Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Sensitivity, Performance and Reproducibility of Microarray Technology in Neuronal Tissue1

Abstract Microarray technology is a powerful technique that allows the simultaneous study of thousands of gene transcripts. During the past two years there has been an explosion of publications describing experiments utilizing microarray technology that range from original research findings from biological paradigms to mathematically modeled systems. However, neuroscientists using microarray technology face significant challenges due to high tissue complexity, low abundance transcripts, and small magnitude changes in transcript levels that have significant biological impact. This manuscript describes a series of studies designed to address issues regarding microarray sensitivity, ability of microarrays to detect subtle changes, and reproducibility of microarray experiments, all in the context of neuronal tissue. From the presentation of these studies, the authors argue that although microarray technology is limited with regards to sensitivity, the outcome of these experiments, if approached with appropriate skepticism, can be fruitful in the generation of hypotheses and seeding of future experiments.
A critical appraisal of propensity‐score matching in the medical literature between 1996 and 2003

Propensity‐score methods are increasingly being used to reduce the impact of treatment‐selection bias in the estimation of treatment effects using observational data. Commonly used propensity‐score methods include covariate adjustment using the propensity score, stratification on the propensity score, and propensity‐score matching. Empirical and theoretical research has demonstrated that matching on the propensity score eliminates a greater proportion of baseline differences between treated and untreated subjects than does stratification on the propensity score. However, the analysis of propensity‐score‐matched samples requires statistical methods appropriate for matched‐pairs data. We critically evaluated 47 articles that were published between 1996 and 2003 in the medical literature and that employed propensity‐score matching. We found that only two of the articles reported the balance of baseline characteristics between treated and untreated subjects in the matched sample and used correct statistical methods to assess the degree of imbalance. Thirteen (28 per cent) of the articles explicitly used statistical methods appropriate for the analysis of matched data when estimating the treatment effect and its statistical significance. Common errors included using the log‐rank test to compare Kaplan–Meier survival curves in the matched sample, using Cox regression, logistic regression, chi‐squared tests, t‐tests, and Wilcoxon rank sum tests in the matched sample, thereby failing to account for the matched nature of the data. We provide guidelines for the analysis and reporting of studies that employ propensity‐score matching. Copyright © 2007 John Wiley & Sons, Ltd.
Histopathological features of flexural melanocytic nevi: a study of 40 cases

Melanocytic nevi in certain locations such as the genital and acral sites may have atypical histologic features simulating melanoma. We studied the microscopic findings of 40 melanocytic nevi of flexural sites (axilla, umbilicus, inguinal creases, pubis, scrotum and perianal area) to verify if flexural nevi show distinctive features similar to melanocytic nevi of the genital skin. The patients were young (mean age 20 years), the lesions were mostly removed for cosmetic reasons and we are not aware of any deaths or complications related to the removed nevi. We found that 22 (55.5%) out of 40 flexural nevi had “a nested and dyshesive pattern” similar to the melanocytic nevi of genital skin. This pattern was characterized by the confluence of enlarged nests with variation in size, shape and position at the dermo‐epidermal junction and by the diminished cohesion of melanocytes. Dermatopathologists should pay attention to the “nested and dyshesive pattern” of flexural nevi that may mimick hystologic changes of melanoma.
A cluster-analytical approach toward physical activity and other health related behaviors.

PURPOSE The purpose of our study was to investigate, on the basis of cluster analysis, whether healthy behavior clusters in a healthy or unhealthy way, whether physical activity can discriminate among those clusters, and whether the groups identified could be characterized by demographic variables. METHODS The relationships between physical activity and other health related behaviors were studied in three age groups, ages 16-25, 35-45, and 50-65. Almost 2400 subjects from a medium-sized Belgian town were interviewed at home to assess their level of physical activity in the past year and to obtain information on other healthy behaviors. RESULTS The two-cluster solution was found to be most reliable in all three age groups. Smoking discriminated most among the clusters. Cluster analysis divided each age group into a healthy and a more unhealthy subgroup, in which the healthy subgroup is larger than the unhealthy one. Sex differences were found in all three age groups, with more men in the unhealthy cluster. Socio-economic differences are especially strong in the two youngest samples. CONCLUSIONS The hypothesis that leisure time physical activity had discriminating power between healthy and unhealthy subgroups was not confirmed. Physical activity seems to be a unique factor in contrast to other health related behaviors. In the future, specific intervention directed at the promotion of physical activity in the population is necessary.
Characterization of the angiogenic activity of zebrafish ribonucleases

Ribonucleases identified from zebrafish possess angiogenic and bactericidal activities. Zebrafish RNases have three intramolecular disulfide bonds, a characteristic structural feature of angiogenin, different from the typical four disulfide bonds of the other members of the RNase A superfamily. They also have a higher degree of sequence homology to angiogenin than to RNase A. It has been proposed that all RNases evolved from these angiogenin‐like progenitors. In the present study, we characterize, in detail, the function of zebrafish RNases in various steps in the process of angiogenesis. We report that zebrafish RNase‐1, ‐2 and ‐3 bind to the cell surface specifically and are able to compete with human angiogenin. Similar to human angiogenin, all three zebrafish RNases are able to induce phosphorylation of extracellular signal‐regulated kinase 1/2 mitogen‐activated protein kinase. They also undergo nuclear translocation, accumulate in the nucleolus and stimulate rRNA transcription. However, zebrafish RNase‐3 is defective in cleaving rRNA precursor, even though it has been reported to have an open active site and has higher enzymatic activity toward more classic RNase substrates such as yeast tRNA and synthetic oligonucleotides. Taken together with the findings that zebrafish RNase‐3 is less angiogenic than zebrafish RNase‐1 and ‐2 as well as human angiogenin, these results suggest that zebrafish RNase‐1 is the ortholog of human angiogenin and that the ribonucleolytic activity of zebrafish RNases toward the rRNA precursor substrate is functionally important for their angiogenic activity.
EVALUATION OF PLASMA GLUCOSE CONTROL IN PREGNANCY COMPLICATED BY CHEMICAL DIABETES

Two‐hourly plasma glucose measurements were made over a 24‐hour period in 24 pregnant women with chemical diabetes treated by dietary carbohydrate restriction alone. The values obtained between midnight and 0600 hours displayed the best correlation with the mean of the diurnal values, the strongest individual correlation being at 0200 hours. During the daytime, the mean of the plasma glucose values before breakfast (0600 hours) and lunch (1200 hours) and two hours after supper (2000 hours) provided the strongest correlation with the mean diurnal value and these are recommended as the routine sampling times for assessment of diabetic control in pregnant women with dietary treatment for chemical diabetes.
Notice of RetractionModel and Simulation on SO2 Removal with Electrostatic Spray

Electricity effect was introduced into wet flue gas desulfurization by lime spray. The better SO2 removal efficiency was gained using WFGD by charged lime spray in little flow. In order to investigate the mechanism of SO2 removal by charged lime spray, model of WFGD by charged lime spray process was established adopting double-film theory, which is applied to analyze the process of mass transfer and predict the absorption efficiency. SO2 removal model is founded by simplifying the process of the mass transfer between liquid and gas and adding the effect of the droplets coulomb and polarization forces which exist in the electrostatic field. The model results indicate that the absorption efficiency is in accordance with experimental data, and the plus electrostatic voltages effect is proved to be true, and the prediction efficiency parameter is direction to the experiment. The foundation of model is academic and important base for the more development of WFGD by charged lime spray.
Determining the General Circulation of the Oceans: A Preliminary Discussion

The classical oceanographic problem of deducing the unknown constant in the dynamic method—the problem of the "level of no motion"—may be treated as a geophysical inverse problem. The unknown "barotropic" velocity may be chosen to satisfy an arbitrary number of conservation laws, subject to perfect geostrophic balance and with explicit use made of the relative errors in the observations. The solution obtained is one of minimum energy. A western North Atlantic region is used to demonstrate the power of the method.
Citizens as Partners: Information, Consultation and Public Participation in Policy-Making

U radu autor prikazuje sadržaj i svoje viđenje knjige Organizacije za ekonomsku suradnju i razvoj objavljene 2001. godine pod naslovom Citizens as Partners: Information, Consultation and Public Participation in Policy-Making.
Safety and efficacy of everolimus in patients with non-clear cell renal cell carcinoma refractory to VEGF-targeted therapy: Subgroup analysis of REACT.

402 Background: Metastatic non-clear cell renal cell carcinoma (mncRCC), which accounts for about 25% of all RCCs, is characterized by resistance to treatment and poor overall survival. Despite recent advances in targeted therapies for patients with mRCC, effective therapies for patients with mncRCC remain limited. The REACT (RAD001 Expanded Access Clinical Trial in RCC) study was initiated to provide patients with mRCC of any histology refractory to VEGF-targeted therapy access to everolimus in advance of regulatory approval. METHODS REACT, an open-label, international, expanded-access program (Clinicaltrials.gov: NCT00655252 ) enrolled patients with measurable or nonmeasurable mRCC of any histology who were intolerant of, or progressed while on, VEGFR-TKI therapy in order to evaluate the long-term safety of everolimus 10 mg daily. Overall incidence of grade 3/4 and serious adverse events (AEs) were recorded, as was tumor response to everolimus according to RECIST criteria. A subgroup analysis of safety and efficacy in patients with mncRCC was performed. RESULTS Of 1367 patients enrolled, 75 patients (5.5%) had mncRCC. Median everolimus treatment duration in the mncRCC subgroup was 12.14 weeks (range, 0.9-49.0 weeks) and in the overall REACT population it was 14.0 weeks (range, 0.1-83.7 weeks). In the mncRCC subgroup, most commonly reported grade 3/4 AEs were anemia (17.3%), dyspnea (10.7%), pleural effusion (9.3%), fatigue (8.0%), and hyperglycemia (6.6%). Best overall response was similar in the mncRCC subgroup and overall population: respectively, 1.3% and 1.7% had partial response and 49.3% and 51.6% had stable disease. CONCLUSIONS Although patients with mncRCC had a slightly lower treatment duration than the overall REACT population, approximately 50% of these patients achieved disease control on treatment. In this subgroup, everolimus was well tolerated, no new safety issues were observed, and the AE profile was consistent with that of the overall population. These encouraging results of the safety and efficacy of everolimus in patients with mncRCC support further evaluation of everolimus in these patients.
Investigation into multiphysics coupling via semiconducting nanophosphors

In an attempt to strengthen the case for the design and manufacture of multi-modal imaging machines capable of simultaneous and synergistic computed tomography (CT) and magnetic resonance imaging (MRI) as proposed by Ge Wang as early as 2012, a series of experiments using various combinations of nanophosphors, agar gels, a fiber optic coupled UV LED, and micro-MRI have been proposed and performed. The aim of these experiments is to elucidate the ability, if any, of UV-excited nanophosphors to modulate MRI parameters (T1, T2, and T2*). The majority of our findings have been difficult to interpret, although some hints of the coupling were seen in previously reported studies. This paper briefly describes the next set experiments and discusses the improvements that need to be made to achieve statistical confidence in any phenomena that may be recorded. This work is an important step in the coupling of seemingly unrelated imaging modalities and could serve as a stepping-stone for further insight into the future of imaging.
Integrating collaborative governance theory with the Advocacy Coalition Framework

Abstract As collaborative governance processes continue to grow in popularity, practitioners and policy scholars alike can benefit from the development of methods to better analyse and evaluate them. This article develops one such method by demonstrating how collaborative governance theory can be integrated with the Advocacy Coalition Framework (ACF) to better explain coalition dynamics, policy-oriented learning and policy change in collaborative contexts. I offer three theoretical propositions that suggest alternate relationships among ACF variables under collaborative governance arrangements and illustrate these propositions using interview data from an original case study of a collaborative governance process in Colorado, USA. The integration of collaborative governance theory with the ACF improves its application in collaborative contexts and provides new theoretical insights into the study and practice of collaborative governance.
Oral squamous cancer cell exploits hnRNP A1 to regulate cell cycle and proliferation

Oral squamous cell carcinoma (OSCC) is a common human malignant tumor with high mortality. So far, the molecular pathogenesis of OSCC remains largely unclear. Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an important multi‐function splicing factor and closely related to tumorigenesis. hnRNP A1 is overexpressed in various tumors, and promotes aerobic glycolysis and elongation of telomere, but the function of hnRNP A1 in cell cycle and proliferation remains unclear. We found that hnRNP A1 was overexpressed in OSCC tissues, and was required for the growth of OSCC cells. Moreover, hnRNP A1 was highly expressed in the G2/M cell cycle phase. Knockdown of hnRNP A1 induced G2/M arrest. DNA microarray assay result showed that hnRNP A1 regulated the expression of a number of target genes associated with G2/M phase. Moreover, hnRNP A1 controlled the alternative splicing of CDK2 exon 5. These findings suggested that hnRNP A1 plays key roles in the regulation of cell cycle progression and pathogenesis of OSCC. J. Cell. Physiol. 230: 2252–2261, 2015. © 2015 Wiley Periodicals, Inc.
Effect of pH and salt bridges on structural assembly: Molecular structures of the monomer and intertwined dimer of the Eps8 SH3 domain

The SH3 domain of Eps8 was previously found to form an intertwined, domain‐swapped dimer. We report here a monomeric structure of the EPS8 SH3 domain obtained from crystals grown at low pH, as well as an improved domain‐swapped dimer structure at 1.8 Å resolution. In the domain‐swapped dimer the asymmetric unit contains two “hybrid‐monomers. ” In the low pH form there are two independently folded SH3 molecules per asymmetric unit. The formation of intermolecular salt bridges is thought to be the reason for the formation of the dimer. On the basis of the monomer SH3 structure, it is argued that Eps8 SH3 should, in principle, bind to peptides containing a PxxP motif. Recently it was reported that Eps8 SH3 binds to a peptide with a PxxDY motif. Because the “SH3 fold” is conserved, alternate binding sites may be possible for the PxxDY motif to bind. The strand exchange or domain swap occurs at the n‐src loops because the n‐src loops are flexible. The thermal b‐factors also indicate the flexible nature of n‐src loops and a possible handle for domain swap initiation. Despite the loop swapping, the typical SH3 fold in both forms is conserved structurally. The interface of the acidic form of SH3 is stabilized by a tetragonal network of water molecules above hydrophobic residues. The intertwined dimer interface is stabilized by hydrophobic and aromatic stacking interactions in the core and by hydrophilic interactions on the surface.
Sharia’h practice at Islamic banks in Pakistan

Purpose Islamic banks provide an alternative financial system based on Sharia’h (Islamic law). However, critics argue that operation at Islamic banks is violating Sharia’h particularly in terms of provision of interest free services, risk sharing and legal contract. The purpose of this paper is to empirically evaluate the Sharia’h practice at Islamic banks in Pakistan by considering some basic principles of Sharia’h. Design/methodology/approach Primary data are collected from 63 branches of Islamic banks in Pakistan. Questionnaire is used as an instrument. The study uses structural equation modeling that includes confirmatory factor analysis and regression analysis. Data are codified and analyzed using SPSS and Amos. Findings This study finds that Islamic banks are providing interest free services, ensuring that transactions and contracts offered by Islamic banks are legal and offering conflict-free environment to customers. In contrast, estimated results expose that Islamic banks are not sharing risk and Sharia’h supervisory board is not performing its role perfectly. Similarly, it is found that organization and distribution of zakat and qard-ul-hassan are weak at Islamic banks. Research limitations/implications Data are collected from Islamabad federal capital of Pakistan that hold just 5 per cent share of Islamic banking industry. This small share may not provide true picture of Islamic banking sector. Practical implications To ensure risk sharing, Islamic banking industry must consider the development of new modes of financing and innovation of more products based on Sharia’h. State Bank of Pakistan should ensure separate regulatory framework that enable Islamic banks to provide qard-ul-hassan, organize and allocate zakat. Originality/value This paper discusses the perception of bankers, who are actually the executors, about Shariah’s practices at Islamic banks in Pakistan. There are not many discussions on this topic that could be found, and hence this could be considered as a significant contribution by this paper to the existing literature of Islamic finance.
Changes in Microbiota Population during Fermentation of Narezushi as Revealed by Pyrosequencing Analysis

Modern Japanese sushi is derived from an archetype, narezushi, which is made by the fermentation of salted fish with rice. Several studies have demonstrated that lactic acid bacteria are dominantly present in narezushi, but no studies have addressed how microbial composition changes during fermentation. In this study, we examined changes in the microbial population in aji (horse mackerel)-narezushi during fermentation by pyrosequencing the 16S ribosomal RNA gene (rDNA). Ribosomal Database Project Classifier analysis revealed that among the 53 genera present, the Lactobacillus population drastically increased during fermentation, while the populations of other bacteria remained unchanged. Basic Local Alignment Search Tool analysis revealed that L. plantarum and L. brevis were the major species. Comparison with other fermented food microbiota indicated high product-dependency of the bacterial composition, which might have been due to the starter-free fermentation process.
Human abuse potential of immediate-release/extended-release versus immediate-release hydrocodone bitartrate/acetaminophen: a randomized controlled trial in recreational users of prescription opioids

Abstract Background. The abuse potential of prescription opioids is well established. This study compared positive, subjective drug effects of single, equal doses of biphasic immediate release (IR)/extended release (ER) hydrocodone bitartrate (HB)/acetaminophen (acetyl-p-aminophenol [APAP]) 7.5/325 mg tablets versus IR HB/APAP 7.5/325-mg tablets and placebo. Methods: Healthy adult recreational users of prescription opioids entered this randomized, double-blind, double-dummy, active- and placebo-controlled, seven-way crossover study. Participants received single, total doses of IR/ER HB/APAP 22.5/975 mg (intact; three active tablets) and 45/1950 mg (intact and crushed [encapsulated]; six active tablets), IR HB/APAP 22.5/975 mg (intact; three active tablets) and 45/1950 mg (intact and crushed [encapsulated]; six active tablets), and placebo. Peak subjective effects (Emax); time to peak effects (TEmax); and area under the drug–effect curves for drug liking, high, and good drug effects were measured using visual analog scales. Median values with 95% confidence interval (CI) were compared using analysis of variance. Results: Among completers (n = 52), IR/ER HB/APAP produced delayed and lower peak effects compared to equal doses of IR HB/APAP. Comparing intact tablets, the drug liking Emax (median [95% CI]) was significantly lower for IR/ER HB/APAP 45/1950 mg (78.0 [73.0, 81.0]) than an equal dose of IR HB/APAP (89.5 [85.0, 93.0]; difference, –8.5 [–12.0, –6.0]; P < 0.001). Similar results were observed for intact IR/ER HB/APAP and IR HB/APAP 22.5/975 mg. Crushing IR/ER HB/APAP 45/1950 mg delayed these effects compared with an equal dose of crushed IR HB/APAP and intact IR/ER HB/APAP. Conclusion. IR/ER HB/APAP resulted in lower subjective positive drug effects than an equal dose of IR HB/APAP. Crushing IR/ER HB/APAP also delayed the onset of subjective effects compared with intact IR/ER HB/APAP. These findings suggest that biphasic IR/ER HB/APAP has lower abuse potential than IR HB/APAP in single equal doses. Registration: This Phase I clinical trial conducted in the USA was not registered.
A Patient Portal for Clinical Trials: Towards Increasing Patient Enrollment

Clinical trials face delays due to the inability to enroll the necessary number of patients. A survey performed on cancer clinical trials demonstrated that American adults are willing to participate in clinical trials, however there is often an inability to recruit the required number of participants to a clinical trial study. To address this deficit, we propose an application that mines patient records, to extract diagnoses via ICD 9 codes obtained by natural language processing (NLP), and links patients with clinical trials relevant to their diagnoses. The patient portal searches relevant clinical trials tailored to a user's personal demographics, allows users to save trials from previous searches, provides a medium to initiate contact with a recruiter prior to enrollment with a click of a button, and presents additional information targeted towards patient needs such as options for continued care, cost of participation and required appointments and procedures. We theorize that this application will improve patients understanding of clinical trial information and potentially increase enrollment rates.