bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causativization of verbs of directed motion in Romance languages
Authors: Pineda Anna 
Published: July 2018

Abstract
The purpose of this paper is to shed light on a particular behavior displayed by verbs of inherently directed motion, the availability of a causative transitive alternate, and how this phenomenon interacts with the presence of clitic se in the intransitive variant. Data from Catalan, Aragonese and Italian varieties, none of which have received much attention in the literature, will prove crucial for our proposal. We adopt an inter-Romance perspective and a nanosyntactic approach to lexicalization in order to refine the correlation Jiménez-Fernández and Tubino (2014, 2017) find for Spanish, where inherently directional motion verbs are claimed to be more easily causativized (entrar el coche ‘go in the car’) in varieties where the use of se in the intransitive forms is also more frequent (Juan se entró ‘Juan se went in’).
Resumed phrases (are always moved, even with in-island resumption)
Authors: Sportiche Dominique 
Published: July 2018

Abstract
On the basis of the properties of resumption in colloquial spoken French, I conclude that resumption of a phrase by a pronominal element always involve run of the mill movement of this phrase, whether the resumptive pronoun is inside an island or not. I propose that such movement can take place in two steps, the first being one of the Left Dislocation options, which feeds a variety of possible second steps (e.g., wh-movement or Clitic Left Dislocation).
Cognate noun constructions in Early Modern English
Authors: Lavidas Nikolaos 
Published: July 2018

Abstract
This paper examines cognate noun constructions (CNCs) (e.g. smile a disarming smile) in Early Modern English, particularly in the first complete English translation of the Bible from the original Greek and Hebrew by William Tyndale. Tyndale’s translation is produced during a period of significant expansion of CNCs in English. It is argued that CNCs in Tyndale are a marker of a particular English biblical register which involves archaic (early) English properties (cognate nouns in PPs) rather than a new tendency for cognate direct objects or the result of a translation effect alone. In other words, it is shown that Tyndale’s translation follows archaic/early English rules, thus deviating both from the new tendency for cognate direct objects and from the source text. This archaic characteristic of CNCs with cognate nouns in PPs instantiates a general tendency in Tyndale’s translation to use archaisms – as evidenced, for instance, in his dispreference of auxiliaries.
Learning structural motif representations for efficient protein structure search
Authors: Liu Yang , Ye Qing , Wang Liwei , Peng Jian 
Published: July 2018

Abstract

Motivation
Given a protein of unknown function, fast identification of similar protein structures from the Protein Data Bank (PDB) is a critical step for inferring its biological function. Such structural neighbors can provide evolutionary insights into protein conformation, interfaces and binding sites that are not detectable from sequence similarity. However, the computational cost of performing pairwise structural alignment against all structures in PDB is prohibitively expensive. Alignment-free approaches have been introduced to enable fast but coarse comparisons by representing each protein as a vector of structure features or fingerprints and only computing similarity between vectors. As a notable example, FragBag represents each protein by a ‘bag of fragments’, which is a vector of frequencies of contiguous short backbone fragments from a predetermined library. Despite being efficient, the accuracy of FragBag is unsatisfactory because its backbone fragment library may not be optimally constructed and long-range interacting patterns are omitted.

Results
Here we present a new approach to learning effective structural motif presentations using deep learning. We develop DeepFold, a deep convolutional neural network model to extract structural motif features of a protein structure. We demonstrate that DeepFold substantially outperforms FragBag on protein structural search on a non-redundant protein structure database and a set of newly released structures. Remarkably, DeepFold not only extracts meaningful backbone segments but also finds important long-range interacting motifs for structural comparison. We expect that DeepFold will provide new insights into the evolution and hierarchical organization of protein structural motifs.

Availability and implementation
https://github.com/largelymfs/DeepFold
The Terabase Search Engine: a large-scale relational database of short-read sequences
Authors: Wilton Richard , Wheelan Sarah J , Szalay Alexander S , Salzberg Steven L 
Published: July 2018

Abstract

Motivation
DNA sequencing archives have grown to enormous scales in recent years, and thousands of human genomes have already been sequenced. The size of these data sets has made searching the raw read data infeasible without high-performance data-query technology. Additionally, it is challenging to search a repository of short-read data using relational logic and to apply that logic across samples from multiple whole-genome sequencing samples.

Results
We have built a compact, efficiently-indexed database that contains the raw read data for over 250 human genomes, encompassing trillions of bases of DNA, and that allows users to search these data in real-time. The Terabase Search Engine enables retrieval from this database of all the reads for any genomic location in a matter of seconds. Users can search using a range of positions or a specific sequence that is aligned to the genome on the fly.

Availability and implementation
Public access to the Terabase Search Engine database is available at http://tse.idies.jhu.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries
Authors: Noor Zainab , Wu Jemma X , Pascovici Dana , Mohamedali Abidali , Molloy Mark P , Baker Mark S , Ranganathan Shoba 
Published: July 2018

Abstract

Summary
Large-scale peptide mass spectrometry (MS)/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a comprehensive set of spectra for identification and quantification of proteins. We have developed a novel web-based R-package (iSwathX) for combining reference libraries that is compatible with different DIA analysis software. This open-source web GUI automates the process of normalization and combination of spectral libraries and provides a user-friendly method for performing library format conversions, analysis and visualizations, with no need for programing familiarity.

Availability and implementation
iSwathX is freely accessible at https://biolinfo.shinyapps.io/iSwathX with the R-package and Shiny source code available from GitHub (https://github.com/znoor/iSwathX).

Supplementary information
Supplementary data are available at Bioinformatics online.
Addressing the gender-knowledge gap in glucose-6-phosphate dehydrogenase deficiency: challenges and opportunities
Authors: Domingo Gonzalo J , Advani Nicole , Satyagraha Ari W , Sibley Carol H , Rowley Elizabeth , Kalnoky Michael , Cohen Jessica , Parker Michael , Kelley Maureen 
Published: July 2018

AbstractGlucose-6-phosphate dehyrdgoenase (G6PD) deficiency is a common X-linked genetic trait, with an associated enzyme phenotype, whereby males are either G6PD deficient or normal, but females exhibit a broader range of G6PD deficiencies, ranging from severe deficiency to normal. Heterozygous females typically have intermediate G6PD activity. G6PD deficiency has implications for the safe treatment for Plasmodium vivax malaria. Individuals with this deficiency are at greater risk of serious adverse events following treatment with the only curative class of anti-malarials, 8-aminoquinolines, such as primaquine. Quantitative diagnostic tests for G6PD deficiency are complex and require sophisticated laboratories. The commonly used qualitative tests, do not discriminate intermediate G6PD activities. This has resulted in poor understanding of the epidemiology of G6PD activity in females and its corresponding treatment ramifications. New simple-to-use quantitative tests, and a momentum to eliminate malaria, create an opportunity to address this knowledge gap. While this will require additional resources for clinical studies, adequate operational research, and appropriate pharmacovigilance, the health benefits from this investment go beyond the immediate intervention for which the G6PD status is first diagnosed.
Global Effects of Focal Brain Tumors on Functional Complexity and Network Robustness: A Prospective Cohort Study
Authors: Hart Michael G , Romero-Garcia Rafael , Price Stephen J , Suckling John 
Published: July 2018

Abstract

BACKGROUND
Neurosurgical management of brain tumors has entered a paradigm of supramarginal resections that demands thorough understanding of peritumoral functional effects. Historically, the effects of tumors have been believed to be local, and long-range effects have not been considered.

OBJECTIVE
To test the hypothesis that tumors affect the brain globally, producing long-range gradients in cortical function.

METHODS
Resting-state functional magnetic resonance imaging (fMRI) data were acquired from 11 participants with glioblastoma and split into discovery and validation datasets in a single-center prospective cohort study. Fractal complexity was computed with a wavelet-based estimator of the Hurst exponent. Distance-related effects of the tumors were tested with a tumor mask-dilation technique and parcellation of the underlying Hurst maps.

RESULTS
Fractal complexity demonstrates a penumbra of suppression in the peritumoral region. At a global level, as distance from the tumor increases, this initial suppression is balanced by a subsequent overactivity before finally normalizing. These effects were best fit by a quadratic model and were consistent across different network construction pipelines. The Hurst exponent was correlated with graph theory measures of centrality including network robustness, but graph theory measures did not demonstrate distance-dependent effects.

CONCLUSION
This work provides evidence supporting the theory that focal brain tumors produce long-range gradients in function. Consequently, the effects of focal lesions need to be interpreted in terms of the global changes on functional complexity and network architecture rather than purely in terms of functional localization. Determining whether peritumoral changes represent potential plasticity may facilitate extended resection of tumors without functional cost.
Survival impact of prolonged postoperative radiation therapy for patients with glioblastoma treated with combined-modality therapy
Authors: Yusuf Mehran B , Gaskins Jeremy , Amsbaugh Mark J , Woo Shiao , Burton Eric 
Published: July 2018

Abstract

Background
Though conventionally fractionated chemoradiation (CRT) is well tolerated by selected patients with newly diagnosed glioblastoma (GBM), adverse health-related and nonhealth-related factors can lead to unplanned interruptions in treatment. The effects of prolonged time to completion (TTC) of radiation therapy (RT) on overall survival (OS) for these patients are unclear.

Methods
The National Cancer Database (NCDB) was queried for all adult patients with newly diagnosed GBM undergoing surgical resection followed by adjuvant CRT with conventionally fractionated RT (6000-6600 cGy in 30-33 fractions) from 2005 to 2012. TTC was defined as the interval from first to last fraction of RT. Recursive partitioning analysis (RPA) was used to determine a threshold for TTC of adjuvant RT. Cox proportional hazards modeling was used to identify covariates associated with OS.

Results
A total of 13489 patients were included in our cohort. Patients who completed adjuvant RT within the RPA-defined threshold of 46 days from initiation of RT (median OS: 14.0 months, 95% confidence interval (CI) 13.7 to 14.3 months) had significantly improved OS compared to patients with TTC of 47 days or greater (median OS: 12.0 months, 95% CI 11.4 to 12.6 months, P < .001). Delays in completing adjuvant RT were relatively common, with 15.0% of patients in our cohort having a TTC of RT of 47 days or greater.

Conclusions
Delays in completing adjuvant RT were associated with a worse survival outcome. Any unnecessary delays in completing adjuvant RT should be minimized while ensuring the safe delivery of therapy.
Loss of lipin 1‐mediated phosphatidic acid phosphohydrolase activity in muscle leads to skeletal myopathy in mice
Authors: Schweitzer George G. , Collier Sara L. , Chen Zhouji , Mccommis Kyle S. , Pittman Sara K. , Yoshino Jun , Matkovich Scot J. , Hsu Fong-Fu , Chrast Roman , Eaton James M. , Harris Thurl E. , Weihl Conrad C. , Finck Brian N. 
Published: July 2018

ABSTRACTLipin 1 regulates glycerolipid homeostasis by acting as a phosphatidic acid phosphohydrolase (PAP) enzyme in the triglyceride‐synthesis pathway and by regulating transcription factor activity. Mutations in human lipin 1 are a common cause of recurrent rhabdomyolysis in children. Mice with constitutive whole‐body lipin 1 deficiency have been used to examine mechanisms connecting lipin 1 deficiency to myocyte injury. However, that mouse model is confounded by lipodystrophy not phenocopied in people. Herein, 2 muscle‐specific mouse models were studied: 1) Lpin1 exon 3 and 4 deletion, resulting in a hypomorphic protein without PAP activity, but which preserved transcriptional coregulatory function; and 2) Lpin1 exon 7 deletion, resulting in total protein loss. In both models, skeletal muscles exhibited a chronic myopathy with ongoing muscle fiber necrosis and regeneration and accumulation of phosphatidic acid and, paradoxically, diacylglycerol. Additionally, lipin 1–deficient mice had abundant, but abnormal, mitochondria likely because of impaired autophagy. Finally, these mice exhibited increased plasma creatine kinase following exhaustive exercise when unfed. These data suggest that mice lacking lipin 1–mediated PAP activity in skeletal muscle may serve as a model for determining the mechanisms by which lipin 1 deficiency leads to myocyte injury and for testing potential therapeutic approaches.—Schweitzer, G. G., Collier, S. L., Chen, Z., McCommis, K. S., Pittman, S. K., Yoshino, J., Matkovich, S. J., Hsu, F.‐F., Chrast, R., Eaton, J. M., Harris, T. E., Weihl, C. C., Finck, B. N. Loss of lipin 1–mediated phosphatidic acid phosphohydrolase activity in muscle leads to skeletal myopathy in mice. FASEB J. 33, 652–667 (2019). www.fasebj.org
Klippel-Feil Syndrome With Auxiliary Anterior Cervical Meningomyelocele and Thoracic Syringomyelia
Authors: Alam Mehtab , Haq Ayaz ul , Shah Muzaffar , Haqqani Usman , Ullah Sajjad 
Published: July 2018

Study Design.
Case report.

Objective.
Since this is the first ever case of a male patient with Klippel-Feil syndrome (KFS) with anterior cervical meningomyelocele and syringomyelia. All four previously reported cases were female patients. This makes this case unique.

Summary of Background Data.
KFS with auxiliary anterior cervical meningomyelocele is a rare entity. To the best of our knowledge so far only four cases are reported.

Methods.
A 22-year-old male patient was presented to neurology outpatient department with 2-year history of left hand paresthesia and progressive weakness. The diagnostic evaluation showed KFS with auxiliary anterior cervical meningomyelocele and thoracic syringomyelia.

Results.
Patient was sent to neurosurgery department for intervention. After discussing the possible risks and complications of intervention he opted for conservative therapy and declined the surgery.

Conclusion.
The paucity of data is the key reason for any recommended protocol for management of such patients but the available literature recommends neurosurgical intervention in symptomatic patients.

Level of Evidence: 5
New perspectives in the therapeutic approach of peripheral T-cell lymphoma
Authors: Gisselbrecht Christian , Sibon David 
Published: July 2018

Purpose of review
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of mature T-cell and natural killer (NK)-cell neoplasms in the WHO 2016 classification. Patient prognosis is poor when treated with CHOP, and there is an unmet need for new drugs. Several agents have been developed for PTCL, and their use is the subject of this review.

Recent findings
Phase 2 studies demonstrated the activity of new drugs in Relapsed/refractory PTCL. Only four compounds were approved by the food and drug administration: romidepsin and belinostat, which are epigenetic modifiers, the antifolate agent pralatrexate, the immuno-conjugate brentuximab vedotin. New combinations have been tested, but the results were disappointing. Given the latest progress in biology, targeted agents are evaluated in different subtypes of PTCL. Relapsed anaplastic large-cell lymphoma exhibits improved prognosis with the approved anti-CD30 drug conjugate brentuximab vedotin. Localized nasal NK/T is treated with radiotherapy and nonanthracycline chemotherapy with L-asparaginase. Recently, immune checkpoint inhibitors demonstrated activity in NK/T lymphoma and can be used in elderly patients.

Summary
Treatment remains a challenge for PTCL, and several targeted drugs provide new approaches. Progress will be made incrementally in the different subtypes. One of the critical situations facing new drugs is the ability to run robust clinical trials in rare diseases.
Forty-year Seasonality Trends in Occurrence of Myocardial Infarction, Ischemic Stroke, and Hemorrhagic Stroke
Authors: Skajaa Nils , Horváth-Puhó Erzsébet , Sundbøll Jens , Adelborg Kasper , Rothman Kenneth J. , Sørensen Henrik Toft 
Published: July 2018

Background:
The occurrence of myocardial infarction (MI), ischemic stroke, and hemorrhagic stroke has decreased in recent years, but trends in seasonal occurrence remain unclear.

Methods:
Using Danish healthcare databases, we identified all patients with a first-time MI, ischemic stroke, or hemorrhagic stroke during the study period (1977–2016). We summarized monthly cases for each disease separately and computed the peak-to-trough ratio as a measure of seasonal occurrence of one cycle. To examine trends over time in seasonal occurrence, we computed the peak-to-trough ratio for each of the 40 years. We also quantified the amount of bias arising from random error in peak-to-trough ratios.

Results:
Before consideration of bias, the peak-to-trough ratio of summarized monthly cases was 1.11 (95% confidence interval [CI] = 1.10, 1.12) for MI, 1.08 (95% CI = 1.07, 1.09) for ischemic stroke, and 1.12 (95% CI = 1.10, 1.14) for hemorrhagic stroke. The peak-to-trough ratio of MI occurrence increased from 1.09 (95% CI = 1.04, 1.15) in 1977 to 1.16 (95% CI = 1.09, 1.23) in 1999. The trend then remained stable. The peak-to-trough ratio of ischemic stroke occurrence declined continuously during the study period, dropping from 1.12 (95% CI = 1.02, 1.24) in 1977 to 1.06 (95% CI = 1.00, 1.12) in 2016. The peak-to-trough ratio of hemorrhagic stroke occurrence remained stable over time. However, after adjusting for potential bias, time trends in peak-to-trough ratios were almost flat.

Conclusions:
We found no substantial seasonality for MI, ischemic stroke, or hemorrhagic stroke occurrence during 1977−2016. Modest peak-to-trough ratios should be interpreted after considering bias induced by random variation.
TOPICAL DORZOLAMIDE FOR CYSTOID MACULAR EDEMA IN BIETTI CRYSTALLINE RETINAL DYSTROPHY
Authors: Khojasteh Hassan , Roohipoor Ramak , Riazi-Esfahani Hamid , Ghasempour Mehrbod 
Published: July 2018

Purpose:
To report a case of Bietti crystalline retinal dystrophy with cystoid macular edema (CME) that was successfully treated with topical carbonic anhydrase inhibitor.

Methods:
A 35-year-old otherwise healthy woman, with a known case of Bietti crystalline retinal dystrophy, presented with progressive visual impairment in her right eye for 3 months. The best-corrected visual acuity was 20/50 in the right eye and 20/25 in the left eye. On the basis of the multimodal imaging findings, the patient was diagnosed with Bietti crystalline retinal dystrophy with unilateral CME. Carbonic anhydrase inhibitor therapy twice a day was initiated.

Results:
Three months later, visual acuity improved to 20/25 in the right eye, and CME had resolved based on spectral domain ocular coherence tomography findings, although the CME reoccurred after discontinuation of the drug. Three months after resuming the therapy, the best-corrected visual acuity improved back to 20/25.

Conclusion:
Cystoid macular edema is one of the main causes of central visual worsening in patients with Bietti crystalline retinal dystrophy. This complication may be resolved with topical carbonic anhydrase inhibitor, resulting in improved anatomical and visual outcomes.
Incidence, Admission Rates, and Economic Burden of Adult Emergency Visits for Chronic Pancreatitis
Authors: Garg Sushil K. , Singh Dupinder , Sarvepalli Shashank , Bazerbachi Fateh , Puthanveedu Nitin D. , Obaitan Itegbemie , Haffar Samir , Goyal Hemant , Sanaka Madhusudhan R. 
Published: July 2018

Introduction:
Chronic pancreatitis (CP) is a common reason for emergency department (ED) visits, but little research has examined ED use by patients with CP.

Materials and Methods:
The Nationwide Emergency Department Sample (2006 to 2012) was interrogated to evaluate trends in adult ED visits for a primary diagnosis of CP (International Classification of Disease, 9th revision, Clinical Modification code: 577.1), the rates of subsequent hospital admission, and total charges. A survey logistic regression model was used to determine factors associated with hospitalization from the ED.

Results:
We identified 253,753 ED visits with a primary diagnosis of CP. No significant trends in annual incidence were noted. However, the ED-to-hospitalization rates decreased by 3% per year (P<0.001) and mean ED charges after adjusting for inflation increased by 11.8% per year (P<0.001). Higher Charlson comorbidity index, current smoker status, alcohol use, and biliary-related CP were associated with hospitalization. In hospitalized patients, length of stay decreased by 2.2% per year (P=0.003) and inpatient charges increased by 2.9% per year (P=0.004).

Conclusions:
Patient characteristics associated with higher risk of hospitalization from the ED deserve further attention.
Is the WHO Creating Unnecessary Confusion Over Breast Milk Substitutes?
Authors: Forsyth Stewart 
Published: July 2018

ABSTRACTA recent statement by WHO that “breast milk substitutes should be understood to include any milks …that are specifically marketed for feeding infants and young children up to the age of 3 years” differs significantly from the definition in the International Code which states “a breast milk substitute is any food being marketed or otherwise presented as a partial or total replacement for breast milk, whether or not suitable for that purpose.” The new interpretation, which lacks consultation and endorsement, is also ambiguous, with the boundaries between breast milk substitutes and complementary foods being blurred during the first 3 years of life. The logical definitions of breast milk substitutes and complementary foods contained within the Code should be maintained and inappropriate promotion of foods and fluids for infants and young children should be addressed through effective regulation of composition and labelling standards.