bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transthyretin-assoziierte familiäre Amyloidpolyneuropathie
Authors: Niemietz Christoph , Röcken Christoph , Schilling Matthias , Stypman Jörg , Uhlig Constantin , Schmidt Hartmut 
Published: March 2018

AbstractTransthyretin-related Familial Amyloid Polyneuropathy (ATTR Amyloidosis, former FAP, here called TTR-FAP) is a rare, progressive autosomal dominant inherited amyloid disease ending fatal within 5 – 15 years after final diagnosis. TTR-FAP is caused by mutations of transthyretin (TTR), which forms amyloid fibrils affecting peripheral and autonomic nerves, the heart and other organs. Due to the phenotypic heterogeneity and partly not specific enough clinical symptoms, diagnosis of TTR-FAP can be complicated. False diagnoses can include idiopathic polyneuropathy, chronic inflammatory demyelinating polyneuropathy, diabetic neuropathy as well as paraneoplastic syndrome. Hence, it is assumed that many cases remain unreported. Early and correct diagnosis of TTR-FAP is crucial, since appropriate therapeutic options exist. TTR-FAP should always be differentially diagnosed, when apart from a progressive peripheral polyneuropathy, additional symptoms as autonomic dysfunction, cardiomyopathy, gastrointestinal disorders, unexpected loss of weight, carpal tunnel syndrome, restrictions of renal function, epileptic fits, and corneal and vitreous body clouding occur. Histological evidence of amyloid and successive immunohistochemical evidence of transthyretin as well as genetic testing for transthyretin mutations, lead to an accurate diagnosis.
Family obligations across European borders: negotiating migration decisions within the families of post-accession migrants in Sweden
Authors: Shmulyar Gréen Oksana , Melander Charlotte 
Published: March 2018

AbstractThe negotiation of migration decisions within the families of post-accession mobile workers from Poland and Romania in Sweden is explored through the concept of family obligations. This study departs from Finch’s (1987) and Mason’s (1996) seminal works, which identified a wide range of supportive (and non-supportive) exchanges and negotiated commitments within families and their kin. Drawing on Mason’s (1996) definition of care as both sentient activity and active sensibility, we seek to understand how migrant parents negotiate their migration decisions as an act of care and responsibility, but also as morally imbued obligations in relation to their children. As an analytical tool, the lifeline method (Davies, 1996) is used to capture key moments and events shaping the migration decisions of European workers’ families, which include their motivations to pursue migration, the gendered patterns of care shaping their migration decisions, and moral reasoning over what is the right thing to do in relation to caring for their children. The analysis shows that mobile families’ decisions to migrate are ‘livelihood strategies’ involving complex and dynamic negotiations over the options and resources of entire families and their kin across generations and transnational locations. While reflecting on their decisions over time, both migrant parents express their genuine involvement in caring responsibilities. However, the actual practice shows that caring is still a gendered activity. Finally, the decision to migrate shows that migration itself can be seen as an act of relational and emotional caring involving moral reasoning, feelings and thoughts through which migrant parents negotiate their “good parenthood”.
Perception of formulaic and novel expressions under acoustic degradation
Authors: Rammell C. Sophia , Van Lancker Sidtis Diana , Pisoni David B. 
Published: March 2018

AbstractBackground: Formulaic expressions, including idioms and other fixed expressions, comprise a significant proportion of discourse. Although much has been written about this topic, controversy remains about their psychological status. An important claim about formulaic expressions, that they are known to native speakers, has seldom been directly demonstrated. This study tested the hypothesis that formulaic expressions are known and stored as whole unit mental representations by performing three perceptual experiments.Method: Listeners transcribed two kinds of spectrally-degraded spoken sentences, half formulaic, and half novel, newly created expressions, matched for grammar and length. Two familiarity ratings, usage and exposure, were obtained from listeners for each expression. Text frequency data for the stimuli and their constituent words were obtained using a spoken corpus.Results: Participants transcribed formulaic more successfully than literal utterances. Usage and familiarity ratings correlated with accuracy, but formulaic utterances with low ratings were also transcribed correctly. Phrase types differed significantly in text frequency, but word frequency counts did not differentiate the two kinds of expressions.Discussion: These studies provide new converging evidence that formulaic expressions are encoded and processed as whole units, supporting a dual-process model of language processing, which assumes that grammatical and formulaic expressions are differentially processed.
Commonly stabilized cytochromes c from deep-sea Shewanella and Pseudomonas
Authors: Fujii Sotaro , Masanari-Fujii Misa , Kobayashi Shinya , Kato Chiaki , Nishiyama Masayoshi , Harada Yoshie , Wakai Satoshi , Sambongi Yoshihiro 
Published: March 2018

Abstract
Two cytochromes c5 (SBcytc and SVcytc) have been derived from Shewanella living in the deep-sea, which is a high pressure environment, so it could be that these proteins are more stable at high pressure than at atmospheric pressure, 0.1 MPa. This study, however, revealed that SBcytc and SVcytc were more stable at 0.1 MPa than at higher pressure. In addition, at 0.1–150 MPa, the stability of SBcytc and SVcytc was higher than that of homologues from atmospheric-pressure Shewanella, which was due to hydrogen bond formation with the heme in the former two proteins. This study further revealed that cytochrome c551 (PMcytc) of deep-sea Pseudomonas was more stable than a homologue of atmospheric-pressure Pseudomonas aeruginosa, and that specific hydrogen bond formation with the heme also occurred in the former. Although SBcytc and SVcytc, and PMcytc are phylogenetically very distant, these deep-sea cytochromes c are commonly stabilized through hydrogen bond formation.
CMV: visualization for RNA and protein family models and their comparisons
Authors: Eggenhofer Florian , Hofacker Ivo L , Backofen Rolf , Höner zu Siederdissen Christian 
Published: March 2018

Abstract

Summary
A standard method for the identification of novel RNAs or proteins is homology search via probabilistic models. One approach relies on the definition of families, which can be encoded as covariance models (CMs) or Hidden Markov Models (HMMs). While being powerful tools, their complexity makes it tedious to investigate them in their (default) tabulated form. This specifically applies to the interpretation of comparisons between multiple models as in family clans. The Covariance model visualization tools (CMV) visualize CMs or HMMs to: I) Obtain an easily interpretable representation of HMMs and CMs; II) Put them in context with the structural sequence alignments they have been created from; III) Investigate results of model comparisons and highlight regions of interest.

Availability and implementation
Source code (http://www.github.com/eggzilla/cmv), web-service (http://rna.informatik.uni-freiburg.de/CMVS).

Supplementary information
Supplementary data are available at Bioinformatics online.
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors
Authors: Lo Monte Matteo , Manelfi Candida , Gemei Marica , Corda Daniela , Beccari Andrea Rosario 
Published: March 2018

Abstract

Motivation
ADP-ribosylation is a post-translational modification (PTM) implicated in several crucial cellular processes, ranging from regulation of DNA repair and chromatin structure to cell metabolism and stress responses. To date, a complete understanding of ADP-ribosylation targets and their modification sites in different tissues and disease states is still lacking. Identification of ADP-ribosylation sites is required to discern the molecular mechanisms regulated by this modification. This motivated us to develop a computational tool for the prediction of ADP-ribosylated sites.

Results
Here, we present ADPredict, the first dedicated computational tool for the prediction of ADP-ribosylated aspartic and glutamic acids. This predictive algorithm is based on (i) physicochemical properties, (ii) in-house designed secondary structure-related descriptors and (iii) three-dimensional features of a set of human ADP-ribosylated proteins that have been reported in the literature. ADPredict was developed using principal component analysis and machine learning techniques; its performance was evaluated both internally via intensive bootstrapping and in predicting two external experimental datasets. It outperformed the only other available ADP-ribosylation prediction tool, ModPred. Moreover, a novel secondary structure descriptor, HM-ratio, was introduced and successfully contributed to the model development, thus representing a promising tool for bioinformatics studies, such as PTM prediction.

Availability and implementation
ADPredict is freely available at www.ADPredict.net.

Supplementary information
Supplementary data are available at Bioinformatics online.
RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules
Authors: Neveu Emilie , Popov Petr , Hoffmann Alexandre , Migliosi Angelo , Besseron Xavier , Danoy Grégoire , Bouvry Pascal , Grudinin Sergei 
Published: March 2018

Abstract

Motivation
The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of spatially proximate molecular conformations. Previously, we introduced the RigidRMSD algorithm to compute the RMSD corresponding to the rigid-body motion of a molecule. In this study, we go beyond the limits of the rigid-body approximation by taking into account conformational flexibility of the molecule. We model the flexibility with a reduced set of collective motions computed with e.g. normal modes or principal component analysis.

Results
The initialization of our algorithm is linear in the number of atoms and all the subsequent evaluations of RMSD values between flexible molecular conformations depend only on the number of collective motions that are selected to model the flexibility. Therefore, our algorithm is much faster compared to the standard RMSD computation for large-scale modeling applications. We demonstrate the efficiency of our method on several clustering examples, including clustering of flexible docking results and molecular dynamics (MD) trajectories. We also demonstrate how to use the presented formalism to generate pseudo-random constant-RMSD structural molecular ensembles and how to use these in cross-docking.

Availability and implementation
We provide the algorithm written in C++ as the open-source RapidRMSD library governed by the BSD-compatible license, which is available at http://team.inria.fr/nano-d/software/RapidRMSD/. The constant-RMSD structural ensemble application and clustering of MD trajectories is available at http://team.inria.fr/nano-d/software/nolb-normal-modes/.

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepSol: a deep learning framework for sequence-based protein solubility prediction
Authors: Khurana Sameer , Rawi Reda , Kunji Khalid , Chuang Gwo-Yu , Bensmail Halima , Mall Raghvendra 
Published: March 2018

Abstract

Motivation
Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imperative to develop novel, highly accurate in silico sequence-based protein solubility predictors. In this work we propose, DeepSol, a novel Deep Learning-based protein solubility predictor. The backbone of our framework is a convolutional neural network that exploits k-mer structure and additional sequence and structural features extracted from the protein sequence.

Results
DeepSol outperformed all known sequence-based state-of-the-art solubility prediction methods and attained an accuracy of 0.77 and Matthew’s correlation coefficient of 0.55. The superior prediction accuracy of DeepSol allows to screen for sequences with enhanced production capacity and can more reliably predict solubility of novel proteins.

Availability and implementation
DeepSol’s best performing models and results are publicly deposited at https://doi.org/10.5281/zenodo.1162886 (Khurana and Mall, 2018).

Supplementary information
Supplementary data are available at Bioinformatics online.
Arioc: GPU-accelerated alignment of short bisulfite-treated reads
Authors: Wilton Richard , Li Xin , Feinberg Andrew P , Szalay Alexander S 
Published: March 2018

Abstract

Motivation
The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can be mitigated by appropriate algorithmic and software-engineering improvements. One strategy is to modify the read-alignment algorithms by integrating the logic related to BS-seq alignment, with the goal of making the software implementation amenable to optimizations that lead to higher speed and greater sensitivity than might otherwise be attainable.

Results
We evaluated this strategy using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic. We integrated the BS-seq computational logic into both GPU and CPU code throughout the Arioc implementation. We then carried out a read-by-read comparison of Arioc's reported alignments with the alignments reported by well-known CPU-based BS-seq read aligners. With simulated reads, Arioc's accuracy is equal to or better than the other read aligners we evaluated. With human sequencing reads, Arioc's throughput is at least 10 times faster than existing BS-seq aligners across a wide range of sensitivity settings.

Availability and implementation
The Arioc software is available for download at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

Supplementary information
Supplementary data are available at Bioinformatics online.
SCOTCH: subtype A coreceptor tropism classification in HIV-1
Authors: Löchel Hannah F , Riemenschneider Mona , Frishman Dmitrij , Heider Dominik 
Published: March 2018

Abstract

Motivation
The V3 loop of the gp120 glycoprotein of the Human Immunodeficiency Virus 1 (HIV-1) is considered to be responsible for viral coreceptor tropism. gp120 interacts with the CD4 receptor of the host cell and subsequently V3 binds either CCR5 or CXCR4. Due to the fact that the CCR5 coreceptor is targeted by entry inhibitors, a reliable prediction of the coreceptor usage of HIV-1 is of great interest for antiretroviral therapy. Although several methods for the prediction of coreceptor tropism are available, almost all of them have been developed based on only subtype B sequences, and it has been shown in several studies that the prediction of non-B sequences, in particular subtype A sequences, are less reliable. Thus, the aim of the current study was to develop a reliable prediction model for subtype A viruses.

Results
Our new model SCOTCH is based on a stacking approach of classifier ensembles and shows a significantly better performance for subtype A sequences compared to other available models. In particular for low false positive rates (between 0.05 and 0.2, i.e. recommendation in the German and European Guidelines for tropism prediction), SCOTCH shows significantly better prediction performances in terms of partial area under the curves and diagnostic odds ratios compared to existing tools, and thus can be used to reliably predict coreceptor tropism for subtype A sequences.

Availability and implementation
SCOTCH can be downloaded/accessed at http://www.heiderlab.de.
Conditional expectation estimation through attributable components
Authors: Tabak Esteban G , Trigila Giulio 
Published: March 2018

Abstract
A general methodology is proposed for the explanation of variability in a quantity of interest x in terms of covariates z = (z1, …, zL). It provides the conditional mean $\bar{x}(z)$ as a sum of components, where each component is represented as a product of non-parametric one-dimensional functions of each covariate zl that are computed through an alternating projection procedure. Both x and the zl can be real or categorical variables; in addition, some or all values of each zl can be unknown, providing a general framework for multi-clustering, classification and covariate imputation in the presence of confounding factors.
The procedure can be considered as a preconditioning step for the more general determination of the full conditional distribution $\boldsymbol{\rho}(x|z) $ through a data-driven optimal-transport barycenter problem. In particular, just iterating the procedure once yields the second order structure (i.e. the covariance) of $\boldsymbol{\rho}(x|z) $.
The methodology is illustrated through examples that include the explanation of variability of ground temperature across the continental United States and the prediction of book preference among potential readers.
Normal Breast Anatomy and Histology
Authors: Apple Sophia K. , Bassett Lawrence W. 
Published: March 2018

Abstract
In this chapter, normal breast anatomy is discussed, with a succinct pictorial summary of breast glandular elements, the chest wall, and the axilla. The locations of breast lesions are often arbitrarily divided into upper outer, upper inner, lower inner, and upper inner quadrants. However, the lobes within a specific quadrant cross over into adjacent quadrants. The terminal duct lobular unit (TDLU) is composed of an interlobular duct and associated lobules with multiple grape-like structures where the milk is secreted and drains into the terminal ducts, interlobular ducts, excretory ducts, lactiferous sinus, lactiferous duct, and the nipple. Axillary lymph nodes are divided into three levels, based on their location in relation to the pectoralis minor muscle. Level I axillary lymph nodes are located below the edge of the pectoralis minor; level II lies posterior to the pectoralis minor; and level III lies medial to the pectoralis minor.
Circumscribed Mass: Cysts, Complicated Cysts, Clustered Microcysts
Authors: Kettler Mark D. 
Published: March 2018

Abstract
Benign cysts can occur in women of all ages, but they have a predilection for women in their 40s and 50s, and are far less common in younger and older women. Most cysts arise at the level of the terminal duct-lobular unit (TDLU); less commonly, cysts are caused by ectasia of central ducts. This chapter, appearing in the section on circumscribed mass, reviews the key clinical and imaging features, differential diagnosis, and management recommendations for primary cystic masses, including simple cysts, complicated cysts, and clustered microcysts. Careful assessment of sonographic features usually allows a definitive diagnosis of these benign entities that do not typically require tissue sampling. Some complex masses containing fluid and/or cystic-appearing components may require tissue sampling for diagnosis.
Spiculated Masses
Authors: Andrejeva Liva , Geisel Jaime L. , Harigopal Malini 
Published: March 2018

Abstract
A spiculated mass is a centrally dense lesion seen on mammography with sharp lines radiating from its margin. The spicules can vary greatly in length, from a few millimeters to several centimeters. In malignant lesions, spicules represent a mixture of tumor cells and fibrosis invading the normal tissue surrounding the lesion. Although a spiculated mass is thought of as a classic finding of malignancy on mammography, ultrasound, and MRI, its differential diagnosis includes benign lesions. However, unless clinical history strongly supports a benign diagnosis, a spiculated mass on any modality typically will require additional workup and biopsy. This chapter reviews the key imaging and clinical features, imaging protocols and pitfalls, differential diagnoses, radiology–pathology correlations, and clinical management recommendations for a spiculated mass. Topics discussed include both malignant and benign masses.
Mass in Lactating Female
Authors: Woldenberg Nina , Joines Melissa M. 
Published: March 2018

Abstract
Timely and accurate diagnosis of a mass in the lactating patient requires comprehensive understanding of the indicated imaging workup. During lactation it is not uncommon for patients to present with a palpable mass that requires evaluation. In patients with a palpable abnormality, diagnostic evaluation should not be delayed due to pregnancy or lactation. In addition, a mass that requires further evaluation may be identified at the time of screening mammography in lactating patients. This chapter, appearing in the section on asymmetry, mass, and distortion, reviews the key imaging and clinical features, imaging protocols and pitfalls, differential diagnoses, and management recommendations for a mass in the lactating patient. Topics discussed include differential considerations of benign and malignant masses in the lactating breast including cysts, focal lobular hyperplasia (focal fibrocystic change), galactocele, abscess, fibroadenoma, lactating adenoma, and pregnancy-associated breast cancer.
Architectural Distortion (Cancer)
Authors: Durand Melissa A. 
Published: March 2018

Abstract
An architectural distortion (AD) is an alteration of the breast parenchyma, which results in radiating lines or spicules emanating from a point without a distinct mass. It can occur as the primary finding, or it may be an associated feature of a mass, asymmetry, or calcifications. AD is a mammographic finding with a high positive predictive value for malignancy and is a major cause of false-negative screening exams. This chapter, appearing in the section on asymmetry, mass, and distortion, reviews the key imaging and clinical features, imaging protocols, differential diagnoses, management recommendations, and potential pitfalls for a malignant architectural distortion. Topics discussed include superimposition of breast tissue, localization, workup of tomosynthesis-detected architectural distortion, and image-guided biopsy options.
Vascular Calcifications
Authors: Holbrook Anna I. 
Published: March 2018

Abstract
Vascular calcifications lie within the artery wall, and appear to be linear, usually in association with blood vessels. The parallel or “tram-track” appearance of the calcifications in opposite walls of the artery is pathognomonic. They are more prevalent with age. They are also associated with diabetes, renal disease, hyperparathyroidism, parity, and history of lactation, and possibly, cardiovascular disease. Vascular calcifications in the breast are within the arterial wall media, where they are known as Mönckeberg medial calcific sclerosis. This chapter reviews the key imaging features, imaging protocols, differential diagnoses, and management recommendations for vascular calcifications. Topics discussed include demographics and comorbidities, linear calcifications, and diagnostic workup.