bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Stepwise Integrated Approach to Personalized Risk Predictions in Stage III Colorectal Cancer
Authors: Salvucci Manuela , Würstle Maximilian L. , Morgan Clare , Curry Sarah , Cremona Mattia , Lindner Andreas U. , Bacon Orna , Resler Alexa J. , Murphy Áine C. , O'Byrne Robert , Flanagan Lorna , Dasgupta Sonali , Rice Nadege , Pilati Camilla , Zink Elisabeth , Schöller Lisa M. , Toomey Sinead , Lawler Mark , Johnston Patrick G. , Wilson Richard , Camilleri-Broët Sophie , Salto-Tellez Manuel , McNamara Deborah A. , Kay Elaine W. , Laurent-Puig Pierre , Van Schaeybroeck Sandra , Hennessy Bryan T. , Longley Daniel B. , Rehm Markus , Prehn Jochen H.M. 
Published: September 2016

Abstract
Purpose: Apoptosis is essential for chemotherapy responses. In this discovery and validation study, we evaluated the suitability of a mathematical model of apoptosis execution (APOPTO-CELL) as a stand-alone signature and as a constituent of further refined prognostic stratification tools.
Experimental Design: Apoptosis competency of primary tumor samples from patients with stage III colorectal cancer (n = 120) was calculated by APOPTO-CELL from measured protein concentrations of Procaspase-3, Procaspase-9, SMAC, and XIAP. An enriched APOPTO-CELL signature (APOPTO-CELL-PC3) was synthesized to capture apoptosome-independent effects of Caspase-3. Furthermore, a machine learning Random Forest approach was applied to APOPTO-CELL-PC3 and available molecular and clinicopathologic data to identify a further enhanced signature. Association of the signature with prognosis was evaluated in an independent colon adenocarcinoma cohort (TCGA COAD, n = 136).
Results: We identified 3 prognostic biomarkers (P = 0.04, P = 0.006, and P = 0.0004 for APOPTO-CELL, APOPTO-CELL-PC3, and Random Forest signatures, respectively) with increasing stratification accuracy for patients with stage III colorectal cancer.
The APOPTO-CELL-PC3 signature ranked highest among all features. The prognostic value of the signatures was independently validated in stage III TCGA COAD patients (P = 0.01, P = 0.04, and P = 0.02 for APOPTO-CELL, APOPTO-CELL-PC3, and Random Forest signatures, respectively). The signatures provided further stratification for patients with CMS1-3 molecular subtype.
Conclusions: The integration of a systems-biology–based biomarker for apoptosis competency with machine learning approaches is an appealing and innovative strategy toward refined patient stratification. The prognostic value of apoptosis competency is independent of other available clinicopathologic and molecular factors, with tangible potential of being introduced in the clinical management of patients with stage III colorectal cancer. Clin Cancer Res; 23(5); 1200–12. ©2016 AACR.
Ipilimumab with Stereotactic Ablative Radiation Therapy: Phase I Results and Immunologic Correlates from Peripheral T Cells
Authors: Tang Chad , Welsh James W. , de Groot Patricia , Massarelli Erminia , Chang Joe Y. , Hess Kenneth R. , Basu Sreyashi , Curran Michael A. , Cabanillas Maria E. , Subbiah Vivek , Fu Siqing , Tsimberidou Apostolia M. , Karp Daniel , Gomez Daniel R. , Diab Adi , Komaki Ritsuko , Heymach John V. , Sharma Padmanee , Naing Aung , Hong David S. 
Published: September 2016

AbstractPurpose: Little prospective data are available on clinical outcomes and immune correlates from combination radiation and immunotherapy. We conducted a phase I trial (NCT02239900) testing stereotactic ablative radiotherapy (SABR) with ipilimumab.Experimental Design: SABR was given either concurrently (1 day after the first dose) or sequentially (1 week after the second dose) with ipilimumab (3 mg/kg every 3 weeks for 4 doses) to five treatment groups: concurrent 50 Gy (in 4 fractions) to liver; sequential 50 Gy (in 4 fractions) to liver; concurrent 50 Gy (in 4 fractions) to lung; sequential 50 Gy (in 4 fractions) to lung; and sequential 60 Gy (in 10 fractions) to lung or liver. MTD was determined with a 3 + 3 dose de-escalation design. Immune marker expression was assessed by flow cytometry.Results: Among 35 patients who initiated ipilimumab, 2 experienced dose-limiting toxicity and 12 (34%) grade 3 toxicity. Response outside the radiation field was assessable in 31 patients. Three patients (10%) exhibited partial response and 7 (23%) experienced clinical benefit (defined as partial response or stable disease lasting ≥6 months). Clinical benefit was associated with increases in peripheral CD8+ T cells, CD8+/CD4+ T-cell ratio, and proportion of CD8+ T cells expressing 4-1BB and PD1. Liver (vs. lung) irradiation produced greater T-cell activation, reflected as increases in the proportions of peripheral T cells expressing ICOS, GITR, and 4-1BB.Conclusions: Combining SABR and ipilimumab was safe with signs of efficacy, peripheral T-cell markers may predict clinical benefit, and systemic immune activation was greater after liver irradiation. Clin Cancer Res; 23(6); 1388–96. ©2016 AACR.
Determinação da curva de crescimento através da lepidologia em diferentes áreas do corpo de Astyanax bimaculatus (Linnaeus, 1758) (Pisces, Characidae), na Represa de Ibitinga, SP
Authors: Giamas Maria Teresa Duarte , Santos Ricardo Amaro do , Vermulm Junior Harry , Campos Elmar Cardoso , Camara Jaime José Casari da 
Published: September 2016

Com o objetivo de determinar a curva de crescimento segundo a expressão de von Bertalanffy, referente à espécie Astyanax bimaculatus presente na Represa de Ibitinga (21°46’S e 48°59’), foi empregado o método de contagem dos anéis etários de escamas. Para a extração destas estruturas, foi também identificada dentre seis áreas, a mais adequada do corpo, quanto à precisão de leitura, segundo WERDER e SOARES18 (1984). Foram examinados 50 exemplares, amostrados no período de julho de 1989 a junho de 1990. Observaram-se 8 classes etárias, e os comprimentos totais médios de 1 a 8 anos foram, respectivamente: 61,03 mm: 75,30 mm; 86,67 mm; 97,92 mm; 109,80 mm; 121,75 mm; 134,13 mm e 144,40 mm. A curva de crescimento determinada foi: ^Lt = 223,14 [1 – e -0,1027 (t + 1,8549) ]
Gains from Trade Liberalization between Heterogeneous Countries: Implications for the Korea–Japan FTA
Authors: Hong Gihoon , Oh Soo Hyun 
Published: September 2016

We study the welfare implications of a bilateral free trade agreement (FTA). The model is based on the recent trade literature that considers search and matching frictions in the labor market. We extend the model by incorporating country-level heterogeneity in terms of production technology, population, and productivity endowment. By calibrating the model to Japanese and Korean data in order to assess the expected outcome of the potential Korea–Japan FTA, we find that when the two countries have the same population size, Japan receives greater benefits from the FTA because its relatively more capital-intensive production allows for quicker output adjustment upon trade liberalization. When we take into account that Japan's population is 2.5 times that of Korea, however, the results show that Korea enjoys a greater surplus because of the market size effect.
The Importance of Spatiotemporal Information in Biological Motion Perception: White Noise Presented with a Step-like Motion Activates the Biological Motion Area
Authors: Callan Akiko , Callan Daniel , Ando Hiroshi 
Published: September 2016

Abstract
Humans can easily recognize the motion of living creatures using only a handful of point-lights that describe the motion of the main joints (biological motion perception). This special ability to perceive the motion of animate objects signifies the importance of the spatiotemporal information in perceiving biological motion. The posterior STS (pSTS) and posterior middle temporal gyrus (pMTG) region have been established by many functional neuroimaging studies as a locus for biological motion perception. Because listening to a walking human also activates the pSTS/pMTG region, the region has been proposed to be supramodal in nature. In this study, we investigated whether the spatiotemporal information from simple auditory stimuli is sufficient to activate this biological motion area. We compared spatially moving white noise, having a running-like tempo that was consistent with biological motion, with stationary white noise. The moving-minus-stationary contrast showed significant differences in activation of the pSTS/pMTG region. Our results suggest that the spatiotemporal information of the auditory stimuli is sufficient to activate the biological motion area.
Nonhomogeneous Boosting for Predictor Selection in Ensemble Postprocessing
Authors: Messner Jakob W. , Mayr Georg J. , Zeileis Achim 
Published: September 2016

AbstractNonhomogeneous regression is often used to statistically postprocess ensemble forecasts. Usually only ensemble forecasts of the predictand variable are used as input, but other potentially useful information sources are ignored. Although it is straightforward to add further input variables, overfitting can easily deteriorate the forecast performance for increasing numbers of input variables. This paper proposes a boosting algorithm to estimate the regression coefficients, while automatically selecting the most relevant input variables by restricting the coefficients of less important variables to zero. A case study with ensemble forecasts from the European Centre for Medium-Range Weather Forecasts (ECMWF) shows that this approach effectively selects important input variables to clearly improve minimum and maximum temperature predictions at five central European stations.
WSR-88D Radar Data Processing at NCEP
Authors: Liu Shun , DiMego Geoff , Guan Shucai , Kumar V. Krishna , Keyser Dennis , Xu Qin , Nai Kang , Zhang Pengfei , Liu Liping , Zhang Jian , Howard Kenneth , Ator Jeff 
Published: September 2016

Abstract
Real-time access to level II radar data became available in May 2005 at the National Centers for Environmental Prediction (NCEP) Central Operations (NCO). Using these real-time data in operational data assimilation requires the data be processed reliably and efficiently through rigorous data quality controls. To this end, advanced radar data quality control techniques developed at the National Severe Storms Laboratory (NSSL) are combined into a comprehensive radar data processing system at NCEP. Techniques designed to create a high-resolution reflectivity mosaic developed at the NSSL are also adopted and installed within the NCEP radar data processing system to generate hourly 3D reflectivity mosaics and 2D-derived products. The processed radar radial velocity and 3D reflectivity mosaics are ingested into NCEP’s data assimilation systems to improve operational numerical weather predictions. The 3D reflectivity mosaics and 2D-derived products are also used for verification of high-resolution numerical weather prediction. The NCEP radar data processing system is described.
Risk Factors for and Management of Postpancreatectomy Hepatic Steatosis
Authors: Takemura N. , Saiura A. , Koga R. , Yamamoto J. , Yamaguchi T. 
Published: September 2016

Background: Relatively little is known about the risk factors and treatments for postpancreatectomy hepatic steatosis. Methods: The records of patients who underwent pancreaticoduodenectomy or total pancreatectomy between 2005 and 2010 and were followed up by periodic imaging were reviewed retrospectively. Risk factors and treatment for postpancreatectomy hepatic steatosis were analyzed. Results: A total of 253 patients were included in the analysis, including 137 males and 116 females, of median (5, 95 percentile) age 67 (47, 81) years. Of these 253 patients, 75 (29.6%) developed postpancreatectomy hepatic steatosis. Multivariable logistic regression analysis showed that female gender ( p = 0.005; odds ratio: 2.387; 95% confidence interval: 1.293–4.386), body mass index > 22.5 kg/m2 ( p = 0.007; odds ratio: 2.330; 95% confidence interval: 1.261–4.307), operative duration > 540 min ( p = 0.018; odds ratio: 2.286; 95% confidence interval: 1.153–4.533), and delayed gastric emptying ( p < 0.001; odds ratio: 4.598; 95% confidence interval: 1.979–10.678) were independent risk factors associated with postpancreatectomy hepatic steatosis. Treatment consisted of maintenance- or high-dose digestive enzyme replacement therapy. Of patients without obvious tumor recurrence after 6 months, 12 of 15 treated with high dose and only 6 of 35 treated with maintenance-dose digestive enzyme replacement therapy showed improvements in postpancreatectomy hepatic steatosis ( p = 0.006). Conclusion: Female gender, obesity, longer operative time, and occurrence of delayed gastric emptying are risk factors for postpancreatectomy hepatic steatosis. High-dose digestive enzyme replacement therapy may improve postpancreatectomy hepatic steatosis.
Validation of the Crohn’s and Ulcerative Colitis questionnaire in patients with acute severe ulcerative colitis
Authors: Hutchings Hayley A , Alrubiay Laith , Watkins Alan , Cheung W‐Y , Seagrove Anne C , Williams John G 
Published: September 2016

BackgroundThe Crohn’s and Ulcerative Colitis questionnaire (CUCQ) has previously been validated in patients with mild to moderate Crohn’s and ulcerative colitis (UC). The aim of this study was to validate the tool in patients with acute severe UC.MethodsWe undertook a validation of the CUCQ in patients recruited to the COmparison of iNfliximab and ciclosporin in STeroid Resistant Ulcerative Colitis Trial (CONSTRUCT). We carried out psychometric analysis to examine the underlying dimensions of the scale, internal consistency and construct validity. We carried out stepwise regression to examine which items accounted for the greatest variance in the scale.ResultsWe obtained complete data for 270 patients. The internal consistency of the CUCQ was excellent (Cronbach’s alpha > 0.8). The CUCQ scores achieved significant correlations with two generic quality of life scales (SF‐12 and EQ‐5D), demonstrating good construct validity. Stepwise regression identified 16 items that accounted for greater than 95% of the variance of the CUCQ. Only three of the eight items selected for a short form in mild to moderate patients were selected for patients with acute severe UC.ConclusionsThe CUCQ demonstrated good validity in our sample of acute severe UC patients. Stepwise regression identified potential to shorten the tool, but that different items would be selected compared with less severe patients. If the tool is to be applied across the spectrum of disease it would be more appropriate to use the full 32 items in the scale. Further work to explore test‐retest is required in acute patients.
A corpus for plant-chemical relationships in the biomedical domain
Authors: Choi Wonjun , Kim Baeksoo , Cho Hyejin , Lee Doheon , Lee Hyunju 
Published: September 2016

Abstract
Background
Plants are natural products that humans consume in various ways including food and medicine. They have a long empirical history of treating diseases with relatively few side effects. Based on these strengths, many studies have been performed to verify the effectiveness of plants in treating diseases. It is crucial to understand the chemicals contained in plants because these chemicals can regulate activities of proteins that are key factors in causing diseases. With the accumulation of a large volume of biomedical literature in various databases such as PubMed, it is possible to automatically extract relationships between plants and chemicals in a large-scale way if we apply a text mining approach. A cornerstone of achieving this task is a corpus of relationships between plants and chemicals.

Results
In this study, we first constructed a corpus for plant and chemical entities and for the relationships between them. The corpus contains 267 plant entities, 475 chemical entities, and 1,007 plant–chemical relationships (550 and 457 positive and negative relationships, respectively), which are drawn from 377 sentences in 245 PubMed abstracts. Inter-annotator agreement scores for the corpus among three annotators were measured. The simple percent agreement scores for entities and trigger words for the relationships were 99.6 and 94.8 %, respectively, and the overall kappa score for the classification of positive and negative relationships was 79.8 %. We also developed a rule-based model to automatically extract such plant–chemical relationships. When we evaluated the rule-based model using the corpus and randomly selected biomedical articles, overall F-scores of 68.0 and 61.8 % were achieved, respectively.

Conclusion
We expect that the corpus for plant–chemical relationships will be a useful resource for enhancing plant research. The corpus is available at http://combio.gist.ac.kr/plantchemicalcorpus.
Risk of Neutropenia-Related Hospitalization in Patients Who Received Colony-Stimulating Factors With Chemotherapy for Breast Cancer
Authors: Agiro Abiy , Ma Qinli , Acheson Anupama Kurup , Wu Sze-jung , Patt Debra A. , Barron John J. , Malin Jennifer L. , Rosenberg Alan , Schilsky Richard L. , Lyman Gary H. 
Published: September 2016

Purpose To describe outcomes after granulocyte colony-stimulating factor (G-CSF) prophylaxis in patients with breast cancer who received chemotherapy regimens with low-to-intermediate risk of induction of neutropenia-related hospitalization. Patients and Methods We identified 8,745 patients age ≥ 18 years from a medical and pharmacy claims database for 14 commercial US health plans. This retrospective analysis included patients with breast cancer who began first-cycle chemotherapy from 2008 to 2013 using docetaxel and cyclophosphamide (TC); docetaxel, carboplatin, and trastuzumab (TCH); or doxorubicin and cyclophosphamide (conventional-dose AC) regimens. Primary prophylaxis (PP) was defined as G-CSF administration within 5 days of beginning chemotherapy. Outcome was neutropenia, fever, or infection-related hospitalization within 21 days of initiating chemotherapy. Multivariable regressions and number-needed-to-treat analyses were used. Results A total of 4,815 patients received TC (2,849 PP; 1,966 no PP); 2,292 patients received TCH (1,444 PP; 848 no PP); and 1,638 patients received AC (857 PP; 781 no PP) regimen. PP was associated with reduced risk of neutropenia-related hospitalization for TC (2.0% PP; 7.1% no PP; adjusted odds ratio [AOR], 0.29; 95% CI, 0.22 to 0.39) and TCH (1.3% PP; 7.1% no PP; AOR, 0.19; 95% CI, 0.12 to 0.30), but not AC (4.7% PP; 3.8% no PP; AOR, 1.21; 95% CI, 0.75 to 1.93) regimens. For the TC regimen, 20 patients (95% CI, 16 to 26) would have to be treated for 21 days to avoid one neutropenia-related hospitalization; with the TCH regimen, 18 patients (95% CI, 13 to 25) would have to be treated. Conclusion Primary G-CSF prophylaxis was associated with low-to-modest benefit in lowering neutropenia-related hospitalization in patients with breast cancer who received TC and TCH regimens. Further evaluation is needed to better understand which patients benefit most from G-CSF prophylaxis in this setting.
Postmastectomy Radiotherapy: An American Society of Clinical Oncology, American Society for Radiation Oncology, and Society of Surgical Oncology Focused Guideline Update
Authors: Recht Abram , Comen Elizabeth A. , Fine Richard E. , Fleming Gini F. , Hardenbergh Patricia H. , Ho Alice Y. , Hudis Clifford A. , Hwang E. Shelley , Kirshner Jeffrey J. , Morrow Monica , Salerno Kilian E. , Sledge George W. , Solin Lawrence J. , Spears Patricia A. , Whelan Timothy J. , Somerfield Mark R. , Edge Stephen B. 
Published: September 2016

Purpose A joint American Society of Clinical Oncology, American Society for Radiation Oncology, and Society of Surgical Oncology panel convened to develop a focused update of the American Society of Clinical Oncology guideline concerning use of postmastectomy radiotherapy (PMRT). Methods A recent systematic literature review by Cancer Care Ontario provided the primary evidentiary basis. The joint panel also reviewed targeted literature searches to identify new, potentially practice-changing data. Recommendations The panel unanimously agreed that available evidence shows that PMRT reduces the risks of locoregional failure (LRF), any recurrence, and breast cancer mortality for patients with T1-2 breast cancer with one to three positive axillary nodes. However, some subsets of these patients are likely to have such a low risk of LRF that the absolute benefit of PMRT is outweighed by its potential toxicities. In addition, the acceptable ratio of benefit to toxicity varies among patients and physicians. Thus, the decision to recommend PMRT requires a great deal of clinical judgment. The panel agreed clinicians making such recommendations for individual patients should consider factors that may decrease the risk of LRF, attenuate the benefit of reduced breast cancer–specific mortality, and/or increase risk of complications resulting from PMRT. When clinicians and patients elect to omit axillary dissection after a positive sentinel node biopsy, the panel recommends that these patients receive PMRT only if there is already sufficient information to justify its use without needing to know additional axillary nodes are involved. Patients with axillary nodal involvement after neoadjuvant systemic therapy should receive PMRT. The panel recommends treatment generally be administered to both the internal mammary nodes and the supraclavicular-axillary apical nodes in addition to the chest wall or reconstructed breast.
Smart Mechanical Dipole: a device for the measurement of sphere motion in behavioral and neurophysiological experiments
Authors: Herzog Hendrik , Mogdans Joachim , Bleckmann Horst 
Published: September 2016

ABSTRACT
Fluid motion and pressure fields induced by vibrating spheres are frequently used to investigate the function of biological mechanosensory systems and artificial sensors. The calibration of the sphere motion amplitude (displacement, velocity, acceleration), time course and vibration direction often demands expensive equipment. To mitigate this requirement, we have developed a high-quality, low-cost device that we term a ‘Smart Mechanical Dipole’. It provides real-time measurement of sphere acceleration along three axes and can be used to obtain an accurate stimulation trace. We applied digital filtering to equalize the frequency response of the vibrating sphere, which also reduced unwanted amplitude and frequency changes in the hydrodynamic signal. In addition, we show that the angular orientation of the rod to which the sphere was attached, i.e. axial versus transverse, but not the immersion depth of the sphere affected sphere vibration behavior.
Signs and symptoms of breast cancer: The practice nurse role
Authors: Harmer Victoria 
Published: September 2016

Breast cancer is the most common cancer in the UK. Victoria Harmer illustrates the role practice nurses can play in promoting breast awareness and the NHS breast screening programme in consultations This article will describe the principles of being breast aware, signs, symptoms and risk factors of breast cancer, and the National Health Service breast screening programme (NHSBSP). The article aims to illustrate that practice nurses are in a privileged and unique position to promote these aspects with the hope this will empower patients as they take more responsibility for their health.