bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomechanical Comparison of Five Posterior Cruciate Ligament Reconstruction Techniques
Authors: Milles Jeffrey , Pfeiffer Ferris , Stannard James , Smith Patrick , Kfuri Mauricio , Cook James , Nuelle Clayton 
Published: October 2016

AbstractNo surgical technique recreates native posterior cruciate ligament (PCL) biomechanics. We compared the biomechanics of five different PCL reconstruction techniques versus the native PCL. Cadaveric knees (n = 20) were randomly assigned to one of five reconstruction techniques: Single bundle all-inside arthroscopic inlay, single bundle all-inside suspensory fixation, single bundle arthroscopic-assisted open onlay (SB-ONL), double bundle arthroscopic-assisted open inlay (DB-INL), and double bundle all-inside suspensory fixation (DB-SUSP). Each specimen was potted and connected to a servo-hydraulic load frame for testing in three conditions: PCL intact, PCL deficient, and PCL reconstructed. Testing consisted of a posterior force up to 100 N at a rate of 1 N/s at four knee flexion angles: 10, 30, 60, and 90 degrees. Three material properties were measured under each condition: load to 5 mm displacement, maximal displacement, and stiffness. Data were normalized to the native PCL, compared across techniques, compared with all PCL-intact knees and to all PCL-deficient knees using one-way analysis of variance. For load to 5 mm displacement, intact knees required significantly (p < 0.03) more load at 30 degrees of flexion than all reconstructions except the DB-SUSP. At 60 degrees of flexion, intact required significantly (p < 0.01) more load than all others except the SB-ONL. At 90 degrees, intact, SB-ONL, DB-INL, and DB-SUSP required significantly more load (p < 0.05). Maximal displacement testing showed the intact to have significantly (p < 0.02) less laxity than all others except the DB-INL and DB-SUSP at 60 degrees. At 90 degrees the intact showed significantly (p < 0.01) less laxity than all others except the DB-SUSP. The intact was significantly stiffer than all others at 30 degrees (p < 0.03) and 60 degrees (p < 0.01). Finally, the intact was significantly (p < 0.05) stiffer than all others except the DB-SUSP at 90 degrees. No technique matched the exact properties of the native PCL, but the double bundle reconstructions more closely recreated the native biomechanics immediately after implantation, with the DB-SUSP coming closest to the native ligament. This study contributes new data for consideration in PCL reconstruction technique choice.
Evolutionary consequences of behavioral diversity
Authors: Stewart Alexander J. , Parsons Todd L. , Plotkin Joshua B. 
Published: October 2016

Significance
Access to a diversity of behavioral choices makes social dynamics rich and difficult to analyze. Individuals are rarely constrained to a binary choice between “cooperate” or “defect,” as many theoretical treatments assume. Here we use game theory to ask what social behaviors will emerge in populations as the number of behavioral choices grows. We show that simple strategies, where players do not vary their behavior much at all, can nonetheless be successful, and that access to a broader range of behavioral choices can cause a population to evolve toward lower levels of cooperation. Finally, we show that access to greater choice in rock–paper–scissors games inevitably leads to behavioral diversity, with players using strategies that make use of all possible choices.
Using seafaring simulations and shortest-hop trajectories to model the prehistoric colonization of Remote Oceania
Authors: Montenegro Álvaro , Callaghan Richard T. , Fitzpatrick Scott M. 
Published: October 2016

Significance
The colonization of Remote Oceania between ∼3400 and 800 B.P.—from multiple origin points and across hundreds or thousands of kilometers of open ocean—represents some of the most impressive population dispersals on Earth. For decades, scholars have sought to explain when and how these occurred. Here we show that seafaring simulation techniques coupled with sophisticated analyses of climatic data, including the role of El Niño Southern Oscillation events and island distribution on ancient voyaging, are critical comparative tools for understanding the variables—culturally, technologically, and environmentally—that structured movement across the world’s largest ocean. These data also pinpoint likely departure points for ancient Pacific Islanders that in some cases support or negate current archaeological and other lines of evidence.
Allelic diversity in an NLR geneBPH9enables rice to combat planthopper variation
Authors: Zhao Yan , Huang Jin , Wang Zhizheng , Jing Shengli , Wang Yang , Ouyang Yidan , Cai Baodong , Xin Xiu-Fang , Liu Xin , Zhang Chunxiao , Pan Yufang , Ma Rui , Li Qiaofeng , Jiang Weihua , Zeng Ya , Shangguan Xinxin , Wang Huiying , Du Bo , Zhu Lili , Xu Xun , Feng Yu-Qi , He Sheng Yang , Chen Rongzhi , Zhang Qifa , He Guangcun 
Published: October 2016

SignificanceInsect pests represent a major constraint that reduces crop yield and quality globally. Host plant resistance is often used as a key tactic to control insect pests, but is frequently overcome by newly emerged insect populations. In nature, plants have developed various strategies for sustainable defense. In this work, we isolated a brown planthopper-resistance gene,BPH9, and show that alleles of this gene locus have been widely used in rice breeding and saved rice production from massive brown planthopper (BPH) damage. Allelic diversity in this gene locus has provided resistance to rice against different BPH populations. Manipulating allelic diversity of the gene may provide a strategy for developing resistant varieties to cope with evolving insect populations with new virulence variation.
Lutein, a carotenoid, suppresses osteoclastic bone resorption and stimulates bone formation in cultures
Authors: Tominari Tsukasa , Matsumoto Chiho , Watanabe Kenta , Hirata Michiko , Grundler Florian MW , Inada Masaki , Miyaura Chisato 
Published: October 2016

Abstract
Lutein, a member of the xanthophyll family of carotenoids, suppressed IL-1-induced osteoclast differentiation and bone resorption. The survival of mature osteoclasts was also suppressed by lutein in cultures. When lutein was added to the cultures of osteoblasts, lutein enhanced the formation of mineralized bone nodules by elevating BMP2 expression and inhibiting sclerostin expression. Lutein may be beneficial for bone health.
Network-based analysis of omics data: the LEAN method
Authors: Gwinner Frederik , Boulday Gwénola , Vandiedonck Claire , Arnould Minh , Cardoso Cécile , Nikolayeva Iryna , Guitart-Pla Oriol , Denis Cécile V , Christophe Olivier D , Beghain Johann , Tournier-Lasserve Elisabeth , Schwikowski Benno 
Published: October 2016

Abstract

Motivation
Most computational approaches for the analysis of omics data in the context of interaction networks have very long running times, provide single or partial, often heuristic, solutions and/or contain user-tuneable parameters.

Results
We introduce local enrichment analysis (LEAN) for the identification of dysregulated subnetworks from genome-wide omics datasets. By substituting the common subnetwork model with a simpler local subnetwork model, LEAN allows exact, parameter-free, efficient and exhaustive identification of local subnetworks that are statistically dysregulated, and directly implicates single genes for follow-up experiments.
Evaluation on simulated and biological data suggests that LEAN generally detects dysregulated subnetworks better, and reflects biological similarity between experiments more clearly than standard approaches. A strong signal for the local subnetwork around Von Willebrand Factor (VWF), a gene which showed no change on the mRNA level, was identified by LEAN in transcriptome data in the context of the genetic disease Cerebral Cavernous Malformations (CCM). This signal was experimentally found to correspond to an unexpected strong cellular effect on the VWF protein. LEAN can be used to pinpoint statistically significant local subnetworks in any genome-scale dataset.

Availability and Implementation
The R-package LEANR implementing LEAN is supplied as supplementary material and available on CRAN (https://cran.r-project.org).

Supplementary information
Supplementary data are available at Bioinformatics online.
tcpl: the ToxCast pipeline for high-throughput screening data
Authors: Filer Dayne L , Kothiya Parth , Setzer R Woodrow , Judson Richard S , Martin Matthew T 
Published: October 2016

Abstract

Motivation
Large high-throughput screening (HTS) efforts are widely used in drug development and chemical toxicity screening. Wide use and integration of these data can benefit from an efficient, transparent and reproducible data pipeline. Summary: The tcpl R package and its associated MySQL database provide a generalized platform for efficiently storing, normalizing and dose-response modeling of large high-throughput and high-content chemical screening data. The novel dose-response modeling algorithm has been tested against millions of diverse dose-response series, and robustly fits data with outliers and cytotoxicity-related signal loss.

Availability and Implementation
tcpl is freely available on the Comprehensive R Archive Network under the GPL-2 license.
ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability
Authors: Hiner Mark C , Rueden Curtis T , Eliceiri Kevin W 
Published: October 2016

Abstract

Summary
ImageJ-MATLAB is a lightweight Java library facilitating bi-directional interoperability between MATLAB and ImageJ. By defining a standard for translation between matrix and image data structures, researchers are empowered to select the best tool for their image-analysis tasks.

Availability and Implementation
Freely available extension to ImageJ2 (http://imagej.net/Downloads). Installation and use instructions available at http://imagej.net/MATLAB_Scripting. Tested with ImageJ 2.0.0-rc-54, Java 1.8.0_66 and MATLAB R2015b.

Supplementary information
Supplementary data are available at Bioinformatics online.
PyBoolNet: a python package for the generation, analysis and visualization of boolean networks
Authors: Klarner Hannes , Streck Adam , Siebert Heike 
Published: October 2016

AbstractMotivationThe goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts.ResultsPyBoolNet is a Python package for working with Boolean networks that supports simple access to model checking via NuSMV, standard graph algorithms via NetworkX and visualization via dot. In addition, state of the art attractor computation exploiting Potassco ASP is implemented. The package is function-based and uses only native Python and NetworkX data types.Availability and Implementationhttps://github.com/hklarner/PyBoolNet
BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods
Authors: Oyetunde Tolutola , Zhang Muhan , Chen Yixin , Tang Yinjie , Lo Cynthia 
Published: October 2016

Abstract

Motivation
Metabolic network reconstructions are often incomplete. Constraint-based and pattern-based methodologies have been used for automated gap filling of these networks, each with its own strengths and weaknesses. Moreover, since validation of hypotheses made by gap filling tools require experimentation, it is challenging to benchmark performance and make improvements other than that related to speed and scalability.

Results
We present BoostGAPFILL, an open source tool that leverages both constraint-based and machine learning methodologies for hypotheses generation in gap filling and metabolic model refinement. BoostGAPFILL uses metabolite patterns in the incomplete network captured using a matrix factorization formulation to constrain the set of reactions used to fill gaps in a metabolic network. We formulate a testing framework based on the available metabolic reconstructions and demonstrate the superiority of BoostGAPFILL to state-of-the-art gap filling tools. We randomly delete a number of reactions from a metabolic network and rate the different algorithms on their ability to both predict the deleted reactions from a universal set and to fill gaps. For most metabolic network reconstructions tested, BoostGAPFILL shows above 60% precision and recall, which is more than twice that of other existing tools.

Availability and Implementation
MATLAB open source implementation (https://github.com/Tolutola/BoostGAPFILL)

Supplementary information
Supplementary data are available at Bioinformatics online.
Meningococcal Disease in Patients With Human Immunodeficiency Virus Infection: A Review of Cases Reported Through Active Surveillance in the United States, 2000–2008
Authors: Harris Christine M. , Wu Henry M. , Li Jianmin , Hall H. Irene , Lee Adria , Zell Elizabeth , Harrison Lee H. , Petit Susan , Farley Monica M. , Lynfield Ruth , Miller Lisa , Nichols Megin , Reingold Arthur , Schaffner William , Thomas Ann , MacNeil Jessica R. , Clark Thomas A. , Cohn Amanda C. 
Published: October 2016

Abstract

Background
Although human immunodeficiency virus (HIV) infection is an established risk factor for several bacterial infections, the association between HIV infection and meningococcal disease remains unclear.

Methods
Expanded chart reviews were completed on persons with meningococcal disease and HIV infection reported from 2000 through 2008 from 9 US sites participating in an active population-based surveillance system for meningococcal disease. The incidence of meningococcal disease among patients meeting Centers for Disease Control and Prevention acquired immune deficiency syndrome (AIDS) surveillance criteria was estimated using data from the National HIV Surveillance System for the participating sites.

Results
Thirty-three cases of meningococcal disease in individuals with HIV infection were reported from participating sites, representing 2.0% of all reported meningococcal disease cases. Most (75.8%) persons with HIV infection were adult males aged 25 to 64 years old. Among all meningococcal disease cases aged 25 to 64 years old, case fatality ratios were similar among HIV-infected and HIV-uninfected persons (13.3% vs 10.6%; P = .6). The cumulative, mean incidence of meningococcal disease among patients aged 25 to 64 years old with HIV infection ever classified as AIDS was 3.5 cases per 100000 person years (95% confidence interval [CI], 2.1–5.6), compared with 0.3 cases per 100000 person years (95% CI, 0.3–0.3) for persons of the same age group not reported to have AIDS (relative risk = 12.9; 95% CI, 7.9–20.9).

Conclusions
Individuals with HIV infection meeting the AIDS surveillance case definition have a higher incidence of meningococcal disease compared with the general adult population.
Antiretroviral Therapy as Prevention of … Pneumococcal Infections?
Authors: Lesourd Anaïs , Leporrier Jérémie , Delbos Valérie , Unal Guillemette , Honoré Patricia , Etienne Manuel , Bouchaud Olivier , Caron François 
Published: October 2016

Abstract

Background
Despite antiretroviral therapy, it is generally believed that the risk for pneumococcal infections (PnIs) is high among patients infected with human immunodeficiency virus (HIV). However, most studies in this field have been conducted before 2010, and the proportion of virologically suppressed patients has drastically increased in these latter years thanks to larger indications and more effective antiretroviral regimens. This study aimed to re-evaluate the current risk of PnI among adult patients infected with HIV.

Methods
The incidence of PnI was evaluated between 1996 and 2014 in 2 French regional hospitals. The 80 most recent cases of PnI (2000–2014) were retrospectively compared with 160 controls (HIV patients without PnI) to analyze the residual risk factors of PnI.

Results
Among a mean annual follow-up cohort of 1616 patients, 116 PnIs were observed over 18 years. The risk factors of PnI among patients infected with HIV were an uncontrolled HIV infection or “classic” risk factors of PnI shared by the general population such as addiction, renal or respiratory insufficiency, or hepatitis B or C coinfection. Pneumococcal vaccination coverage was low and poorly targeted, because only 5% of the cases had been previously vaccinated. The incidence of invasive PnIs among HIV patients with a nonvirologically suppressed infection or comorbidities was 12 times higher than that reported in the general population at the country level (107 vs 9/100000 patients), whereas the incidence among virologically suppressed HIV patients without comorbidities was lower (7.6/100000 patients).

Conclusions
Human immunodeficiency virus infection no longer per se seems to be a significant risk factor for PnI, suggesting a step-down from a systematic to an “at-risk patient” targeted pneumococcal vaccination strategy.
Exploring NICU Nurses' Affective Responses to End-of-Life Care
Authors: Lewis Stephanie Lacefield 
Published: October 2016

Background:
The survival rate for infants born with life-threatening problems has improved greatly over the last few decades. Nevertheless, infants still die in neonatal intensive care units (NICUs) every day. Despite existing standards of care, some aspects of end-of-life care (EOLC) are still not delivered consistently. Little is known about how NICU nurses' individual experiences affect EOLC.

Purpose:
The purpose of this study was to explore, through lived and told stories, the affective, interactional, and meaning-related responses that NICU nurses have while caring for dying infants and their families. Coping strategies and changes in practice were also explored.

Methods:
Thirty-six members of the National Association of Neonatal Nurses submitted written narratives about an EOLC experience during which the nurse experienced strong emotions.

Findings:
Narrative analysis revealed many affective responses, but 3 were the most frequent: responsibility, moral distress, and identification. Coping methods included healthy and less healthy strategies, such as colleague support, informal and formal debriefing, practicing intentional gratefulness, avoidance, and compartmentalization. Changes in practice identified were universally described as professional growth through the use of reflective practice.

Implications for Practice & Research:
Educators should discuss the range of emotions experienced by caregivers related to EOLC and healthy coping strategies and encourage the use of reflective practice as a facilitator of professional growth. Nurse leaders should promote supportive environments in NICUs and ensure debriefing opportunities for nurses who have recently cared for a dying infant. Future research should focus on formulating interventions to utilize debriefing with NICU nurses and perhaps the development of EOLC mentors.
Change in Psychosocial Health Status Over 5 Years in Relation to Adults’ Hearing Ability in Noise
Authors: Stam Mariska , Smit Jan H. , Twisk Jos W. R. , Lemke Ulrike , Smits Cas , Festen Joost M. , Kramer Sophia E. 
Published: October 2016

Objectives:
The aim of this study was to establish the longitudinal relationship between hearing ability in noise and psychosocial health outcomes (i.e., loneliness, anxiety, depression, distress, and somatization) in adults aged 18 to 70 years. An additional objective was to determine whether a change in hearing ability in noise over a period of 5 years was associated with a change in psychosocial functioning. Subgroup effects for a range of factors were investigated.

Design:
Longitudinal data of the web-based Netherlands Longitudinal Study on Hearing (NL-SH) (N = 508) were analyzed. The ability to recognize speech in noise (i.e., the speech-reception-threshold [SRTn]) was measured with an online digit triplet test at baseline and at 5-year follow-up. Psychosocial health status was assessed by online questionnaires. Multiple linear regression analyses and longitudinal statistical analyses (i.e., generalized estimating equations) were performed.

Results:
Poorer SRTn was associated longitudinally with more feelings of emotional and social loneliness. For participants with a high educational level, the longitudinal association between SRTn and social loneliness was significant. Changes in hearing ability and loneliness appeared significantly associated only for specific subgroups: those with stable pattern of hearing aid nonuse (increased emotional and social loneliness), who entered matrimony (increased social loneliness), and low educational level (less emotional loneliness). No significant longitudinal associations were found between hearing ability and anxiety, depression, distress, or somatization.

Conclusions:
Hearing ability in noise was longitudinally associated with loneliness. Decline in hearing ability in noise was related to increase in loneliness for specific subgroups of participants. One of these subgroups included participants whose hearing deteriorated over 5 years, but who continued to report nonuse of hearing aids. This is an important and alarming finding that needs further investigation.
Database studies: an increasing trend in the United States orthopaedic literature
Authors: Sivasundaram Lakshmanan , Pannell William , Heckmann Nathanael , Alluri Ram K. , Omid Reza , “Rick” Hatch George F. 
Published: October 2016

Background:
There has been a recent increase in the number of orthopaedic publications using large-scale databases. The purpose of this study was to examine current database publication trends in the United States orthopaedic literature. In addition, we briefly discuss the strengths and limitations of the most utilized databases.

Methods:
PubMed was queried, and all abstracts and text were screened by two authors to insure that they reported on an orthopaedic topic using database findings. Studies from international databases, single-center databases, specialty-specific registries, and review articles were excluded. Annual and subspecialty trends were analyzed using Spearman correlation. Significance was set at P<0.05.

Results:
Our initial search yielded 1080 articles, of which 306 met inclusion criteria. There was a significant increase in the number of database studies published from 2004 to 2014, and an almost two-fold increase in the number of published studies from 2013 to 2014. The Journal of Bone and Joint Surgery, Spine (Phila Pa 1976), and Clinical Orthopaedics and Related Research had the most database publications over the period examined. Spine, joints, and sports subspecialties published the most database studies.

Conclusions:
There has been a large increase in the number of database studies published in United States orthopaedic literature, with the most dramatic increase observed between 2013 and 2014. Understanding the general strengths and limitations of these databases, as well as the differences between the various types of databases, is essential to fully understand this medium of orthopaedic research.