gaussian phylogenetic models. For time-intensive Bayesian inferences, we recommend combining this technique with adaptive Metropolis sampling. Beyond Gaussian models, the parallel tree traversal can be applied to numerous other models, including discrete trait and birth-death population dynamics models. Currently, SPLITT supports multi-core shared memory architectures, but can be extended to distributed memory architectures as well as graphical processing units.
Mutations alter RNA-mediated conversion of human prions
Authors: Alred Erik J. , Lodangco Izra D. , Gallaher Jennifer , Hansmann Ulrich 
Published: December 2017

AbstractPrion diseases are connected with self-replication and self-propagation of mis-folded proteins. The rate-limiting factor is the formation of the initial seed. We have recently studied early stages in the conversion between functional PrPC and the infectious scrapie PrPSC form, triggered by the binding of RNA. Here, we study how this process is modulated by the prion sequence. We focus on residues 129 and 178, which are connected to the hereditary neurodegenerative disease Fatal Familial Insomnia.
Fitness traits of deoxynivalenol and nivalenol-producing Fusarium graminearum species complex strains from wheat
Authors: Nicolli C.P. , Machado F.J. , Spolti P. , Del Ponte E.M. 
Published: December 2017

AbstractFusarium graminearum of the 15-acetyl(A)deoxynivalenol(D0N) chemotype is the main cause of Fusarium head blight (FHB) of wheat in south of Brazil. However, 3-ADON and nivalenol(NIV) chemotypes have been found in other members of the species complex causing FHB in wheat. To improve our understanding of the pathogen ecology, we assessed a range of fitness-related traits in a sample of 30 strains representatives of 15-ADON (F. graminearum), 3-ADON (F. cortaderiae and F. austroamericanum) and NIV (F. meridionale and F. cortaderiae). These included: perithecia formation on three cereal-based substrates, mycelial growth at two suboptimal temperatures, sporulation and germination, pathogenicity towards a susceptible and a moderately resistant cultivar and sensitivity to tebuconazole. The most important trait favoring F. graminearum was its 2x higher sexual fertility (> 40% PPI = perithecia production index) than the other species (< 30% PPI); PPI varied among substrates (maize > rice > wheat). In addition, sensitivity to tebuconazole appeared lower in F. graminearum which had the only strain with EC50 > 1 ppm. In the pathogenicity assays, the DON-producers were generally more aggressive (1.5 to 2x higher final severity) towards the two cultivars, with 3-ADON or 15-ADON leading to higher area under the severity curve than the NIV strains in the susceptible and moderately resistant cv., respectively. There was significant variation among strains of a same species with regards asexual fertility (mycelial growth, macroconidia production and germination), which suggest a strain-rather than a species-specific differences. These results contribute new knowledge to improve our understanding of the pathogen-related traits that may explain the dominance of certain members of the species complex in specific wheat agroecosystems.
Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems
Authors: Liu Qing , Wang Chun , Jiao Xiaozhen , Zhang Huawei , Song Lili , Li Yanxin , Gao Caixia , Wang Kejian 
Published: December 2017

AbstractThe CRISPR/Cas system has been extensively applied to make precise genetic modifications in various organisms. Despite its importance and widespread use, large-scale mutation screening remains time-consuming, labour-intensive and costly. Here, we describe a cheap, practicable and high-throughput screening strategy that allows parallel screening of 96 × N (N denotes the number of targets) genome-modified sites. The strategy simplified and streamlined the process of next-generation sequencing (NGS) library construction by fixing the bridge sequences and barcoding primers. We also developed Hi-TOM (available at http://www.hi-tom.net/hi-tom/), an online tool to track the mutations with precise percentage. Analysis of the samples from rice, hexaploid wheat and human cells reveals that the Hi-TOM tool has high reliability and sensitivity in tracking various mutations, especially complex chimeric mutations that frequently induced by genome editing. Hi-TOM does not require specially design of barcode primers, cumbersome parameter configuration or additional data analysis. Thus, the streamlined NGS library construction and comprehensive result output make Hi-TOM particularly suitable for high-throughput identification of all types of mutations induced by CRISPR/Cas systems.