bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global wetland contribution to 2000–2012 atmospheric methane growth rate dynamics
Authors: Poulter Benjamin , Bousquet Philippe , Canadell Josep G , Ciais Philippe , Peregon Anna , Saunois Marielle , Arora Vivek K , Beerling David J , Brovkin Victor , Jones Chris D , Joos Fortunat , Gedney Nicola , Ito Akihito , Kleinen Thomas , Koven Charles D , McDonald Kyle , Melton Joe R , Peng Changhui , Peng Shushi , Prigent Catherine , Schroeder Ronny , Riley William J , Saito Makoto , Spahni Renato , Tian Hanqin , Taylor Lyla , Viovy Nicolas , Wilton David , Wiltshire Andy , Xu Xiyan , Zhang Bowen , Zhang Zhen , Zhu Qiuan 
Published: September 2017

Abstract
Increasing atmospheric methane (CH4) concentrations have contributed to approximately 20% of anthropogenic climate change. Despite the importance of CH4 as a greenhouse gas, its atmospheric growth rate and dynamics over the past two decades, which include a stabilization period (1999–2006), followed by renewed growth starting in 2007, remain poorly understood. We provide an updated estimate of CH4 emissions from wetlands, the largest natural global CH4 source, for 2000–2012 using an ensemble of biogeochemical models constrained with remote sensing surface inundation and inventory-based wetland area data. Between 2000–2012, boreal wetland CH4 emissions increased by 1.2 Tg yr−1 (−0.2–3.5 Tg yr−1), tropical emissions decreased by 0.9 Tg yr−1 (−3.2−1.1 Tg yr−1), yet globally, emissions remained unchanged at 184 ± 22 Tg yr−1. Changing air temperature was responsible for increasing high-latitude emissions whereas declines in low-latitude wetland area decreased tropical emissions; both dynamics are consistent with features of predicted centennial-scale climate change impacts on wetland CH4 emissions. Despite uncertainties in wetland area mapping, our study shows that global wetland CH4 emissions have not contributed significantly to the period of renewed atmospheric CH4 growth, and is consistent with findings from studies that indicate some combination of increasing fossil fuel and agriculture-related CH4 emissions, and a decrease in the atmospheric oxidative sink.
High-resolution model for estimating the economic and policy implications of agricultural soil salinization in California
Authors: Welle Paul D , Mauter Meagan S 
Published: September 2017

AbstractThis work introduces a generalizable approach for estimating the field-scale agricultural yield losses due to soil salinization. When integrated with regional data on crop yields and prices, this model provides high-resolution estimates for revenue losses over large agricultural regions. These methods account for the uncertainty inherent in model inputs derived from satellites, experimental field data, and interpreted model results. We apply this method to estimate the effect of soil salinity on agricultural outputs in California, performing the analysis with both high-resolution (i.e. field scale) and low-resolution (i.e. county-scale) data sources to highlight the importance of spatial resolution in agricultural analysis. We estimate that soil salinity reduced agricultural revenues by $3.7 billion ($1.7–$7.0 billion) in 2014, amounting to 8.0 million tons of lost production relative to soil salinities below the crop-specific thresholds. When using low-resolution data sources, we find that the costs of salinization are underestimated by a factor of three. These results highlight the need for high-resolution data in agro-environmental assessment as well as the challenges associated with their integration.
On the volume of locally conformally flat 4-dimensional closed hypersurface
Authors: Cui Qing , Sun Linlin 
Published: September 2017

Let

M
M

be a 5-dimensional Riemannian manifold with

S
e

c
M

∈
[
0
,
1
]

Sec_M\in [0,1]

and

Σ
\Sigma

be a locally conformally flat closed hypersurface in

M
M

with mean curvature function

H
H

. We prove that there exists

ε
0

>
0

\varepsilon _0>0

such that

∫
Σ

(
1
+

H
2

)
2

≥

4

π
2

3

χ
(
Σ
)
,

\begin{align} \int _\Sigma (1+H^2)^2 \ge \frac {4\pi ^2}{3}\chi (\Sigma ), \end{align}

provided

|
H
|
≤

ε
0

\vert H\vert \le \varepsilon _0

, where

χ
(
Σ
)

\chi (\Sigma )

is the Euler number of

Σ
\Sigma

. In particular, if

Σ
\Sigma

is a locally conformally flat minimal hypersphere in

M
M

, then

V
o
l
(
Σ
)
≥
8

π
2

/

3

Vol(\Sigma ) \ge 8\pi ^2/3

, which partially answers a question proposed by Mazet and Rosenberg. Moreover, we show that if

M
M

is (some special but large class) rotationally symmetric, then the inequality (\ref{V1}) holds for all

H
H

.
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
Authors: Papili Gao Nan , Ud-Dean S M Minhaz , Gandrillon Olivier , Gunawan Rudiyanto 
Published: September 2017

AbstractMotivationSingle cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired.ResultsWe developed SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) for the inference of GRNs from single cell transcriptional profiles. We focused on time-stamped cross-sectional expression data, commonly generated from transcriptional profiling of single cells collected at multiple time points after cell stimulation. SINCERITIES recovers directed regulatory relationships among genes by employing regularized linear regression (ridge regression), using temporal changes in the distributions of gene expressions. Meanwhile, the modes of the gene regulations (activation and repression) come from partial correlation analyses between pairs of genes. We demonstrated the efficacy of SINCERITIES in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. The case studies showed that SINCERITIES could provide accurate GRN predictions, significantly better than other GRN inference algorithms such as TSNI, GENIE3 and JUMP3. Moreover, SINCERITIES has a low computational complexity and is amenable to problems of extremely large dimensionality. Finally, an application of SINCERITIES to single cell expression data of T2EC chicken erythrocytes pointed to BATF as a candidate novel regulator of erythroid development.Availability and implementationMATLAB and R version of SINCERITIES are freely available from the following websites: http://www.cabsel.ethz.ch/tools/sincerities.html and https://github.com/CABSEL/SINCERITIES. The single cell THP-1 and T2EC transcriptional profiles are available from the original publications (Kouno et al., 2013; Richard et al., 2016). The in silico single cell data are available on SINCERITIES websites.Supplementary informationSupplementary data are available at Bioinformatics online.
Interactive network visualization in Jupyter notebooks: visJS2jupyter
Authors: Rosenthal Sara Brin , Len Julia , Webster Mikayla , Gary Aaron , Birmingham Amanda , Fisch Kathleen M 
Published: September 2017

Abstract

Motivation
Network biology is widely used to elucidate mechanisms of disease and biological processes. The ability to interact with biological networks is important for hypothesis generation and to give researchers an intuitive understanding of the data. We present visJS2jupyter, a tool designed to embed interactive networks in Jupyter notebooks to streamline network analysis and to promote reproducible research.

Results
The tool provides functions for performing and visualizing useful network operations in biology, including network overlap, network propagation around a focal set of genes, and co-localization of two sets of seed genes. visJS2jupyter uses the JavaScript library vis.js to create interactive networks displayed within Jupyter notebook cells with features including drag, click, hover, and zoom. We demonstrate the functionality of visJS2jupyter applied to a biological question, by creating a network propagation visualization to prioritize risk-related genes in autism.

Availability and implementation
The visJS2jupyter package is distributed under the MIT License. The source code, documentation and installation instructions are freely available on GitHub at https://github.com/ucsd-ccbb/visJS2jupyter. The package can be downloaded at https://pypi.python.org/pypi/visJS2jupyter.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry
Authors: Wandy Joe , Zhu Yunfeng , van der Hooft Justin J J , Daly Rónán , Barrett Michael P , Rogers Simon 
Published: September 2017

Abstract

Motivation
We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualizations.

Results
Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a data set onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service.

Availability and implementation
The website can be found at http://ms2lda.org, while the source code is available at https://github.com/sdrogers/ms2ldaviz under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Psychic vs. Economic Barriers to Vaccine Take-Up: Evidence from a Field Experiment in Nigeria
Authors: Sato Ryoko , Takasaki Yoshito 
Published: September 2017

Abstract
This paper experimentally evaluates the relative importance of psychic costs of tetanus vaccination compared to monetary costs among women in rural Nigeria. We compare vaccine take-up between two conditions to receive cash incentives: clinic attendance vs. vaccine take-up. Because the only difference between these two conditions is whether a woman was required to receive a vaccine upon arrival at the clinic, the difference in clinic attendance between these two groups captures the psychic costs of vaccination. Contrary to conventional wisdom, we find no evidence for significant psychic costs. Priming about disease severity increases the perceived severity of disease, but not vaccine take-up. Monetary costs strongly affect vaccination decisions.
Hamstring Autograft Reconstruction of the Anterior Tibial Tendon
Authors: Karnovsky Sydney C. , Drakos Mark C. 
Published: September 2017

Injuries to the tibialis anterior tendon (TAT) are rarely reported in the literature, and, in existing reports, there are varied treatment options. Many authors recommend operative treatment over conservative treatment in young, healthy, and active patients, in order to give the patient as much strength back as possible and to allow them to avoid the use of a brace. Different types of operative repair have been described, including: extensor digitorum longus transfer, extensor hallucis longus transfer, plantaris transfer, Achilles autograft, as well as gracilis and semitendinosus autografts and allografts. We advocate using a hamstring autograft, either gracilis in isolation, semitendinosus in isolation, or a combination of the 2, depending on the size of the patient’s tendons, to operatively reconstruct ruptured TATs.
Level of Evidence: Diagnostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Predictors of Weight-Related Quality of Life in Adolescents Who Are Overweight or Obese
Authors: Ievers-Landis Carolyn E. , Olayinka Oluwatomisin , Burant Christopher , Moore Shirley 
Published: September 2017

ABSTRACT:

Objective:
Weight-related quality of life (WRQOL) is a type of health-related QOL that may serve as a patient-reported outcome of the potential burden of overweight. The present study uses structural equation modeling path analysis methods to examine body mass index (BMI) and other potential predictors of WRQOL components among adolescents who were overweight/obese from predominantly low-income, urban households.

Methods:
Baseline data were obtained from 360 participants (10–13 year olds; 57.8% female; 76.7% black; average BMI of 27.12) and their parents/legal guardians from a randomized, controlled, treatment trial. Youth completed measures of WRQOL, depressive symptoms, and family/friend social support for healthy eating. Parents completed measures of demographics and child social problems.

Results:
The initial model included BMI, gender, parent education, family/friend social support for healthy eating, child social problems, body esteem and social life WRQOL, and depressive symptoms. The final model fit the data well (χ2 = 27.738; df = 16; p = .034). Higher BMI was indirectly related to lower social life and body esteem WRQOL through greater social problems. Physical comfort and family relations WRQOL were unrelated to BMI and were not included. Lower social life and body esteem related to more depressive symptoms. Family/friend discouragement for healthy eating was associated with lower body esteem; also, family discouragement was related to lower social life.

Conclusion:
Body mass index may not directly relate to WRQOL but may be associated through other factors, including child social problems. Interventions should screen for and treat mood and social problems and address family/friend support for healthy eating.
Validation of a Unilateral Cleft Lip Surgical Outcomes Evaluation Scale for Surgeons and Laypersons
Authors: Campbell Alex , Restrepo Carolina , Deshpande Gaurav , Tredway Caroline , Bernstein Sarah M. , Patzer Rachel , Wendby Lisa , Schonmeyr Bjorn 
Published: September 2017

Background:
A standardized evaluation tool is needed for the assessment of surgical outcomes in cleft lip surgery. Current scales for evaluating unilateral cleft lip/nose (UCL/N) aesthetic outcomes are limited in their reliability, ease of use, and application. The Unilateral Cleft Lip Surgical Outcomes Evaluation (UCL SOE) scale measures symmetry of 4 components and sums these for a total score. The purpose of this study was to validate the SOE as a reliable tool for use by both surgeons and laypersons.

Methods:
Twenty participants (9 surgeons and 12 laypeople) used the SOE to evaluate 25 sets of randomly selected presurgical and postsurgical standardized photographs of UCL/N patients. Interrater reliability for surgeon and laypeople was determined using an intraclass correlation coefficient (ICC).

Results:
Individual surgeons and laypeople both reached an ICC in the "fair to good" range (ICC = 0.42 and 0.59, respectively). Averaging 2 evaluators in the surgeon group improved the ICC to 0.58 and in the laypeople group to 0.74, respectively. Averaging 3 evaluators increased the ICC for surgeons to the "good" range (ICC = 0.71) and the ICC for laypeople to the "very good" range (ICC = 0.82).

Conclusions:
Surgeon and layperson raters can reliably use the SOE to assess the aesthetics results after surgical repair of UCL/N, and improved reliability and reproducibility is achieved by averaging the scores of multiple reviewers.
A Technique for Reduction of Edentulous Fractures Using Dentures and SMARTLock Hybrid Fixation System
Authors: Carlson Anna Rose , Shammas Ronnie Labib , Allori Alexander Christopher , Powers David Bryan 
Published: September 2017

Summary:
Establishing anatomic reduction of an edentulous mandible fracture is a frequently acknowledged challenge in craniomaxillofacial trauma surgery. In this study, we report a novel method for the reduction of the edentulous mandible fracture, via fabrication of modified Gunning splints using existing dentures and SMARTLock hybrid arch bars. This technique dramatically simplifies the application of an arch bar to dentures, obviates the need for the fabrication of impressions and custom splints, and eliminates the lag time associated with the creation of splints. Furthermore, this method may be used with or without adjunctive rigid internal fixation. The technique described herein of creating Gunning splints with SMARTLock hybrid arch bars provides surgeons with a simple, rapid, single-stage solution for reduction of mandibular fractures in the edentulous patient.
Validation of the Unilateral Cleft Lip Severity Index for Surgeons and Laypersons
Authors: Campbell Alex , Restrepo Carolina , Deshpande Gaurav , Bernstein Sarah M. , Tredway Caroline , Wendby Lisa , Schonmeyr Bjorn 
Published: September 2017

Background:
Severity of the primary unilateral cleft lip/nose deformity (UCL/N) is postulated to play a key role in postoperative complications, aesthetic result, and need for secondary surgery. There is no validated and widely accepted classification scheme of initial cleft severity. The purpose of this study was to validate the Unilateral Cleft Lip Cleft Severity Index as a reliable tool for evaluating presurgical UCL/N deformity by both surgeons and laypersons.

Methods:
Twenty-five participants (10 surgeons and 15 laypeople) evaluated 25 sets of randomly selected presurgical standardized photographs of UCL/N patients. Each participant rated patients on a scale of 1–4 using the Cleft Severity Index. Interrater reliability for surgeons, laypersons, and all participants was determined using an intraclass correlation coefficient. Histograms and regression analysis were performed to compare average ratings between groups.

Results:
Interrater reliability for all groups was classified as "very good" determined by intraclass correlation coefficients of 0.837 (laymen), 0.885 (surgeons), and 0.848 (all participants). These results indicate that there was a high degree of interrater across all 3 groups and that both surgeons and laypersons can reliability rate cleft severity using the Cleft Severity Index.

Conclusions:
This study validates the use of the Cleft Severity Index by both surgeons and laypersons as a reliable tool for evaluating the degree of presurgical severity of patients with UCL/N. The Unilateral Cleft Lip Cleft Severity Index can thus serve as a reproducible and reliable grading system for primary UCL/N deformity and to categorize patients for future outcomes studies.
Gaps in Current Knowledge and Priorities for Future Research in Dry Eye
Authors: Saldanha Ian J. , Dickersin Kay , Hutfless Susan T. , Akpek Esen K. 
Published: September 2017

Purpose:
Dry eye, a common yet underrecognized and evolving field, has few recommended treatment algorithms, mostly based on expert consensus rather than robust research evidence. There are high costs associated with managing dry eye and conducting research to identify effective and safe long-term treatments. To support evidence-based management of dry eye, our purpose was to identify and prioritize important clinical research questions for future clinical research.

Methods:
We translated recommendations from the American Academy of Ophthalmology's 2013 Preferred Practice Patterns for dry eye into answerable clinical research questions about treatment effectiveness. Clinicians around the world who manage patients with dry eye rated each question's importance from 0 (not important) to 10 (very important) using a 2-round online Delphi survey. We considered questions as “important” if ≥75% of respondents assigned a rating of 6 or more in round 2. We mapped the identified important clinical research questions to reliable systematic reviews published up to March 2016.

Results:
Seventy-five clinicians from at least 21 countries completed both Delphi rounds. Among the 58 questions, 24 met our definition of “important”: 9/24 and 7/24 addressed topical and systemic treatments, respectively. All 4 questions with the highest 25th percentiles addressed topical treatments. Although 6/24 “important” questions were associated with 4 existing reliable systematic reviews, none of these reviews came to a definitive conclusion about treatment effectiveness.

Conclusions:
We identified gaps pertaining to treatment options for dry eye. Future clinical research on the management of dry eye should strongly consider these prioritized questions.
Change in Eyelid Position Following Muller’s Muscle Conjunctival Resection With a Standard Versus Variable Resection Length
Authors: Rootman Daniel B. , Sinha Kunal R. , Goldberg Robert A. 
Published: September 2017

Purpose:
This study compares the use of a standard 7 mm resection length to a variable 4:1 ratio of resection length to desired elevation nomogram when performing Muller’s muscle conjunctival resection surgery.

Methods:
In this cross-sectional case control study, 2 groups were defined. The first underwent Muller’s muscle conjunctival resection surgery with a standard 7 mm resection length and the second underwent the same surgery with a variable resection length determined by a 4:1 ratio of resection length to desired elevation nomogram. Groups were matched for age (within 5 years) and sex. Pre- and postoperative photographs were measured digitally. Change in upper marginal reflex distance 1 (MRD1) and final MRD1 were the primary outcome measures. The study was powered to detect a 1 mm difference in MRD1 to a beta error of 0.95.

Results:
No significant preoperative differences between the groups were noted. No significant difference in final MRD1 (0.1 mm; p = 0.74) or change in MRD1 (0.2 mm; p = 0.52) was noted. Mean resection length to elevation ratios were 3.9:1 for standard group and 4.3:1 for the variable group (p = 0.54).

Conclusion:
The authors were not able to detect a significant difference in final MRD1 or change in MRD1 for patients undergoing Muller’s muscle conjunctival resection surgery with standard or variable resection lengths. These results tend to argue against a purely mechanical mechanism for Muller’s muscle conjunctival resection surgery.