Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Medical Diagnosis by Ranking Clusters Across the Symptom-Disease Network

The rapid growth of medical recording data has increased the demand for automated analysis. An important problem in recent medical research is automated medical diagnosis, which is to infer likely diseases for the observed symptoms. Existing approaches typically perform the inference on a sparse bipartite graph with two sets of nodes representing diseases and symptoms, respectively. By using this graph, existing methods basically assume no direct dependency exists between diseases (or symptoms), which may not be true in practice. To address this limitation, we propose to integrate two domain networks encoding similarities between diseases and those between symptoms to avoid information loss as well as to alleviate the sparsity problem of the bipartite graph. Another limitation of the existing methods is that they usually output a ranked list of diseases mixed from very different etiologies which greatly limits their practical usefulness. An ideal method should allow a clustered structure in the disease ranking list so that both similar and different diseases can be easily identified. Therefore, we formulate automated diagnosis as a novel cross-domain cluster ranking problem, which identifies and ranks the disease clusters simultaneously in the symptom-disease network. Our formulation employs a joint learning scheme in which the dual procedures of cluster finding and cluster ranking are coupled and mutually reinforced. Experimental results on real-world datasets demonstrate the effectiveness of our method.
The Community Parent Education Program (COPE): Treatment Effects in a Clinical and a Community-based Sample

The present study is the first European evaluation of the Canadian parent training programme called Community Parent Education Program (COPE). In addition, it is the first to examine the effects of the COPE programme in different types of clinical and nonclinical samples. The main findings were that COPE was found to be effective in reducing conduct problems, hyperactivity/impulsivity, daily problem behaviours, parental stress, and lack of perceived parental control. However, the programme was not effective in reducing inattention, social competence deficits, or peer problems. Interestingly, the significant group effects were a result of significant differences between the two nonclinical intervention groups and the waiting-list control group, whereas the clinical intervention group did not differ significantly from the control group with regard to either child or parental variables. This points to the importance of evaluating parent training programmes in groups with different levels of severity so that parents are offered the type of training programme most suitable for their child's needs.
Short versus long gonadotropin-releasing hormone analogue suppression protocols in advanced age women undergoing IVF/ICSI

Abstract Objective: To compare the effective of two GnRH-a protocols for ovarian stimulation in advanced age women undergoing IVF/ICSI cycles. Study design: A total of 1149 IVF-ET/ICSI cycles were retrospectively identified. The cycles were divided two groups, namely a long-protocol group and a short-protocol group. Results: The numbers of oocytes retrieved, and high-quality embryos in the long-protocol group were significantly greater than those in the short-protocol group. In the long-protocol group, the implantation and pregnancy rates were 17.22% and 33.67%, respectively, and these values were significantly higher than those in the short-protocol group (8.24% and 15.96%, p < 0.05). Conclusions: Our study demonstrated that the long protocol was superior to the short protocol for advanced age women.
Shifts in Value Chain Governance and Upgrading in the European Periphery of Automotive Production: Evidence from Bursa, Turkey

This paper examines shifts in value chain governance and upgrading in the automotive component production node of Bursa in Turkey. Component suppliers in Bursa have gained design and product-development competences, one result of which is that European and global firms have turned to the creation of modular value chains for the sourcing of components from these suppliers. This paper considers the implications of the insertion of Turkish suppliers into modular value chains on suppliers' upgrading, and reveals that, despite the diffusion of design and product-development competences to suppliers in Bursa, cutting-edge innovation activities such as marketing and branding continue to remain the domain of the lead firms. It is argued that although Turkish suppliers seem to be successful in upgrading to take on design and product-development tasks, this has been more due to the willingness of global lead firms to relinquish these functions than to the success of Turkish suppliers in encroaching upon these once core competences of their customers. It is concluded that power asymmetries in global automotive value chains continue to exist, and that lead firms continue to have a major influence on the type of upgrading strategies that are open to their suppliers.
Distributional and Efficiency Effects of Marine Protected Areas: A Study of the Northeast Atlantic Cod Fishery

We study the distributional and efficiency effects of marine protected areas using the Northeast Atlantic cod stock as an example. A model with two players targeting different age groups of cod is developed to examine how protected areas may affect payoffs to the players under cooperation and non-cooperation. We find that depending on the ex ante and ex post management regime, win-win, lose-lose, or win-lose outcomes may emerge with the implementation of marine protected areas. When the ex post management is cooperation, both players gain, while ex post non-cooperative behavior results in gains only to one of the players. (JEL Q22, Q28)
J. Clifford Richardson and 50 years of progressive supranuclear palsy

Objective: To trace the historical events leading to Richardson’s clinical description of progressive supranuclear palsy (PSP) in the context of subsequent observations of its clinical heterogeneity and pathologic overlap with other tauopathies. Background: Fifty years ago, Canadian neurologist J. Clifford Richardson identified patients in Toronto with a syndrome of supranuclear vertical gaze palsy, pseudobulbar palsy, axial rigidity-in-extension, and cognitive impairment. In his seminal description, Richardson predicted that further clinicopathologic observations would broaden the clinical syndrome and that this was unlikely to be a disorder restricted to the Toronto region. Methods: The recollections of two of Richardson’s contemporaries and archival material from his time were used as primary materials. Publications that follow the evolution of his observations were examined. Results: Recent factor analysis of pathologically verified PSP cases has confirmed the accuracy and uniformity of the original classic clinical description of PSP and vindicated Richardson’s prediction of clinical variants. Most notably, a presentation with Parkinson syndrome and absent gaze palsy has been identified, with less severe PSP-tau pathology. Conclusions: In recognition of his seminal observations, we propose that the classic clinical presentation of PSP-tau pathology be renamed Richardson’s disease, and that the commonest clinical variant be termed PSP-parkinsonism. GLOSSARY: AD = Alzheimer disease; ALS = amyotrophic lateral sclerosis; PAGF = pure akinesia with gait freezing; PDC = parkinsonism-dementia complex; PEP = postencephalitic parkinsonism; PSP = progressive supranuclear palsy; PSP-P = PSP-parkinsonism; QSBB = Queen Square Brain Bank.
Urinary 8-iso-Prostaglandin F2&agr; as a Risk Marker in Patients With Coronary Heart Disease: A Matched Case-Control Study

Background—Oxidative stress is involved in the pathophysiology of atherosclerosis, diabetes mellitus, hypertension, obesity, and cigarette smoking, all of these being risk factors for coronary heart disease (CHD). We tested the hypothesis that risk factors of CHD are associated with abundant systemic oxidative stress. Methods and Results—We conducted a case-control study with 93 CHD patients and 93 control subjects frequency-matched by age and sex. Urinary excretion of the F2-isoprostane 8-iso-prostaglandin (PG) F2&agr; and its major urinary metabolite, 2,3-dinor-5,6-dihydro-8-iso-PGF2&agr;, were measured by gas chromatography–tandem mass spectrometry. Body mass index, systolic blood pressure, and C-reactive protein were elevated in CHD patients (P <0.01). Urinary 8-iso-PGF2&agr; and 2,3-dinor-5,6-dihydro-8-iso-PGF2&agr; also differed, from 77 (interquartile range, 61–101) to 139 (93–231) pmol/mmol creatinine and from 120 (91–151) to 193 (140–275) pmol/mmol in control subjects and case subjects, respectively (P <0.001). 8-iso-PGF2&agr; and its metabolite were highly correlated (Spearman’s &rgr;=0.664, P <0.001). HDL cholesterol was diminished in CHD patients (P <0.001). All of these characteristics predicted CHD in univariate analysis. In a multivariate model, the odds ratios were increased only for 8-iso-PGF2&agr; (≥131 pmol/mmol, P <0.001) and C-reactive protein (>3 mg/L, P <0.01), ie, by 30.8 (95% CI, 7.7–124) and 7.2 (1.9–27.6), respectively. 8-iso-PGF2&agr; was found to be a novel marker in addition to known risk factors of CHD, ie, diabetes mellitus, hypercholesterolemia, hypertension, and smoking. Urinary excretion of 8-iso-PGF2&agr; correlated with the number of risk factors for all subjects (P <0.001 for trend). Conclusions—8-iso-PGF2&agr; is a sensitive and independent risk marker of CHD.
Potential of extensification of European agriculture for a more sustainable food system, focusing on nitrogen

Most global strategies for future food security focus on sustainable intensification of production of food and involve increased use of nitrogen fertilizer and manure. The external costs of current high nitrogen (N) losses from agriculture in the European Union, are 0.3–1.9% of gross domestic product (GDP) in 2008. We explore the potential of sustainable extensification for agriculture in the EU and The Netherlands by analysing cases and scenario studies focusing on reducing N inputs and livestock densities. Benefits of extensification are higher local biodiversity and less environmental pollution and therefore less external costs for society. Extensification also has risks such as a reduction of yields and therewith a decrease of the GDP and farm income and a smaller contribution to the global food production, and potentially an i0ncrease of global demand for land. We demonstrate favourable examples of extensification. Reducing the N fertilization rate for winter wheat in Northwest Europe to 25–30% below current N recommendations accounts for the external N cost, but requires action to compensate for a reduction in crop yield by 10–20%. Dutch dairy and pig farmers changing to less intensive production maintain or even improve farm income by price premiums on their products, and/or by savings on external inputs. A scenario reducing the Dutch pig and poultry sector by 50%, the dairy sector by 20% and synthetic N fertilizer use by 40% lowers annual N pollution costs by 0.2–2.2 billion euro (40%). This benefit compensates for the loss of GDP in the primary sector but not in the supply and processing chain. A 2030 scenario for the EU27 reducing consumption and production of animal products by 50% (demitarean diet) reduces N pollution by 10% and benefits human health. This diet allows the EU27 to become a food exporter, while reducing land demand outside Europe in 2030 by more than 100 million hectares (2%), which more than compensates increased land demand when changing to organic farming. We conclude that in Europe extensification of agriculture is sustainable when combined with adjusted diets and externalization of environmental costs to food prices.
Effect of nutrition changes on foods selected by students in a middle school-based diabetes prevention intervention program: the HEALTHY experience.

BACKGROUND The HEALTHY primary prevention trial developed an integrated multicomponent intervention program to moderate risk factors for type 2 diabetes in middle schools. The nutrition component aimed to improve the quality of foods and beverages served to students. Changes in the School Breakfast Program (SBP), National School Lunch Program (NSLP), and à la carte venues are compared to the experience of control schools. METHODS The intervention was implemented in 21 middle schools from winter 2007 through spring 2009 (following a cohort of students from sixth through eighth grades); 21 schools acted as observed controls. The nutrition component targeted school food service environmental change. Data identifying foods and nutrients served (selected by students for consumption) were collected over a 20-day period at baseline and end of study. Analysis compared end of study values for intervention versus control schools. RESULTS Intervention schools more successfully limited dessert and snack food portion size in NSLP and à la carte and lowered fat content of foods served. Servings of high-fiber grain-based foods and/or legumes were improved in SBP but not NSLP. Intervention and control schools eliminated >1% fat milk and added-sugar beverages in SBP, but intervention schools were more successful in NSLP and à la carte. CONCLUSION The HEALTHY program demonstrated significant changes in the nutritional quality of foods and beverages served in the SBP, NSLP, and à la carte venues, as part of an effort to decrease childhood obesity and support beneficial effects in some secondary HEALTHY study outcomes.
The impact of pediatric traumatic brain injury (TBI) on family functioning: a systematic review.

PURPOSE To explore the impact moderate to severe traumatic brain injury (TBI) in a child has on family functioning. METHODS The search was conducted using 9 bibliographic databases for articles published between 1980 and 2013. Two reviewers independently screened for inclusion and assessed study quality. Two reviewers extracted study data and a third checked for completeness and accuracy. Findings are presented by three domains: injury-related burden and stress, family adaptability, and family cohesion. RESULTS Nine observational studies were included. Across the studies, differences between study groups for family functioning varied, but there was a trend for more dysfunction in families whose child had a severe TBI as compared to families whose child had a moderate TBI or orthopedic injury. In three studies, injury-associated burden was persistent post-injury and was highest in families whose child had a severe TBI followed by families with a child who had a moderate TBI. One study found fathers reported more family dysfunction caused by their child's injury compared to mothers. Two studies found that mothers' adaptability depended on social support and stress levels while fathers' adaptability was independent of these factors and injury severity. CONCLUSION Moderate to severe TBI has a significant, long-standing impact on family functioning. Factors associated with family adaptability vary by parental role.
Identification of Dp71 Isoforms in the Platelet Membrane Cytoskeleton

Utrophin is a component of the platelet membrane cytoskeleton and participates in cytoskeletal reorganization (Earnest, J. P., Santos, G. F., Zuerbig, S., and Fox, J. E. B. (1995) J. Biol. Chem. 270, 27259–27265). Although platelets do not contain dystrophin, the identification of smaller C-terminal isoforms of dystrophin, including Dp71, which are expressed in a wide range of nonmuscle tissues and cell lines, has not been investigated. In this report, we have identified Dp71 protein variants of 55–60 kDa (designated Dp71Δ110) in the membrane cytoskeleton of human platelets. Both Dp71Δ110and utrophin sediment from lysed platelets along with the high speed detergent-insoluble pellet, which contains components of the membrane cytoskeleton. Like the membrane cytoskeletal proteins vinculin and spectrin, Dp71Δ110 and utrophin redistributed from the high speed detergent-insoluble pellet to the integrin-rich low speed pellet of thrombin-stimulated platelets. Immunoelectron microscopy provided further evidence that Dp71Δ110 was localized to the submembranous cytoskeleton. In addition to Dp71Δ110, platelets contained several components of the dystrophin-associated protein complex, including β-dystroglycan and syntrophin. To better understand the potential function of Dp71Δ110, collagen adhesion assays were performed on platelets isolated from wild-type or Dp71-deficient (mdx3cv) mice. Adhesion to collagen in response to thrombin was significantly decreased in platelets isolated from mdx3cv mice, compared with wild-type platelets. Collectively, our results provide evidence that Dp71Δ110is a component of the platelet membrane cytoskeleton, is involved in cytoskeletal reorganization and/or signaling, and plays a role in thrombin-mediated platelet adhesion.
DNA repair and cancer: Lessons from mutant mouse models

DNA damage, if the repair process, especially nucleotide excision repair (NER), is compromised or the lesion is repaired by some other error‐prone mechanism, causes mutation and ultimately contributes to neoplastic transformation. Impairment of components of the DNA damage response pathway (e.g., p53) is also implicated in carcinogenesis. We currently have considerable knowledge of the role of DNA repair genes as tumor suppressors, both clinically and experimentally. The deleterious clinical consequences of inherited defects in DNA repair system are apparent from several human cancer predisposition syndromes (e.g., NER‐compromised xeroderma pigmentosum [XP] and p53‐deficient Li‐Fraumeni syndrome). However, experimental studies to support the clinical evidence are hampered by the lack of powerful animal models. Here, we review in vivo experimental data suggesting the protective function of DNA repair machinery in chemical carcinogenesis. We specifically focus on the three DNA repair genes, O6‐methylguanine‐DNA methyltransferase gene (MGMT), XP group A gene (XPA) and p53. First, mice overexpressing MGMT display substantial resistance to nitrosamine‐induced hepatocarcinogenesis. In addition, a reduction of spontaneous liver tumors and longer survival times were evident. However, there are no known mutations in the human MGMT and therefore no associated cancer syndrome. Secondly, XPA mutant mice are indeed prone to spontaneous and carcinogen‐induced tumorigenesis in internal organs (which are not exposed to sunlight). The concomitant loss of p53 resulted in accelerated onset of carcinogenesis. Finally, p53 null mice are predisposed to brain tumors upon transplacental exposure to a carcinogen. Accumulated evidence in these three mutant mouse models firmly supports the notion that the DNA repair system is vital for protection against cancer.
The Impact of State Minimum Wages on Child Poverty in Female-Headed Families

ABSTRACT Several state governments set minimum wage levels above the federal level, and some automatically index them to inflation. This article uses the variation in real minimum wages both over time and across states to examine how minimum wages have affected poverty rates of children living in female-headed households. These children are among the most vulnerable members of society and are increasingly likely to feel the impact of such policy actions due to the growing presence of their mothers in low-wage labor markets. Evidence based on state-level panel data for the years 1991 to 2002 shows that minimum wages have significantly reduced child poverty rates, after controlling for a number of other potentially relevant factors. These findings are robust to alternative measures of poverty, sample definition, estimation technique, and variable selection.
Feature-based image stitching with repetitive patterns using local phase quantization

Stitching images with repeated patterns is one of the hard tasks in computer vision. Unfortunately, available algorithms do not have enough accuracy to register these kinds of images. This problem is due to lack of discriminative information of corresponding points of images. To overcome this shortcoming, a novel method for feature-based image stitching is proposed. In the proposed method, the SIFT descriptor is utilized to extract and match robust keypoints from each image. Texture information is achieved by using the local phase quantization (LPQ) around each keypoint. Then, a distinctive feature histogram is obtained based on LPQ. Finally, the symmetric Kullback-Leibler divergence (SKLD) is used as a dissimilarity measure between corresponding points to reject mismatches. Experimental results demonstrate that the proposed method can efficiently eliminate ambiguities in image stitching and successfully register images with repeated patterns.
HuR Contributes to TRAIL Resistance by Restricting Death Receptor 4 Expression in Pancreatic Cancer Cells

Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal cancers, in part, due to resistance to both conventional and targeted therapeutics. TRAIL directly induces apoptosis through engagement of cell surface Death Receptors (DR4 and DR5), and has been explored as a molecular target for cancer treatment. Clinical trials with recombinant TRAIL and DR-targeting agents, however, have failed to show overall positive outcomes. Herein, we identify a novel TRAIL resistance mechanism governed by Hu antigen R (HuR, ELAV1), a stress-response protein abundant and functional in PDA cells. Exogenous HuR overexpression in TRAIL-sensitive PDA cell lines increases TRAIL resistance whereas silencing HuR in TRAIL-resistant PDA cells, by siRNA oligo-transfection, decreases TRAIL resistance. PDA cell exposure to soluble TRAIL induces HuR translocation from the nucleus to the cytoplasm. Furthermore, it is demonstrated that HuR interacts with the 3′-untranslated region (UTR) of DR4 mRNA. Pre-treatment of PDA cells with MS-444 (Novartis), an established small molecule inhibitor of HuR, substantially increased DR4 and DR5 cell surface levels and enhanced TRAIL sensitivity, further validating HuR's role in affecting TRAIL apoptotic resistance. NanoString analyses on the transcriptome of TRAIL-exposed PDA cells identified global HuR-mediated increases in antiapoptotic processes. Taken together, these data extend HuR's role as a key regulator of TRAIL-induced apoptosis. Implications: Discovery of an important new HuR-mediated TRAIL resistance mechanism suggests that tumor-targeted HuR inhibition increases sensitivity to TRAIL-based therapeutics and supports their re-evaluation as an effective treatment for PDA patients. Mol Cancer Res; 14(7); 599–611. ©2016 AACR.
Contingent Valuation: From Dubious to Hopeless

Approximately 20 years ago, Peter Diamond and I wrote an article for this journal analyzing contingent valuation methods. At that time Peter's view was that contingent valuation was hopeless, while I was dubious but somewhat more optimistic. But 20 years later, after millions of dollars of largely government-funded research, I have concluded that Peter's earlier position was correct and that contingent valuation is hopeless. In this paper, I selectively review the contingent valuation literature, focusing on empirical results. I find that three long-standing problems continue to exist: 1) hypothetical response bias that leads contingent valuation to overstatements of value; 2) large differences between willingness to pay and willingness to accept; and 3) the embedding problem which encompasses scope problems. The problems of embedding and scope are likely to be the most intractable. Indeed, I believe that respondents to contingent valuation surveys are often not responding out of stable or well-defined preferences, but are essentially inventing their answers on the fly, in a way which makes the resulting data useless for serious analysis. Finally, I offer a case study of a prominent contingent valuation study done by recognized experts in this approach, a study that should be only minimally affected by these concerns but in which the answers of respondents to the survey are implausible and inconsistent.