bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a Patient-Completed Caprini Risk Score for Venous Thromboembolism Risk Assessment
Authors: Fuentes H. , Paz L. , Al-Ogaili A. , Andrade X. , Oramas D. , Salazar-Adum J. , Diaz-Quintero L. , Acob C. , Tafur A. , Caprini J. 
Published: October 2017

Introduction Individualized risk assessment for venous thromboembolism (VTE) using the Caprini risk score (CRS), coupled with targeted prophylaxis based on the score, is effective in reducing postoperative VTE. Critics contend that using this tool is time consuming for health care providers. We decided to create a patient-completed CRS and conducted a prospective study to compare the scores calculated by a patient with those calculated by a blinded physician for the same patient.
Methods In phase 1, we interviewed patients in our deep vein thrombosis (DVT) support group who had a history of thrombosis and included their family members to determine areas of misunderstanding in the original CRS. We created a patient-completed form based on these interviews. In phase 2, we further optimized the questions after a CRS-trained, blinded physician scored 20 hospitalized patients during the pilot study. In the final (third) phase, we measured the agreement level between the new form filled out by the trained physicians and those filled out by the patients. The study was approved by our local institutional review board. Using PASS version 11, we determined that a sample size of 37 individuals achieves a power of 80%, to detect a 0.1 difference between the null hypothesis correlation of 0.5 and the alternative hypothesis correlation of 0.7 using a two-sided hypothesis test with a significance level of 0.05. We tabulated the individuals' answers and categorized the scores by using SPSS version 23 to estimate the kappa value, linear correlation, and the Bland–Altman test. A kappa value greater than 0.8 indicated an “almost perfect agreement.”
Results We tested the first patient-completed CRS version (phase 2) in a 20-patient pilot study. A poor agreement was observed with the body mass index (BMI) responses in multiple iterations, and so we excluded the BMI calculation from the final patient-completed CRS form. We recruited 42 patients with an average age of 55, mostly female (45%), who completed less than college education (62%) to fill out the updated CRS form (phase 3). An almost perfect agreement was found for both the individual questions and the overall score comparing physician and patient answers, resulting in a high correlation (r = 0.95). In Bland–Altman, we did not find any trend for extreme values.
Conclusion We created and validated a patient-completed CRS form that has an excellent agreement level with the physician-completed form. From the results, the physician only needs to calculate the BMI. The average time for a patient to complete the form was 5 minutes. The average time for the physician to finalize the score was approximately 6 minutes. Implementation studies are needed to assess the correlation of the aggregated score, derived from this form, with the occurrence of perioperative VTE.
Vorsicht Brandgefahr
Authors: Schwab Gisela 
Published: October 2017

Zusammenfassung
Checkliste Die Gefahr, dass es im OP zu Verbrennungen am Patienten oder zu
einer Explosion am Tisch kommt, wird häufig unterschätzt. Wir stellen Ihnen die
häufigsten Gefahrenquellen vor und geben Tipps, wie sich Brände oder
Verbrennungen vermeiden lassen.
HIV und Malaria: Auswirkungen und Interaktionen zwischen Antimalariamedikamenten und antiretroviraler Therapie
Authors: Brehm Thomas , Schmiedel Stefan 
Published: October 2017

ZusammenfassungHIV und Malaria sind weltweit 2 der wichtigsten Infektionskrankheiten und gemeinsam für über 2 Mio. Todesfälle pro Jahr verantwortlich. Koinfektionen treten insbesondere in Subsahara-Afrika häufig auf. Die Infektionen scheinen sich gegenseitig zu begünstigen und den jeweiligen Krankheitsverlauf auf vielfältige Weise negativ zu beeinflussen. HIV-positive Reisende in Malariaendemiegebiete sind keinem allgemein erhöhten Malariarisiko ausgesetzt, jedoch müssen bei Chemoprophylaxe oder notfallmäßigen Selbstbehandlung vielfältige Wechselwirkungen zwischen Antimalariamedikamenten und antiretroviraler Therapie beachtet werden.
Mediated populism, culture and media form
Authors: Higgins Michael 
Published: October 2017

AbstractThis comment seeks to identify some key concerns in the study of mediated populism. The paper highlights the relationship between populism and political conditions, noting that the weak party structures and non-conventional party-media relations that characterise populist actors applies across the political left and right, who engage strategically according to media conditions. In setting out the terms in which mediated populism operates, the paper stresses the turn to emotionality in media, with a particular prominence on the expression of aggressiveness. It links with the rise of participatory media, with an attendant shift in the style and form of language to characterise political discussion and influences on legitimate political speech. The paper then looks at the use of “fake news” as a means of positioning media within the discredited elite, warranting the easy dismissal of hostile content. While showing how the political and media environment provides fertile grounds for populism, and the extent to which populism is encouraged by media affordances, the article concludes by recommending the purposeful cultivation by media of alternative and proactive forms of inclusion and emotional engagement.
Suffixation as a Place Naming Strategy in the Central Pacific and its Implications for Prehistory
Authors: Geraghty Paul 
Published: October 2017

This article uses comparative linguistic data to arrive at some generalizations about the place naming practices of the early inhabitants of the Central Pacific (Fiji, Rotuma, and Polynesia) who are believed to have arrived there some three thousand years ago. In particular it focuses on a pair of suffixes, -(C)a and -(C)aga, that had similar functions of nominalization and were therefore used quite extensively in various types of derivation, including place naming. Many place names so formed are indicators of the environment that prevailed when the place was named, so have great potential value in the reconstruction of prehistory.
CE–MS-based metabolomics reveals the metabolic profile of maitake mushroom (Grifola frondosa) strains with different cultivation characteristics
Authors: Sato Mayumi , Miyagi Atsuko , Yoneyama Shozo , Gisusi Seiki , Tokuji Yoshihiko , Kawai-Yamada Maki 
Published: October 2017

Abstract
Maitake mushroom (Grifola frondosa [Dicks.] Gray) is generally cultured using the sawdust of broadleaf trees. The maitake strain Gf433 has high production efficiency, with high-quality of fruiting bodies even when 30% of the birch sawdust on the basal substrate is replaced with conifer sawdust. We performed metabolome analysis to investigate the effect of different cultivation components on the metabolism of Gf433 and Mori52 by performing CE–MS on their fruiting bodies in different cultivation conditions to quantify the levels of amino acids, organic acids, and phosphorylated organic acids. We found that amino acid and organic acid content in Gf433 were not affected by the kind of sawdust. However, Gf433 contained more organic acids and less amino acids than Mori52, and Gf433 also contained more chitin compared with Mori52. We believe that these differences in the metabolome contents of the two strains are related to the high production efficiency of Gf433.
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
Authors: Blin Kai , Kim Hyun Uk , Medema Marnix H , Weber Tilmann 
Published: October 2017

AbstractMany drugs are derived from small molecules produced by microorganisms and plants, so-called natural products. Natural products have diverse chemical structures, but the biosynthetic pathways producing those compounds are often organized as biosynthetic gene clusters (BGCs) and follow a highly conserved biosynthetic logic. This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. However, mining for a variety of BGCs quickly approaches a complexity level where manual analyses are no longer possible and require the use of automated genome mining pipelines, such as the antiSMASH software. In this review, we discuss the principles underlying the predictions of antiSMASH and other tools and provide practical advice for their application. Furthermore, we discuss important caveats such as rule-based BGC detection, sequence and annotation quality and cluster boundary prediction, which all have to be considered while planning for, performing and analyzing the results of genome mining studies.
A fast fiducial marker tracking model for fully automatic alignment in electron tomography
Authors: Han Renmin , Zhang Fa , Gao Xin 
Published: October 2017

Abstract

Motivation
Automatic alignment, especially fiducial marker-based alignment, has become increasingly important due to the high demand of subtomogram averaging and the rapid development of large-field electron microscopy. Among the alignment steps, fiducial marker tracking is a crucial one that determines the quality of the final alignment. Yet, it is still a challenging problem to track the fiducial markers accurately and effectively in a fully automatic manner.

Results
In this paper, we propose a robust and efficient scheme for fiducial marker tracking. Firstly, we theoretically prove the upper bound of the transformation deviation of aligning the positions of fiducial markers on two micrographs by affine transformation. Secondly, we design an automatic algorithm based on the Gaussian mixture model to accelerate the procedure of fiducial marker tracking. Thirdly, we propose a divide-and-conquer strategy against lens distortions to ensure the reliability of our scheme. To our knowledge, this is the first attempt that theoretically relates the projection model with the tracking model. The real-world experimental results further support our theoretical bound and demonstrate the effectiveness of our algorithm. This work facilitates the fully automatic tracking for datasets with a massive number of fiducial markers.

Availability and implementation
The C/C ++ source code that implements the fast fiducial marker tracking is available at https://github.com/icthrm/gmm-marker-tracking. Markerauto 1.6 version or later (also integrated in the AuTom platform at http://ear.ict.ac.cn/) offers a complete implementation for fast alignment, in which fast fiducial marker tracking is available by the ‘-t’ option.

Supplementary information
Supplementary data are available at Bioinformatics online.
ARCS: scaffolding genome drafts with linked reads
Authors: Yeo Sarah , Coombe Lauren , Warren René L , Chu Justin , Birol Inanç 
Published: October 2017

Abstract

Motivation
Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA—a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics.

Results
Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiens genome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts.

Availability and implementation
https://github.com/bcgsc/ARCS/

Supplementary information
Supplementary data are available at Bioinformatics online.
PESTO: Parameter EStimation TOolbox
Authors: Stapor Paul , Weindl Daniel , Ballnus Benjamin , Hug Sabine , Loos Carolin , Fiedler Anna , Krause Sabrina , Hroß Sabrina , Fröhlich Fabian , Hasenauer Jan 
Published: October 2017

Abstract

Summary
PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, for which the user can provide a deterministic objective function in MATLAB.

Availability and implementation
PESTO is a MATLAB toolbox, freely available under the BSD license. The source code, along with extensive documentation and example code, can be downloaded from https://github.com/ICB-DCM/PESTO/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Wach Modules, Regulator Maps, and $\varepsilon$-Isomorphisms in Families
Authors: Bellovin Rebecca , Venjakob Otmar 
Published: October 2017

Abstract
We prove the “local $\varepsilon$-isomorphism” conjecture of Fukaya and Kato [13] for certain crystalline families of $G_{{\mathbf{Q}_p}}$-representations. This conjecture can be regarded as a local analog of the Iwasawa main conjecture for families. Our work extends earlier work of Kato for rank-$1$ modules (cf. [33]), of Benois and Berger for crystalline $G_{{\mathbf{Q}_p}}$-representations with respect to the cyclotomic extension (cf. [1]), as well as of Loeffler et al. (cf. [21]) for crystalline $G_{{\mathbf{Q}_p}}$-representations with respect to abelian $p$-adic Lie extensions of ${\mathbf{Q}_p}$. Nakamura [24, 25] has also formulated a version of Kato’s $\varepsilon$-conjecture for affinoid families of $(\varphi,\Gamma)$-modules over the Robba ring, and proved his conjecture in the rank-$1$ case. He used this case to construct an $\varepsilon$-isomorphism for families of trianguline $(\varphi,\Gamma)$-modules, depending on a fixed triangulation. Our results imply that this $\varepsilon$-isomorphism is independent of the chosen triangulation for certain crystalline families. The main ingredient of our proof consists of the construction of families of Wach modules generalizing work of Wach and Berger [6] and following Kisin’s approach to the construction of potentially semi-stable deformation rings [18].
CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines
Authors: Soysal Ergin , Wang Jingqi , Jiang Min , Wu Yonghui , Pakhomov Serguei , Liu Hongfang , Xu Hua 
Published: October 2017

AbstractExisting general clinical natural language processing (NLP) systems such as MetaMap and Clinical Text Analysis and Knowledge Extraction System have been successfully applied to information extraction from clinical text. However, end users often have to customize existing systems for their individual tasks, which can require substantial NLP skills. Here we present CLAMP (Clinical Language Annotation, Modeling, and Processing), a newly developed clinical NLP toolkit that provides not only state-of-the-art NLP components, but also a user-friendly graphic user interface that can help users quickly build customized NLP pipelines for their individual applications. Our evaluation shows that the CLAMP default pipeline achieved good performance on named entity recognition and concept encoding. We also demonstrate the efficiency of the CLAMP graphic user interface in building customized, high-performance NLP pipelines with 2 use cases, extracting smoking status and lab test values. CLAMP is publicly available for research use, and we believe it is a unique asset for the clinical NLP community.
Handwritten digit recognition using neural networks and dynamic zoning with stroke-based descriptors
Authors: Álvarez-León David , Fernández-Díaz Ramón-Ángel , Sánchez-Gonzalez Lidia , Alija-Pérez José-Manuel 
Published: October 2017

Abstract
This article presents an Off-line handwritten digit recognition approach based on neural networks. We define a numeric character as a composition of vertical and horizontal strokes. After the preprocessing, we use dynamic zoning to retrieve the positions where vertical strokes – the main strokes — are joined to horizontal strokes. These features are recorded into a representative string and verified using a custom matching pattern. Finally, a multilayer perceptron neural network is fed with the previous data to raise the learning process. The results gathered from the experiments performed on the well-known MNIST handwritten database are compared against other proposals providing promising results.
Predictive Factors for Corneal Clearance After Descemetorhexis Without Endothelial Keratoplasty
Authors: Davies Emma , Jurkunas Ula , Pineda Roberto 
Published: October 2017

Purpose:
To study preoperative factors that possibly contribute to corneal clearance after Descemetorhexis without endothelial keratoplasty (DWEK) and to determine the most successful surgical technique for the procedure.

Methods:
Retrospective chart review of 17 eyes of 13 patients with Fuchs corneal endothelial dystrophy that underwent central 4-mm DWEK.

Results:
Baseline age, pachymetry, and endothelial cell count were not statistically significantly different between eyes that cleared 0 to 2 months, 3 to 5 months, 6 to 8 months, or that failed to clear. All eyes that failed to clear had DWEK performed using scoring followed by the stripping technique. Postoperative endothelial cell counts steadily increased over time after the procedure, even in eyes that failed to clear.

Conclusions:
DWEK when performed with a Descemetorhexis technique results in corneal clearance in the majority of cases regardless of baseline demographics, with clearance typically 3 months after the procedure. Further studies are needed to investigate environmental factors, such as possible growth factors in the anterior chamber, that may influence clearing in these cases.
Signatures of Selection in the Human Antibody Repertoire: Selective Sweeps, Competing Subclones, and Neutral Drift
Authors: Horns Felix , Vollmers Christopher , Dekker Cornelia L. , Quake Stephen R. 
Published: October 2017

AbstractAntibodies are created and refined by somatic evolution in B cell populations, which endows the human immune system with the ability to recognize and eliminate diverse pathogens. However, the evolutionary processes that sculpt antibody repertoires remain poorly understood. Here, using an unbiased repertoire-scale approach, we show that the molecular signatures of evolution are evident in human B cell lineages and reveal how antibodies evolve somatically. We measured the dynamics and genetic diversity of B cell responses of five adults longitudinally before and after influenza vaccination using high-throughput antibody repertoire sequencing. We identified vaccine-responsive B cell lineages that carry signatures of selective sweeps driven by positive selection, and discovered that they often display evidence for selective sweeps favoring multiple subclones. We also found persistent B cell lineages that exhibit stable population dynamics and carry signatures of neutral drift. By exploiting the linkage between B cell fitness and antibody binding affinity, we demonstrated the potential for using signatures of selection to identify antibodies with high binding affinity. This quantitative characterization reveals that antibody repertoires are shaped by an unexpectedly broad spectrum of evolutionary processes and shows how signatures of evolutionary history can be harnessed for antibody discovery and engineering.One Sentence SummaryMolecular signatures of somatic evolution reveal that diverse evolutionary processes ranging from strong positive selection to neutral drift sculpt human antibodies.
Blind estimation and correction of microarray batch effect
Authors: Varma Sudhir 
Published: October 2017

AbstractMicroarray batch effect (BE) has been the primary bottleneck for large-scale integration of data from multiple experiments. Current BE correction methods either need known batch identities (ComBat)or have the potential to overcorrect, by removing true but unknown biological differences (SVA).Even though the effects of technical differences on measured expression have been published, there are no BE correction algorithms that take the approach of predicting technical effects from parameters computed from a fixed reference sample set. We show that a set of signatures, each of which is a vector the length of the number of probes, calculated on a Reference set of microarray samples can predict much of the batch effect in other Validation sets. We present a rationale of selecting a Reference set of samples designed to estimate technical differences without removing biological differences. Putting both together, we introduce the Batch Effect Signature Correction (BESC) algorithm that uses the BES calculated on the Reference set to efficiently predict and remove BE. Using two independent Validation sets, we show that BESC is capable of removing batch effect without removing unknown but true biological differences. Much of the variations due to batch effect is shared between different microarray datasets. That shared information can be used to predict signatures (i.e. directions of perturbation) due to batch effect in new datasets. The correction is blind (without needing to re-compute the parameters on new samples to be corrected), single sample, (each sample is corrected independently of each other) and conservative (only those perturbations known to be likely to be due to technical differences are removed ensuring that unknown but important biological differences are maintained). Those three characteristics make it ideal for high-throughput correction of samples for a microarray data repository. An R Package besc implementing the algorithm is available from http://explainbio.com.