bluuebunny/crossref_metadata_2025_split huggingface dataset:
Narrow-band imaging in the diagnosis of deep submucosal colorectal cancers: a systematic review and meta-analysis
Authors: Zhang Qing-Wei , Teng La-Mei , Zhang Xin-Tian , Zhang Jing-Jing , Zhou Ying , Zhou Zhi-Rui , Hou Yi-Chao , Ge Zhi-Zheng , Li Xiao-Bo 
Published: May 2017

Abstract
Background and aims Magnifying endoscopy with narrow-band imaging (M-NBI) has been widely used in the differential diagnosis of deep submucosal colorectal cancers (dSMCs) from superficial submucosal cancers (sSMCs) and intramucosal neoplasms. We aimed to pool the diagnostic efficacy of M-NBI and compare it with that of magnifying chromoendoscopy (M-CE) in diagnosing colorectal dSMC.
Methods PubMed, EMBASE, and the Cochrane Library were searched to identify eligible studies. Meeting abstracts were also searched. A bivariate mixed-effects binary regression model was used in the meta-analysis to calculate the pooled diagnostic efficacy of M-NBI and compare it with that of M-CE in the diagnosis of dSMC. Subgroup analyses and meta-regression were conducted to explore sources of heterogeneity.
Results We included 17 studies: 14 full texts and 3 meeting abstracts. The pooled sensitivity, specificity, and area under the summary receiver operating characteristic curve (AUC) with 95 % confidence intervals (CIs) in diagnosing dSMC were 74 % (66 % – 81 %; I2 = 84.6 %), 98 % (94 % – 99 %; I2 = 94.4 %), and 0.91 (0.88 – 0.93), respectively, for M-NBI. The pooled sensitivity, specificity and AUC (95 %CI) were 84 % (76 % – 89 %; I2 = 76.9 %), 97 % (94 % – 99 %; I2 = 90.2 %), and 0.97 (0.95 – 0.98), respectively, for M-CE. M-NBI had lower sensitivity (P < 0.01) than M-CE with similar specificity (P = 0.32). Subgroup analyses and meta-regression indicated that endoscopic diagnostic criteria, study type, endoscope type, risk of index test bias, and histopathological diagnostic criteria might be the sources of heterogeneity.
Conclusions M-NBI and M-CE had comparable specificities in diagnosing dSMC, but the sensitivity of M-NBI was slightly lower than that of M-CE.
Der Roux-Y-Magenbypass zur Therapie der Adipositas bei Jugendlichen: Analyse des Gewichtsverlaufs und des Einflusses auf Komorbiditäten im Vergleich zu adipösen Erwachsenen
Authors: Benedix Frank , Kusibab Marek , Adolf Daniela , Lorenz Eric , Wolff Stefanie , Lippert Hans , Manger Thomas , Stroh Christine 
Published: May 2017

Zusammenfassung
Hintergrund Die Adipositas repräsentiert eines der ernsthaftesten medizinischen Probleme unserer Zeit. Neben der Zunahme der Adipositas im Erwachsenenalter zeigt sich auch bei Jugendlichen eine besorgniserregende Entwicklung. Die bariatrische Chirurgie hat sich zu einer sicheren und effektiven Therapieoption bei Adipositas im Erwachsenenalter etabliert. Bei Jugendlichen werden diese Eingriffe noch kontrovers diskutiert. Die derzeit verfügbare Evidenz bez. Sicherheit und Effektivität ist limitiert.
Material und Methoden Im Rahmen der multizentrischen Beobachtungsstudie „Qualitätssicherung in der operativen Therapie der Adipositas“ werden seit dem 01.01.2005 die Daten von Patienten, die sich in Deutschland wegen einer Adipositas einem chirurgischen Eingriff unterzogen haben, prospektiv erfasst. Für die vorliegende Studie wurden alle Patienten berücksichtigt, bei denen im Zeitraum von 01.01.2005 bis 31.12.2014 ein primärer Roux-Y-Magenbypass (RYGB) wegen einer Adipositas durchgeführt wurde.
Ergebnisse Insgesamt wurden 370 Jugendliche (≤ 21 Jahre) und 16 840 Erwachsene untersucht. Im Jahr 2014 repräsentierte der RYGB den zweithäufigsten bariatrischen Eingriff für beide Gruppen. Bei den Jugendlichen zeigte sich ein höherer initialer BMI (49,2 vs. 47,9 kg/m2, p < 0,01), der Anteil assoziierter Nebenerkrankungen war niedriger (67,8 vs. 87,4%, p < 0,01). Die Operationsdauer (104,9 vs. 113,0 min, p < 0,01) sowie die Krankenhausverweildauer (5,2 vs. 5,9 Tage; p < 0,01) unterschieden sich signifikant zwischen beiden Gruppen. Keiner der jugendlichen Adipösen entwickelte eine Anastomoseninsuffizienz, verglichen mit einer Leckagerate von 1,6% bei den Erwachsenen (p = 0,04). Die Mortalitätsrate betrug 0,2% in der Gruppe der Erwachsenen. Keiner der adipösen Jugendlichen verstarb postoperativ. Der mittlere prozentuale Übergewichtsverlust (% EWL) war nach 12 (69,9 vs. 68,2%; p = 0,97) bzw. 24 Monaten (72,6 vs. 72,1%; p = 1,0) für beide Gruppen vergleichbar. Bei Jugendlichen mit vorbestehender arterieller Hypertonie fand sich im Vergleich zu Erwachsenen eine höhere Remissionsrate.
Schlussfolgerung Der RYGB kann bei jugendlichen Adipösen mit einer niedrigeren Morbidität und Mortalität durchgeführt werden. Trotz aller Limitierungen einer Registerstudie und der geringen Follow-up-Rate zeigt sich, dass die Ergebnisse im kurzfristigen Verlauf denen nach RYGB bei Erwachsenen mindestens vergleichbar sind. Der Fokus zukünftiger Studien muss auf der Evaluation des Langzeitverlaufs liegen.
Universal transition from unstructured to structured neural maps
Authors: Weigand Marvin , Sartori Fabio , Cuntz Hermann 
Published: May 2017

Significance
To save wiring, neurons in the brain that are connected to one another should be located in close vicinity. We use computational models based on multidimensional scaling to explore the implications of this simple premise regarding the organization of the visual cortex. Assuming only that neurons with similar orientation preference are more strongly connected, we predict the emergence of characteristic pinwheels where preferred orientations organize in a continuous circular manner. We find that a universal transition exists between completely unstructured and such structured neural maps when increasing neuron numbers even without changing the selectivity of the connections. Our results are a simple explanation for the existence of salt-and-pepper arrangements in rodents and pinwheel arrangements in cat visual cortex.
Multiscale model predicts increasing focal adhesion size with decreasing stiffness in fibrous matrices
Authors: Cao Xuan , Ban Ehsan , Baker Brendon M. , Lin Yuan , Burdick Jason A. , Chen Christopher S. , Shenoy Vivek B. 
Published: May 2017

Significance
Focal adhesions play crucial roles in mechanotransduction and regulate processes such as spreading, proliferation, differentiation, and motility. It is well known that cells develop larger adhesions when cultured on stiffer elastic hydrogels, but the native extracellular matrix (ECM) is fibrous, nonlinear, and dissipative. We developed a multiscale model showing that adhesion size decreases with increasing stiffness in fibrous matrices, in excellent agreement with our experiments on engineered fibrous matrices. Our model shows that this is due to the feedback between cell contractility and the physical remodeling of ECM, which does not exist in elastic substrates. The basic stiffness–adhesion size principle uncovered can be applied to understand tumor progression fundamentally or to better design biomaterial scaffolds to control cell behavior.
Introduction: what is a tragedy?
Authors: Wells Stanley 
Published: May 2017

Abstract
Around half of Shakespeare’s plays are tragedies in the most basic sense of the word, with the death of their central character or characters. The Introduction explains that just as Shakespeare’s comedies often verge on tragedy, so his tragedies frequently offer a wittily ironic perspective on the action. This suggests that when Shakespeare set about looking for a story to dramatize he was more concerned to find one that offered possibilities for a variety of dramatic effects than for one that would fit neatly into the traditional kinds of drama. It also notes that Shakespeare was aware of, and influenced by, the Roman tragedies of Seneca and the comic dramatist Plautus.
Tragedies on the stages of Shakespeare’s time
Authors: Wells Stanley 
Published: May 2017

Abstract
Tragedies were immensely popular at the time Shakespeare came on the theatrical scene. The brightest star among Shakespeare’s early contemporaries was Christopher Marlowe, a prolific dramatist who had a seminal influence on his contemporaries and successors. Shakespeare also learnt much from the less prolific Thomas Kyd. ‘Tragedies on the stages of Shakespeare’s time’ explains that the form and style of Shakespeare’s plays were determined partly by the physical conditions of the playhouses within which they were to be acted; the nature of the companies that performed them; the conventions of dramatic presentation at the time; and to a lesser extent the expectations of those who went to see them.
Hamlet
Authors: Wells Stanley 
Published: May 2017

Abstract
‘Hamlet’ explains the textual fluidity of the play and how it has therefore been subject to a wider range of interpretation than most; it is different every time it is acted. Though every version has the same basic central story of Hamlet’s revenge for his father’s murder, each inevitably presents a more or less subtly different narrative, some omitting whole scenes and even major story threads. All this helps to explain why the play—and its central character—have been subject to an exceptionally wide range of interpretation. The most familiar image of the play is the young prince contemplating a skull, the overriding theme being how people react to death.
King Lear
Authors: Wells Stanley 
Published: May 2017

Abstract
‘King Lear’ explains that for readers, as well as for performers, the play may seem a daunting intellectual and emotional challenge. It tells a deeply tragic story, a story of national and familial division and paternal oppression, of hypocritical deception, of developing enmity, and of profound physical cruelty. The story of the play—related to that of Cinderella and her two ugly sisters—has something of the nature of a parable, in which characters divide easily into the good and the bad; and profoundly serious though the play is, it is shot through with comedy, though admittedly it’s often a grotesque, ironic sort of comedy.
Epilogue: why might we enjoy tragedies?
Authors: Wells Stanley 
Published: May 2017

Abstract
‘Epilogue: why might we enjoy tragedies?’ considers why we pay good money to subject ourselves to displays of misery, cruelty, suicide, murder—even cannibalism. Perhaps central to the appeal of Shakespeare’s tragedies is that through dramatic, well-shaped stories with lyricism, rhetorical force, complex variety, and frequent ironic and comic perspective, they give us a sense of sharing in and facing up to the ultimate realities of human existence; the intermingling in our lives of joy and sorrow, love and hatred; conflicting impulses of kindness and cruelty; the inevitability of death; the pathos of human endeavour to mitigate its terrors; and the mystery inherent in the human condition.
Tumor phylogeny inference using tree-constrained importance sampling
Authors: Satas Gryte , Raphael Benjamin J 
Published: May 2017

Abstract

Motivation
A tumor arises from an evolutionary process that can be modeled as a phylogenetic tree. However, reconstructing this tree is challenging as most cancer sequencing uses bulk tumor tissue containing heterogeneous mixtures of cells.

Results
We introduce Probabilistic Algorithm for Somatic Tree Inference (PASTRI), a new algorithm for bulk-tumor sequencing data that clusters somatic mutations into clones and infers a phylogenetic tree that describes the evolutionary history of the tumor. PASTRI uses an importance sampling algorithm that combines a probabilistic model of DNA sequencing data with a enumeration algorithm based on the combinatorial constraints defined by the underlying phylogenetic tree. As a result, tree inference is fast, accurate and robust to noise. We demonstrate on simulated data that PASTRI outperforms other cancer phylogeny algorithms in terms of runtime and accuracy. On real data from a chronic lymphocytic leukemia (CLL) patient, we show that a simple linear phylogeny better explains the data the complex branching phylogeny that was previously reported. PASTRI provides a robust approach for phylogenetic tree inference from mixed samples.

Availability and Implementation
Software is available at compbio.cs.brown.edu/software.

Supplementary information
Supplementary data are available at Bioinformatics online.
Assembling draft genomes using contiBAIT
Authors: O’Neill Kieran , Hills Mark , Gottlieb Mike , Borkowski Matthew , Karsan Aly , Lansdorp Peter M 
Published: May 2017

Abstract

Summary
Massively parallel sequencing is now widely used, but data interpretation is only as good as the reference assembly to which it is aligned. While the number of reference assemblies has rapidly expanded, most of these remain at intermediate stages of completion, either as scaffold builds, or as chromosome builds (consisting of correctly ordered, but not necessarily correctly oriented scaffolds separated by gaps). Completion of de novo assemblies remains difficult, as regions that are repetitive or hard to sequence prevent the accumulation of larger scaffolds, and create errors such as misorientations and mislocalizations. Thus, complementary methods for determining the orientation and positioning of fragments are important for finishing assemblies. Strand-seq is a method for determining template strand inheritance in single cells, information that can be used to determine relative genomic distance and orientation between scaffolds, and find errors within them. We present contiBAIT, an R/Bioconductor package which uses Strand-seq data to repair and improve existing assemblies.

Availability and Implementation
contiBAIT is available on Bioconductor. Source files available from GitHub.

Supplementary information
Supplementary data are available at Bioinformatics online.
An efficient graph kernel method for non-coding RNA functional prediction
Authors: Navarin Nicolò , Costa Fabrizio 
Published: May 2017

Abstract

Motivation
The importance of RNA protein-coding gene regulation is by now well appreciated. Non-coding RNAs (ncRNAs) are known to regulate gene expression at practically every stage, ranging from chromatin packaging to mRNA translation. However the functional characterization of specific instances remains a challenging task in genome scale settings. For this reason, automatic annotation approaches are of interest. Existing computational methods are either efficient but non-accurate or they offer increased precision, but present scalability problems.

Results
In this article, we present a predictive system based on kernel methods, a type of machine learning algorithm grounded in statistical learning theory. We employ a flexible graph encoding to preserve multiple structural hypotheses and exploit recent advances in representation and model induction to scale to large data volumes. Experimental results on tens of thousands of ncRNA sequences available from the Rfam database indicate that we can not only improve upon state-of-the-art predictors, but also achieve speedups of several orders of magnitude.

Availability and implementation
The code is available from http://www.bioinf.uni-freiburg.de/~costa/EDeN.tgz.
EEG datasets for motor imagery brain–computer interface
Authors: Cho Hohyun , Ahn Minkyu , Ahn Sangtae , Kwon Moonyoung , Jun Sung Chan 
Published: May 2017

Abstract

Background:
Most investigators of brain–computer interface (BCI) research believe that BCI can be achieved through induced neuronal activity from the cortex, but not by evoked neuronal activity. Motor imagery (MI)–based BCI is one of the standard concepts of BCI, in that the user can generate induced activity by imagining motor movements. However, variations in performance over sessions and subjects are too severe to overcome easily; therefore, a basic understanding and investigation of BCI performance variation is necessary to find critical evidence of performance variation. Here we present not only EEG datasets for MI BCI from 52 subjects, but also the results of a psychological and physiological questionnaire, EMG datasets, the locations of 3D EEG electrodes, and EEGs for non-task-related states.

Findings:
We validated our EEG datasets by using the percentage of bad trials, event-related desynchronization/synchronization (ERD/ERS) analysis, and classification analysis. After conventional rejection of bad trials, we showed contralateral ERD and ipsilateral ERS in the somatosensory area, which are well-known patterns of MI. Finally, we showed that 73.08% of datasets (38 subjects) included reasonably discriminative information.

Conclusions:
Our EEG datasets included the information necessary to determine statistical significance; they consisted of well-discriminated datasets (38 subjects) and less-discriminative datasets. These may provide researchers with opportunities to investigate human factors related to MI BCI performance variation, and may also achieve subject-to-subject transfer by using metadata, including a questionnaire, EEG coordinates, and EEGs for non-task-related states.
Ontogenetic development of otolith shape during settlement of juvenile Barents Sea cod (Gadus morhua)
Authors: Irgens Christian , Kjesbu Olav S , Folkvord Arild 
Published: May 2017

Abstract
This study documents how settlement of juvenile Atlantic cod (Gadus morhua) in the Barents Sea affects otolith growth and morphology. A simple method to objectively discriminate between age 0 and age 1 cod sampled in late summer was demonstrated by using only two otolith morphometric descriptors: area and perimeter. In the pre-settled 0-group cod, otolith lobe formation clearly increased with fish size, resulting in high otolith crenulation. This trend was disrupted during settlement, resulting in noticeably less crenulated otoliths of the settled 1-group cod sampled in winter. Combined observations of otolith shape, fish size, and body condition suggest that environmental factors associated with settlement during autumn, particularly reduced food intake, directly affect lobe formation leading to less crenulated otoliths. Comparably reduced body condition and otolith crenulation of 0-group cod in bottom trawls (vs. pelagic trawls) may indicate early settlement or vertical exploratory behaviour in the Barents Sea Ecosystem Survey (in August–September) and, thus, an underrepresentation of 0-group cod from pelagic trawling.
The superior colliculus and the steering of saccades toward a moving visual target
Authors: Goffart Laurent , Cecala Aaron , Gandhi Neeraj 
Published: May 2017

ABSTRACTFollowing the suggestion that a command encoding the expected here-and-now target location feeds the oculomotor system during interceptive saccades, we tested whether this command originates in the deep superior colliculus (SC). Monkeys generated saccades to targets that were static or moving along the preferred axis, away from (outward) or toward a fixated target (inward) with a constant speed (20°/s). Vertical and horizontal motions were also tested. Extracellular activity of 57 saccade-related neurons was recorded in 3 monkeys. The movement field (MF) parameters (boundaries, center and firing rate) were estimated after spline fitting the relation between the saccade amplitude and the average firing rate of the motor burst. During radial motion, the inner MF boundary shifted in the same direction as the target motion for some neurons, not all. During vertical motion, both lower and upper boundaries were shifted upward during upward motion whereas the upper boundary only shifted during downward motions. For horizontal motions, the medial boundaries were not changed. The MF center was shifted only for outward motion. Regardless of the motion direction, the average firing rate was consistently reduced during interceptive saccades. Our study shows an involvement of the saccade-related burst of SC neurons in steering the gaze toward a moving target. When observed, the shifts of MF boundary in the direction of target motion correspond to commands related to antecedent target locations. The absence of shift in the opposite direction shows that SC activity does not issue predictive commands related to the future target location.SIGNIFICANCE STATEMENTBy comparing the movement field (MF) of saccade-related neurons between saccades toward static and moving targets, we show that the motor burst issued by neurons in the superior colliculus does not convey commands related to the future location of a moving target. During interceptive saccades, the active population consists of a continuum of neurons, ranging from cells exhibiting a shift in the center or boundary of their MF to cells which exhibit no change. The shifts correspond to residual activity related to the fact that the active population does not change as fast as the target in the visual field. By contrast, the absence of shift indicates commands related to the current target location, as if it were static.
Gene2Function: An integrated online resource for gene function discovery
Authors: Hu Yanhui , Comjean Aram , Mohr Stephanie E. ,   the FlyBase Consortium, Perrimon Norbert , Agapite Julie , Broll Kris , Crosby Madeline , Dos Santos Gilberto , Emmert David , Falls Kathleen , Gelbart Susan Russo , Gramates Sian , Matthews Beverley , Perrimon Norbert , Sutherland Carol , Tabone Chris , Zhou Pinglei , Zytkovicz Mark , Antonazzo Giulia , Attrill Helen , Brown Nicholas , Fexova Silvie , Jones Tamsin , Larkin Aoife , Marigold Steven , Milburn Gillian , Rey Alix , Urbano Jose-Maria , Czoch Brian , Goodman Josh , Grumbling Gary , Kaufman Thomas , Strelets Victor , Thurmond James , Baker Phill , Cripps Richard , Werner-Washburne Margaret 
Published: May 2017

AbstractOne of the most powerful ways to develop hypotheses regarding biological functions of conserved genes in a given species, such as in humans, is to first look at what is known about function in another species. Model organism databases (MODs) and other resources are rich with functional information but difficult to mine. Gene2Function (G2F) addresses a broad need by integrating information about conserved genes in a single online resource.
Patterns of female entrepreneurial activities in Turkey
Authors: Kalemci Tuzun Ipek , Araz Takay Bahar 
Published: May 2017

PurposeThis study aims to identify and understand the challenges, motivational factors and future needs of female entrepreneurs in Ankara, Turkey.Design/methodology/approachThe study uses the qualitative analysis methodology and uses the qualitative data analysis software, MAXQDA 11. A total of 41 randomly selected female entrepreneurs from the city of Ankara and rural areas of the Ankara region participated in semi-structured in-depth interviews. A total of 284 codes were defined.FindingsResults indicate that female entrepreneurs are mostly intrinsically motivated and are driven by the desire to achieve and to become independent. The socially constructed role of women in Turkey is the primary challenge faced by female entrepreneurs in both urban and rural areas. Moreover, the major future needs identified for female entrepreneurs are support from public institutions and access to managerial consultants.Originality/valueThere are limited number of studies that closely examine the characteristics of female entrepreneurship activity and their challenges/motivations in Turkey. This research contributes to the existing literature through its qualitative nature and by highlighting differences in urban and rural female entrepreneurs. Moreover, the results of this study are useful for policy makers to evaluate the future needs of female entrepreneurs and the programs that will be needed to overcome the challenges facing female entrepreneurs in the entrepreneurial process.