bluuebunny/crossref_metadata_2025_split huggingface dataset:
Die mentale Welt der Anderen
Authors: Mohnke S. , Walter H. , Tantchik W. 
Published: July 2018

ZusammenfassungDas menschliche Gehirn verfügt über eine Reihe von Mechanismen, die uns in die Lage versetzen, die verborgenen mentalen Prozesse unserer Mitmenschen zu erkennen und zu verstehen. Diese Fähigkeiten werden unter dem Begriff Theory of Mind oder Mentalisieren zusammengefasst und haben sich in den letzten Jahrzehnten als bedeutendes Forschungsgebiet verschiedener Disziplinen – von der Entwicklungspsychologie über die kognitiven Neurowissenschaften bis zur Psychiatrie – etabliert. Dieser Artikel gibt einen kurzen Überblick über die Geschichte sowie Gegenwart der Forschung zu Theory of Mind. Im Fokus stehen die neuronalen Grundlagen dieser Fähigkeiten, neben der Beziehung von Theory of Mind zu dem verwandten Konzept der Empathie und der angenommenen Bedeutung des Spiegelneuronensystems werden auch Veränderungen im Verlauf der Entwicklung sowie Störungen im Rahmen psychiatrischer Erkrankungen thematisiert.
Mentalisierungsbasierte Therapie für Patienten mit Borderline-Persönlichkeitsstörung
Authors: Volkert J. , Bark C. , Taubner S. 
Published: July 2018

ZusammenfassungDie Mentalisierungsbasierte Therapie (MBT) wurde ursprünglich für die Behandlung von Patienten mit Borderline Persönlichkeitsstörung (BPS) entwickelt. Das multi-dimensionale Konzept des Mentalisierens beschreibt die imaginative Fähigkeit, das eigene Verhalten und das Verhalten anderer Menschen durch Zuschreibung mentaler Gründe interpretieren zu können und gilt als ein zentrales Merkmal zur Erklärung der Ätiopathogenese von schweren Persönlichkeitsstörungen (insbesondere BPS). Die MBT versteht sich als eine integrative, manualisierte Methode mit psychodynamischen Wurzeln, die mittlerweile auch für andere Störungsbilder (wie z.B. Depressionen, Essstörungen) und verschiedene Altersgruppen adaptiert wurde. Die MBT umfasst Einzel- und Gruppensitzungen, ist auf ca. 12–18 Monate ausgelegt und kann im stationären und ambulanten Setting durchgeführt werden. Sie verfolgt mithilfe einer spezifischen offenen und neugierigen therapeutischen Haltung des „Nicht-Wissens” und MBT-spezifischen Interventionen (z.B. „Stop, Rewind, Explore” oder „Challenge” das Ziel, die Mentalisierungsfähigkeiten in affektiv bedeutsamen Beziehungen zu fördern. Es liegen bereits einige Wirksamkeitsnachweise von randomisiert-kontrollierten Studien für die MBT vor, jedoch sind weitere Untersuchungen zur spezifischen Wirksamkeit und transdiagnostische Weiterentwicklungen notwendig.
Extraction and accuracy assessment of DTMs derived from remotely sensed and field surveying approaches in GIS framework
Authors: Rizeei Hossein Mojaddadi , Pradhan Biswajeet 
Published: July 2018

Abstract
Generating a high precision continuous surface is a key capability required in most geographic information system (GIS) applications. In fact the most commonly used surface type is a digital elevation model (DEM). Recently, there are some sources of remote sensing data that provide DEM information such as; LiDAR, InSAR and ASTER GDEM which ranged from very high to low spatial resolution. However, new methods of topographic field surveying still highly on demand e.g. Differential GPS and Total station devices. In both method of capturing the terrain elevation the post processing need to be applied to create a continuous surface from point clouds. Geostatistical analysis were used to interpolate the taken sample points from site into continuous surface. In current research, we examined the height accuracy of LiDAR point clouds and total station dataset with three non-adoptive interpolation models including, invers distance weightage (IDW), nearest neighbour (NN) and radial basis function (RBF) based on referenced DGPS points. RMSE and R square regression analysis were conducted to reveal the most accurate approaches in pilot study area. The results showed Lidar surveying (less than 0.5 meter RMSE) has higher height accuracy compared to Total station surveying (above 1 meter in RMSE) to extract DTM in flat area; while consumed less computational processing time. Moreover, IDW was the best and accurate interpolation model in both datasets to generate raster cautious terrain model.
A fast adaptive algorithm for computing whole-genome homology maps
Authors: Jain Chirag , Koren Sergey , Dilthey Alexander , Phillippy Adam M , Aluru Srinivas 
Published: July 2018

Abstract

Motivation
Whole-genome alignment is an important problem in genomics for comparing different species, mapping draft assemblies to reference genomes and identifying repeats. However, for large plant and animal genomes, this task remains compute and memory intensive. In addition, current practical methods lack any guarantee on the characteristics of output alignments, thus making them hard to tune for different application requirements.

Results
We introduce an approximate algorithm for computing local alignment boundaries between long DNA sequences. Given a minimum alignment length and an identity threshold, our algorithm computes the desired alignment boundaries and identity estimates using kmer-based statistics, and maintains sufficient probabilistic guarantees on the output sensitivity. Further, to prioritize higher scoring alignment intervals, we develop a plane-sweep based filtering technique which is theoretically optimal and practically efficient. Implementation of these ideas resulted in a fast and accurate assembly-to-genome and genome-to-genome mapper. As a result, we were able to map an error-corrected whole-genome NA12878 human assembly to the hg38 human reference genome in about 1 min total execution time and &lt;4 GB memory using eight CPU threads, achieving significant improvement in memory-usage over competing methods. Recall accuracy of computed alignment boundaries was consistently found to be &gt;97% on multiple datasets. Finally, we performed a sensitive self-alignment of the human genome to compute all duplications of length ≥1 Kbp and ≥90% identity. The reported output achieves good recall and covers twice the number of bases than the current UCSC browser’s segmental duplication annotation.

Availability and implementation
https://github.com/marbl/MashMap
Effusion: prediction of protein function from sequence similarity networks
Authors: Yunes Jeffrey M , Babbitt Patricia C 
Published: July 2018

Abstract

Motivation
Critical evaluation of methods for protein function prediction shows that data integration improves the performance of methods that predict protein function, but a basic BLAST-based method is still a top contender. We sought to engineer a method that modernizes the classical approach while avoiding pitfalls common to state-of-the-art methods.

Results
We present a method for predicting protein function, Effusion, which uses a sequence similarity network to add context for homology transfer, a probabilistic model to account for the uncertainty in labels and function propagation, and the structure of the Gene Ontology (GO) to best utilize sparse input labels and make consistent output predictions. Effusion’s model makes it practical to integrate rare experimental data and abundant primary sequence and sequence similarity. We demonstrate Effusion’s performance using a critical evaluation method and provide an in-depth analysis. We also dissect the design decisions we used to address challenges for predicting protein function. Finally, we propose directions in which the framework of the method can be modified for additional predictive power.

Availability and implementation
The source code for an implementation of Effusion is freely available at https://github.com/babbittlab/effusion.

Supplementary information
Supplementary data are available at Bioinformatics online.
TIMING 2.0: high-throughput single-cell profiling of dynamic cell–cell interactions by time-lapse imaging microscopy in nanowell grids
Authors: Lu Hengyang , Li Jiabing , Martinez-Paniagua Melisa A , Bandey Irfan N , Amritkar Amit , Singh Harjeet , Mayerich David , Varadarajan Navin , Roysam Badrinath 
Published: July 2018

Abstract

Motivation
Automated profiling of cell–cell interactions from high-throughput time-lapse imaging microscopy data of cells in nanowell grids (TIMING) has led to fundamental insights into cell–cell interactions in immunotherapy. This application note aims to enable widespread adoption of TIMING by (i) enabling the computations to occur on a desktop computer with a graphical processing unit instead of a server; (ii) enabling image acquisition and analysis to occur in the laboratory avoiding network data transfers to/from a server and (iii) providing a comprehensive graphical user interface.

Results
On a desktop computer, TIMING 2.0 takes 5 s/block/image frame, four times faster than our previous method on the same computer, and twice as fast as our previous method (TIMING) running on a Dell PowerEdge server. The cell segmentation accuracy (f-number = 0.993) is superior to our previous method (f-number = 0.821). A graphical user interface provides the ability to inspect the video analysis results, make corrective edits efficiently (one-click editing of an entire nanowell video sequence in 5–10 s) and display a summary of the cell killing efficacy measurements.

Availability and implementation
Open source Python software (GPL v3 license), instruction manual, sample data and sample results are included with the Supplement (https://github.com/RoysamLab/TIMING2).

Supplementary information
Supplementary data are available at Bioinformatics online.
Functional Subdivisions of Magnocellular Cell Groups in Human Basal Forebrain: Test–Retest Resting-State Study at Ultra-high Field, and Meta-analysis
Authors: Yuan Rui , Biswal Bharat B , Zaborszky Laszlo 
Published: July 2018

Abstract
The heterogeneous neuronal subgroups of the basal forebrain corticopetal system (BFcs) have been shown to modulate cortical functions through their cholinergic, gamma-aminobutyric acid-ergic, and glutamatergic projections to the entire cortex. Although previous studies suggested that the basalo-cortical projection system influences various cognitive functions, particularly via its cholinergic component, these studies only focused on certain parts of the BFcs or nearby structures, leaving aside a more systematic picture of the functional connectivity of BFcs subcompartments. Moreover, these studies lacked the high-spatial resolution and the probability maps needed to identify specific subcompartments. Recent advances in the ultra-high field 7T functional magnetic resonance imaging (fMRI) provided potentially unprecedented spatial resolution of functional MRI images to study the subdivision of the BFcs. In this study, the BF space containing corticopetal cells was divided into 3 functionally distinct subdivisions based on functional connection to cortical regions derived from fMRI. The overall functional connection of each BFcs subdivision was examined with a test-retest study. Finally, a meta-analysis was used to study the related functional topics of each BF subdivision. Our results demonstrate distinct functional connectivity patterns of these subdivisions along the rostrocaudal axis of the BF. All three compartments have shown consistent segregation and overlap at specific target regions including the hippocampus, insula, thalamus, and the cingulate gyrus, suggesting functional integration and separation in BFcs.
Atypical Local and Distal Patterns of Occipito-frontal Functional Connectivity are Related to Symptom Severity in Autism
Authors: Jao Keehn R Joanne , Nair Sangeeta , Pueschel Ellyn B , Linke Annika C , Fishman Inna , Müller Ralph-Axel 
Published: July 2018

Abstract
Autism spectrum disorders (ASDs) are increasingly prevalent neurodevelopmental disorders characterized by sociocommunicative impairments. Growing consensus indicates that neurobehavioral abnormalities require explanation in terms of interconnected networks. Despite theoretical speculations about increased local and reduced distal connectivity, links between local and distal functional connectivity have not been systematically investigated in ASDs. Specifically, it remains open whether hypothesized local overconnectivity may reflect isolated versus overly integrative processing. Resting state functional MRI data from 57 children and adolescents with ASDs and 51 typically developing (TD) participants were included. In regional homogeneity (ReHo) analyses, pericalcarine visual cortex was found be locally overconnected (ASD &gt; TD). Using this region as seed in whole-brain analyses, we observed overconnectivity in distal regions, specifically middle frontal gyri, for an ASD subgroup identified through k-means clustering. While in this subgroup local occipital to distal frontal overconnectivity was associated with greater symptom severity, a second subgroup showed the opposite pattern of connectivity and symptom severity correlations. Our findings suggest that increased local connectivity in ASDs is region-specific and may be partially associated with more integrative long-distance connectivity. Results also highlight the need to test for subtypes, as differential patterns of brain–behavior links were observed in two distinct subgroups of our ASD cohort.
Endoscopic Endonasal Resection of Orbital Apex Cavernous Hemangioma: 2-Dimensional Operative Video
Authors: Marcellino Chris R , Peris-Celda Maria , Link Michael J , Stokken Janalee K 
Published: July 2018

Abstract
A 52-yr-old woman was referred to a tertiary medical center for evaluation of 2 yr of progressive visual symptoms and 1 yr of retro-orbital pressure. Her ophthalmologic exam was unrevealing except for mild asymmetrical impairment in color perception. A gadolinium contrast-enhanced magnetic resonance image of the head showed a left extraconal orbital apex lesion consistent with cavernous hemangioma. Computed tomography reveled bony remodeling of the medial-inferior orbital walls with superior orbital fissure expansion.
The lesion was endoscopically resected and confirmed by pathological analysis. The endoscopic approach is demonstrated in detail, including correlation with cadaveric anatomic specimens‡. During the approach, a rescue nasoseptal flap was raised in case the orbit required further support after tumor resection, but was replaced as this was not needed. This patient had a brief period of postoperative diplopia, which resolved 1 wk after surgery. Her subjective visual deficits and pressure have also resolved.
Advantages of the endoscopic approach include improved direct visualization of the lesion, lack of external skin incisions, avoidance of significant neurovascular retraction, and shorter hospital stays than alternative orbitotomy or craniotomy approaches. This 4-handed approach demands endoscopic expertise of 2 surgeons, and is often performed by rhinology-neurosurgery or rhinology-ophthalmology surgical teams. The risk of postoperative diplopia should be discussed with the patient during informed consent.

‡ Anatomic specimen photography courtesy Dr Peris-Celda.
The Impact of Introducing a Physical Medicine and Rehabilitation Trauma Consultation Service to an Academic Level 1 Trauma Center
Authors: Robinson Lawrence R. , Tam Alan K. H. , MacDonald Shannon L. , Hanada Edwin Y. , Berbrayer David , Abdullahi Abdikarim , Camilotti Bruna G. , Tien Homer 
Published: July 2018

Objective
Previous retrospective studies suggest that early physical medicine and rehabilitation (PM&R) consultation for trauma patients improves outcome and reduces acute care length of stay (LOS). There have not been controlled studies to evaluate this impact. This study assesses the impact of PM&R consultations on acute trauma patients.

Design
This study compared measured outcomes before and after the introduction of a PM&R consultation service to the trauma program at a large academic hospital. The primary outcome measure was acute care LOS.

Results
The 274 historical controls and 76 patients who received a PM&R consultation were not different in injury severity score, age, or sex. Length of stay was not different between the two groups. However, when early (≤8 days after injury) versus late (>8 days) consults were compared, the early group had a markedly lower LOS (12 vs. 30 days, P < 0.001). When adjusted for injury severity score, an early consult was associated with an 11.8-day lower LOS (P < 0.001). The early consult group also had fewer complications and less usage of benzodiazepines and antipsychotics.

Conclusions
An acute care PM&R consultation of 8 days or less after admission is associated with a shorter acute care LOS, fewer complications, and less use of benzodiazepines and antipsychotics.
Biotrophic interactions disentangled: In situ localisation of mRNAs to decipher plant and algal pathogen – host interactions at the single cell level
Authors: Badstöber Julia , Gachon Claire M. M. , Ludwig-Müller Jutta , Sandbichler Adolf M. , Neuhauser Sigrid 
Published: July 2018

SummaryPlant-pathogen interactions follow spatiotemporal developmental dynamics where gene expression in pathogen and host undergo crucial changes. It is of great interest to detect, quantify and localise where and when key genes are active or inactive. Here, we adapt single molecule FISH techniques to demonstrate presence and activity of mRNAs using phytomyxids in their plant and algal host from laboratory and field materials. This allowed to monitor and quantify the expression of genes from the clubroot pathogen Plasmodiophora brassicae, several species of its Brassica hosts, and of several brown algae, including the genome model Ectocarpus siliculosus, infected with the phytomyxid Maullinia ectocarpii. We show that mRNAs are localised along a spatiotemporal gradient, thus providing proof-of-concept of the usefulness of these methods. These methods are easily adaptable to any interaction between microbes and their algal or plant host, and have the potential to increase our understanding of processes underpinning complex plant-microbe interactions.
Evolution of limb development in cephalopod mollusks
Authors: Tarazona Oscar A. , Lopez Davys H. , Slota Leslie A. , Cohn Martin J. 
Published: July 2018

AbstractCephalopod mollusks evolved numerous anatomical novelties, including arms and tentacles, but little is known about the developmental mechanisms underlying cephalopod limb evolution. Here we show that all three axes of cuttlefish limbs are patterned by the same signaling networks that act in vertebrates and arthropods, although they evolved limbs independently. In cuttlefish limb buds,Hedgehogis expressed anteriorly. Posterior transplantation ofHedgehog-expressing cells induced mirror-image limb duplications. Bmp and Wnt signals, which establish dorsoventral polarity in vertebrate and arthropod limbs, are similarly polarized in cuttlefish. Inhibition of Bmp2/4 dorsally caused ectopic expression ofNotum,which marks the ventral sucker field, and ectopic sucker development. Cuttlefish also show proximodistal regionalization ofHth,Exd, Dll,Dac,Sp8/9, andWntexpression, which delineates arm and tentacle sucker fields. These results suggest that cephalopod limbs evolved by parallel activation of a genetic program for appendage development that was present in the bilaterian common ancestor.
SuperFreq: Integrated mutation detection and clonal tracking in cancer
Authors: Flensburg Christoffer , Sargeant Tobias , Oshlack Alicia , Majewski Ian 
Published: July 2018

AbstractAnalysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that drive progression. Existing approaches for clonal tracking from sequencing data typically require the user to combine multiple tools that are not purpose-built for this task. Furthermore, most methods require a matched normal (non-tumour) sample, which limits the scope of application. We developed SuperFreq, a cancer exome sequencing analysis pipeline that integrates identification of somatic single nucleotide variants (SNVs) and copy number alterations (CNAs) and clonal tracking for both. SuperFreq does not require a matched normal and instead relies on unrelated controls. When analysing multiple samples from a single patient, SuperFreq cross checks variant calls to improve clonal tracking, which helps to separate somatic from germline variants, and to resolve overlapping CNA calls. To demonstrate our software we analysed 304 cancer-normal exome samples across 33 cancer types in The Cancer Genome Atlas (TCGA) and evaluated the quality of the SNV and CNA calls. We simulated clonal evolution through in silico mixing of cancer and normal samples in known proportion. We found that SuperFreq identified 93% of clones with a cellular fraction of at least 50% and mutations were assigned to the correct clone with high recall and precision. In addition, SuperFreq maintained a similar level of performance for most aspects of the analysis when run without a matched normal. SuperFreq is highly versatile and can be applied in many different experimental settings for the analysis of exomes and other capture libraries. We demonstrate an application of SuperFreq to leukaemia patients with diagnosis and relapse samples.SuperFreq is implemented in R and available on github at https://github.com/ChristofferFlensburg/SuperFreq.
Studying the fate of tumor extracellular vesicles at high spatio-temporal resolution using the zebrafish embryo
Authors: Hyenne Vincent , Ghoroghi Shima , Collot Mayeul , Harlepp Sébastien , Bauer Jack , Mercier Luc , Busnelli Ignacio , Lefebvre Olivier , Fekonja Nina , Machado Pedro , Bons Joanna , Delalande François , Amor Ana Isabel , Silva Susana Garcia , Verweij Frederik J. , Niel Guillaume Van , Schwab Yannick , Peinado Héctor , Carapito Christine , Klymchenko Andrey S. , Goetz Jacky G. 
Published: July 2018

SummaryTumor extracellular vesicles (tumor EVs) mediate the communication between tumor and stromal cells mostly to the benefit of tumor progression. Notably, tumor EVs have been reported to travel in the blood circulation, reach specific distant organs and locally modify the microenvironment. However, visualizing these eventsin vivostill faces major hurdles. Here, we show a new method for tracking individual circulating tumor EVs in a living organism: we combine novel, bright and specific fluorescent membrane probes, MemBright, with the transparent zebrafish embryo as an animal model. We provide the first description of tumor EVs’ hemodynamic behavior and document their arrest before internalization. Using transgenic lines, we show that circulating tumor EVs are uptaken by endothelial cells and blood patrolling macrophages, but not by leukocytes, and subsequently stored in acidic degradative compartments. Finally, we prove that the MemBright can be used to follow naturally released tumor EVsin vivo. Overall, our study demonstrates the usefulness and prospects of zebrafish embryo to track tumor EVsin vivo.HighlightsMemBright, a new family of membrane probes, allows for bright and specific staining of EVsZebrafish melanoma EVs are very similar to human and mouse melanoma EVs in morphology and protein contentThe zebrafish embryo is an adapted model to precisely track tumor EVs dynamics and fate in a living organism from light to electron microscopyCirculating tumor EVs are rapidly uptaken by endothelial cells and patrolling macrophagesCorrelated light and electron microscopy can be used in zebrafish to identify cells and compartments uptaking tumor EVsBlurbDispersion of tumor extracellular vesicles (EVs) throughout the body promotes tumor progression. However the behavior of tumor EVs in body fluids remains mysterious due to their small size and the absence of adapted animal model. Here we show that the zebrafish embryo can be used to track circulating tumor EVsin vivoand provide the first high-resolution description of their dissemination and uptake.