bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records
Authors: Savova Guergana K. , Tseytlin Eugene , Finan Sean , Castine Melissa , Miller Timothy , Medvedeva Olga , Harris David , Hochheiser Harry , Lin Chen , Chavan Girish , Jacobson Rebecca S. 
Published: November 2017

Abstract
Precise phenotype information is needed to understand the effects of genetic and epigenetic changes on tumor behavior and responsiveness. Extraction and representation of cancer phenotypes is currently mostly performed manually, making it difficult to correlate phenotypic data to genomic data. In addition, genomic data are being produced at an increasingly faster pace, exacerbating the problem. The DeepPhe software enables automated extraction of detailed phenotype information from electronic medical records of cancer patients. The system implements advanced Natural Language Processing and knowledge engineering methods within a flexible modular architecture, and was evaluated using a manually annotated dataset of the University of Pittsburgh Medical Center breast cancer patients. The resulting platform provides critical and missing computational methods for computational phenotyping. Working in tandem with advanced analysis of high-throughput sequencing, these approaches will further accelerate the transition to precision cancer treatment. Cancer Res; 77(21); e115–8. ©2017 AACR.
Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images
Authors: Spagnolo Daniel M. , Al-Kofahi Yousef , Zhu Peihong , Lezon Timothy R. , Gough Albert , Stern Andrew M. , Lee Adrian V. , Ginty Fiona , Sarachan Brion , Taylor D. Lansing , Chennubhotla S. Chakra 
Published: November 2017

Abstract
We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71–74. ©2017 AACR.
Rapid Intraoperative Diagnosis of Pediatric Brain Tumors Using Stimulated Raman Histology
Authors: Hollon Todd C. , Lewis Spencer , Pandian Balaji , Niknafs Yashar S. , Garrard Mia R. , Garton Hugh , Maher Cormac O. , McFadden Kathryn , Snuderl Matija , Lieberman Andrew P. , Muraszko Karin , Camelo-Piragua Sandra , Orringer Daniel A. 
Published: November 2017

Abstract
Accurate histopathologic diagnosis is essential for providing optimal surgical management of pediatric brain tumors. Current methods for intraoperative histology are time- and labor-intensive and often introduce artifact that limit interpretation. Stimulated Raman histology (SRH) is a novel label-free imaging technique that provides intraoperative histologic images of fresh, unprocessed surgical specimens. Here we evaluate the capacity of SRH for use in the intraoperative diagnosis of pediatric type brain tumors. SRH revealed key diagnostic features in fresh tissue specimens collected from 33 prospectively enrolled pediatric type brain tumor patients, preserving tumor cytology and histoarchitecture in all specimens. We simulated an intraoperative consultation for 25 patients with specimens imaged using both SRH and standard hematoxylin and eosin histology. SRH-based diagnoses achieved near-perfect diagnostic concordance (Cohen's kappa, κ &gt; 0.90) and an accuracy of 92% to 96%. We then developed a quantitative histologic method using SRH images based on rapid image feature extraction. Nuclear density, tumor-associated macrophage infiltration, and nuclear morphology parameters from 3337 SRH fields of view were used to develop and validate a decision-tree machine-learning model. Using SRH image features, our model correctly classified 25 fresh pediatric type surgical specimens into normal versus lesional tissue and low-grade versus high-grade tumors with 100% accuracy. Our results provide insight into how SRH can deliver rapid diagnostic histologic data that could inform the surgical management of pediatric brain tumors.
Significance: A new imaging method simplifies diagnosis and informs decision making during pediatric brain tumor surgery. Cancer Res; 78(1); 278–89. ©2017 AACR.
Genetic Variation at the
ADAMTS7
Locus is Associated With Reduced Severity of Coronary Artery Disease
Authors: Chan Kenneth , Pu Xiangyuan , Sandesara Pratik , Poston Robin N. , Simpson Iain A. , Quyyumi Arshed A. , Ye Shu , Patel Riyaz S. 
Published: November 2017

Background

Genome‐wide association studies identified
ADAMTS
7 as a risk locus for coronary artery disease (
CAD
). Functional studies suggest that
ADAMTS
7 may promote cellular processes in atherosclerosis. We sought to examine the association between genetic variation at
ADAMTS
7 and measures of atherosclerosis using histological, angiographic, and clinical outcomes data.

Methods and Results

The lead
CAD
‐associated single‐nucleotide polymorphism rs3825807 at the
ADAMTS
7 locus was genotyped. The G allele (reduced
ADAMTS
7 function) was associated with a smaller fibrous cap (
P
=0.017) and a smaller percentage area of α‐actin (smooth muscle cell marker) in the intima (
P
=0.017), but was not associated with calcification or plaque thickness, following ex vivo immunohistochemistry analysis of human coronary plaques (n=50; mean age 72.2±11.3). In two independent cohorts (Southampton Atherosclerosis Study [n=1359; mean age 62.5±10.3; 70.1% men] and the Emory Cardiovascular Biobank [Em
CAB
; n=2684; mean age 63.8±11.3; 68.7% men]), the G allele was associated with 16% to 19% lower odds of obstructive
CAD
(Southampton Atherosclerosis Study: odds ratio, 0.81; 95% confidence interval, 0.67–0.98; Em
CAB
: odds ratio, 0.84; 95% confidence interval, 0.75–0.95) with similar effects for multivessel, left anterior descending, and proximal
CAD
. Furthermore, each copy of the G allele was associated with lower angiographic severity Gensini score (Southampton Atherosclerosis Study,
P
=0.026; Em
CAB
,
P
<0.001), lower Sullivan Extent score (Southampton Atherosclerosis Study,
P
=0.029; Em
CAB
,
P
<0.001), and a 23% lower risk of incident revascularization procedures (EmCAB: hazard ratio, 0.76; 95% confidence interval, 0.59–0.98). There were no associations with all‐cause mortality or incident myocardial infarction.

Conclusions

Genetic variation at the

ADAMTS
7

locus is associated with several complementary
CAD
phenotypes, supporting the emerging role of
ADAMTS
7 in atherosclerosis and may represent a potential drug target.
Why Nuclear Energy Programs Rarely Lead to Proliferation
Authors: Miller Nicholas L. 
Published: November 2017

Abstract
The conventional wisdom suggests that states with nuclear energy programs are more likely to seek or acquire nuclear weapons. Yet there is a dearth of systematic empirical work that directly assesses this proposition. A systematic analysis of the historical evidence suggests that the link between nuclear energy programs and proliferation is overstated. Although such programs increase the technical capacity of a state to build nuclear weapons, they have important countervailing political effects that limit the odds of proliferation. Specifically, nuclear energy programs increase the likelihood that parallel nuclear weapons programs will be detected and face counterproliferation pressures; they also increase the costliness of nonproliferation sanctions. Contrary to the conventional wisdom, states with nuclear energy programs historically have not been significantly more likely to seek or acquire nuclear weapons. A combination of qualitative and quantitative evidence supports the plausibility of the countervailing political effects of nuclear energy programs.
Does Weather Forecasting Relate to Foraging Productivity? An Empirical Test among Three Hunter-Gatherer Societies
Authors: Reyes-García Victoria , Fernández-Llamazares Álvaro , Guèze Maximilien , Gallois Sandrine 
Published: November 2017

Abstract
Previous research has studied the association between ethnoclimatological knowledge and decision-making in agriculture and pastoral activities but has paid scant attention to how ethnoclimatological knowledge might affect hunting and gathering, an important economic activity for many rural populations. The work presented here tests whether people who can forecast temperature and rain display higher hunting and gathering returns (measured as kilograms per hour for hunting and cash equivalent for gathering). Data were collected among three indigenous, small-scale, subsistence-based societies largely dependent on hunting and gathering for their livelihoods: the Tsimane’ (Amazonia, n = 107), the Baka (Congo basin, n = 164), and the Punan Tubu (Borneo, n = 103).The ability to forecast rainfall and temperature varied from one society to another, but the average consistency between people’s 1-day rainfall and temperature forecasts and instrumental measurements was low. This study found a statistically significant positive association between consistency in forecasting rain and the probability that a person engaged in hunting. Conversely, neither consistency in forecasting rain nor consistency in forecasting temperature were associated in a statistically significant way with actual returns to hunting or gathering activities. The authors discuss methodological limitations of the approach, suggesting improvements for future work. This study concludes that, other than methodological issues, the lack of strong associations might be partly explained by the fact that an important characteristic of local knowledge systems, including ethnoclimatological knowledge, is that they are widely socialized and shared.
Somatic mutations and clonal hematopoiesis in congenital neutropenia
Authors: Xia Jun , Miller Christopher A. , Baty Jack , Ramesh Amrita , Jotte Matthew R. M. , Fulton Robert S. , Vogel Tiphanie P. , Cooper Megan A. , Walkovich Kelly J. , Makaryan Vahagn , Bolyard Audrey A. , Dinauer Mary C. , Wilson David B. , Vlachos Adrianna , Myers Kasiani C. , Rothbaum Robert J. , Bertuch Alison A. , Dale David C. , Shimamura Akiko , Boxer Laurence A. , Link Daniel C. 
Published: November 2017

Key PointsHematopoietic stem/progenitor mutation burden is not increased in SCN. Clonal hematopoiesis due to mutations of TP53 is present in the majority of patients with SDS.
Patients’ priorities in selecting chronic lymphocytic leukemia treatments
Authors: Mansfield Carol , Masaquel Anthony , Sutphin Jessie , Weiss Elisa , Gutierrez Meghan , Wilson Jennifer , Boeri Marco , Li Jia , Reyes Carolina 
Published: November 2017

Key PointsCLL patients value higher PFS but would accept significant reductions in PFS to avoid serious adverse events. Adding even modest out-of-pocket costs changed treatment choices for hypothetical treatments, suggesting patients are sensitive to cost.
Shrink rethink: rebranding psychiatry
Authors: Crabb Jim , Barber Lee , Masson Neil 
Published: November 2017

SummaryNegative public attitudes towards psychiatry hinder individuals coming for treatment and prevent us from attracting and retaining the very brightest and best doctors. As psychiatrists we are skilled in using science to change the thoughts and behaviours of individuals, however, we lack the skills to engage entire populations. Expertise in this field is the preserve of branding, advertising and marketing professionals. Techniques from these fields can be used to rebrand psychiatry at a variety of levels from national recruitment drives to individual clinical interactions between psychiatrists and their patients.
Decentralized Learning Framework of Meta-Survival Analysis for Developing Robust Prognostic Signatures
Authors: Cui Yi , Li Bailiang , Li Ruijiang 
Published: November 2017

Purpose A significant hurdle in developing reliable gene expression–based prognostic models has been the limited sample size, which can cause overfitting and false discovery. Combining data from multiple studies can enhance statistical power and reduce spurious findings, but how to address the biologic heterogeneity across different datasets remains a major challenge. Better meta-survival analysis approaches are needed. Material and Methods We presented a decentralized learning framework for meta-survival analysis without the need for data aggregation. Our method consisted of a series of proposals that together alleviated the influence of data heterogeneity and improved the performance of survival prediction. First, we transformed the gene expression profile of every sample into normalized percentile ranks to obtain platform-agnostic features. Second, we used Stouffer’s meta-z approach in combination with Harrell’s concordance index to prioritize and select genes to be included in the model. Third, we used survival discordance as a scale-independent model loss function. Instead of generating a merged dataset and training the model therein, we avoided comparing patients across datasets and individually evaluated the loss function on each dataset. Finally, we optimized the model by minimizing the joint loss function. Results Through comprehensive evaluation on 31 public microarray datasets containing 6,724 samples of several cancer types, we demonstrated that the proposed method has outperformed (1) single prognostic genes identified using conventional meta-analysis, (2) multigene signatures trained on single datasets, (3) multigene signatures trained on merged datasets as well as by other existing meta-analysis methods, and (4) clinically applicable, established multigene signatures. Conclusion The decentralized learning approach can be used to effectively perform meta-analysis of gene expression data and to develop robust multigene prognostic signatures.
Survival As a Quality Metric of Cancer Care: Use of the National Cancer Data Base to Assess Hospital Performance
Authors: Shulman Lawrence N. , Palis Bryan E. , McCabe Ryan , Mallin Kathy , Loomis Ashley , Winchester David , McKellar Daniel 
Published: November 2017

Purpose: Survival is considered an important indicator of the quality of cancer care, but the validity of different methodologies to measure comparative survival rates is less well understood. We explored whether the National Cancer Data Base (NCDB) could serve as a source of unadjusted and risk-adjusted cancer survival data and whether these data could be used as quality indicators for individual hospitals or in the aggregate by hospital type. Methods: The NCDB, an aggregate of > 1,500 hospital cancer registries, was queried to analyze unadjusted and risk-adjusted hazards of death for patients with stage III breast cancer (n = 116,787) and stage IIIB or IV non–small-cell lung cancer (n = 252,392). Data were analyzed at the individual hospital level and by hospital type. Results: At the hospital level, after risk adjustment, few hospitals had comparative risk-adjusted survival rates that were statistically better or worse. By hospital type, National Cancer Institute–designated comprehensive cancer centers had risk-adjusted survival ratios that were statistically significantly better than those of academic cancer centers and community hospitals. Conclusion: Using the NCDB as the data source, survival rates for patients with stage III breast cancer and stage IIIB or IV non–small-cell lung cancer were statistically better at National Cancer Institute–designated comprehensive cancer centers when compared with other hospital types. Compared with academic hospitals, risk-adjusted survival was lower in community hospitals. At the individual hospital level, after risk adjustment, few hospitals were shown to have statistically better or worse survival, suggesting that, using NCDB data, survival may not be a good metric to determine relative quality of cancer care at this level.
The Effect of an Inpatient Smoking Cessation Treatment Program on Hospital Readmissions and Length of Stay
Authors: van den Broek‐Altenburg Eline M. , Atherly Adam J. 
Published: November 2017

BACKGROUNDMost clinical research involving tobacco dependence treatment is related to outpatient interventions and focuses on health outcomes. Inpatient smoking cessation treatment has been found to be cost‐effective in the Canadian healthcare system, but the finding's applicability to US health systems is unclear.OBJECTIVEThe objective of this study is to estimate the impact of an inpatient tobacco cessation treatment program on 30‐day readmission rates and length of stay (LOS).METHODSParticipants were 28,994 patients admitted to the hospital between July 2012 and July 2014. Smokers were identified through the electronic medical records system and were offered cessation treatment. Program effects were estimated by using a difference‐in‐differences approach, comparing all smokers to all nonsmokers before versus after introduction of the program. Readmission rates were modeled by using probit regression; LOS was modeled by using truncated negative binomial regression. Models controlled for age, sex, race, payer, hospital department, severity of illness, and intensive care unit days.RESULTSThe hospital‐initiated smoking cessation intervention had no significant effect on 30‐day readmission rates or LOS. Other control variables had the expected signs and were statistically significant.CONCLUSIONSThe evaluation of an inpatient tobacco dependence treatment did not find significant short‐term changes in healthcare utilization in the first 30 days after initial hospitalization.
Association Between Anemia and Fatigue in Hospitalized Patients: Does the Measure of Anemia Matter?
Authors: Prochaska Micah T. , Newcomb Richard , Block Graham , Park Brian , MD David O. Meltzer 
Published: November 2017

BACKGROUNDRestrictive blood transfusion practices in hospitalized patients with anemia have reduced the use of transfusion. Consequently, hospitalized patients are more likely to have lower hemoglobin (Hb) concentrations. Lower Hb is associated with increased fatigue in ambulatory patients. However, it is not known whether anemia is associated with fatigue in hospitalized patients. It is also unclear how to best measure anemia in hospitalized patients because Hb levels generally vary over a hospital stay.OBJECTIVETo assess multiple Hb‐based measures of anemia in hospitalized patients and test whether these are associated with fatigue.DESIGNProspective observational study.SETTINGUrban, academic medical center.PATIENTSHospitalized general medicine patients, age ≥50 years, with any Hb < 9 g/dL.INTERVENTIONPatients' anemia‐related fatigue was measured during hospitalization.MEASUREMENTSMeasures of anemia were created for each patient based on the Hb values from their hospitalization (mean, median, minimum, maximum, admission, and discharge). Fatigue was measured using the Functional Assessment of Chronic Illness Therapy (FACIT)‐Fatigue subscale.RESULTSSeven hundred eighty‐four patients participated. Minimum Hb was strongly associated with fatigue. Patients with a minimum Hb of < 8 g/dL had higher fatigue levels (mean FACIT [standard deviation] Hb < 7 g/dL: 25 [13], 7 g/dL ≤ Hb <8 g/dL: 25 [14] Hb ≥8 g/dL: 29 [14], P ≤ 0.001) and were more likely to report high levels of fatigue (FACIT‐Fatigue < 27) (56% vs 41%; P = 0.002). Mean Hb had a less robust association with fatigue than minimum Hb, and no other measure of Hb was associated with patients' fatigue levels.CONCLUSIONMinimum Hb is associated with fatigue while hospitalized and may help identify patients for interventions to address anemia‐related fatigue.
PENCEGAHAN PENCOKLATAN ENZIMATIK PADA PORANG KUNING (Amorphophallus oncophyllus)
Authors: Wardhani Dyah Hesti , Arif Atmadja Ariel , Rinaldy Nugraha Christo 
Published: November 2017

Abstract ENZYMATIC BROWNING INHIBITION OF YELLOW PORANG (Amorphophallus oncophyllus). Glucomannan is widely used in the cosmetics, food and health industry due to its high viscosity. One sources of local glucomannan is yellow porang tuber (Amorphophallus oncophyllus). Unfortunately, the content of carotenoids, polyphenoloxidases and tannins of the tuber is high enough and causing brownish color of the flour. Sodium acid pyrophosphat (Na2H2P2O7) or SAPP is a safe whitening agent used as an food additive and categorized as generally recognized as safe (GRAS). The purpose of this work was to study the enzymatic browning inhibition of yellow porang using SAPP as well as its effect on glucomannan content. Extended maceration time up to 3 h did not increase the degree of whiteness and glucomannan levels significantly. 2% of Na2H2P2O7 increased the degrees of whiteness into 50,33. Higher degree of whiteness was obtained in maseration of the flour than that of slurry, wet chips and dried chips. In these three variables, increasing degree of whiteness was in line with the glucomannan content. SAPP provided the highest degree of whiteness (61.48), however, the highest glucomannan samples (75.08%) was obtained at maceration using NaHSO3. Keywords: Amorphophallus oncophyllus; degree of whiteness; glucomannan; yellow porang Abstrak Glukomanan banyak digunakan di industri kosmetik, makanan dan kesehatan karena viskositas yang tinggi. Salah satu sumber glukomanan lokal adalah umbi porang kuning (Amorphophallus oncophyllus). Sayangnya, kandungan karoten, polyphenoloxidases dan tannins pada umbi ini cukup tinggi menyebabkan tepung yang dihasilkan berwarna kecoklatan yang tidak diinginkan oleh pengguna. Sodium acid pyrophosphat (Na2H2P2O7) atau SAPP merupakan bahan pemutih yang aman digunakan sebagai zat additif dan dikategorikan dan termasuk ”generally recognized as safe” (GRAS). Tujuan penelitian ini yaitu mempelajari pencegahan pencoklatan pada porang kuning menggunakan SAPP serta efeknya terhadap kadar glukomanan. Peningkatan waktu maserasi hingga 3 jam tidak meningkatkan derajat putih dan kadar glukomanan secara signifikan. Konsentrasi SAPP 2% memberikan derajat putih 50,33. Maserasi tepung porang memberikan derajat putih tertinggi dibanding maserasi slurry, chips basah maupun chips kering. Pada ketiga variabel tersebut, kenaikan kadar glukomanan sejalan dengan derajat putihnya. Penggunaan SAPP pada tepung menghasilkan derajat putih tertinggi yaitu 61,48 namun kadar glukomanan tertinggi (75,08%) dicapai pada sampel yang dimaserasi menggunakan NaHSO3. Kata kunci: Amorphophallus oncophyllus; derajat putih; glukomanan; porang kuning