bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining the nature of intra-speaker subject case variation
Authors: Nowenstein Iris Edda 
Published: February 2017

Abstract
Extensive syntactic surveys show that variation in subject case appears in both Insular Scandinavian languages. The results furthermore indicate that intra-speaker variation is widespread and that Person-Specific Retention (PSR) is one of the characteristics of the variation in both Icelandic and Faroese. Many questions on the nature of the variation remain unanswered and no formal account of the PSR has been provided. In this paper I shed light on the subject by presenting new data from Icelandic, Faroese and heritage North-American Icelandic. Experimental language acquisition data can be particularly decisive regarding the nature of the intra-speaker variation and the variation and PSR can be accounted for formally within Yang’s (2002, 2016) variational model of acquisition.
Variation in dative in Faroese
Authors: Petersen Hjalmar P. 
Published: February 2017

Abstract
The aim of this article is to investigate variation in object case marking in Faroese and the ongoing change from dative objects to accusative objects in Modern Faroese. In this investigation I try to determine what influences this change: Is it influenced by the morphological form of the noun phrase, the semantics of the verb, language contact with Danish or an interaction between these three factors? Furthermore it is necessary to see if synonymous Nom/Acc native verbs influence Nom/Dat verbs. To seek answers to these questions I conducted three different grammaticality judgment tests among young people, 17–20 years of age, in the Faroe Islands, and I have compared these data with the results of a search in a text database (teldni.fo/tekstasavn).
Avoiding Genitive in Icelandic
Authors: Jónsson Jóhannes Gísli 
Published: February 2017

Abstract
The genitive is a highly idiosyncratic case for arguments in Icelandic. Hence it is sometimes substituted for by other cases, i.e. by structural case of subjects (nominative) and direct objects (accusative) or by the productive lexical dative case in other instances. Genitive objects of adjectives can only be replaced by dative, since dative is the only regular case for objects of adjectives. Genitive can also be replaced by dative in certain contexts of agreement or concord. Dative is a better alternative in such instances than nominative and accusative because dative and genitive share the property of being KPs (Kase Phrases) in the sense of Bayer, Bader and Meng (2001). This analysis is independently supported by facts about noun inflection in Icelandic.
Dimensions of Variation
Authors: Ussery Cherlon 
Published: February 2017

Abstract
This chapter provides an in-depth investigation of both inter-speaker and intra-speaker variation in agreement with nominative objects and ECM nominative subjects. We both build on previous observations and report the findings of recent fieldwork. We show that in addition to a general dative intervention effect, clause boundaries, expletives, and singular datives are interveners for some speakers. We propose that Icelandic ECM clauses are either TP or vP and that the number feature on datives is visible for some speakers, contra previous research.
Inverse attraction in Icelandic relative clauses
Authors: Wood Jim , Sigurðsson Einar Freyr , Nowenstein Iris Edda 
Published: February 2017

Abstract
We introduce “inverse attraction” (IA) (Bianchi 1999: 93) in non-standard Icelandic, a nearly unstudied phenomenon that provides special insight into relative clause formation, specificially regarding the copy deletion that occurs in the “matching analysis” derivation of relatives. Descriptively, IA seems to involve deletion of the higher, rather than the lower copy of the relative head. In order to study this phenomenon in more detail, we conducted a judgment study with 130 Icelandic-speaking participants. The results of our study indicate that the acceptability of IA depends on the matrix and embedded cases involved, on the position of the gap inside the relative clause, and on the position of the whole relativized DP.
Variation in copular agreement in Insular Scandinavian
Authors: Hartmann Jutta , Heycock Caroline 
Published: February 2017

Abstract
This paper explores the syntax of agreement in Insular Scandinavian in copular clauses with two potential goals for agreement. Data from three production experiments – one in Faroese and two in Icelandic – establish several new facts. First, in both languages agreement with the second nominal (DP2) is possible/preferred. Second, there is considerable variation (both within and between languages, and indeed speakers) in the patterns observed. Third, Icelandic shows a surprising pattern of "partial" agreement with DP2 – agreement in number but not person. We discuss the implications for current theorising about agreement, proposing that in these languages, at least, agreement is downwards, and that the available agreement options depend in part on the syntactic position of DP1 when agreement is established.
God particles in the perspective of The AlQuran Surah Yunus: 61 and modern science
Authors: Jumini Sri 
Published: February 2017

Abstract
The Qur'an is the book of Allah revealed to guide human beings, settting the rules of life to enable them to achieve happiness in this world and hereafter. The Qur'an has mentioned various scientific nature detailly and accurately so we are able to find new knowledge which is previously unknown by human being. One was about the God particle (Higgs Boson). This article aims to provide a deeper understanding of the concept of the Higgs Boson, the Higgs Boson explained this concept in detail relatated to 1) Perspective of science 2) Perspective of Al-Qur'an 3) Development of technology or science and technology. This study is a qualitative research using library research (library research) that examines and analyzes the books relating directly or indirectly. The results of the analysis states that 1) The concept of the Higgs Boson particle in terms of basic science is also the reason why almost all elementary particles have a greater mass, 2) The concept of the Higgs Boson in the Qur'an is implied from the results of the comparison interpretation of the commentators in Surah Yunus paragraph 61 related to Atom concepts and smaller particles theory of (Higgs Boson), interpretation of Al-Maraghi, and Al-Misbah. 3) The concept of the Higgs Boson in science and technology provide the most advance technology and it is the greatest achievement in the world of science and technology.
MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets
Authors: Fort Alexandre , Panousis Nikolaos I , Garieri Marco , Antonarakis Stylianos E , Lappalainen Tuuli , Dermitzakis Emmanouil T , Delaneau Olivier 
Published: February 2017

Abstract

Motivation
Large genomic datasets combining genotype and sequence data, such as for expression quantitative trait loci (eQTL) detection, require perfect matching between both data types.

Results
We described here MBV (Match BAM to VCF); a method to quickly solve sample mislabeling and detect cross-sample contamination and PCR amplification bias.

Availability and Implementation
MBV is implemented in C ++ as an independent component of the QTLtools software package, the binary and source codes are freely available at https://qtltools.github.io/qtltools/.

Supplementary information
Supplementary data are available at Bioinformatics online.
sfinx: an R package for the elimination of false positives from affinity purification–mass spectrometry datasets
Authors: Titeca Kevin , Meysman Pieter , Laukens Kris , Martens Lennart , Tavernier Jan , Eyckerman Sven 
Published: February 2017

Abstract

Summary
We describe sfinx, an R package providing access to the straightforward filtering index (SFINX) for the separation of true positive from false positive protein interactions in affinity purification – mass spectrometry datasets. This package maintains the reliability and user-friendliness of the SFINX web site interface but is faster, unlimited in input size, and can be run locally within R.

Availability and Implementation
The sfinx R package is available for download at the comprehensive R archive network (CRAN) https://cran.r-project.org/web/packages/sfinx/ under the Apache License 2.0.

Supplementary information
Supplementary data are available at Bioinformatics online.
STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies
Authors: Pei Jingwen , Wu Yufeng 
Published: February 2017

Abstract

Motivation
It is well known that gene trees and species trees may have different topologies. One explanation is incomplete lineage sorting, which is commonly modeled by the coalescent process. In multispecies coalescent, a gene tree topology is observed with some probability (called the gene tree probability) for a given species tree. Gene tree probability is the main tool for the program STELLS, which finds the maximum likelihood estimate of the species tree from the given gene tree topologies. However, STELLS becomes slow when data size increases. Recently, several fast species tree inference methods have been developed, which can handle large data. However, these methods often do not fully utilize the information in the gene trees.

Results
In this paper, we present an algorithm (called STELLS2) for computing the gene tree probability more efficiently than the original STELLS. The key idea of STELLS2 is taking some ‘shortcuts’ during the computation and computing the gene tree probability approximately. We apply the STELLS2 algorithm in the species tree inference approach in the original STELLS, which leads to a new maximum likelihood species tree inference method (also called STELLS2). Through simulation we demonstrate that the gene tree probabilities computed by STELLS2 and STELLS have strong correlation. We show that STELLS2 is almost as accurate in species tree inference as STELLS. Also STELLS2 is usually more accurate than several existing methods when there is one allele per species, although STELLS2 is slower than these methods. STELLS2 outperforms these methods significantly when there are multiple alleles per species.

Availability and Implementation
The program STELLS2 is available for download at: https://github.com/yufengwudcs/STELLS2

Supplementary information
Supplementary data are available at Bioinformatics online.
Simulome: a genome sequence and variant simulator
Authors: Price Adam , Gibas Cynthia 
Published: February 2017

Abstract

Summary
Simulome provides a powerful and easy to use tool for creating prokaryotic pseudo-genomes. It provides options that can be used in combination to create mutated variants of the simulated genome, which allows for controlled testing of specific genomic conditions. Simulome can be used in combination with real reads generated from next-generation sequencing platforms, or with simulated reads.

Availability and Implementation
Simulome is available for download at https://github.com/price0416/Simulome and is free for use under the MIT license.
Impact of Timing of Intervention Among 397 Consecutively Treated Brainstem Cavernous Malformations
Authors: Zaidi Hasan A. , Mooney Michael A. , Levitt Michael R. , Dru Alexander B. , Abla Adib A. , Spetzler Robert F. 
Published: February 2017

Abstract

BACKGROUND
Surgical resection of brainstem cavernous malformations (BSCMs) is challenging, and patient selection and timing of intervention remain controversial.

OBJECTIVE
To evaluate the impact of surgical timing and predictors of neurological outcome after surgical resection of BSCMs.

METHODS
Consecutive adult patients (≥18 years) with BSCMs undergoing surgical resection between 1985 and 2014 by the senior author (RFS) were retrospectively reviewed. Patient demographics, lesion characteristics, imaging results, surgical approach, and perioperative and long-term neurological morbidity were analyzed.

RESULTS
Data were analyzed for a total of 397 adult patients (160, 40% male). On univariate analysis, a greater proportion of patients treated within 6 weeks of hemorrhage had an improved Glasgow Outcome Scale score (P = .06). On logistic regression analysis, patients treated within 6 weeks of hemorrhage experienced improved clinical outcomes (odds ratio = 1.73; 95% confidence interval = 1.06-2.83; P = .03).

CONCLUSIONS
Although BSCM surgery is associated with significant perioperative morbidity and mortality, favorable long-term hemorrhage rates and symptom resolution can be achieved in a carefully selected group of patients. Overall, patients treated acutely, within 6 weeks, benefited the most from surgical intervention.
Does Adjunctive Tigecycline Improve Outcomes in Severe-Complicated, Nonoperative Clostridium difficile Infection?
Authors: LaSalvia Mary T. , Branch-Elliman Westyn , Snyder Graham M. , Mahoney Monica V. , Alonso Carolyn D. , Gold Howard S. , Wright Sharon B. 
Published: February 2017

Abstract
Severe Clostridium difficile infection is associated with a high rate of mortality; however, the optimal treatment for severe- complicated infection remains uncertain for patients who are not candidates for surgical intervention. Thus, we sought to evaluate the benefit of adjunctive tigecycline in this patient population using a retrospective cohort adjusted for propensity to receive tigecycline. We found that patients who received tigecycline had similar outcomes to those who did not, although the small sample size limited power to adjust for comorbidities and severity of illness.
Influence of Antibiotics on the Detection of Bacteria by Culture-Based and Culture-Independent Diagnostic Tests in Patients Hospitalized With Community-Acquired Pneumonia
Authors: Harris Aaron M. , Bramley Anna M. , Jain Seema , Arnold Sandra R. , Ampofo Krow , Self Wesley H. , Williams Derek J. , Anderson Evan J. , Grijalva Carlos G. , McCullers Jonathan A. , Pavia Andrew T. , Wunderink Richard G. , Edwards Kathryn M. , Winchell Jonas M. , Hicks Lauri A. 
Published: February 2017

Abstract

Background
Specimens collected after antibiotic exposure may reduce culture-based bacterial detections. The impact on culture-independent diagnostic tests is unclear. We assessed the effect of antibiotic exposure on both of these test results among patients hospitalized with community-acquired pneumonia (CAP).

Methods
Culture-based bacterial testing included blood cultures and high-quality sputum or endotracheal tube (ET) aspirates; culture-independent testing included urinary antigen testing (adults) for Streptococcus pneumoniae and Legionella pneumophila and polymerase chain reaction (PCR) on nasopharyngeal and oropharyngeal (NP/OP) swabs for Mycoplasma pneumoniae and Chlamydia pneumoniae. The proportion of bacterial detections was compared between specimens collected before and after either any antibiotic exposure (prehospital and/or inpatient) or only prehospital antibiotics and increasing time after initiation of inpatient antibiotics.

Results
Of 4678 CAP patients, 4383 (94%) received antibiotics: 3712 (85%) only inpatient, 642 (15%) both inpatient and prehospital, and 29 (&lt;1%) only prehospital. There were more bacterial detections in specimens collected before antibiotics for blood cultures (5.2% vs 2.6%; P &lt; .01) and sputum/ET cultures (50.0% vs 26.8%; P &lt; .01) but not urine antigen (7.0% vs 5.7%; P = .53) or NP/OP PCR (6.7% vs 5.4%; P = .31). For all diagnostic testing, bacterial detections declined with increasing time between inpatient antibiotic administration and specimen collection.

Conclusions
Bacteria were less frequently detected in culture-based tests collected after antibiotics and in culture-independent tests that had longer intervals between antibiotic exposure and specimen collection. Bacterial yield could improve if specimens were collected promptly, preferably before antibiotics, providing data for improved antibiotic selection.
On the Road to Professionalism
Authors: Chestnut David H. 
Published: February 2017

Abstract
Many observers have concluded that we have a crisis of professionalism in the practice of medicine. In this essay, the author identifies and discusses personal attributes and commitments important in the development and maintenance of physician professionalism: humility, servant leadership, self-awareness, kindness, altruism, attention to personal well-being, responsibility and concern for patient safety, lifelong learning, self-regulation, and honesty and integrity. Professionalism requires character, but character alone is not enough. We need others to help and encourage us. And in turn, as physician leaders, we help shape the culture of professionalism in our practice environment. Professionalism is not something we learn once, and no physician is perfectly professional at all times, in all circumstances. Professionalism is both a commitment and a skill—a competency—that we practice over a lifetime.
Validation and Calibration of the Risk Stratification Index
Authors: Chamoun George F. , Li Linyan , Chamoun Nassib G. , Saini Vikas , Sessler Daniel I. 
Published: February 2017

Abstract

Background
The Risk Stratification Index was developed from 35 million Medicare hospitalizations from 2001 to 2006 but has yet to be externally validated on an independent large national data set, nor has it been calibrated. Finally, the Medicare Analysis and Provider Review file now allows 25 rather than 9 diagnostic codes and 25 rather than 6 procedure codes and includes present-on-admission flags. The authors sought to validate the index on new data, test the impact of present-on-admission codes, test the impact of the expansion to 25 diagnostic and procedure codes, and calibrate the model.

Methods
The authors applied the original index coefficients to 39,753,036 records from the 2007–2012 Medicare Analysis data set and calibrated the model. The authors compared their results with 25 diagnostic and 25 procedure codes, with results after restricting the model to the first 9 diagnostic and 6 procedure codes and to codes present on admission.

Results
The original coefficients applied to the 2007–2012 data set yielded C statistics of 0.83 for 1-yr mortality, 0.84 for 30-day mortality, 0.94 for in-hospital mortality, and 0.86 for median length of stay—values nearly identical to those originally reported. Calibration equations performed well against observed outcomes. The 2007–2012 model discriminated similarly when codes were restricted to nine diagnostic and six procedure codes. Present-on-admission models were about 10% less predictive for in-hospital mortality and hospital length of stay but were comparably predictive for 30-day and 1-yr mortality.

Conclusions
Risk stratification performance was largely unchanged by additional diagnostic and procedure codes and only slightly worsened by restricting analysis to codes present on admission. The Risk Stratification Index, after calibration, thus provides excellent discrimination and calibration for important health services outcomes and thus appears to be a good basis for making hospital comparisons.
Nerve Root Compression Increases Spinal Astrocytic Vimentin in Parallel With Sustained Pain and Endothelial Vimentin in Association With Spinal Vascular Reestablishment
Authors: Smith Jenell R. , Lee Jasmine , Winkelstein Beth A. 
Published: February 2017

Study Design.
Temporal immunohistochemistry analysis of spinal cord tissue from a rat model of cervical radiculopathy.

Objective.
The goal was to measure spinal endothelial and astrocytic vimentin expression after a painful nerve root compression to define spinal cellular expression of vimentin in the context of pain.

Summary of Background Data.
The intermediate filament, vimentin, is expressed in a variety of cell types in the spinal cord and is modulated in response to neural pathologies. Early after nerve root compression spinal astrocytes become activated and blood-spinal cord barrier (BSCB) breakdown occurs in parallel with development of pain-related behaviors; these spinal responses remain activated as does the presence of pain. In addition to vimentin, glial fibrillary acidic protein (GFAP) expression is a hallmark of astrocyte activation. In contrast, vascular endothelial cells down-regulate vimentin expression in parallel with vascular breakdown. It is not known whether spinal astrocytes and endothelial cells modulate their expression of vimentin in response to a painful neural injury.

Methods.
Mechanical hyperalgesia was measured and spinal cord tissue was harvested at days 1 and 7 after a unilateral nerve root compression in rats. Vimentin was coimmunolabeled with GFAP to label astrocytes and von Willebrand factor (VWF) for endothelial cells in the spinal cord on the side of injury.

Results.
Spinal astrocytic vimentin increases by day 7 after nerve root compression, corresponding to when mechanical hyperalgesia is maintained. Spinal endothelial vimentin increases as early as day 1 after a painful compression and is even more robust at day 7.

Conclusion.
The delayed elevation in spinal astrocytic vimentin corresponding to sustained mechanical hyperalgesia supports its having a relationship with pain maintenance. Further, since BSCB integrity has been shown to be reestablished by day 7 after a painful compression, endothelial expressed vimentin may help to fortify spinal vasculature contributing to BSCB stability.

Level of Evidence: N/A
Successful Treatment of Classic Kaposi Sarcoma With Long-Pulse Neodymium-Doped Yttrium Aluminum Garnet Laser: A Preliminary Study
Authors: Özdemir Mustafa , Balevi Ali 
Published: February 2017

BACKGROUND
Kaposi sarcoma (KS) is a systemic disease that can present with cutaneous lesions with or without internal involvement, mostly caused by infection with human herpesvirus-8. The treatment options include surgical excision, cryotherapy, radiotherapy, intralesional chemotherapy, laser, and elastic stockings for the prevention of lymphedema.

OBJECTIVE
This article presents 7 cases with classic KS treated with the long-pulse neodymium:yttrium–aluminum–garnet (Nd:YAG) laser.

METHODS
Forty-nine lesions of 7 KS patients (5 stage 1, 2 stage 2A) were treated with Nd:YAG laser with a spot size of 4 to 6 mm and a fluence of 180 J/cm2 increased by 10 J/cm2 in the neighboring area to a maximum of 260 J/cm2. The pulse sequencing was 1.5, and delay time was 5 milliseconds. Sessions were continued at 4-week intervals for 2 to 4 sessions.

RESULTS
All patients exhibited clinical and histological improvement. One session was sufficient for small lesions, whereas coalescing and multicentric lesions required up to 4 sessions. All the lesions healed in 2 to 4 weeks, with the only complication being mild atrophic scars.

CONCLUSION
With the advantage of penetrating into deeper sites than other lasers, long-pulse Nd:YAG is an efficient and safe local treatment alternative especially for papulonodular and deeper lesions located on bony structures.