bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing linkage maps in the genomics era with MapDisto 2.0
Authors: Heffelfinger Christopher , Fragoso Christopher A , Lorieux Mathias 
Published: March 2017

Abstract

Motivation
Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM).

Results
MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface.

Availability and Implementation
The program is available free of charge at mapdisto.free.fr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using local ecological knowledge to inform fisheries assessment: measuring agreement among Polish fishermen about the abundance and condition of Baltic cod (Gadus morhua)
Authors: Figus Elizabeth , Carothers Courtney , Beaudreau Anne H 
Published: March 2017

AbstractAlthough fisheries managers often attempt to incorporate stakeholders’ views into development of policy options, integration of fishermen’s local ecological knowledge into biological assessments remains uncommon. Using the case of the eastern Baltic cod (Gadus morhua) resource, this article documented local ecological knowledge about a managed fishery stock. In 2012 and 2013, local media reported that fishermen were observing increased occurrences of cod with poor body condition (“skinny” cod) in their catches from waters off Poland. Polish cod fishermen were interviewed (n = 31) to quantify the strength of their agreement about the abundance and body condition of cod. Agreement among fishermen was assessed about trends in abundance and occurrence of “skinny” cod, as well as the mechanisms explaining those patterns. Cultural consensus analysis showed strong agreement among Polish fishermen that “skinny” cod may be attributed to overfishing on sprat, a key prey species. Fishermen and scientists observed similar declines in the abundance and condition of cod along the Polish coastline; however, they may perceive causes of those changes differently. Generalized additive models were used to show that trends in fishermen’s observations of abundance and “skinny” cod occurrence may be partially explained by variation in temperature, salinity, and sprat abundance.
Baptism by fire: the pivotal role of ancient conflagrations in evolution of the Earth's flora
Authors: He Tianhua , Lamont Byron B 
Published: March 2017

AbstractFire became a defining feature of the Earth's processes as soon as land plants evolved 420 million years ago and has played a major role in shaping the composition and physiognomy of many ecosystems ever since. However, there remains a general lack of appreciation of the place of fire in the origin, evolution, ecology and conservation of the Earth's biodiversity. We review the literature on the presence of fire throughout the Earth's history following the evolution of land plants and examine the evidence for the origin and evolution of adaptive functional traits, biomes and major plant groups in relation to fire. We show that: (1) fire activities have fluctuated throughout geological time due to variations in climate, and more importantly in atmospheric oxygen, as these affected fuel levels and flammability; (2) fire promoted the early evolution and spread of major terrestrial plant groups; (3) fire has shaped the floristics, structure and function of major global biomes; and (4) fire has initiated and maintained the evolution of a wide array of fire-adapted functional traits since the evolution of land plants. We conclude that fire has been a fundamental agent of natural selection on terrestrial plants throughout the history of life on the Earth's land surface. We suggest that a paradigm shift is required to reassess ecological and evolutionary theories that exclude a role for fire, and also there is a need to review fire-suppression policies on ecosystem management and biodiversity conservation in global fire-prone regions.
Recognition and management of Clostridium difficile in older adults
Authors: Sams Anna Wentz , Kennedy-Malone Laurie 
Published: March 2017

Abstract:

Clostridium difficile infection (CDI) is increasing in the outpatient setting, and older adults are at a higher risk for contracting CDI and experiencing poor outcomes. NPs may see this infection in the primary care setting. This article focuses on the presentation, treatment, and clinical practice implications for CDI in community-dwelling older adults.
Age-Based Normative Measurements of the Pediatric Pelvis
Authors: Oetgen Matthew E. , Andelman Steven , Martin Benjamin D. 
Published: March 2017

Objectives:
Pediatric pelvic trauma is associated with high rates of morbidity and mortality. Current classifications do not take into account age-dependent quantitative differences of the pediatric pelvis making accurate diagnosis of pathologic diastasis of the pubic symphysis, sacroiliac (SI) joints, and triradiate cartilage difficult. The purpose of this study was to establish age-based normative values for the width of the pubic symphysis, SI joints, and the triradiate cartilage of the pediatric pelvis.

Methods:
All computed tomographic (CT) scans of the abdomen and pelvis from patients between the ages 2 and 16 years over a 3-year period at a single institution were evaluated. Patients were excluded if the CT was performed as part of a trauma evaluation or for a history of neuromuscular disease or spinopelvic instrumentation. A total of 821 CT were included. The width of pubic symphysis, right and left SI joints, and each limb of the triradiate cartilages was measured using the PACS digital measurement tool. Left and right measurements of the SI joints and triradiate cartilage were combined and reported together.

Results:
From age 2 to 16 years, the average widths of the SI joint and pubic symphysis decreased from 3.11 to 1.80 mm and 5.55 to 3.69 mm, respectively. The average widths of the 3 limbs of the triradiate cartilage also slightly decreased from age 2 until closure: ilioischial, iliopubic, and ischiopubic cartilages decreasing from 3.72 to 2.74 mm, 4.42 to 3.52 mm, and 3.08 to 2.97 mm, respectively.

Conclusions:
This study demonstrates an age-dependent decrease in width of the pubic symphysis and left and right SI joints. By contrast, the widths of the triradiate cartilage remain relatively stable until closure. We believe that these age-based normative values will aid in future diagnosis of pathologic diastasis of these areas of the pediatric pelvis.
Proximal Femoral Shortening After Cephalomedullary Nail Insertion for Intertrochanteric Fractures
Authors: Gilat Ron , Lubovsky Omri , Atoun Ehud , Debi Ronen , Cohen Ornit , Weil Yoram A. 
Published: March 2017

Objective:
To assess the incidence of proximal femoral shortening (PFS) and its effect on the patient outcomes when intertrochanteric fractures were treated with a cephalomedullary nail (CMN).

Design:
Retrospective cohort study.

Settings:
Level II trauma center.

Patients:
Forty-eight consecutive patients with OTA/AO 31-A intertrochanteric fractures.

Intervention:
All patients were treated with a Gamma3 CMN (Stryker, Kalamazoo, MI).

Methods:
PFS was assessed for abductor lever arm (x vector), femoral height (y vector), and overall shortening (z vector) on anteroposterior radiographs. Fixation success and retained ambulatory capacity were noted.

Results:
Shortening of >5 mm of the x, y, and z vectors was evident in 18, 20, and 29 patients, respectively. Shortening of >10 mm of the x, y, and z vectors was measured in 5, 6, and 8 patients, respectively. Mean shortening of the x, y, and z vectors was 4.5, 5.5, and 7 mm, respectively. Greater PFS was found to be associated with fixation failure and inability to retain ambulatory capacity, independently (P ≤ 0.05 and P ≤ 0.025, respectively). Of note, an unstable fracture pattern was not found to be associated with greater PFS.

Conclusions:
PFS is a common phenomenon after CMN of intertrochanteric fractures with a Gamma CMN. In addition, greater PFS seems to be associated with fixation failure and inability to retain ambulatory capacity postoperatively.

Level of Evidence:
Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Clinical and Functional Results of 119 Patients With Knee Dislocations
Authors: Scarcella Nicholas R. , Weinberg Douglas S. , Bowen Stephen , Vallier Heather A. 
Published: March 2017

Objectives:
To describe clinical results and functional outcomes of knee dislocations treated with a consistent strategy within our institution.

Design:
Retrospective case series.

Setting:
Level 1 trauma center.

Patients:
One hundred nineteen patients were treated at one institution between 2000 and 2014 for knee dislocation.

Main Outcome Measurements:
Knee range of motion, functional instability, and complications were recorded. Musculoskeletal Function Assessment (MFA) and Lysholm scores were obtained after minimum of 1 year.

Results:
Sixty-three early complications were noted in 36 patients (32%), with an overall amputation rate of 9.2% (8 early and 3 late amputations). Of the patients who retained their limb, 4.5% reported instability. Open knee dislocations were associated with amputation (26% vs. 1.3%, P < 0.001). Popliteal arterial injuries were associated with more amputation (31% vs. 3.2%, P = 0 < 0.001), infection (37% vs. 8%, P = 0.002), and deep venous thrombosis (32% vs. 8.8%, P = 0.014). Patients with wound infection were more likely to develop heterotopic ossification (36% vs. 9.4%, P = 0.017) and less knee motion (77.5 vs. 117 degrees P = 0.049). Knee motion improved over time for all patients with a mean arc of 86 degrees at 3 months, 109 degrees at 6 months, and 115 degrees at 12 months. An Injury Severity Score of ≥20 was associated with less knee motion (97 vs. 121 degrees P = 0.029). Mean Lysholm score was 86.7, and mean MFA score was 35.7 after mean follow-up of 90 months and 82 months, respectively.

Conclusions:
Few patients (4.5%) experienced functional instability. However, early complications occurred frequently (32%) as expected, particularly in patients with open injuries and/or arterial injury. Limitations in knee motion were associated with high Injury Severity Score, infection, and heterotopic ossification. Mean knee scores were good, consistent with reasonable knee function, although MFA scores suggest a lower level of generalized function.

Level of Evidence:
Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
A Retrospective Case-Matched Cost Comparison of Surgical Treatment of Melanoma and Nonmelanoma Skin Cancer in the Outpatient Versus Operating Room Setting
Authors: Johnson Ryan P. , Butala Niraj , Alam Murad , Lawrence Naomi 
Published: March 2017

BACKGROUND
To date, no study has used authentic billing data in a case–control matched fashion to examine the cost of treating skin cancer in different settings.

OBJECTIVE
To compare the cost of surgical treatment of skin cancer in the outpatient versus operating room setting using matched cases based on patient and skin cancer characteristics.

METHODS
ICD-9 diagnosis codes for skin cancers were used to find patients who had a malignant excision current procedural terminology code in the operating room setting during 2010 to 2014. Patient and skin cancer characteristics were used to match cases to those treated as an outpatient. A total of 36 cases (18 operating room and 18 outpatient) had the required information and characteristics to be matched and analyzed for cost. Health status was determined using the American Society of Anesthesiologists anesthesia grading scale.

RESULTS
No statistically significant differences were found in the age (p > 0.9) or American Society of Anesthesiologists scores (p > 0.6) of the outpatient and operating room cases. The median cost for outpatient cases was $1,745. For operating room cases, the median cost was $11,323. This was a statistically significant difference (p < 0.001).

CONCLUSION
The outpatient setting remains a cost-effective location to treat skin cancer compared with the operating room.
Population Pharmacokinetics of Gemcitabine and dFdU in Pancreatic Cancer Patients Using an Optimal Design, Sparse Sampling Approach
Authors: Serdjebi Cindy , Gattacceca Florence , Seitz Jean-François , Fein Francine , Gagnière Johan , François Eric , Abakar-Mahamat Abakar , Deplanque Gael , Rachid Madani , Lacarelle Bruno , Ciccolini Joseph , Dahan Laetitia 
Published: March 2017

Background:
Gemcitabine remains a pillar in pancreatic cancer treatment. However, toxicities are frequently observed. Dose adjustment based on therapeutic drug monitoring might help decrease the occurrence of toxicities. In this context, this work aims at describing the pharmacokinetics (PK) of gemcitabine and its metabolite dFdU in pancreatic cancer patients and at identifying the main sources of their PK variability using a population PK approach, despite a sparse sampled-population and heterogeneous administration and sampling protocols.

Methods:
Data from 38 patients were included in the analysis. The 3 optimal sampling times were determined using KineticPro and the population PK analysis was performed on Monolix. Available patient characteristics, including cytidine deaminase (CDA) status, were tested as covariates. Correlation between PK parameters and occurrence of severe hematological toxicities was also investigated.

Results:
A two-compartment model best fitted the gemcitabine and dFdU PK data (volume of distribution and clearance for gemcitabine: V1 = 45 L and CL1 = 4.03 L/min; for dFdU: V2 = 36 L and CL2 = 0.226 L/min). Renal function was found to influence gemcitabine clearance, and body surface area to impact the volume of distribution of dFdU. However, neither CDA status nor the occurrence of toxicities was correlated to PK parameters.

Conclusions:
Despite sparse sampling and heterogeneous administration and sampling protocols, population and individual PK parameters of gemcitabine and dFdU were successfully estimated using Monolix population PK software. The estimated parameters were consistent with previously published results. Surprisingly, CDA activity did not influence gemcitabine PK, which was explained by the absence of CDA-deficient patients enrolled in the study. This work suggests that even sparse data are valuable to estimate population and individual PK parameters in patients, which will be usable to individualize the dose for an optimized benefit to risk ratio.
Comparison of Noncontact Specular and Confocal Microscopy for Evaluation of Corneal Endothelium
Authors: Huang Jianyan , Maram Jyotsna , Tepelus Tudor C. , Sadda Srinivas R. , Chopra Vikas , Lee Olivia L. 
Published: March 2017

Purpose:
To compare endothelial cell analysis obtained by noncontact specular and confocal microscopy, using the Konan NSP-9900 and Nidek ConfoScan4 systems, respectively.

Methods:
Three groups including 70 healthy eyes, 49 eyes with Fuchs endothelial corneal dystrophy (FECD), and 78 eyes with glaucoma were examined with both the Konan NSP-9900 specular microscope and the Nidek ConfocScan4 confocal microscope. Certified graders at the Doheny Image Reading Center compared corneal endothelial images from both instruments side by side to assess image quality. Endothelial cell density (ECD) measurements were calculated and compared using three different modalities: (1) each instrument's fully automated analysis; (2) each instrument's semiautomatic analysis with grader input; and (3) manual grading methods by certified grader.

Results:
All normal eyes yielded gradable endothelial images, and most but not all glaucomatous eyes yielded images with high enough image quality to allow grading. In addition, in corneas with severe FECD, poor image quality precluded ECD grading by specular microscopy in 20 eyes (40.8%) but in only 4 (8.2%) confocal images from the same eyes. For the gradable images, the ECD values obtained using the manual grading method from either device were comparable with no statistically significant difference (P>0.05) between specular and confocal devices. Machine-generated ECD values were significantly different from manual results, measuring greater in all cases with specular microscopy. Machine-generated ECD values from confocal microscopy also differed significantly from manual determinations, but not in a consistent direction. Semiautomatic methods for both instruments obtained clinically acceptable ECD values.

Conclusions:
Automatic machine-generated ECD measurements differed significantly from manual assessments of corneal endothelium by both specular and confocal microscopy, suggesting that automated results should be used with caution. But ECD values derived manually were comparable between the two devices in both normal and glaucomatous eyes, suggesting that manually graded images from the two instruments can be used interchangeably for reliable ECD measurements. Because of a higher proportion of gradable images, confocal microscopy may be superior to specular microscopy for ECD measurements in FECD.
Effects of Myopic Orthokeratology on Visual Performance and Optical Quality
Authors: Liu Guihua , Chen Zhi , Xue Feng , Li Jing , Tian Mi , Zhou Xingtao , Wei Ruihua 
Published: March 2017

Objectives:
To analyze the changes in visual performance and optical quality after orthokeratology (ortho-k) treatment and its correlation with the magnitude of lens decentration and the diameter of treatment zone (TxZ).

Methods:
A prospective study was conducted in 27 eyes of 27 patients wearing ortho-k contact lens. Area under log contrast sensitivity function (AULCSF), modulation transfer function cutoff values (MTFcutoff), Strehl ratio (SR), and objective scattering index (OSI) were measured and compared before and 1 month after ortho-k lens treatment. Refractive sphere, astigmatism, and diameter and decentration of TxZ were tested against the change in AULCSF, MTFcutoff, SR, and OSI after ortho-k treatment in stepwise multiple linear regression models.

Results:
Objective scattering index significantly increased and AULCSF, MTFcutoff, and SR significantly decreased after ortho-k lens wear (all P<0.001). The mean TxZ diameter was 3.61±0.26 mm, and the mean magnitude of TxZ decentration was 0.60±0.16 mm. The amount of lens decentration significantly correlated with the change in AULCSF and MTFcutoff (P=0.027 and P=0.005, respectively). The diameter of TxZ significantly correlated with the change in MTFcutoff and SR (P=0.005 and P=0.024, respectively).

Conclusions:
Visual and optical quality decreases after ortho-k treatment, which can be alleviated by a larger TxZ diameter and a smaller lens decentration.
Minimally Invasive Aortic Valve Replacement via Right Anterior Minithoracotomy and Central Aortic Cannulation
Authors: Bethencourt Daniel M. , Le Jennifer , Rodriguez Gabriela , Kalayjian Robert W. , Thomas Gregory S. 
Published: March 2017

Objective This study reports the evolution of a minimally invasive aortic valve replacement (mini-AVR) technique that uses a right anterior minithoracotomy approach with central cannulation, for a 13-year period. This technique has become our standard approach for isolated primary AVR in nearly all patients. Methods This observational study evaluated perioperative clinical outcomes of patients 18 years or older who underwent mini-AVR from November 2003 to June 2015. Results The mini-AVR technique was used in 202 patients during two periods of 2003 to 2009 (n = 65, “early”) and 2010 to 2015 (n = 137, “late”). The mean ± SD age was 72.5 ± 12.9 years and 60% were male. Demographic parameters were statistically similar between the study periods, except for increased body weight in the later period (75.3 ± 14.7 vs 80.9 ± 20.8 kg, P = 0.03). The mean cardiopulmonary bypass and aortic cross-clamp times were significantly different by each year and Bonferroni adjustment, with significant decreases in cardiopulmonary bypass and aortic cross-clamp times beginning 2006. Compared with the early study period, late study period patients were more often extubated intraoperatively (52% vs 12%, P < 0.001), had less frequent prolonged ventilator use postoperatively (6% vs 16%, P = 0.018), required fewer blood transfusions (mean, 2.0 ± 2.3 U vs 3.6 ± 3.0 U; P = 0.011), and had shorter postoperative stay (6.3 ± 4.5 days vs 8.0 ± 5.9 days, P = 0.026). Numerically, fewer postoperative strokes (1% vs 6%, P = 0.09) and fewer reoperations for bleeding (3% vs 6%, P = 0.3) occurred in the late period. In-hospital mortality did not differ (1/65 early vs 3/137 late). Conclusions Overall mini-AVR intraoperative and postoperative clinical outcomes improved for this 13-year experience.
Using a Mixed Methods Approach to Examine Practice Characteristics Associated With Implementation of an Adult Immunization Intervention Using the 4 Pillars Practice Transformation Program
Authors: Hawk Mary , Nowalk Mary Patricia , Moehling Krissy K. , Pavlik Valory , Raviotta Jonathan M. , Brown Anthony E. , Zimmerman Richard K. , Ricci Edmund M. 
Published: March 2017

Abstract:
Adult immunization rates are consistently suboptimal, exacting significant human and financial burden of preventable disease. Practice-level interventions to improve immunization rates have produced mixed results. The context of change critically affects implementation of evidence-based interventions. We conducted a randomized controlled cluster trial of the 4 Pillars Practice Transformation Program to increase adult vaccination rates in primary care practices and used qualitative methods to test intervention effects and understand practice characteristics associated with implementation success. We conducted qualitative interviews with staff from 14 practices to assess implementation experiences. Thematic analysis of data pointed to the importance of quality improvement history, communication and practice leadership, Immunization Champion leadership effectiveness, and organizational flexibility. Practices were scored on these characteristics and grouped into four types: Low Implementers, Medium Implementers, High Implementers, and Public/University Practices. Intervention uptake and immunization rate changes were compared, and a significant increase in influenza vaccination rates (3.9 percentage points [PPs]; p = .038) was observed for High Implementers only. Significant increases in Tdap vaccination rates were observed for High Implementers (9.3 PP; p = 0.006) and the Public/University groups (6.5 PP; p = 0.012), but not other groups. Practice characteristics may be critical factors in predicting intervention success.