bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fully-covered esophageal stent migration rates in benign and malignant disease: a multicenter retrospective study
Authors: Thomas Samuel , Siddiqui Ali , Taylor Linda , Parbhu Sheeva , Cao Christopher , Loren David , Kowalski Thomas , Adler Douglas 
Published: May 2019

Abstract
Background and study aims Stent migration is a common complication of fully-covered self-expanding metal stents (FCSEMS), but the rate of clinically relevant migration as defined by stent migration followed by reintervention via endoscopy for stent replacement is unknown. The goal of this study is to gain insight into the total migration rate and clinically relevant migration rate of different types of FCSEMS placed within benign and malignant strictures with specific attention paid to stent manufacturer, diameter, and length.
Patients and methods Multicenter retrospective analysis of endoscopic data from patients with FCSEMS placed within benign or malignant strictures. FCSEMS used included a variety of sizes and manufacturers.
Results A total of 369 patients were included, 161 of whom had benign strictures and 208 of whom had malignant strictures. The total migration rate and clinically relevant migration rate in benign strictures were 30 % and 17 %, respectively. For benign strictures, Wallflex stents had a clinically relevant migration rate of 15 %, compared to Endomaxx stents with 19 %, and Evolution stents with 25 % (P = 0.52). The total migration rate and clinically relevant migration rates in malignant strictures were 23 % and 14 %, respectively. Evolution stents had a significantly higher clinically relevant migration rate (29 %) than the Wallflex stents (7 %) and the endomaxx stents (12 %), P = 0.003.
Conclusion This study is the largest to investigate migration rates for FCSEMS in benign and malignant strictures. Clinically relevant migration is a relatively common occurrence with all stent types studied and better anti-migration features are needed.
Importance of Temperament in Individualized Homeopathic Prescription: Evaluation by an Open, Randomized, Pilot Trial
Authors: Sultana Najne , Samanta Amitava , Koley Munmun , Saha Subhranil 
Published: May 2019

Background The importance of temperament in the selection of an individualized homeopathic medicine has not been evaluated systematically. The current study explored this under-researched area.
Materials and Methods A prospective, open, randomized (1:1), two parallel arms, pilot trial was performed on patients suffering from various chronic diseases. Each patient's temperament was assessed using a newly developed “temperament diagnostic questionnaire”. Outcome measures were health status using the EQ-5D-5L questionnaire and a visual analog scale (VAS) of patient's self-rated health, measured at baseline and at 3 months. Homeopathic medicines were prescribed on the basis of individualization, randomly with or without accounting for individual temperament, and patients grouped accordingly (temperament(+) and temperament(−)). Baseline comparability of the two groups was checked, followed by analysis of group differences. A p-value < 0.01 was considered as statistically significant.
Results Fifty protocol-compliant patients were analyzed. The two groups were comparable at baseline. Over 3 months of intervention, there was significant improvement (p < 0.01) in each group. Though improvement in the EQ-5D-5L score was greater in the temperament(+) group (mean difference, 2.4; 95% confidence interval [CI], 0.2 to 4.5), the change did not achieve the threshold for statistical significance (p = 0.029). Improvement in VAS score was significantly greater in the temperament(+) group than in temperament(–) patients (mean difference, 15.2; 95% CI, 4.9 to 25.4; p = 0.004).
Conclusion Considering temperament as a key element of individualized prescription may enhance health improvement from homeopathic treatment in chronic diseases. Independently replicated rigorous trials with validated scales are warranted.
Trial Registration CTRI/2018/03/012433.
Novel Drivers of the Inflammatory Response in Liver Injury and Fibrosis
Authors: Wree Alexander , Holtmann Theresa Maria , Inzaugarat Maria Eugenia , Feldstein Ariel E. 
Published: May 2019

AbstractHepatocyte demise as well as signals released by stressed hepatocytes have been now recognized as important triggers of liver inflammation. While traditional concepts classically viewed hepatocyte cell death to occur by either a nonlytic, noninflammatory form (apoptosis), or lytic, proinflammatory nonregulated cell death (necrosis), recent studies have provided evidence for additional mechanisms that can contribute to both acute and chronic liver damage. Two novel forms of cell death, pyroptosis and necroptosis, are of particular importance as they are highly regulated and intrinsically proinflammatory. Additionally, stressed hepatocytes may also release signals to attract and activate monocytes into proinflammatory macrophages. In this review, the authors discuss recent developments supporting the role of novel triggers of liver inflammation in various forms of liver injury and their potential translational implications.
Soft Tissue Coverage for Defects around the Knee Joint
Authors: R. Ravindra Bharathi , Ramkumar Sanjai , Venkatramani Hari 
Published: May 2019

AbstractSoft tissue injuries around the knee present a challenge for providing a cover when there is loss of tissue. Various flaps comprising of skin and muscles around the joint have been described. Understanding the anatomical basis and the design of these flaps can aid in choosing the right flap for a given situation. A prompt cover of the defects aids in quicker healing and quicker rehabilitation of the patient.
Aesthetic Earlobe Reduction: A Practical Geometric Modification with Natural Contour Preservation
Authors: Tatar Sedat , Sezgin Billur 
Published: May 2019

AbstractEarlobe elongation is one of the signs of aging process and surgical correction is warranted for earlobe ptosis. Most of the earlobe reduction techniques result with scars on the anterior or inferior aspect of the earlobe or unnatural appearance. The authors present a modified technique for earlobe reduction and reshaping that results with an acceptable scar set on the natural groove of the anterior surface of the earlobe. Nine healthy female patients were operated for earlobe reduction. The postoperative and preoperative otobasion inferius (O)–subaurale (S) distances of these patients were evaluated. According to the measurements, the preoperative mean O–S distance of the right lobule was 13.1 ± 1.8 mm and the left lobule was 12.8 ± 1.9 mm, while the postoperative O–S distance of the right side was 3.4 ± 1 mm and the left side was 3.4 ± 0.7 mm (Table 2). This translated to an approximate pre- and postoperative O–S distance difference of 9 mm, a significant reduction that resulted with ideal O–S values. The presented approach has numerous advantages including inconspicuous scarring, smooth lateral earlobe contours, and undisturbed free borders. This was a Level IV therapeutic study.
Role for polo-like kinase 4 in mediation of cytokinesis
Authors: Press Michael F. , Xie Bin , Davenport Simon , Zhou Yu , Guzman Roberta , Nolan Garry P. , O’Brien Neil , Palazzolo Michael , Mak Tak W. , Brugge Joan S. , Slamon Dennis J. 
Published: May 2019

SignificancePolo-like kinase 4 (PLK4), a known cell cycle regulatory protein, localizes to the centrosome during S-phase and facilitates centrosome duplication. We show that phospho-serine305-PLK4 is subsequently redistributed to kinetochores (metaphase and anaphase), midzone during cleavage furrow formation (anaphase and telophase), and midbody (cytokinesis) during the cell cycle, and is required for cell division. Inhibition of PLK4 kinase activity prevents cytokinesis, leading to polyploidy and vulnerability to anaphase or mitotic catastrophe. The role of PLK4 in cytokinesis is consistent with its role as a potential target for cancer therapy.
Substrate inhibition imposes fitness penalty at high protein stability
Authors: Adkar Bharat V. , Bhattacharyya Sanchari , Gilson Amy I. , Zhang Wenli , Shakhnovich Eugene I. 
Published: May 2019

Significance
Why highly stable proteins are not commonly observed in mesophilic organisms is an important evolutionary question. It has been suggested that high stability has a fitness cost in the form of loss of activity. However, this hypothesis has not yet been experimentally demonstrated. Here, we use an essential bacterial enzyme adenylate kinase (Adk) to explore this hypothesis and show that, as Adk’s stability increases, one of its own substrates inhibits its activity. Bacterial strains carrying such stable Adks show substantial fitness defects, which can be mapped to the loss of Adk activity due to substrate inhibition. Overall, our study adds “substrate inhibition” to the “toolbox” that is used to rationalize the stability distribution of proteins.
Spontaneous and directed symmetry breaking in the formation of chiral nanocrystals
Authors: Hananel Uri , Ben-Moshe Assaf , Diamant Haim , Markovich Gil 
Published: May 2019

SignificanceProcesses which break symmetry have always attracted the interest of scientists, as they are at the heart of many natural phenomena, from particle physics to biology. In life, the mirror symmetry breaking of biomolecules has been the subject of extensive debate and theoretical modeling. Hence, well-controlled model systems which break chiral symmetry are of great interest. We report on chiral amplification in the formation of chiral inorganic nanocrystals, leading to random breaking of mirror symmetry below a critical temperature. This symmetry breaking can be sensitively directed to a particular handedness by specific chiral biomolecules. The observed symmetry breaking is analyzed as a phase transition analogous to the ferromagnetic–paramagnetic transition in metals.
Developmental integration and evolution of labile plasticity in a complex quantitative character in a multiperiodic environment
Authors: Lande Russell 
Published: May 2019

SignificanceMany quantitative characters undergo continuous reversible development, or labile plasticity, which may be determined by multiple components of plasticity acting on different time scales. Thermal adaptation in mammals includes transient fat deposition and fur growth, shivering and sweating or panting, and movement between warm and cold microhabitats, adapting individuals to annual and daily temperature cycles. With a single component of plasticity, adaptation is constrained by filtering environmental frequencies above the development rate and by component costs of plasticity. For a character with multiple components of plasticity, some patterns of development integration among the components can alleviate these constraints and facilitate evolutionary changes that greatly improve labile plasticity tracking complex environmental cycles in the optimum phenotype.
Definiteness in Germanic and Balto-Slavic
Authors: Askedal John Ole 
Published: May 2019

Abstract
The present paper is concerned with overt marking of definiteness, and to a lesser extent indefiniteness, in Germanic and Balto-Slavic from a historical perspective, concentrating on the main functional or formation types as well as general aspects of the historical development of (in)definiteness marking in the Germanic, Baltic and Slavic languages. By way of conclusion, I offer some tentative areal perspectives concerning definiteness marking in Germanic and Balto-Slavic.
Relevance of the dairy cow biodiversity in the development of a profitable and environmentally sustainable livestock.
Authors: Curone G. , Filipe J. , Cremonesi P. , Piccioli-Cappelli F. , Trevisi E. , Amadori M. 
Published: May 2019

Abstract
The theme of the loss of biodiversity in recent years has become increasingly important as highlighted by the United Nations General Assembly which declared the 2011-2020 period as the United Nations Decade on Biodiversity. In this context, the preservation and rational use of autochthonous cattle breeds play a key role in the maintenance of the biodiversity. The animal husbandry of the twenty-first century has brought about a decline in biodiversity of bovine breeds, due to the abandonment of autochthonous cows in favour of more productive cosmopolitan breeds. The intense selection for milk traits applied on the cosmopolitan breeds has resulted nowadays in peculiar physiological features, which have impaired some immune defence mechanisms, increasing the incidence of infectious and metabolic diseases, and worsened both fertility and longevity. The situation is dramatically different within the autochthonous breeds. These animals, despite the apparent 'low production', present some important characteristics like great rusticity, frugality, longevity, disease resistance and resilience. They are able to adapt to marginal habitats and extensive production systems, maintaining adequate milk and meat production of high quality, using diets based on forage or pasture, which reduce also the competition with the human society for the food sources. These features make these animals the first choice in marginal areas where they can guarantee an economic return to farmers and play an important environmental role by helping the preservation of the habitats and landscapes.
Effects of Lorentz Breaking on the Accretion onto a Schwarzschild-like Black Hole*
Authors: Yang Rong-Jia , Gao He , Zheng Yao-Guang , Wu Qin 
Published: May 2019

Abstract

We formulate and solve the problem of spherically symmetric, steady state, adiabatic accretion onto a Schwarzschild-like black hole obtained recently. We derive the general analytic expressions for the critical points, the critical velocity, the critical speed of sound, and subsequently the mass accretion rate. The case for polytropic gas is discussed in detail. We find the parameter characterizing the breaking of Lorentz symmetry will slow down the mass accretion rate, while has no effect on the gas compression and the temperature profile below the critical radius and at the event horizon.
Repulsive Polarons in One-Dimensional Fermi Gases*
Authors: Song Ya-Dong , Barthwal Sachin 
Published: May 2019

Abstract

Using the variational method, we study the properties of a spin-down impurity immersed in a one-dimensional (1D) spin-up Fermi sea. With repulsive interactions between them, the impurity is dressed up by surrounding particles in Fermi sea and forms a polaron. We clearly calculate the binding energy, effective mass, momentum distribution, Tan contact, and pair correlation. Even in strong repulsive regimes, the results can agree with the exact Bethe Ansatz results. The repulsive polaron energy E+ is below Fermi energy EF and no negative effective masses are found in whole interaction regimes, unequal masses polarons are also calculated. We show a clear momentum distribution and calculate the Tan contact from three different aspects. Furthermore, we explore the particle-hole excitation and find that the hole terms in Fermi sea have a great influence on the polaron energy and contact in repulsive regime. These results show that the variational method can still be used effectively in 1D repulsive polaron system.
In Living Color: Early “Impressions” of Slavery and the Limits of Living History
Authors: Swanson Drew 
Published: May 2019

Abstract
In the 1970s, American historical sites began to more thoroughly and critically interpret slavery’s history, with a few institutions employing living history as an interpretive form. At sites like Virginia’s Mount Vernon and Colonial Williamsburg, the hope is that these historical “impressions” will engage audiences with a more authentic or credible representation of racial bondage. An earlier wave of living historical representations of slavery suggest the challenges and hazards of embodied history, however. In the late nineteenth and early twentieth centuries, a significant number of southern sites employed African American interpreters who claimed to have been born into slavery, often on the very sites where they were currently working. Historical attractions used the “authenticity” and “credibility” of these interpreters to advance the narrative of a happy Old South. Historians have noted these performances as part of the sectional reconciliation of the Jim Crow era, but have rarely interpreted them as public history. Although the contemporary living history of slavery has different—and far better—goals than impressions of a century past, this long history of embodied bondage suggests the implicit dangers of interpreting slavery and race through living people.
Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects
Authors: Tiuryn Jerzy , Szczurek Ewa 
Published: May 2019

AbstractMotivationPerturbation experiments constitute the central means to study cellular networks. Several confounding factors complicate computational modeling of signaling networks from this data. First, the technique of RNA interference (RNAi), designed and commonly used to knock-down specific genes, suffers from off-target effects. As a result, each experiment is a combinatorial perturbation of multiple genes. Second, the perturbations propagate along unknown connections in the signaling network. Once the signal is blocked by perturbation, proteins downstream of the targeted proteins also become inactivated. Finally, all perturbed network members, either directly targeted by the experiment, or by propagation in the network, contribute to the observed effect, either in a positive or negative manner. One of the key questions of computational inference of signaling networks from such data are, how many and what combinations of perturbations are required to uniquely and accurately infer the model?ResultsHere, we introduce an enhanced version of linear effects models (LEMs), which extends the original by accounting for both negative and positive contributions of the perturbed network proteins to the observed phenotype. We prove that the enhanced LEMs are identified from data measured under perturbations of all single, pairs and triplets of network proteins. For small networks of up to five nodes, only perturbations of single and pairs of proteins are required for identifiability. Extensive simulations demonstrate that enhanced LEMs achieve excellent accuracy of parameter estimation and network structure learning, outperforming the previous version on realistic data. LEMs applied to Bartonella henselae infection RNAi screening data identified known interactions between eight nodes of the infection network, confirming high specificity of our model and suggested one new interaction.Availability and implementationhttps://github.com/EwaSzczurek/LEMSupplementary informationSupplementary data are available at Bioinformatics online.
NRStitcher: non-rigid stitching of terapixel-scale volumetric images
Authors: Miettinen Arttu , Oikonomidis Ioannis Vogiatzis , Bonnin Anne , Stampanoni Marco 
Published: May 2019

Abstract

Summary
In modern microscopy, the field of view is often increased by obtaining an image mosaic, where multiple sub-images are taken side-by-side and combined post-acquisition. Mosaic imaging often leads to long imaging times that can increase the probability of sample deformation during the acquisition due to, e.g. changes in the environment, damage caused by the radiation used to probe the sample or biologically induced deterioration. Here we propose a technique, based on local phase correlation, to detect the deformations and construct an artifact-free image mosaic from deformed sub-images. The implementation of the method supports distributed computing and can be used to generate teravoxel-size mosaics. We demonstrate its capabilities by assembling a 5.6 teravoxel tomographic image mosaic of microvasculature in whole mouse brain. The method is compared to existing rigid stitching implementations designed for very large datasets, and observed to create artifact-free image mosaics in comparable runtime with the same hardware resources.

Availability and implementation
The stitching software and C++/Python source code are available at GitHub (https://github.com/arttumiettinen/pi2) along with an example dataset and user instructions.
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions
Authors: Hou Qingzhen , De Geest Paul F G , Griffioen Christian J , Abeln Sanne , Heringa Jaap , Feenstra K Anton 
Published: May 2019

AbstractMotivationInterpretation of ubiquitous protein sequence data has become a bottleneck in biomolecular research, due to a lack of structural and other experimental annotation data for these proteins. Prediction of protein interaction sites from sequence may be a viable substitute. We therefore recently developed a sequence-based random forest method for protein–protein interface prediction, which yielded a significantly increased performance than other methods on both homomeric and heteromeric protein–protein interactions. Here, we present a webserver that implements this method efficiently.ResultsWith the aim of accelerating our previous approach, we obtained sequence conservation profiles by re-mastering the alignment of homologous sequences found by PSI-BLAST. This yielded a more than 10-fold speedup and at least the same accuracy, as reported previously for our method; these results allowed us to offer the method as a webserver. The web-server interface is targeted to the non-expert user. The input is simply a sequence of the protein of interest, and the output a table with scores indicating the likelihood of having an interaction interface at a certain position. As the method is sequence-based and not sensitive to the type of protein interaction, we expect this webserver to be of interest to many biological researchers in academia and in industry.Availability and implementationWebserver, source code and datasets are available at www.ibi.vu.nl/programs/serendipwww/.Supplementary informationSupplementary data are available at Bioinformatics online.
Conserved growth rate and age structure of Xenopus laevis in the edge and core of an expanding population
Authors: Courant Julien , Adil Layla , De Kegel Barbara , Adriaens Dominique , Herrel Anthony 
Published: May 2019

Abstract
Invasive species represent a unique opportunity to study the evolutionary mechanisms driving range expansions. Although range expansion is expected to be associated with increased reproduction and dispersal at the range edge, Xenopus laevis seems to decrease its reproductive investment and to enhance dispersal at the range edge. Evidence of increased dispersal at the edge of expanding populations occurring simultaneously with a faster growth rate has been reported for other organisms. Here, we focused on the growth rate and age structure at the range edge vs. the range core in an expanding population of X. laevis. We used skeletochronology to characterize the age of 250 individuals captured at the range core and edge of this expanding population. Using the Von Bertalanffy equation, we then compared individual growth rates between locations. We found no significant changes in growth rate or age structure between edge and core samples. This result suggests that the reduced investment in reproduction recorded in another study at the range edge might compensate for the increased dispersal without impacting growth in this population. This implies that the resource allocation in an expanding population might thus be more diverse than commonly assumed.