LLukas22/scidocs huggingface dataset:
Cluster analysis and its application to healthcare claims data: a study of end-stage renal disease patients who initiated hemodialysis

BACKGROUND
Cluster analysis (CA) is a frequently used applied statistical technique that helps to reveal hidden structures and "clusters" found in large data sets. However, this method has not been widely used in large healthcare claims databases where the distribution of expenditure data is commonly severely skewed. The purpose of this study was to identify cost change patterns of patients with end-stage renal disease (ESRD) who initiated hemodialysis (HD) by applying different clustering methods.


METHODS
A retrospective, cross-sectional, observational study was conducted using the Truven Health MarketScan® Research Databases. Patients aged ≥18 years with ≥2 ESRD diagnoses who initiated HD between 2008 and 2010 were included. The K-means CA method and hierarchical CA with various linkage methods were applied to all-cause costs within baseline (12-months pre-HD) and follow-up periods (12-months post-HD) to identify clusters. Demographic, clinical, and cost information was extracted from both periods, and then examined by cluster.


RESULTS
A total of 18,380 patients were identified. Meaningful all-cause cost clusters were generated using K-means CA and hierarchical CA with either flexible beta or Ward's methods. Based on cluster sample sizes and change of cost patterns, the K-means CA method and 4 clusters were selected: Cluster 1: Average to High (n = 113); Cluster 2: Very High to High (n = 89); Cluster 3: Average to Average (n = 16,624); or Cluster 4: Increasing Costs, High at Both Points (n = 1554). Median cost changes in the 12-month pre-HD and post-HD periods increased from $185,070 to $884,605 for Cluster 1 (Average to High), decreased from $910,930 to $157,997 for Cluster 2 (Very High to High), were relatively stable and remained low from $15,168 to $13,026 for Cluster 3 (Average to Average), and increased from $57,909 to $193,140 for Cluster 4 (Increasing Costs, High at Both Points). Relatively stable costs after starting HD were associated with more stable scores on comorbidity index scores from the pre-and post-HD periods, while increasing costs were associated with more sharply increasing comorbidity scores.


CONCLUSIONS
The K-means CA method appeared to be the most appropriate in healthcare claims data with highly skewed cost information when taking into account both change of cost patterns and sample size in the smallest cluster.
Organization of lipids in milks, infant milk formulas and various dairy products: role of technological processes and potential impacts

The microstructure of milk fat in processed dairy products is poorly known despite its importance in their functional, sensorial and nutritional properties. However, for the last 10 years, several research groups including our laboratory have significantly contributed to increasing knowledge on the organization of lipids in situ in dairy products. This paper provides an overview of recent advances on the organization of lipids in the milk fat globule membrane using microscopy techniques (mainly confocal microscopy and atomic force microscopy). Also, this overview brings structural information about the organization of lipids in situ in commercialized milks, infant milk formulas and various dairy products (cream, butter, buttermilk, butter serum and cheeses). The main mechanical treatment used in the dairy industry, homogenization, decreases the size of milk fat globules, changes the architecture (composition and organization) of the fat/water interface and affects the interactions between lipid droplets and the protein network (concept of inert vs active fillers). The potential impacts of the organization of lipids and of the alteration of the milk fat globule membrane are discussed, and technological strategies are proposed, in priority to design biomimetic lipid droplets in infant milk formulas.
Specification-Based Test Repair Using a Lightweight Formal Method

When a program evolves, its test suite must be modified to reflect changes in requirements or to account for new feature additions. This problem of modifying tests as a program evolves is termed test repair. Existing approaches either assume that updated implementation is correct, or assume that most test repairs require simply fixing compilation errors caused by refactoring of previously tested implementation. This paper focuses on the problem of repairing semantically broken or outdated tests by leveraging specifications. Our technique, Spectr, employs a lightweight formal method to perform specification-based repair. Specifically, Spectr supports the Alloy language for writing specifications and uses its SAT-based analyzer for repairing JUnit tests. Since Spectr utilizes specifications, it works even when the specification is modified but the change has not yet been implemented in code—in such a case, Spectr is able to repair tests that previous techniques would not even consider as candidates for test repair. An experimental evaluation using a suite of subject programs with pre-conditions and post-conditions shows Spectr can effectively repair tests even for programs that perform complex manipulation of dynamically allocated data.
An architecture for Malay Tweet normalization

Research in natural language processing has increasingly focused on normalizing Twitter messages. Currently, while different well-defined approaches have been proposed for the English language, the problem remains far from being solved for other languages, such as Malay. Thus, in this paper, we propose an approach to normalize the Malay Twitter messages based on corpus-driven analysis. An architecture for Malay Tweet normalization is presented, which comprises seven main modules: (1) enhanced tokenization, (2) In-Vocabulary (IV) detection, (3) specialized dictionary query, (4) repeated letter elimination, (5) abbreviation adjusting, (6) English word translation, and (7) de-tokenization. A parallel Tweet dataset, consisting of 9000 Malay Tweets, is used in the development and testing stages. To measure the performance of the system, an evaluation is carried out. The result is promising whereby we score 0.83 in BLEU against the baseline BLEU, which scores 0.46. To compare the accuracy of the architecture with other statistical approaches, an SMT-like normalization system is implemented, trained, and evaluated with an identical parallel dataset. The experimental results demonstrate that we achieve higher accuracy by the normalization system, which is designed based on the features of Malay Tweets, compared to the SMT-like system. 2014 Elsevier Ltd. All rights reserved.
Community and Team Member Factors that Influence the Early Phase Functioning of Community Prevention Teams: The PROSPER Project

This research examines the early development of community teams in a specific university–community partnership project called PROSPER (Spoth et al., Prev Sci 5:31–39, 2004). PROSPER supports local community teams in rural areas and small towns to implement evidence-based programs intended to support positive youth development and reduce early substance use. The study evaluated 14 community teams and included longitudinal data from 108 team members. Specifically, it examined how community demographics and team member characteristics, perceptions, and attitudes at initial team formation were related to local team functioning 6 months later, when teams were planning for prevention program implementation. Findings indicate that community demographics (poverty), perceived community readiness, characteristics of local team members (previous collaborative experience) and attitudes toward prevention played a substantial role in predicting the quality of community team functioning 6 months later. Editors’ Strategic Implications: The authors identify barriers to successful long-term implementation of prevention programs and add to a small, but important, longitudinal research knowledge base related to community coalitions.
Effects of atorvastatin on early recurrent ischemic events in acute coronary syndromes: the MIRACL study: a randomized controlled trial.

CONTEXT
Patients experience the highest rate of death and recurrent ischemic events during the early period after an acute coronary syndrome, but it is not known whether early initiation of treatment with a statin can reduce the occurrence of these early events.


OBJECTIVE
To determine whether treatment with atorvastatin, 80 mg/d, initiated 24 to 96 hours after an acute coronary syndrome, reduces death and nonfatal ischemic events.


DESIGN AND SETTING
A randomized, double-blind trial conducted from May 1997 to September 1999, with follow-up through 16 weeks at 122 clinical centers in Europe, North America, South Africa, and Australasia.


PATIENTS
A total of 3086 adults aged 18 years or older with unstable angina or non-Q-wave acute myocardial infarction.


INTERVENTIONS
Patients were stratified by center and randomly assigned to receive treatment with atorvastatin (80 mg/d) or matching placebo between 24 and 96 hours after hospital admission.


MAIN OUTCOME MEASURES
Primary end point event defined as death, nonfatal acute myocardial infarction, cardiac arrest with resuscitation, or recurrent symptomatic myocardial ischemia with objective evidence and requiring emergency rehospitalization.


RESULTS
A primary end point event occurred in 228 patients (14.8%) in the atorvastatin group and 269 patients (17.4%) in the placebo group (relative risk [RR], 0.84; 95% confidence interval [CI], 0.70-1.00; P =.048). There were no significant differences in risk of death, nonfatal myocardial infarction, or cardiac arrest between the atorvastatin group and the placebo group, although the atorvastatin group had a lower risk of symptomatic ischemia with objective evidence and requiring emergency rehospitalization (6.2% vs 8.4%; RR, 0.74; 95% CI, 0.57-0.95; P =.02). Likewise, there were no significant differences between the atorvastatin group and the placebo group in the incidence of secondary outcomes of coronary revascularization procedures, worsening heart failure, or worsening angina, although there were fewer strokes in the atorvastatin group than in the placebo group (12 vs 24 events; P =.045). In the atorvastatin group, mean low-density lipoprotein cholesterol level declined from 124 mg/dL (3.2 mmol/L) to 72 mg/dL (1.9 mmol/L). Abnormal liver transaminases (>3 times upper limit of normal) were more common in the atorvastatin group than in the placebo group (2.5% vs 0.6%; P<.001).


CONCLUSION
For patients with acute coronary syndrome, lipid-lowering therapy with atorvastatin, 80 mg/d, reduces recurrent ischemic events in the first 16 weeks, mostly recurrent symptomatic ischemia requiring rehospitalization.
Personalized Mortality Prediction Driven by Electronic Medical Data and a Patient Similarity Metric

BACKGROUND
Clinical outcome prediction normally employs static, one-size-fits-all models that perform well for the average patient but are sub-optimal for individual patients with unique characteristics. In the era of digital healthcare, it is feasible to dynamically personalize decision support by identifying and analyzing similar past patients, in a way that is analogous to personalized product recommendation in e-commerce. Our objectives were: 1) to prove that analyzing only similar patients leads to better outcome prediction performance than analyzing all available patients, and 2) to characterize the trade-off between training data size and the degree of similarity between the training data and the index patient for whom prediction is to be made.


METHODS AND FINDINGS
We deployed a cosine-similarity-based patient similarity metric (PSM) to an intensive care unit (ICU) database to identify patients that are most similar to each patient and subsequently to custom-build 30-day mortality prediction models. Rich clinical and administrative data from the first day in the ICU from 17,152 adult ICU admissions were analyzed. The results confirmed that using data from only a small subset of most similar patients for training improves predictive performance in comparison with using data from all available patients. The results also showed that when too few similar patients are used for training, predictive performance degrades due to the effects of small sample sizes. Our PSM-based approach outperformed well-known ICU severity of illness scores. Although the improved prediction performance is achieved at the cost of increased computational burden, Big Data technologies can help realize personalized data-driven decision support at the point of care.


CONCLUSIONS
The present study provides crucial empirical evidence for the promising potential of personalized data-driven decision support systems. With the increasing adoption of electronic medical record (EMR) systems, our novel medical data analytics contributes to meaningful use of EMR data.
Changes in liraglutide-induced body composition are related to modifications in plasma cardiac natriuretic peptides levels in obese type 2 diabetic patients

BACKGROUND AND AIMS
Liraglutide treatment can improve glycemic control with a concomitant weight loss, but the underlying mechanism on weight loss is not completely understood. Cardiac natriuretic peptides (NPs) can resist body fat accumulation through increasing adipocytes lypolysis. In this study, we tested the hypothesis that liraglutide-induced weight loss was associated with increased plasma NPs concentrations.


METHODS
Thirty-one outpatients with type 2 diabetes (T2D) treated with metformin and other oral antidiabetic drugs except for thiazolidinediones (TZDs) were subcutaneously administered with liraglutide for 12 weeks. Body composition, abdominal visceral adipose tissue areas (VAT) and subcutaneous adipose tissue areas (SAT) were assessed at pre- and post-treatment by dual-energy X-ray absorptiometry (DXA) scanning and abdominal computerized tomography (CT). Plasma atrial natriuretic peptides (ANP) and B-type ventricular natriuretic peptides (BNP) concentrations were tested by commercial ELISA Kit quantitatively.


RESULTS
Following 12-week liraglutide treatment, body weight, waist circumference, total fat and lean mass, fat percentage, SAT and VAT areas were significantly reduced from baseline. Concurrently, plasma ANP and BNP levels were significantly increased following 12-week liraglutide treatment. There were significant correlations between the reductions in body compositions and the increases in both plasma ANP and BNP levels.


CONCLUSIONS
There were significant correlations between increases in both plasma ANP and BNP levels and changes in liraglutide-induced body composition. Our data implied that increases in plasma NPs may add a novel dimension to explain how liraglutide induces weight loss.
Syphilis: a reemerging infection.

Rates of primary and secondary syphilis have increased in the past decade, warranting renewed attention to the diagnosis and treatment of this disease. Men who have sex with men are particularly affected; however, increases in infection rates have also been noted in women, as well as in all age groups and ethnicities. Physicians need to vigilantly screen high-risk patients. The concurrent rise in congenital syphilis also requires special attention and reemphasizes the need for continued early prenatal care and syphilis screening for all pregnant women. Syphilis infection in patients coinfected with human immunodeficiency virus has also become more common. New experimental diagnostic approaches, including using the B cell chemoattractant chemokine (CXC motif) ligand 13 as a cerebrospinal fluid marker, may help identify suspected neurosyphilis cases. Additionally, point-of-care immunochromatographic strip testing has been suggested for screening high-risk populations in developing countries. Nontreponemal screening tests followed by treponemal confirmatory tests continue to be standard diagnostics; however, interpreting false-negative and false-positive test results, and identifying serofast reactions, can be challenging. Although doxycycline, tetracycline, ceftriaxone, and azithromycin have been used to successfully treat syphilis, penicillin remains the drug of choice in all stages of infection and is the therapy recommended by the Centers for Disease Control and Prevention. Close follow-up is necessary to ensure treatment success.
Naturalizing Racial Differences Through Comedy: Asian, Black, and White Views on Racial Stereotypes in Rush Hour 2

In this paper, we examine the ideological implications of racial stereotypes in comedy through a textual and audience analysis of Rush Hour 2. Although Asian, Black, and White focus group participants differentially engaged with racial stereotypes in the film, most participants, regardless of race, found the film’s racial jokes inoffensive. Many Asian and Black participants found a positive source of pleasure in the negative portrayals of their own race and did not produce oppositional discourse. Our study suggests that the generic conventions and textual devices of comedy encourage the audience to naturalize racial differences rather than to challenge racial stereotypes.
Critical review on video game evaluation heuristics: social games perspective

This paper presents the first step in creating design and evaluation heuristics for social games which emerge from the domain of social media. Initial high level heuristics for social games are offered by reviewing four existing video game heuristic models and analyzing two social games design frameworks.
Single-center experience of laparoscopic left pancreatic resection in 359 consecutive patients: changing the surgical paradigm of left pancreatic resection

Laparoscopic distal pancreatectomy (LDP) is increasingly performed for lesions of the body and tail of the pancreas. We analyzed the clinical characteristics of the largest series of patients to date who underwent LDP at a single center, as well as their outcomes, to reassess the surgical paradigm for left pancreatic resection. We retrospectively reviewed the records of 359 patients who underwent LDP at Asan Medical Center, Seoul, Korea, for pancreatic neoplasms between March 2005 and December 2010. Of the 359 patients, 323 (90%) had benign or low-grade malignant neoplasms and 36 (10%) had malignancies. The most common diagnosis was intraductal papillary mucinous neoplasm (IPMN) in 72 patients (21.2%). There were 24 patients (6.7%) with pancreatic ductal adenocarcinoma (PDAC). We found that 178 patients (49.6%) underwent spleen-preserving LDP (SP-LDP): 150 (84.3%) by main splenic vessel preservation, and 28 (15.7%) supported by short gastric and gastroepiploic vessels (Warshaw technique). Postoperative complications occurred in 43 (12%) patients, including 25 (7%) with pancreatic fistula (ISGPF grade B, C), but there was no death. Median operative time was 195 (range, 78–480) min, and median postoperative hospital stay was 8 (range, 4–37) days. The proportion of patients with pancreatic lesions who underwent LDP increased from 8.6% in 2005 to 66.9% in 2010. Kaplan–Meier analysis showed that the 1- and 2-year overall survival rates in the 24 patients with PDAC were 85.2% each. LDP is feasible, safe, and effective for the treatment of benign and low-grade malignant lesions of the pancreas. The increased use of LDP for left-sided pancreatic lesions, including malignant lesions, represents a paradigm shift from open distal pancreatectomy.
The effect of stress doses of hydrocortisone during septic shock on posttraumatic stress disorder in survivors

BACKGROUND
Exposure to intense physical and psychological stress during septic shock can result in posttraumatic stress disorder in survivors. Patients with chronic posttraumatic stress disorder often show sustained reductions in serum cortisol concentration. This investigation examines whether increasing serum cortisol levels with hydrocortisone treatment during septic shock reduces the incidence of posttraumatic stress disorder in survivors.


METHODS
Patients (n = 20) were recruited from a prospective, randomized double-blind study on the hemodynamic effects of hydrocortisone during septic shock. Eleven patients had received placebo and nine stress doses of hydrocortisone. Posttraumatic stress disorder was diagnosed 31 months (median) after intensive care unit discharge using SCID-IV (DSM-IV-criteria). Furthermore, the number of categories of traumatic memory from ICU treatment was determined in both groups at that time.


RESULTS
Only one of nine patients from the hydrocortisone group developed posttraumatic stress disorder, compared with seven of 11 patients in the placebo group (p =.02). There was no significant difference with regard to the number of categories of traumatic memory between the hydrocortisone and placebo groups.


CONCLUSIONS
The administration of hydrocortisone during septic shock in a dosage similar to the endogenous maximal production rate was associated with a lower incidence of posttraumatic stress disorder in long-term survivors, which seems to be independent of the number of categories of traumatic memory.
The diameter response of retinal arterioles in diabetic maculopathy is reduced during hypoxia and is unaffected by the inhibition of cyclo-oxygenase and nitric oxide synthesis

Diabetic retinopathy is accompanied with changes in the diameter regulation and oxygenation of retinal vessels. Previous studies have shown that in normal persons and in diabetic patients without retinopathy hypoxia-induced vasodilatation is mediated by cyclo-oxygenase (COX) products and nitric oxide (NO). The purpose of the present study was to study whether these effects can be reproduced in patients with diabetic maculopathy. Eighteen patients with diabetic maculopathy aged 29–57 years were examined using the Dynamic Vessel Analyzer. The resting diameter and the diameter changes of retinal arterioles during isometric exercise and flicker stimulation were studied before and during breathing a hypoxic gas mixture. The examinations were also performed before and during intravenous infusion of the NOS inhibitor L-NMMA, and were repeated on a second day after topical administration of the COX-inhibitor diclofenac. The diameter of retinal arterioles showed no significant change during hypoxia or L-NMMA infusion, or after topical application of diclofenac (p > 0.25 for all comparisons). The resting diameter of the venules was significantly increased during hypoxia (p = 0.003) and decreased during L-NMMA infusion (p < 0.0001). The diameter of retinal venules during isometric exercise increased significantly during hypoxia (p = 0.01). Flicker stimulation induced significant dilatation of the venules, which was significantly reduced during hypoxia and increased during L-NMMA infusion (p < 0.0001 for all comparisons). Hypoxia-induced dilatation of retinal arterioles is severely reduced in patients with diabetic maculopathy. Future intervention studies aimed at normalizing the diameter regulation of retinal arterioles in diabetic patients should preferentially be conducted in the early stages of the disease where the potential for changing the vessel diameter is preserved. ClinicalTrials.gov identifier: NCT01689090
A Formal Language-Based Approach in Biology

This paper presents an overview of computational biology approaches and surveys some of the natural computing models using, in both cases, a formal language-based approach.