bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of increasing dietary level of a commercial liquid supplement on growth performance and carcass characteristics in feedlot steers
Authors: Felix Tara L , Long Chloe J , Stierwalt Madeline R , Carvalho Pedro H V , Blalock Howard M 
Published: April 2018

Abstract
Feeding cattle liquid supplements has become increasingly popular in the feedlot industry; however, optimal inclusion of liquid supplements in feedlot cattle diets is not known. The objectives of this study were to determine the optimal inclusion of liquid supplementation to maximize growth performance and improve carcass characteristics, as well as estimate the energy value of liquid supplementation when used as a direct corn replacement, for feedlot steers fed a concentrate-based diet. Two hundred and eighty steer calves were stratified by BW into light (BW = 208 ± 9 kg; n = 24) and heavy (BW = 275 ± 8 kg; n = 16) pens. Pens within BW block were randomly assigned to 1 of 4 supplements: 1) dry at 4.5% inclusion (0LIQ), 2) liquid (a proprietary blend from Quality Liquid Feeds; Dodgeville, WI) at 4.5% inclusion (4.5LIQ), 3) liquid at 9% inclusion (9LIQ), or 4) liquid at 13.5% inclusion (13.5LIQ). The remainder of the diet was 47.5% to 55.5% dry rolled corn, 20% corn silage, and 20% modified wet distillers grains with solubles (DM basis). Data were analyzed as a randomized complete block design and linear and quadratic were examined to determine effects of increasing dietary concentrations of liquid. Steers fed 4.5LIQ and 9LIQ had greater (quadratic; P ≤ 0.05) final BW, HCW, and NEm and NEg, and less DMI as a percent of BW compared to steers fed 13.5LIQ. Steers fed 0LIQ were intermediate and not different from other treatments. However, ADG and total BW gain did not differ (P ≥ 0.15) among treatments. Despite the lack of treatment effect on live measures of gain, feeding steers 4.5LIQ and 9LIQ resulted in greater carcass ADG (quadratic; P = 0.03), total carcass gain (quadratic; P = 0.04), and more efficient carcass gain (quadratic; P ≤ 0.01) compared to carcasses from steers fed 13.5LIQ. Feeding steers a liquid supplement at 9% of the diet, DM allowed for the greatest final BW and ADG in this study; however, there was no benefit of increasing liquid to 13.5%.
The Impact of Epidemiological Factors and Treatment Interventions on Survival in Patients With Signet Ring Cell Carcinoma of the Pancreas
Authors: Patel Mausam , Hans Harliv S. , Pan Kelsey , Khan Humza , Donath Elie , Caldera Humberto 
Published: April 2018

Objectives:
Primary pancreatic signet ring cell carcinoma (SRCC) is a rare histologic variant of pancreatic carcinoma. A population-based analysis of pancreatic SRCC was performed to determine the predictive effects of epidemiological factors and treatment interventions on overall survival (OS) and disease-specific survival (DSS).

Materials and Methods:
The Surveillance, Epidemiology, and End Results registry was searched for pancreatic SRCC cases diagnosed between January 1, 1973 and December 31, 2013. Statistical analysis was performed using the Fisher exact test, χ2 analysis, Kaplan-Meier method, log-rank test, and Cox proportional hazards regression.

Results:
The mean age among 497 patients was 66.6 years (SD, 11.9). Most patients were white (82.7%) and male (54.5%). The 1-, 2-, and 5-year OS rates were 17%, 9%, and 4%, respectively, while the corresponding 1-, 2-, and 5-year rates for DSS were 18%, 10%, and 5%, respectively. On univariable analysis; age, site, grade, stage, and treatment were predictive of OS and DSS (P<0.05). On multivariable analysis; radiation improved OS and DSS (adjusted hazard ratio [aHR], 0.592 and 0.589, respectively), pancreatectomy improved OS and DSS (aHR, 0.360 and 0.355, respectively), and combination therapy improved OS and DSS (aHR, 0.295 and 0.286, respectively). Age, site, and stage were also independent predictors of OS and DSS. Subgroup analysis demonstrated treatment to be an independent predictor of OS and DSS in localized/regional disease, in distant disease, and in patients diagnosed between 2000 and 2013.

Conclusions:
Age, site, stage, and treatment independently predict OS and DSS in pancreatic SRCC.
Verrucous Plaque With Unusually Large Candida Blastoconidia: A Unique Clinicopathological Presentation of Systemic Mucocutaneous Candidiasis
Authors: Rozas-Muñoz Eduardo , Mozos Ana , Mir-Bonafé Juan F. , Cubiró Xavier , Sánchez-Reus Ferran , Monteagudo Carlos , Puig Lluís 
Published: April 2018

Abstract:
Mucocutaneous candidiasis is a common infection affecting both immunocompetent and immunosuppressed individuals. Diversity in the clinical and histopathological presentation of mucocutaneous candidiasis is well known. However, the occurrence of cutaneous verrucous lesions and giant yeast-like structures has been rarely reported. In this article, we describe a case of disseminated mucocutaneous candidiasis in an immunosuppressed patient who presented as a verrucous plaque on the scrotum with giant Candida blastoconidia. This peculiar presentation expands the clinicopathological spectrum of mucocutaneous candidiasis and highlights the wide range of clinical manifestations and great morphologic variability of this common fungal infection.
Dyadic analysis of siblings' relationship quality, behavioural responses, and pain experiences during experimental pain
Authors: Schinkel Meghan G. , Chambers Christine T. , Corkum Penny , Jacques Sophie 
Published: April 2018

Abstract
Research on family factors in paediatric pain has primarily focused on parents; the role of siblings has been largely ignored. This study examined whether sibling relationship quality was related to siblings' behaviours during experimental pain, and whether the behaviours of an observing sibling were related to children's pain outcomes. Ninety-two sibling dyads between 8 and 12 years old completed both observational and questionnaire measures of sibling relationship quality. Children took turns completing the cold-pressor task (CPT) in a counterbalanced order with their sibling present. Pain outcomes (intensity, fear, and tolerance) were recorded for each sibling, and the behaviour of the observing and participating siblings during the CPT were coded as attending, nonattending, and coping/encouragement. Structural equation modelling, using the actor–partner interdependence model, was conducted to analyse the dyadic data. While participating in the CPT with their sibling present, greater levels of warmth and positivity in the sibling relationship were related to children engaging in more nonattending behaviours and less attending behaviours. Greater levels of attending behaviours by the observing child was related to the sibling having a lower pain tolerance, and greater levels of coping/encouragement behaviours by the observing child was related to the sibling reporting greater pain intensity and fear during the CPT. Children with warmer/positive sibling relationships were more likely to respond to acute pain by shifting the focus away from their pain experience (eg, through distraction) when a sibling was present. Pain-focused behaviours by an observing sibling are related to greater child pain and fear during experimental pain.
Determinants of Severity in Acute Pancreatitis
Authors: Sternby Hanna , Bolado Federico , Canaval-Zuleta Héctor J. , Marra-López Carlos , Hernando-Alonso Ana I. , del-Val-Antoñana Adolfo , García-Rayado Guillermo , Rivera-Irigoin Robin , Grau-García Francisco J. , Oms Lluís , Millastre-Bocos Judith , Pascual-Moreno Isabel , Martínez-Ares David , Rodríguez-Oballe Juan A. , López-Serrano Antonio , Ruiz-Rebollo María L. , Viejo-Almanzor Alejandro , González-de-la-Higuera Belén , Orive-Calzada Aitor , Gómez-Anta Ignacio , Pamies-Guilabert José , Fernández-Gutiérrez-del-Álamo Fátima , Iranzo-González-Cruz Isabel , Pérez-Muñante Mónica E. , Esteba María D. , Pardillos-Tomé Ana , Zapater Pedro , de-Madaria Enrique 
Published: April 2018

Objective:
The aim of this study was to compare and validate the different classifications of severity in acute pancreatitis (AP) and to investigate which characteristics of the disease are associated with worse outcomes.

Summary of Background Data:
AP is a heterogeneous disease, ranging from uneventful cases to patients with considerable morbidity and high mortality rates. Severity classifications based on legitimate determinants of severity are important to correctly describe the course of disease.

Methods:
A prospective multicenter cohort study involving patients with AP from 23 hospitals in Spain. The Atlanta Classification (AC), Revised Atlanta Classification (RAC), and Determinant-based Classification (DBC) were compared. Binary logistic multivariate analysis was performed to investigate independent determinants of severity.

Results:
A total of 1655 patients were included; 70 patients (4.2%) died. RAC and DBC were equally superior to AC for describing the clinical course of AP. Although any kind of organ failure was associated with increased morbidity and mortality, persistent organ failure (POF) was the most significant determinant of severity. All local complications were associated with worse outcomes. Infected pancreatic necrosis correlated with high morbidity, but in the presence of POF, it was not associated to higher mortality when compared with sterile necrotizing pancreatitis. Exacerbation of previous comorbidity was associated with increased morbidity and mortality.

Conclusion:
The RAC and DBC both signify an advance in the description and differentiation of AP patients. Herein, we describe the complications of the disease independently associated to morbidity and mortality. Our findings are valuable not only when designing future studies on AP but also for the improvement of current classifications.
Minimally Invasive Lobectomy Is Associated With Lower Noncancer-specific Mortality in Elderly Patients
Authors: Hristov Boris , Eguchi Takashi , Bains Sarina , Dycoco Joe , Tan Kay See , Isbell James M. , Park Bernard J. , Jones David R. , Adusumilli Prasad S. 
Published: April 2018

Objective:To investigate cancer- and noncancer-specific mortality following lobectomy by minimally invasive surgery (MIS) versus open thoracotomy in elderly patients with nonsmall cell lung cancer (NSCLC).Background:Two-thirds of patients with NSCLC are ≥65 years of age. As age increases, the risk of competing events, such as noncancer death, also increases.Methods:Elderly patients (≥65 yrs of age) who have undergone curative-intent lobectomy for stage I-III NSCLC without induction therapy (2002–2013) were included (n=1,303). Of those, 607 patients had undergone MIS and 696 had undergone thoracotomy. Propensity-score matching was performed to identify pairs of thoracotomy and MIS patients with comparable clinical characteristics (eg, year of surgery, comorbidities, and pulmonary function). Association between surgical approach (MIS vs thoracotomy) and lung cancer-specific and noncancer-specific cumulative incidence of death (CID) was analyzed using competing risks approach.Results:Following propensity score matching of patients who had undergone thoracotomy (n=338) versus MIS (n=338), MIS was associated with shorter length of stay (P<0.001), lower noncancer-specific 1-year mortality (P=0.027), and lower noncancer-specific CID (P=0.014) compared with thoracotomy; there was no difference in lung cancer-specific CID between surgical approaches. On multivariable analysis, thoracotomy was a significant risk factor for noncancer-specific death (subhazard ratio 2.45, 95% CI 1.18–5.06,P=0.016) independent of age, sex, and diffusion capacity of the lungs for carbon monoxide.Conclusion:In a propensity score-matched cohort, multivariable analysis has indicated that lobectomy performed by MIS is associated with lower incidence of noncancer-specific mortality compared with lobectomy performed by open thoracotomy in elderly patients with NSCLC.
Postoperative Surgical Site Infections
Authors: Ali-Mucheru Mariam N. , Seville Maria T. , Miller Vickie , Sampathkumar Priya , Etzioni David A. 
Published: April 2018

Objective:
To characterize agreement in the ascertainment of surgical site infections (SSIs) between the National Surgical Quality Improvement Program (NSQIP), National Healthcare Safety Network (NHSN), and administrative data.

Background:
The NSQIP, NHSN, and administrative data are the primary systems used to monitor and report SSIs for the purpose of quality control and benchmarking of hospitals and surgeons. These systems have different methods for identifying SSIs.

Methods:
We queried the NHSN, NSQIP, and administrative data systems for patients who had an operation at 1 of 4 hospitals within a single health system between January 2013 and September 2015. The detection of an SSI during a postoperative hospitalization was the outcome of analysis. Any SSI detected by one (or more) of these systems was analyzed by 2 reviewers to determine the presence of discrete elements of documentation constituting evidence of SSI. Concordance between the 3 systems (NHSN, NSQIP, and administrative data) was analyzed using Cohen's kappa.

Results:
After application of appropriate exclusion criteria, a cohort of 9447 inpatient operations was analyzed. In total, 130 SSIs were detected by 1 or more of the 3 systems, with reported SSI rates of 0.5% (NHSN), 0.7% (administrative data), and 1.0% (NSQIP). Of these 130 SSIs, only 17 SSIs were reported by all 3 systems. The concordance between these 3 systems was moderate (kappa values NSQIP-NHSN = 0.50 [0.40–0.60], administrative-NHSN = 0.36 [0.24–0.47], and administrative-NSQIP = 0.47 [0.38–0.57]). Chart review found that reasons for discordance were related to issues of different criteria as well as inaccuracies.

Conclusion:
There is significant discordance in the determination of SSIs reported by the NHSN, NSQIP, and administrative data. The differences and limitations of each of these systems have to be recognized, especially when using these data for quality reports and pay for performance.
Survival Implications of Increased Utilization of Local Excision for cT1N0 Esophageal Cancer
Authors: Sturm Emily C. , Zahnd Whitney E. , Mellinger John D. , Ganai Sabha 
Published: April 2018

Objective:
We hypothesized that patients with cT1N0 esophageal cancer undergoing local excision would have lower survival compared with esophagectomy due to potential discordant staging.

Background:
Local excision has become an attractive alternative for management of early esophageal cancer, avoiding the morbidity of esophagectomy. It is uncertain if occult nodal metastasis impacts survival.

Methods:
An observational study was conducted using the National Cancer Database (1998–2012) for patients with clinical T1N0 esophageal cancer who underwent local excision (n = 1625) or esophagectomy (n = 3255).

Results:
The proportion of patients undergoing local excision increased from 12% in 1998 to 50% in 2012 (P < 0.001). After esophagectomy, 61% of cT1N0 cancers had concordant clinical and pathological staging, with 5.2% having positive nodal disease; 37% were staged concordant after local excision, with excess missing data (60%). Ninety-day mortality was 7.4% after esophagectomy compared with 2.8% after local excision (P < 0.001). While no significant difference was seen in unadjusted survival, adjusted Cox regression analysis indicated worse survival after esophagectomy compared with local excision for all cases [hazard ratio (HR) 1.57, 95% confidence interval (CI) 1.27–1.95] and for patients with concordant staging (HR 1.68, 95% CI 1.23–2.28).

Conclusions:
Local excision for cT1N0 esophageal cancer has increased over time. Contrary to our hypothesis, despite incomplete nodal staging, patients undergoing local excision have favorable survival, particularly in the adenocarcinoma subgroup. This may reflect early differences in mortality due to differences in procedure-related complications and/or selection bias. As this study has limited power to compare outcomes between T1a and T1b cancers, further analysis is warranted.
Factors Associated With Prolonged Warm Ischemia Time Among Deceased Donor Kidney Transplant Recipients
Authors: Vinson Amanda J. , Rose Caren , Kiberd Bryce A. , Odutayo Ayodele , Kim S. Joseph , Alwayn Ian , Tennankore Karthik K. 
Published: April 2018

Background
Prolonged warm ischemia time (WIT) is associated with graft failure and mortality, however less is known about factors associated with prolonged WIT.

Methods
In a cohort of United States deceased donor kidney transplant recipients identified using the Scientific Registry of Transplant Recipients (Jan 2005-Dec 2013), we identified factors associated with prolonged WIT (defined as ≥ 30 minutes versus 10-30 minutes) using hierarchical multilevel models adjusting for center effect, and WIT as a continuous variable using multiple linear regression of log-transformed data.

Results
Among 55 829 patients, potentially modifiable risk factors associated with prolonged WIT included increased recipient body mass index (BMI) (odds ratio [OR], 1.57; 95% confidence interval [CI], 1.44-1.72 for BMI > 35), right donor kidney (OR, 1.14; 95% CI, 1.08-1.19), and a prolonged cold ischemic time (OR, 1.23; 95% CI, 1.13-1.33 for cold ischemia time > 24 hours). Transplanting a right kidney into an obese recipient further prolonged WIT (OR, 1.75; 95% CI, 1.55-1.98; for BMI > 35), increasing overall WIT by 11.0%. There was no correlation between median WIT for a given center and annual center transplant rate (pairwise correlation coefficient, 0.0898).

Conclusions
In conclusion, several modifiable factors are associated with prolonged WIT and may represent strategies to improve WIT and subsequent posttransplant outcomes.
Intra-tumor heterogeneity defines treatment-resistant HER2+ breast tumors
Authors: Rye Inga H. , Trinh Anne , Sætersdal Anna , Nebdal Daniel , Lingjærde Ole Christian , Almendro Vanessa , Polyak Kornelia , Børresen-Dale Anne-Lise , Helland Åslaug , Markowetz Florian , Russnes Hege G. 
Published: April 2018

AbstractTargeted therapy for patients with HER2 positive (HER2+) breast cancer has improved the overall survival, but many patients still suffer relapse and death of the disease. Intra-tumor heterogeneity of both estrogen receptor (ER) and HER2 expression has been proposed to play a key role in treatment failure, but little work has been done to comprehensively study this heterogeneity at the single-cell level.In this study, we explored the clinical impact of intra-tumor heterogeneity of ER protein expression, HER2 protein expression, and HER2 gene copy number alterations. Using combined immunofluorescence and in situ hybridization on tissue sections followed by a validated computational approach, we analyzed more than 13,000 single tumor cells across 37 HER2+ breast tumors. The samples were taken both before and after neoadjuvant chemotherapy plus HER2-targeted treatment, enabling us to study tumor evolution as well.We found that intra-tumor heterogeneity for HER2 copy number varied substantially between patient samples. Highly heterogeneous tumors were associated with significantly shorter disease-free survival and fewer long-term survivors. Patients for which HER2 characteristics did not change during treatment had a significantly worse outcome.This work shows the impact of intra-tumor heterogeneity in molecular diagnostics for treatment selection in HER2+ breast cancer patients and the power of computational scoring methods to evaluate in situ molecular markers in tissue biopsies.
Container-based bioinformatics with Pachyderm
Authors: Novella Jon Ander , Khoonsari Payam Emami , Herman Stephanie , Whitenack Daniel , Capuccini Marco , Burman Joachim , Kultima Kim , Spjuth Ola 
Published: April 2018

AbstractMotivation:Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages, and (iii) a data management layer that tracks data as it moves through the processing pipeline.Results:Pachyderm is an open-source workflow system and data management framework that fulfills these needs by creating a data pipelining and data versioning layer on top of projects from the container ecosystem, having Kubernetes as the backbone for container orchestration. We adapted Pachyderm and demonstrated its attractive properties in bioinformatics. A Helm Chart was created so that researchers can use Pachyderm in multiple scenarios. The Pachyderm File System was extended to support block storage. A wrapper for initiating Pachyderm on cloud-agnostic virtual infrastructures was created. The benefits of Pachyderm are illustrated via a large metabolomics workflow, demonstrating that Pachyderm enables efficient and sustainable data science workflows while maintaining reproducibility and scalability.Availability:Pachyderm is available from https://github.com/pachyderm/pachyderm. The Pachyderm Helm Chart is available from https://github.com/kubernetes/charts/tree/master/stable/pachyderm. Pachyderm is available out-of-the-box from the PhenoMeNal VRE (https://github.com/phnmnl/KubeNow-plugin) and general Kubernetes environments instantiated via KubeNow. The code of the workflow used for the analysis is available on GitHub (https://github.com/pharmbio/LC-MS-Pachyderm).Contact:jon.novella@farmbio.uu.se
Deciphering hybrid larch reaction norms using random regression
Authors: Marchal Alexandre , Schlichting Carl D. , Gobin Rémy , Balandier Philippe , Millier Frédéric , Muñoz Facundo , Pâques Luc E. , Sánchez Leopoldo 
Published: April 2018

ABSTRACTThe link between phenotypic plasticity and heterosis is a broad fundamental question, with stakes in breeding. We report a case-study evaluating temporal series of wood ring traits of hybrid larch (Larix decidua×L. kaempferiand reciprocal) in relation to soil water availability. Growth rings record the tree plastic responses to past environmental conditions, and we used random regressions to estimate the reaction norms of ring width and wood density with respect to water availability. We investigated the role of phenotypic plasticity on the construction of hybrid larch heterosis and on the expression of its quantitative genetic parameters. The data came from an intra-/interspecific diallel mating design between both parental species. Progenies were grown in two environmentally contrasted sites, in France. Ring width plasticity with respect to water availability was confirmed, as all three taxa produced narrower rings under the lowest water availability. Hybrid larch appeared to be the most plastic taxon as its superiority over its parental species increased with increasing water availability. Despite the low heritabilities of the investigated traits, we found that the quantitative genetic parameters varied along the water availability gradient. Finally, by means of a complementary simulation, we demonstrated that random regression can be applied to model the reaction norms of non-repeated records of phenotypic plasticity bound by a family structure. Random regression is a powerful tool for the modeling of reaction norms in various contexts, especially perennial species.