bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noun-modifying constructions and relativization in the central and western Caucasus
Authors: Nichols Johanna 
Published: February 2017

Abstract
Languages of the Nakh-Daghestanian family in the central and eastern Caucasus uniformly use gap strategies for relativization and GNMCC’s, despite different contact histories. Languages to the west and southwest (West Caucasian, Kartvelian) are very different, using relative pronouns and finite verbs. Despite long contact there is almost no accommodation of eastern and western types to each other. This sharp typological divide is a continuation of a larger Eurasian divide between western languages, which use finite relativization with relative pronouns, and eastern ones, which use participles and gaps. The stability of the divide in the Caucasus and its evident antiquity there are testimony to the non-Sprachbund status of the Caucasus.
Conclusion
Authors: Comrie Bernard , Sells Peter , Matsumoto Yoshiko 
Published: February 2017

Abstract
In this conclusion, we address three issues: a) the geographic extent of GNMCCs in Eurasia, including considerations of areal phenomena resulting from language contact; b) delimiting GNMCCs from other constructions, in particular those that in Japanese fall under GNMCCs; and c) structural properties that favor or disfavor GNMCCs.
The role of botanic gardens in the twenty-first century.
Authors: Krishnan S. , Novy A. 
Published: February 2017

Abstract
Botanic gardens and their functions and role in society have evolved over time. Originally established for study of medicinal plants in the mid-sixteenth century, they morphed into active sites for introduction, cultivation and dissemination of economically important crops during European expansion of colonies in Asia, America and Africa during the seventeenth-nineteenth centuries. During the second half of the twentieth century, importance was placed on the need for conservation and sustainable use of biodiversity. In the twenty-first century, botanic gardens are challenged to address issues that extend beyond the garden walls by placing social and environmental responsibility as key mission drivers.
Partial Identification Methods for Evaluating Food Assistance Programs: A Case Study of the Causal Impact of SNAP on Food Insecurity
Authors: Gundersen Craig , Kreider Brent , Pepper John V. 
Published: February 2017

AbstractWe illustrate how partial identification methods can be used to provide credible inferences on the causal impacts of food assistance programs, focusing on the impact that the Supplemental Nutrition Assistance Program (SNAP, formerly known as the Food Stamp Program) has on food insecurity among households with children. Recent research applies these methods to address two key issues confounding identification: missing counterfactuals and nonrandomly misclassified treatment status. In this paper, we illustrate and extend the recent literature by using data from the Survey of Income and Program Participation (SIPP) to study the robustness of prior conclusions. The SIPP confers important advantages: the detailed information about income and eligibility allows us to apply a modified discontinuity design to sharpen inferences, and the panel nature allows us to reduce uncertainty about true participation status. We find that SNAP reduces the prevalence of food insecurity in households with children by at least six percentage points.
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis
Authors: Zhang Yun , Topham David J , Thakar Juilee , Qiu Xing 
Published: February 2017

Abstract

Motivation
Gene set enrichment analyses (GSEAs) are widely used in genomic research to identify underlying biological mechanisms (defined by the gene sets), such as Gene Ontology terms and molecular pathways. There are two caveats in the currently available methods: (i) they are typically designed for group comparisons or regression analyses, which do not utilize temporal information efficiently in time-series of transcriptomics measurements; and (ii) genes overlapping in multiple molecular pathways are considered multiple times in hypothesis testing.

Results
We propose an inferential framework for GSEA based on functional data analysis, which utilizes the temporal information based on functional principal component analysis, and disentangles the effects of overlapping genes by a functional extension of the elastic-net regression. Furthermore, the hypothesis testing for the gene sets is performed by an extension of Mann-Whitney U test which is based on weighted rank sums computed from correlated observations. By using both simulated datasets and a large-scale time-course gene expression data on human influenza infection, we demonstrate that our method has uniformly better receiver operating characteristic curves, and identifies more pathways relevant to immune-response to human influenza infection than the competing approaches.

Availability and Implementation
The methods are implemented in R package FUNNEL, freely and publicly available at: https://github.com/yunzhang813/FUNNEL-GSEA-R-Package.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pseudoalignment for metagenomic read assignment
Authors: Schaeffer L , Pimentel H , Bray N , Melsted P , Pachter L 
Published: February 2017

Abstract

Motivation
Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains.

Results
We find that the recent idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software, making it possible and practical for the first time to analyze abundances of individual genomes in metagenomics projects.

Availability and Implementation
Pipeline and analysis code can be downloaded from http://github.com/pachterlab/metakallisto
Surgical Performance in Minimally Invasive Surgery Plus Recombinant Tissue Plasminogen Activator for Intracerebral Hemorrhage Evacuation Phase III Clinical Trial
Authors: Fam Maged D , Hanley Daniel , Stadnik Agnieszka , Zeineddine Hussein A , Girard Romuald , Jesselson Michael , Cao Ying , Money Lynn , McBee Nichol , Bistran-Hall Amanda J , Mould W Andrew , Lane Karen , Camarata Paul J , Zuccarello Mario , Awad Issam A 
Published: February 2017

Abstract

BACKGROUND
Minimally invasive thrombolytic evacuation of intracerebral hematoma is being investigated in the ongoing phase III clinical trial of Minimally Invasive Surgery plus recombinant Tissue plasminogen activator for Intracerebral hemorrhage Evacuation (MISTIE III).

OBJECTIVE
To assess the accuracy of catheter placement and efficacy of hematoma evacuation in relation to surgical approach and surgeon experience.

METHODS
We performed a trial midpoint interim assessment of 123 cases that underwent the surgical procedure. Accuracy of catheter placement was prospectively assessed by the trial Surgical Center based on prearticulated criteria. Hematoma evacuation efficacy was evaluated based on absolute volume reduction, percentage hematoma evacuation, and reaching the target end-of-treatment volume of <15 mL. One of 3 surgical trajectories was used: anterior (A), posterior (B), and lobar (C). Surgeons were classified based on experience with the MISTIE procedure as prequalified, qualified with probation, and fully qualified.

RESULTS
The average hematoma volume was 49.7 mL (range 20.0-124), and the mean evacuation rate was 71% (range 18.4%-99.8%). First placed catheters were 58% in good position, 28% suboptimal (but suitable to dose), and 14% poor (requiring repositioning). Posterior trajectory (B) was associated with significantly higher rates of poor placement (35%, P = .01). There was no significant difference in catheter placement accuracy among surgeons of varying experience. Hematoma evacuation efficacy was not significantly different among the 3 surgical approaches or different surgeons’ experience.

CONCLUSION
Ongoing surgical education and quality monitoring in MISTIE III have resulted in consistent rates of hematoma evacuation despite technical challenges with the surgical approaches and among surgeons of varying experience.
1-(2,4-Dibromophenyl)-3,6,6-trimethyl-1,5,6,7-tetrahydro-4H-indazol-4-one
Authors: Chao Po-Kuan , Ueng Shau-Hua , Ou Li-Chin , Yeh Teng-Kuang , Chang Wan-Ting , Chang Hsiao-Fu , Chen Shu-Chun , Tao Pao-Luh , Law Ping-Yee , Loh Horace H. , Cheng Ming-Fu , Chuang Jian-Ying , Chen Chiung-Tong , Shih Chuan , Yeh Shiu-Hwa 
Published: February 2017

Abstract

Background
The authors investigated the pharmacology and signaling pathways of the opioid receptors modulated by compound 1, 1-(2,4-dibromophenyl)-3,6,6-trimethyl-1,5,6,7-tetrahydro-4H-indazol-4-one.

Methods

In vitro studies of compound 1 were assessed by using a radioligand-binding assay (n = 3), a cyclic adenosine monophosphate assay (n = 3), a β-arrestin assay (n = 3), an internalization assay (n = 3), and an immunohistochemistry (n = 8). In vivo studies of compound 1 were characterized using a tail-flick test (n = 5 to 6), tail-clip test (n = 7), von Frey hair test (n = 5), and charcoal meal test (n = 5).

Results
Compound 1 elicited robust effects in μ-opioid (mean ± SD; binding affinity: 15 ± 2 nM; cyclic adenosine monophosphate assay: 24 ± 6 nM), δ-opioid (82 ± 7 nM; 1.9 ± 0.1 μM), and κ-opioid (76 ± 9 nM; 1.4 ± 0.5 μM) receptor–expressing cells. Compound 1 acts as a full agonist of β-arrestin-2 recruitment in μ-opioid (1.1 ± 0.3 μM) and δ-opioid (9.7 ± 1.9 μM) receptor–expressing cells. Compound 1 caused less gastrointestinal dysfunction (charcoal meal test: morphine: 82 ± 5%; compound 1: 42 ± 5%) as well as better antinociception in mechanical pain hypersensitivity (tail-clip test: morphine: 10 ± 3 s; compound 1: 19 ± 1 s) and in cancer-induced pain (von Frey hair test: morphine: 0.1 ± 0.1 g; compound 1: 0.3 ± 0.1 g) than morphine at equi-antinociceptive doses.

Conclusions
Compound 1 produced antinociception with less gastrointestinal dysfunction than morphine.
Directional Microphone Contralateral Routing of Signals in Cochlear Implant Users: A Within-Subjects Comparison
Authors: Wimmer Wilhelm , Kompis Martin , Stieger Christof , Caversaccio Marco , Weder Stefan 
Published: February 2017

Objectives:
For medical or financial reasons, bilateral cochlear implantation is not always possible in bilaterally deafened patients. In such cases, a contralateral routing of signals (CROS) device could complement the monaural implant. The goal of our study was to compare the benefit of three different conditions: (1) unilateral cochlear implant (CI) alone, (2) unilateral CI complemented with a directional CROS microphone, and (3) bilateral CIs.

Design:
Twelve bilateral experienced CI users were tested. Speech reception in noise and sound localization were measured in the three above-mentioned conditions. Patients evaluated which condition they presumed to be activated and the subjective benefit on a hearing scale.

Results:
Compared with the unilateral CI condition, the additional CROS device provided significantly better speech intelligibility in noise when speech signals came from the front or side of the CROS microphone. Only small subjective improvement was observed. Bilateral-activated CIs further improved the hearing performance. This was the only condition where sound localization was possible. Subjective evaluation showed a clear preference for the bilateral CI treatment.

Conclusions:
In bilateral deafened patients, bilateral implantation is the most preferable form of treatment. However, patients with one implant only could benefit from an additional directional microphone CROS device.
Developing a Community of Practice for HIV Care: Supporting Knowledge Translation in a Regional Training Initiative
Authors: Gallagher Donna M. , Hirschhorn Lisa R. , Lorenz Laura S. , Piya Priyatam 
Published: February 2017

Introduction:
Ensuring knowledgeable, skilled HIV providers is challenged by rapid advances in the field, diversity of patients and providers, and the need to retain experienced providers while training new providers. These challenges highlight the need for education strategies, including training and clinical consultation to support translation of new knowledge to practice. New England AIDS Education and Training Center (NEAETC) provides a range of educational modalities including academic peer detailing and distance support to HIV providers in six states. We describe the interprofessional perspectives of HIV providers who participated in this regional program to understand success and areas for strengthening pedagogical modality, content, and impact on clinical practice.

Methods:
This 2013 to 2014 mixed-methods study analyzed quantitative programmatic data to understand changes in training participants and modalities and used semistructured interviews with 30 HIV providers and coded for preidentified and emerging themes.

Results:
Since 2010, NEAETC evolved modalities to a greater focus on active learning (case discussion, clinical consultation), decreasing didactic training by half (18–9%). This shift was designed to move from knowledge transfer to translation, and qualitative findings supported the value of active learning approaches. Providers valued interactive trainings and presentation of cases supporting knowledge translation. On-site training encouraged peer networking and sharing of lessons learned. Diversity in learning priorities across providers and sites validated NEAETC's approach of tailoring topics to local needs and encouraging regional networking.

Discussion:
Tailored approaches resulted in improved provider-reported capacity, peer learning, and support. Future evaluations should explore the impact of this multipronged approach on supporting a community of practice and empowerment of provider teams.
Generalized Indeterminate Cell Histiocytosis Presenting as Eroded Papules and Crusts
Authors: Li Yaping , Bai Harrison Xiao , Su Chang , Zhang Guiying 
Published: February 2017

Abstract:
Indeterminate cell histiocytosis (ICH) is a very rare histiocytic disease. We reported a case of generalized ICH presenting as eroded papules and crusts, accompanied with intermittent fever, pulmonary disorder, lymphadenectasis in the mediastinum, and the retroperitoneum. The histopathology indicated a neoplasm that was composed of small nests of large cells with ample pale cytoplasm. Immunohistochemistry results and the absence of Birbeck granules led us to the diagnosis of ICH. Four months later, the patient died of anemia, ascites, and swelling of the limbs.
Choroidal Vessel Diameters in Pseudoexfoliation and Pseudoexfoliation Glaucoma Analyzed Using Spectral-Domain Optical Coherence Tomography
Authors: Sarrafpour Soshian , Adhi Mehreen , Zhang Jason Y. , Duker Jay S. , Krishnan Chandrasekharan 
Published: February 2017

Purpose of the Study:
The purpose of the study was to analyze choroidal vessel diameters in pseudoexfoliation (PXF) and pseudoexfoliation glaucoma (PXFG) using spectral-domain optical coherence tomography (SD-OCT).

Materials and Methods:
Fifty patients (100 eyes) with PXF and PXFG who underwent high-definition 1-line raster SD-OCT imaging at New England Eye Center, Boston, were retrospectively identified and divided into unilateral PXFG (26 patients, 52 eyes), unilateral PXF (4 patients, 8 eyes), bilateral PXFG (4 patients, 8 eyes), and bilateral PXF (16 patients, 32 eyes). Eyes with concomitant chorioretinal pathology, history of shunting/filtering for glaucoma, and significant anisometropia were excluded. SD-OCT scans were divided into subfoveal, central, and peripheral zones and choroidal vessel diameters were measured.

Results:
In patients with unilateral PXFG, mean choroidal vessel diameter was 12.9 μm smaller in the affected eyes when compared with their contralateral eyes (45.7 vs. 58.6 μm; P<0.0001) with the greatest reduction (16.6 μm) in the subfoveal zone (49.0 vs. 65.6 μm; P<0.0001). In patients with unilateral PXF, the mean choroidal vascular diameter was 13.3 μm smaller in the affected eyes when compared with their contralateral eyes (42.8 vs. 56.1 μm; P=0.02). As expected, no significant difference was observed between the 2 eyes of patients with bilateral PXFG (45.5 vs. 45.7 μm; P=0.95) and bilateral PXF (51.4 vs. 50.2 μm; P=0.52).

Conclusions:
Choroidal vessel diameters are smaller in the affected eyes of patients with unilateral PXF and PXFG when compared with their contralateral unaffected eyes. These changes appear to be independent of the presence or absence of glaucoma. Future studies may identify the choroidal vascular changes and their relationship with the pathogenesis of these conditions.
Emotional Intelligence of Nurse Managers
Authors: Prufeta Patricia 
Published: February 2017

OBJECTIVE
The purposes of this study are to determine the level of emotional intelligence (EI) among nurse managers (NMs) in an academic medical center and determine the relationship of EI and demographic variables.

BACKGROUND
Emotional intelligence is a concept that warrants further research in nursing because there is a huge gap in knowledge about nurse leaders’ EI.

METHODS
Data were collected from 38 NMs recruited from a large academic medical center in the Northeast.

RESULTS
Mean EI scores among NMs were average. Nurse managers with less than 2 years of experience had statistically significant lower “using emotions” branch score and strategic EI. Nurse managers with a masters’ degree in nursing scored significantly higher in using emotions branch score than did those with a masters’ degree in a related field.

CONCLUSION
Opportunities exist to enhance the EI of NMs.
Impact of Role Stressors on the Health of Nurse Managers
Authors: Udod Sonia A. , Cummings Greta , Care W. Dean , Jenkins Megan 
Published: February 2017

OBJECTIVE
A qualitative exploratory inquiry was used to understand nurse managers’ (NMs’) perceptions of their role stressors, coping strategies, and self-health related outcomes as a result of frequent exposure to stressful situations in their role.

BACKGROUND
Strong nursing leadership is required for desirable staff, patient, and organizational outcomes. A stressed NM will negatively influence staff nurse satisfaction and retention, patient outcomes, and organizational performance. Stress can affect NMs’ mental and physical heath, leading to job dissatisfaction and turnover.

METHODS
A qualitative exploratory inquiry was conducted using semistructured interviews with 23 NMs and 1 focus group interview.

RESULTS
Findings suggest that coping strategies may be inadequate, given the intensity and demands of the manager role, and could negatively impact NMs’ long-term health.

CONCLUSIONS
Senior nurse leaders can significantly impact the health and productivity of NMs by minimizing the adverse effects of role stress and foster a positive work environment.
Multiple Organ Dysfunction in Children Mechanically Ventilated for Acute Respiratory Failure*
Authors: Weiss Scott L. , Asaro Lisa A. , Flori Heidi R. , Allen Geoffrey L. , Wypij David , Curley Martha A. Q. 
Published: February 2017

Objectives:
The impact of extrapulmonary organ dysfunction, independent from sepsis and lung injury severity, on outcomes in pediatric acute respiratory failure is unclear. We sought to determine the frequency, timing, and risk factors for extrapulmonary organ dysfunction and the independent association of multiple organ dysfunction syndrome with outcomes in pediatric acute respiratory failure.

Design:
Secondary observational analysis of the Randomized Evaluation of Sedation Titration for Respiratory Failure cluster-randomized prospective clinical trial conducted between 2009 and 2013.

Setting:
Thirty-one academic PICUs in the United States.

Patients:
Two thousand four hundred forty-nine children mechanically ventilated for acute respiratory failure enrolled in Randomized Evaluation of Sedation Titration for Respiratory Failure.

Measurements and Main Results:
Organ dysfunction was defined using criteria published for pediatric sepsis. Multiple organ dysfunction syndrome was defined as respiratory dysfunction one or more extrapulmonary organ dysfunctions. We used multivariable logistic regression to identify risk factors for multiple organ dysfunction syndrome, and logistic or proportional hazards regression to compare clinical outcomes. All analyses accounted for PICU as a cluster variable. Overall, 73% exhibited extrapulmonary organ dysfunction, including 1,547 (63%) with concurrent multiple organ dysfunction syndrome defined by onset on day 0/1 and 244 (10%) with new multiple organ dysfunction syndrome with onset on day 2 or later. Most patients (93%) with indirect lung injury from sepsis presented with concurrent multiple organ dysfunction syndrome, whereas patients with direct lung injury had both concurrent (56%) and new (12%) multiple organ dysfunction syndrome. Risk factors for concurrent multiple organ dysfunction syndrome included older age, illness severity, sepsis, cancer, and moderate/severe lung injury. Risk factors for new multiple organ dysfunction syndrome were moderate/severe lung injury and neuromuscular blockade. Both concurrent and new multiple organ dysfunction syndrome were associated with 90-day in-hospital mortality (concurrent: adjusted odds ratio, 6.54; 95% CI, 3.00–14.25 and new: adjusted odds ratio, 3.21; 95% CI, 1.48–6.93) after adjusting for sepsis, moderate/severe lung injury, and other baseline characteristics.

Conclusions:
Extrapulmonary organ dysfunction was common, generally occurred concurrent with respiratory dysfunction (especially in sepsis), and was a major risk factor for mortality in pediatric acute respiratory failure.