bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuklearmedizinische Verfahren zur Diagnostik der Spondylodiszitis
Authors: Davis K. , Happel C. , Heller M. , Vogl T. , Rauschmann M. , Grünwald F. 
Published: November 2017

ZusammenfassungEs existieren zahlreiche nuklearmedizinische Verfahren zur Detektion einer Spondylodiszitis (SP), welche sich in ihrer diagnostischen Wertigkeit teils deutlich unterscheiden. Während sich die Leukozyten- beziehungsweise Antikörperszintigrafie aufgrund mangelnder Sensitivität und Spezifität nicht bewährt hat, zeigt die Skelettszintigrafie gute Ergebnisse und kommt insbesondere bei Kontraindikationen zur MRT zum Einsatz. Die 18F-FDG-PET hat sich inzwischen als führende Diagnostik der SP in der nuklearmedizinischen Bildgebung durchgesetzt. Insbesondere im Vergleich zur MRT, welche bis dato den Gold-Standard der morphologisch-diagnostischen Bildgebung der SP darstellt, liefert die 18F-FDG-PET deutliche Vorteile. So zeigt sich die 18F-FDG-PET bezüglich der Differenzierung zwischen degenerativen und entzündlichen Veränderungen, der frühen Detektion der Erkrankung sowie der Evaluation des Therapieansprechens überlegen. Insgesamt liefert die Kombination aus 18F-FDG-PET und MRT eine nahezu 100 %ig korrekte Detektion infektiöser SP.
Die konservative und operative Therapie der unspezifischen Spondylodiszitis
Authors: Bogert Jochen , Tateen Aimen , Hempfing Axel 
Published: November 2017

ZusammenfassungDie pyogene Spondylodiszitis entsteht meist endogen durch eine Bakteriämie, aber auch exogene Ursachen wie etwa wirbelsäulennahe Infiltrationen können sie hervorrufen. Es besteht eine zunehmende Inzidenz der Erkrankung, die noch immer mit einer signifikanten Mortalität der in vielen Fällen immunsupprimierten und hochbetagten Patienten einhergeht. Eine frühzeitige Diagnosestellung durch Bildgebung und Erregerisolierung ist entscheidend für ein gutes Behandlungsergebnis. Die überwiegende Zahl der Patienten kann konservativ behandelt werden, wichtig sind ein frühzeitiger Beginn der antibiotischen Therapie sowie eine adäquate Ruhigstellung. Operative Therapieziele sind neben der Dekompression und Infektsanierung die Stabilisation und Deformitätenkorrektur. Es kommen rein dorsale offene Verfahren, ggf. mit Ausräumung der Bandscheibe und TLIF, sowie minimalinvasive Stabilisierungen zur Anwendung. Bei ausgeprägten ventralen Destruktionen, Fehlstellungen und Abszedierungen muss durch einen separaten ventralen Zugang debridiert und stabilisiert werden. In der überwiegenden Zahl der Fälle können gute Behandlungsergebnisse erreicht werden, in Einzelfällen bestehen jedoch große therapeutische Herausforderungen. Individuelle Therapieentscheidungen sind notwendig, da einerseits die Literatur keine eindeutigen Behandlungsleitlinien vorgibt und es sich andererseits um teils hochbetagte und multimorbide Patienten handelt.
Prostatakarzinom imitiert metastasiertes Bronchialkarzinom – Ein Fallbericht
Authors: Drosos Konstantinos , Höfner Klaus 
Published: November 2017

ZusammenfassungEs wird über den Fall eines PSA-negativen und lokal fortgeschrittenen azinären Prostatakarzinoms berichtet, das bei thyroid transcription factor-1 (TTF-1) Expression eine Metastase eines bereits behandelten Bronchialkarzinoms imitierte. Unseres Wissens ist ein TTF-1 positiv azinäres Prostatakarzinom bisher nur ein Mal in der Literatur dokumentiert. Die Bestimmung des Immunophänotyps des Karzinoms mit Napsin A, CK7 und CK20 in Kombination mit der Beurteilung des gesamten Krankheitsverhaltens waren für die definitive Diagnose eines primären Prostatakarzinoms entscheidend.
Die konservative und operative Therapie bei kindlichen Spondylodiszitiden und der spezifischen Spondylitis
Authors: Ruf Michael , Drumm Jörg , Berthold Christophe , Gregor Ostrowski , Pitzen Tobias 
Published: November 2017

ZusammenfassungIn diesem Artikel werden die Besonderheiten der konservativen und operativen Therapie bei der kindlichen Spondylodiszitis und der spezifischen, tuberkulösen Spondylitis besprochen. Beides sind seltene Erkrankungen, bei beiden gibt es sinnvolle konservative Therapieansätze und bei beiden stellen Deformitäten im weiteren Verlauf häufige und ernsthafte Komplikationen dar.
Schädel-Hirn-Trauma
Authors: Clauberg Ralf , Hattingen Elke 
Published: November 2017

ZusammenfassungEin Schädel-Hirn-Trauma ist im jungen und mittleren Alter in erster Linie Folge eines Unfalls mit Auto, Motorrad, Fahrrad oder anderen Transportmitteln. Bei älteren Menschen ist dagegen häufiger ein Sturz die Ursache. Im folgenden Beitrag werden das diagnostische Vorgehen und typische Verletzungen im Rahmen eines Schädel-Hirn-Traumas dargestellt.
The economic impact of using single-operator cholangioscopy for the treatment of difficult bile duct stones and diagnosis of indeterminate bile duct strictures
Authors: Deprez Pierre , Garces Duran Rodrigo , Moreels Tom , Furneri Gianluca , Demma Federica , Verbeke Len , Van der Merwe Schalk , Laleman Wim 
Published: November 2017

Abstract
Background and study aim Conventional endoscopic retrograde cholangiopancreatography (ERCP) combines endoscopy and radiography to diagnose and treat pathological conditions of the bile duct. The aim of the present analysis was to evaluate the clinical and economic impact of the use of single-operator intraductal cholangioscopy (IDC), which allows for direct visualization of the bile duct, as an alternative to ERCP for the treatment of difficult bile duct stones and the diagnosis of bile duct strictures.
Patients and methods The clinical and economic consequences of single-operator IDC use were evaluated using two decision-tree models, one for management of difficult-to-remove stones and one for stricture diagnosis. A hospital perspective was adopted. Data to populate the models were derived from two Belgian hospitals that specialize in endoscopic procedures of the bile duct. Overall, the examined population consisted of 62 patients with difficult stones and 49 patients with indeterminate strictures.
Results In the model for difficult stone management, the use of IDC determined a decrease in the number of procedures (– 27 % relative reduction) and costs (– €73 000; – 11 % relative reduction) when compared with ERCP. In the model for stricture diagnosis, the use of IDC determined a decrease in the number of procedures (– 31 % relative reduction) and costs (– €13 000; – 5 % relative variation) when compared with ERCP.
Conclusions The single-operator IDC system performed better than ERCP for the treatment of difficult bile duct stones and the diagnosis of bile duct strictures, and reduced the overall expenditure in hospitals in Belgium.
How to communicate effectively with policymakers: combine insights from psychology and policy studies
Authors: Cairney Paul , Kwiatkowski Richard 
Published: November 2017

AbstractTo communicate effectively in policymaking systems, actors need to understand how policymakers process evidence and the environment in which they operate. Therefore, we combine psychology and policy studies to produce a three-step strategy. First, do not bombard people with evidence. Human beings have too much information to process, and they use heuristics to filter information to make decisions quickly. Synthesise and frame evidence to help you tailor it to the ways in which policymakers demand and understand information. Second, find the right time to act. Timing matters during key individuals’ patterns of thinking and the alignment of conditions in political systems. Third, engage with real world policymaking rather than waiting for a ‘rational’ and orderly process to appear. To present evidence during mythical stages of a ‘policy cycle’ is misguided, and to ‘speak truth to power’ without establishing legitimacy and building trust may be counterproductive. Our overall message is pragmatic, not Machiavellian: effective communication requires the suppliers of evidence to see the world from the perspective of their audience and understand the policy process in which they engage.
Moral discourse in the Twitterverse
Authors: Sterling Joanna , Jost John T. 
Published: November 2017

Abstract
We analyzed Twitter language to explore hypotheses derived from moral foundations
theory, which suggests that liberals and conservatives prioritize different
values. In Study 1, we captured 11
million tweets from nearly 25,000 U.S. residents and observed that liberals
expressed fairness concerns more often than conservatives, whereas conservatives
were more likely to express concerns about group loyalty, authority, and purity.
Increasing political sophistication exacerbated ideological differences in
authority and group loyalty. At low levels of sophistication, liberals used more
harm language, but at high levels of sophistication conservatives referenced
harm more often. In Study 2, we
analyzed 59,000 tweets from 388 members of the U.S. Congress. Liberal
legislators used more fairness- and harm-related words, whereas conservative
legislators used more authority-related words. Unexpectedly, liberal legislators
used more language pertaining to group loyalty and purity. Follow-up analyses
suggest that liberals and conservatives in Congress use similar words to
emphasize different policy priorities.
Student perspectives on assessment for learning
Authors: DeLuca Christopher , Chapman-Chin Allison E. A. , LaPointe-McEwan Danielle , Klinger Don A. 
Published: November 2017

ABSTRACTAssessment for learning (AfL) has become a widespread approach across many educational systems. To date, AfL research has emphasized teachers’ knowledge, skills, and practices, with few studies examining students’ responses to an AfL pedagogical approach. The purpose of this research was to focus directly on students’ perspectives on their use and value of AfL approaches through a survey of 1079 K–12 students and portfolio‐based interviews with 12 purposefully selected students. Survey data were analyzed through descriptive and inferential statistics across grade levels. Interview data were analyzed using standard thematic coding processes. Students most frequently used and valued teacher feedback and success criteria to support their learning. Peer feedback was the least valued AfL approach for all students. Some significant differences between grade levels were noted. Our results suggest that using AfL approaches is a learned behaviour; students need to be explicitly taught about AfL concepts, terminology, and use over time. This study also highlights that AfL implementation requires sustained focus, research, and support in schools and classrooms for students to value and fully benefit from assessment‐based teaching.
Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1
Authors: Park Jeongbin , Bae Sangsu 
Published: November 2017

AbstractSummaryFollowing the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5′-TTTN-3′ at the 5′ ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time.Availability and implementationFree access at http://www.rgenome.net/cpf1-database/.
3dRPC: a web server for 3D RNA–protein structure prediction
Authors: Huang Yangyu , Li Haotian , Xiao Yi 
Published: November 2017

Abstract

RNA–protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA–protein complexes. 3dRPC is an algorithm for prediction of 3D RNA–protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA–protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction.

Availability and implementation
The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC.
Identifying simultaneous rearrangements in cancer genomes
Authors: Oesper Layla , Dantas Simone , Raphael Benjamin J 
Published: November 2017

Abstract

Motivation
The traditional view of cancer evolution states that a cancer genome accumulates a sequential ordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such as chromothripsis, where a large number of mutations instead occur simultaneously. A number of potential signatures of chromothripsis have been proposed. In this work, we provide a rigorous formulation and analysis of the ‘ability to walk the derivative chromosome’ signature originally proposed by Korbel and Campbell. In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, the H/T alternating fraction, which allows us to overcome some of the limitations of the original signature.

Results
We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion.

Availability and implementation
An implementation of the H/T alternating fraction is available at https://bitbucket.org/oesperlab/ht-altfrac.

Supplementary information
Supplementary data are available at Bioinformatics online.
glactools: a command-line toolset for the management of genotype likelihoods and allele counts
Authors: Renaud Gabriel 
Published: November 2017

Abstract

Motivation
Research projects involving population genomics routinely need to store genotyping information, population allele counts, combine files from different samples, query the data and export it to various formats. This is often done using bespoke in-house scripts, which cannot be easily adapted to new projects and seldom constitute reproducible workflows.

Results
We introduce glactools, a set of command-line utilities that can import data from genotypes or population-wide allele counts into an intermediate representation, compute various operations on it and export the data to several file formats used by population genetics software. This intermediate format can take two forms, one to store per-individual genotype likelihoods and a second for allele counts from one or more individuals. glactools allows users to perform operations such as intersecting datasets, merging individuals into populations, creating subsets, perform queries (e.g. return sites where a given population does not share an allele with a second one) and compute summary statistics to answer biologically relevant questions.

Availability and implementation
glactools is freely available for use under the GPL. It requires a C ++ compiler and the htslib library. The source code and the instructions about how to download test data are available on the website (https://grenaud.github.io/glactools/).

Supplementary information
Supplementary data are available at Bioinformatics online.
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
Authors: Audano Peter A , Ravishankar Shashidhar , Vannberg Fredrik O 
Published: November 2017

Abstract

Motivation
The standard protocol for detecting variation in DNA is to map millions of short sequence reads to a known reference and find loci that differ. While this approach works well, it cannot be applied where the sample contains dense variants or is too distant from known references. De novo assembly or hybrid methods can recover genomic variation, but the cost of computation is often much higher. We developed a novel k-mer algorithm and software implementation, Kestrel, capable of characterizing densely packed SNPs and large indels without mapping, assembly or de Bruijn graphs.

Results
When applied to mosaic penicillin binding protein (PBP) genes in Streptococcus pneumoniae, we found near perfect concordance with assembled contigs at a fraction of the CPU time. Multilocus sequence typing (MLST) with this approach was able to bypass de novo assemblies. Kestrel has a very low false-positive rate when applied to the whole genome, and while Kestrel identified many variants missed by other methods, limitations of a purely k-mer based approach affect overall sensitivity.

Availability and implementation
Source code and documentation for a Java implementation of Kestrel can be found at https://github.com/paudano/kestrel. All test code for this publication is located at https://github.com/paudano/kescases.

Supplementary information
Supplementary data are available at Bioinformatics online.
Classifying next-generation sequencing data using a zero-inflated Poisson model
Authors: Zhou Yan , Wan Xiang , Zhang Baoxue , Tong Tiejun 
Published: November 2017

AbstractMotivationWith the development of high-throughput techniques, RNA-sequencing (RNA-seq) is becoming increasingly popular as an alternative for gene expression analysis, such as RNAs profiling and classification. Identifying which type of diseases a new patient belongs to with RNA-seq data has been recognized as a vital problem in medical research. As RNA-seq data are discrete, statistical methods developed for classifying microarray data cannot be readily applied for RNA-seq data classification. Witten proposed a Poisson linear discriminant analysis (PLDA) to classify the RNA-seq data in 2011. Note, however, that the count datasets are frequently characterized by excess zeros in real RNA-seq or microRNA sequence data (i.e. when the sequence depth is not enough or small RNAs with the length of 18–30 nucleotides). Therefore, it is desired to develop a new model to analyze RNA-seq data with an excess of zeros.ResultsIn this paper, we propose a Zero-Inflated Poisson Logistic Discriminant Analysis (ZIPLDA) for RNA-seq data with an excess of zeros. The new method assumes that the data are from a mixture of two distributions: one is a point mass at zero, and the other follows a Poisson distribution. We then consider a logistic relation between the probability of observing zeros and the mean of the genes and the sequencing depth in the model. Simulation studies show that the proposed method performs better than, or at least as well as, the existing methods in a wide range of settings. Two real datasets including a breast cancer RNA-seq dataset and a microRNA-seq dataset are also analyzed, and they coincide with the simulation results that our proposed method outperforms the existing competitors.Availability and implementationThe software is available at http://www.math.hkbu.edu.hk/∼tongt.Supplementary informationSupplementary data are available at Bioinformatics online.
ProphTools: general prioritization tools for heterogeneous biological networks
Authors: Navarro Carmen , Martínez Victor , Blanco Armando , Cano Carlos 
Published: November 2017

Abstract

Background
Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data.

Results
We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization.

Conclusions
ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality.
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome
Authors: Fu Xinhua , Li Jingjing , Tian Yu , Quan Weipeng , Zhang Shu , Liu Qian , Liang Fan , Zhu Xinlei , Zhang Liangsheng , Wang Depeng , Hu Jiang 
Published: November 2017

Abstract

Background
Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis.

Findings
Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions.

Conclusions
We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution.