bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinematic Analysis of the Posterior Cruciate Ligament, Part 1
Authors: Kennedy Nicholas I. , Wijdicks Coen A. , Goldsmith Mary T. , Michalski Max P. , Devitt Brian M. , Årøen Asbjørn , Engebretsen Lars , LaPrade Robert F. 
Published: September 2013

Background: The posterior cruciate ligament (PCL) is composed of 2 functional bundles and has an essential role in knee function and stability. There is, however, a limited understanding of the role of each individual bundle through the full range of knee flexion. Hypothesis: Both bundles provide restraint to posterior tibial translation across a full range of knee flexion. At higher angles of knee flexion (>90°), the intact PCL also imparts significant rotational stability. Study Design: Controlled laboratory study. Methods: Twenty matched-paired, human cadaveric knees (mean age, 55.2 years; range, 51-59 years; 6 male and 4 female pairs) were used to evaluate the kinematics of an intact, anterolateral bundle (ALB) sectioned, posteromedial bundle (PMB) sectioned, and complete PCL sectioned knee. A 6 degree of freedom robotic system was used to assess knee stability with an applied 134-N posterior tibial load, 5-N·m external and internal rotation torques, 10-N·m valgus and varus torques, and a coupled 100-N posterior tibial load and 5-N external rotation torque at 0°, 15°, 30°, 45°, 60°, 75°, 90°, 105°, and 120°. Results: All sectioned states had significant increases compared with intact in posterior translation, internal rotation, and external rotation at all tested flexion angles, with the exception of the ALB sectioned state at 75° of flexion for external rotation. The significant increases (mean ± standard deviation) in posterior translation during a 134-N posterior tibial load at 90° of flexion were 0.9 ± 0.6 mm, 2.6 ± 1.8 mm, and 11.7 ± 4.0 mm for the PMB, ALB, and complete PCL sectioned states, respectively, compared with the intact state. The largest significant increases in internal rotation were in the PMB and complete PCL sectioned states at 105° of flexion, 1.3° ± 1.0° and 2.8° ± 2.1°, respectively. Conclusion: Both the ALB and the PMB assume a significant role in resisting posterior tibial translation, at all flexion angles, suggesting a codominant relationship. The PCL provided a significant constraint to internal rotation beyond 90° of flexion. Clinical Relevance: This information broadens the understanding of native knee kinematics and provides a template for the evaluation of single- and double-bundle PCL reconstructions.
Maternal Anxiety and Breastfeeding
Authors: Adedinsewo Demilade A. , Fleming Alison S. , Steiner Meir , Meaney Michael J. , Girard Amy Webb ,   on behalf of the MAVAN team
Published: September 2013

Background: Maternal anxiety and depression may impair maternal intention, motivation, and self-efficacy in multiple domains associated with child health including breastfeeding. Objective: We tested the hypothesis that mothers who experience substantial anxiety during pregnancy or the postpartum period are at increased risk for reduced initiation, exclusivity, and continuation of breastfeeding. Methods: We obtained data on 255 Canadian pregnant women from the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) study recruited between June 2004 and February 2009. We utilized data collected from 18 to 23 weeks gestation through 12 months postpartum. Multivariate logistic regression was used to assess whether scores on the Hamilton Anxiety Scale (HAM-A) and State-Trait Anxiety Inventory (STAI) were associated with initiation, exclusivity, and continuation of breastfeeding. Results: Prenatal anxiety was not associated with breastfeeding outcomes. In adjusted models, a single point increase in HAM-A scores at 3 months postpartum was associated with an 11% reduction in the odds of exclusive breastfeeding at 6 months (adjusted odds ratio [aOR] = 0.89; 95% CI, 0.80-0.99). A single point increase in STAI State and STAI Trait scores at 3 months postpartum was associated with a 4% (aOR = 0.96; 95% CI, 0.92-0.99) and 7% (aOR = 0.93; 95% CI, 0.86-1.00) reduction, respectively, in the odds of any breastfeeding at 12 months. Conclusion: Our findings suggest a relationship between maternal anxiety and reduced exclusivity and continuation of breastfeeding. Maternal anxiety should be actively monitored and managed appropriately in the postpartum period to support optimal breastfeeding practices.
Cardioprotective effects of fish omega-3 fatty acids on doxorubicin-induced cardiotoxicity in rats
Authors: Uygur R , Aktas C , Tulubas F , Alpsoy S , Topcu B , Ozen OA 
Published: September 2013

The aim of this study was to investigate the protective effects of fish omega-3 (n-3) fatty acids on doxorubicin (DOX)-induced acute cardiotoxicity. A total of 24 rats were divided into three groups: control, DOX-treated, and DOX treated with fish n-3 fatty acids. Control group received 0.4 ml/kg/day of saline intragastrically. The rats in the fish n-3 fatty acid-pretreated group were given 400 mg/kg/day fish n-3 fatty acids for 30 days by intragastric intubation. To induce acute cardiotoxicity, DOX (30 mg/kg) was injected intraperitoneally by a single dose and the rats were killed after 48 h. DOX treatment caused severe damage in heart tissues. Disorganization of myocardial muscle fibers, myofibrillar loss, and cardiotoxic myocardial fibers with cytoplasmic vacuoles were seen. Fish n-3 fatty acid-treated rats showed an improved histological appearance in the DOX-treated group. Our data indicate a significant reduction in the activity of terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling in cardiomyocytes of the DOX-treated group with fish n-3 fatty acids therapy. The DOX-treated with fish n-3 fatty acids group showed a significant decrease in malondialdehyde levels, and an increase in superoxide dismutase and glutathione peroxidase activities in comparison with the DOX-treated group. This study showed that fish n-3 fatty acids may be a suitable cardioprotector against acute toxic effects of DOX.
The serum levels of adiponectin and leptin in mustard lung patients
Authors: Rokni Yazdi H , Lari SM , Attaran D , Ayatollahi H , Mohsenizadeh A 
Published: September 2013

Introduction: Chronic obstructive pulmonary disease (COPD) due to sulfur mustard (SM), known as mustard lung, is an important late pulmonary complication of SM poisoning. Due to the possible role of systemic inflammation in mustard lung, we evaluated the serum levels of adiponectin and leptin in these patients. Materials and methods: Thirty nonsmoker mustard lung patients in stable phase were enrolled into this study. Also, 30 COPD and 21 healthy participants were entered as control groups. Complete lung function tests were performed in the participants. The serum levels of adiponectin and leptin were measured in all groups. Results: There were no statistically significant differences in mean adiponectin and leptin levels among the groups ( p = 0.38 and p = 0.35, respectively). There was a downward trend in leptin to adiponectin ratio from lower to higher stages of global initiative for chronic obstructive lung disease guidelines in mustard lung patients, which was not statistically significant ( p = 0.8). Conclusion: Our results showed that there is no difference in mean adipokine levels in stable mustard lung patients compared with control groups. There was a foot-point in the alterations of serum adipokines regarding the severity of COPD, which needs to be documented by larger sample group.
Measuring Pain Perceptions and Medication Taking Behavior at the End of Life
Authors: Hutt Evelyn , Fink Regina M. , Nelson-Marten Paula , Jones Jacqueline , Kutner Jean S. 
Published: September 2013

Background: Understanding why some patients with terminal illness are reluctant to take sufficient medication to control pain is critical to effective pain management. Objective: As a first step toward exploring the pain medication-taking behavior of palliative care patients, this pilot study tested a survey regarding pain medication adherence, medication beliefs, and quality of life (QoL). Design: Convenience sample; survey. Setting/Subjects: Six patients receiving inpatient Palliative Care consultations at an academic medical center answered questions about their outpatient pain medication-taking behavior. Measurements: Medication Adherence Report Scale (MARS), Beliefs about Medications Questionnaire (BMQ), Brief Pain Inventory (BPI), closed-response items from a pain medication adherence study in terminally ill patients, the McGill Quality of Life Questionnaire (McGill), and demographic items. Results: The battery of questionnaires took approximately 53 minutes; five of six participants were able to complete all items. Respondents reported moderate to severe pain (mean 4.3/10 for pain on average; 7/10 for worst pain in past 24 hours), and excellent medication adherence. When asked how much relief was provided by pain therapies, respondents reported a mean 73% (range 50-100%) relief. They expressed little concern about addiction, but more concern about medication-induced nausea and constipation. Overall QoL was good (mean 6.8/10, range 5-10, higher score better), with notably high scores in existential and support domains. Conclusions: Inpatients receiving palliative care consultation were able to complete interviewer-administered questionnaires regarding their pain perceptions, medications, and QoL. Further studies using these instruments are feasible and could inform shared decision making about pain management.
Circadian Variation of Stent Thrombosis and the Effect of More Robust Platelet Inhibition
Authors: Mogabgab Owen , Wiviott Stephen D. , Cannon Christopher P. , Sloan Sarah , Sabatine Marc S. , Antman Elliott M. , Braunwald Eugene , Giugliano Robert P. 
Published: September 2013

Background: The well-described morning peak in the onset of acute coronary syndromes has been partly attributed to increased platelet activity upon arising. It has been suggested that stent thrombosis (ST) exhibits a similar pattern. We assessed whether a diurnal variation in ST occurs, and whether more robust antiplatelet therapy with prasugrel (vs clopidogrel) can attenuate a morning excess. Methods and Materials: Patients from the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition with Prasugrel–Thrombolysis in Myocardial Infarction (TRITON-TIMI) 38 trial (N = 13 608) with adjudicated ST classified per the Academic Research Consortium definitions of definite (N = 135) and probable (N = 27) were grouped into prespecified 8-hour intervals by time of onset: early (6 am-2 pm), late-day (2 pm-10 pm), and overnight (10 pm-6 am). We compared the rates per 1000 patients of ST across time intervals and stratified by treatment and stent type. Results: A diurnal variation in definite/probable ST was observed with rates of 6.5, 3.7, and 2.1 for early, late-day, and overnight intervals, respectively ( P < .001), per 1000 patients treated. A sensitivity analysis excluding periprocedural acute-ST (<24 hours after index percutaneous coronary intervention [PCI]) resulted in similar findings (5.2, 2.5, and 1.8 per 1000, P < .001). The circadian variation in ST was observed in patients on clopidogrel (9.7, 4.8, and 3.1 per 1000, P < .001) with the highest rate of ST early in the day. Patients on prasugrel also demonstrated a circadian variation with particularly low rates of overnight ST (3.4, 3.0, and 1.1 per 1000, P = .020). Conclusions: In TRITON-TIMI 38 trial, the timing of ST exhibited a significant diurnal variation similar to that seen with onset of other acute coronary syndromes. ST occurred less frequently among patients randomized to prasugrel compared to clopidogrel with the greatest absolute reduction (6.2 per 1000 patients) in events earlier in the day when platelet activity is known to be highest.
Molecular approaches for improved clotting factors for hemophilia
Authors: Kaufman Randal J. , Powell Jerry S. 
Published: September 2013

AbstractHemophilia is caused by a functional deficiency of one of the coagulation proteins. Therapy for no other group of genetic diseases has seen the progress that has been made for hemophilia over the past 40 years, from a life expectancy in 1970 of ∼20 years for a boy born with severe hemophilia to essentially a normal life expectancy in 2013 with current prophylaxis therapy. However, these therapies are expensive and require IV infusions 3 to 4 times each week. These are exciting times for hemophilia because several new technologies that promise extended half-lives for factor products, with potential for improvements in quality of life for persons with hemophilia, are in late-phase clinical development.
In silico characterization of a novel pathogenic deletion mutation identified in XPA gene in a Pakistani family with severe xeroderma pigmentosum
Authors: Nasir Muhammad , Ahmad Nafees , Sieber Christian MK , Latif Amir , Malik Salman Akbar , Hameed Abdul 
Published: September 2013

Abstract

Background
Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation.

Results
The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system.

Conclusions
Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain.
BGFit: management and automated fitting of biological growth curves
Authors: Veríssimo André , Paixão Laura , Neves Ana Rute , Vinga Susana 
Published: September 2013

Abstract

Background
Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from microbiology and oncology, the need for a software that allows researchers to easily organize experimental data and simultaneously extract relevant parameters in an efficient way is crucial.

Results
BGFit provides a web-based unified platform, where a rich set of dynamic models can be fitted to experimental time-series data, further allowing to efficiently manage the results in a structured and hierarchical way. The data managing system allows to organize projects, experiments and measurements data and also to define teams with different editing and viewing permission. Several dynamic and algebraic models are already implemented, such as polynomial regression, Gompertz, Baranyi, Logistic and Live Cell Fraction models and the user can add easily new models thus expanding current ones.

Conclusions
BGFit allows users to easily manage their data and models in an integrated way, even if they are not familiar with databases or existing computational tools for parameter estimation. BGFit is designed with a flexible architecture that focus on extensibility and leverages free software with existing tools and methods, allowing to compare and evaluate different data modeling techniques. The application is described in the context of bacterial and tumor cells growth data fitting, but it is also applicable to any type of two-dimensional data, e.g. physical chemistry and macroeconomic time series, being fully scalable to high number of projects, data and model complexity.
Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle
Authors: Serão Nick VL , González-Peña Dianelys , Beever Jonathan E , Faulkner Dan B , Southey Bruce R , Rodriguez-Zas Sandra L 
Published: September 2013

Abstract

Background
General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50 K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency – residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) – were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.

Results
For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value < 0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value < 0.001) including, 9nucleotide binding; ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.

Conclusions
The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.
Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits
Authors: Fletcher Richard S , Mullen Jack L , Yoder Seth , Bauerle William L , Reuning Gretchen , Sen Saunak , Meyer Eli , Juenger Thomas E , McKay John K 
Published: September 2013

Abstract

Background
The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery.

Results
In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait.

Conclusions
The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.
Incubation periods of viral gastroenteritis: a systematic review
Authors: Lee Rachel M , Lessler Justin , Lee Rose A , Rudolph Kara E , Reich Nicholas G , Perl Trish M , Cummings Derek AT 
Published: September 2013

AbstractBackgroundAccurate knowledge of incubation period is important to investigate and to control infectious diseases and their transmission, however statements of incubation period in the literature are often uncited, inconsistent, and/or not evidence based.MethodsIn a systematic review of the literature on five enteric viruses of public health importance, we found 256 articles with incubation period estimates, including 33 with data for pooled analysis.ResultsWe fit a log-normal distribution to pooled data and found the median incubation period to be 4.5 days (95% CI 3.9-5.2 days) for astrovirus, 1.2 days (95% CI 1.1-1.2 days) for norovirus genogroups I and II, 1.7 days (95% CI 1.5-1.8 days) for sapovirus, and 2.0 days (95% CI 1.4-2.4 days) for rotavirus.ConclusionsOur estimates combine published data and provide sufficient quantitative detail to allow for these estimates to be used in a wide range of clinical and modeling applications. This can translate into improved prevention and control efforts in settings with transmission or the risk of transmission.