Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis issues for gene expression array data.

Gene expression array technologies are rapidly emerging for use in various genome-wide studies in biology and medicine (1)(2)(3). Results from the recently completed sequencing of the human genome predict that the number of genes in the human genome is much smaller (∼33 000 genes) than anticipated (4). This implies that the major complexity in biological mechanisms in humans lies in the synergistic effects among various genes. Therefore, to decipher the secrets of our life and, ultimately, to find the cures for many human diseases, biologists must deal with multiple genes and their interactive transcripts simultaneously. High-throughput biotechnologies, including gene chip approaches, will play an important role in these studies (5). However, quality control over thousands of gene expression values and full utilization of the information from these high-throughput data are extremely difficult, and important issues in quality control and bioinformatic approaches have not been resolved (6)(7). A series of careful analyses on the variability of array instrumentation and on the statistical evaluation of gene expression intensities are required for reliable and consistent inference on gene chip data. Specifically, sources of error and their confidence levels on these high-throughput measurements need to be better understood because some can significantly alter our inferences and conclusions (8). The purpose of this report is to dispel three common misconceptions about array experiments. It often is believed that reproducibility of gene expression data is high enough to perform bioinformatic discovery without a replicated chip experiment and that duplicated array data are necessary only for confirmation of such a discovery, which may help publication in high-standard journals. Investigators who have successfully obtained resources for high-cost gene chip experiments must optimize their experimental strategy for their study goals within limited resources. Therefore, for an initial study, single-chip experiments for each …
Individual, Social, and Environmental Correlates of Healthy and Unhealthy Eating

Background. Few studies use comprehensive ecological approaches considering multilevel factors to understand correlates of healthy (and unhealthy) dietary intake. The aim of this study was to examine the association between individual, social, and environmental factors on composite measures of healthy and unhealthy dietary intake in adults. Method. Participants (n = 565) of the Australian RESIDential Environments (RESIDE) project self-reported dietary intake, home food availability, and behavioral and perceived social and physical environmental inﬂuences on food choices. A geographic information system measured proximity of supermarkets from each participant’s home. “Healthy” and “unhealthy” eating scores were computed based on adherence to dietary guidelines. Univariate and multivariate models were constructed using linear regression. Results. After full adjustment, “healthy” eating (mean = 6.25, standard deviation [SD] = 1.95) was significantly associated with having confidence to prepare healthy meals (β = 0.34; 95% confidence interval [CI] = [0.13, 0.55]); having more healthy (β = 0.13; 95% CI = [0.09-0.16]) and fewer unhealthy (β = −0.04; 95% CI = [−0.06, −0.02]) foods available at home; and having a supermarket within 800 meters of home (β = 1.39; 95% CI = [0.37, 2.404]). “Unhealthy” eating (mean = 3.53, SD = 2.06) was associated with being male (β = 0.39; 95% CI = [0.02, 0.75]), frequently eating takeaway (β = 0.33; 95% CI = [0.21, 0.46]) and cafe or restaurant meals (β = 0.20; 95% CI = [0.06, 0.33]) and having fewer healthy (β = −0.07; 95% CI = [−0.10, −0.03]) and more unhealthy (β = 0.09; 95% CI = [0.07, 0.10]) foods available within the home. Conclusion. Initiatives to improve adherence to dietary guidelines and reduce the consumption of unhealthy foods needs to be multifaceted; addressing individual factors and access to healthy food choices in both the home and neighborhood food environment. Ensuring proximity to local supermarkets, particularly in new suburban developments, appears to be an important strategy for facilitating healthy eating.
Agency, access, and Anopheles: neighborhood health perceptions and the implications for community health interventions in Accra, Ghana

Background Social and environmental factors are increasingly recognized for their ability to influence health outcomes at both individual and neighborhood scales in the developing urban world. Yet issues of spatial heterogeneity in these complex environments may obscure unique elements of neighborhood life that may be protective or harmful to human health. Resident perceptions of neighborhood effects on health may help to fill gaps in our interpretation of household survey results and better inform how to plan and execute neighborhood-level health interventions. Objective We evaluate differences in housing and socioeconomic indicators and health, environment, and neighborhood perceptions derived from the analysis of a household survey and a series of focus groups in Accra, Ghana. We then explore how neighborhood perceptions can inform survey results and ultimately neighborhood-level health interventions. Design Eleven focus groups were conducted across a socioeconomically stratified sample of neighborhoods in Accra, Ghana. General inductive themes from the focus groups were analyzed in tandem with data collected in a 2009 household survey of 2,814 women. In-depth vignettes expand upon the three most salient emergent themes. Results Household and socioeconomic characteristics derived from the focus groups corroborated findings from the survey data. Focus group and survey results diverged for three complex health issues: malaria, health-care access, and sense of personal agency in promoting good health. Conclusion Three vignettes reflecting community views about malaria, health-care access, and sense of personal agency in promoting good health highlight the challenges facing community health interventions in Accra and exemplify how qualitatively derived neighborhood-level health effects can help shape health interventions.
A Word Clustering Approach to Domain Adaptation: Effective Parsing of Biomedical Texts

We present a simple and effective way to perform out-of-domain statistical parsing by drastically reducing lexical data sparseness in a PCFG-LA architecture. We replace terminal symbols with unsupervised word clusters acquired from a large newspaper corpus augmented with biomedical targetdomain data. The resulting clusters are effective in bridging the lexical gap between source-domain and target-domain vocabularies. Our experiments combine known self-training techniques with unsupervised word clustering and produce promising results, achieving an error reduction of 21% on a new evaluation set for biomedical text with manual bracketing annotations.
Luhmann's Slip Box -- What can we Learn from the Device for Knowledge Representation in Requirements Engineering?

This paper is a thought experiment in finding struc tures for the elicitation of requirements on top of struc tures for retrieving requirements. We transfer from structures used by the German sociologist Niklas Luhmann, who applied a wooden slip box to collect notes on processed literature. Each slip contains bib liographic information and Luhmann's thoughts to the referenced content. In this paper we propose to use Luhmann's slip box approach for requirements engi neering, by enhancing it to a multi user suited to sort requirements in a requirements repository.
A Randomized Controlled Trial Evaluating the Role of Honey in Reducing Pain Due to Radiation Induced Mucositis in Head and Neck Cancer Patients

Background: There are various drugs tried for relieving pain associated with radiation-induced mucositis. This paper aims to study role of honey in relieving pain due to radiation induced mucositis in head and neck cancer patients receiving concomitant chemoradiation. Materials and Methods: A randomized controlled trial on 78 subjects (40 in test group and 38 in control group) was undertaken to study the analgesic effect of honey, but the analysis of 69 patients was done as nine patients (four in test and five in control group) were lost to follow-up or left treatment in between the study. All patients were advised to do salt-soda and benzydamine mouth gargles, alternatively every 3 hours. Test group patients additionally received 20 ml honey three times a day during the entire course of radiation treatment and 3 months following radiation therapy (RT). Results: Honey significantly reduced the severity of mucositis associated pain and resulted in lesser treatment gaps and a decrease in overall radiotherapy treatment duration. None of the test group and majority of controls (51.5%) had severe pain score during the 7th week of RT. The same pattern was seen in the post-RT period. Mean pain score was significantly different in both groups during all weeks during and upto 6 weeks post-RT (mean score of 3.08 and 6.54 for test and control respectively at 7th week RT, P < 0.001). Conclusion: Honey being a cheap, palatable, and natural medicament can be used for decreasing pain associated with radiation-induced mucositis in cancer patients.
Cell-Free RNA Content in Peripheral Blood as Potential Biomarkers for Detecting Circulating Tumor Cells in Non-Small Cell Lung Carcinoma

Circulating tumor cells (CTCs) have been implicated in tumor progression and prognosis. Techniques detecting CTCs in the peripheral blood of patients with non-small cell lung carcinoma (NSCLC) may help to identify individuals likely to benefit from early systemic treatment. However, the detection of CTCs with a single marker is challenging, owing to low specificity and sensitivity and due to the heterogeneity and rareness of CTCs. Herein, the probability of cell-free RNA content in the peripheral blood as a potential biomarker for detecting CTCs in cancer patients was investigated. An immunomagnetic enrichment of real-time reverse-transcription PCR (RT-PCR) technology for analysis of CTCs in NSCLC patients was also developed. The mRNA levels of four candidate genes, cytokeratin 7 (CK7), E74-like factor 3 (ELF3), epidermal growth factor receptor (EGFR), and erythropoietin-producing hepatocellular carcinoma receptor B4 (EphB4) that were significantly elevated in tumor tissues and peripheral blood mononuclear cells (PBMCs) were determined. The expression of CK7 and ELF3 in tumor tissues and EGFR in PBMCs was associated with lymph node metastasis (all p < 0.05). The expression of CK7 in PBMCs was correlated with age and EphB4 in PBMCs correlated with histopathological type, respectively (all p < 0.05). The expression of all four genes in tumor tissues and PBMCs was significantly correlated with the clinical stage (all p < 0.01). Survival analysis showed that the patients with enhanced expression of CK7, ELF3, EGFR, and EphB4 mRNA in PBMCs had poorer disease-free survival (DFS) and overall survival (OS) than those without (all p < 0.0001). The present study showed that this alteration of cell-free RNA content in peripheral blood might have clinical ramifications in the diagnosis and treatment of NSCLC patients.
Time Course of ECG Depolarization and Repolarization Changes during Ischemia in PTCA Recordings

Summary Objectives: In this work we studied the temporal evolution of changes in the electrocardiogram (ECG) as a consequence of the induced ischemia during prolonged coronary angioplasty, comparing the time course of indexes reflecting depolarization and those reflecting repolarization. Methods: We considered both local (measured at specific points of the ECG) and global (obtained from the Karhunen-Loève transform) indexes. In particular, the evolution of Q, R and S wave amplitudes during ischemia was analyzed with respect to classical indexes such as ST level. As a measurement of sensitivity we used an Ischemic Changes Sensor (ICS), which reflects the capacity of an index to detect changes in the ECG. Results: The results showed that, in leads with low-amplitude ST-T complexes, the S wave amplitude was more sensitive in detecting ischemia than was the commonly used index ST60. It was found that in such leads the S wave amplitude initially exhibited a delayed response to ischemia when compared to ST60, but its performance was better from the second minute of occlusion. The global indexes describing the ST-T complex were, in terms of the ICS, superior to the S wave amplitude for ischemia detection. Conclusions: Ischemic ECG changes occur both at repolarization and depolarization, with alterations in the depolarization period appearing later in time. Local indexes are less sensitive to ischemia than global ones.
German Children ’ s Welfare Between Economy and Ideology

The objective of this study is to present selected dimensions of child welfare in contemporary Germany. The study’s argumentation does not apply descriptive logic, but rather an explicitly analytical perspective. The central thesis is that the welfare and well-being of children in Germany are influenced to a high extent by a clear discrepancy between children’s real forms of living (and those of their immediate family) on one hand, and ideological constructions of ‘a good childhood’ and the resulting ‘institutional framework’ of children’s lives on the other. Economic modernisation and policy decisions appear to be increasingly distancing themselves from the demands and needs of children and their life worlds. As a result, German society and the German welfare state – in contrast to the self-conception of the Scandinavian countries, for example – are considered ‘structurally indifferent’ (Bundesministerium für Familie und Senioren – BMFuS, 1994) towards children and families. Both the demands of modern economic life and the basic political-institutional conditions make it difficult for parents and potential parents to organise their lives with children, and have a negative effect on the well-being and happiness of children. The causes of these contradictions between modern children’s lives, on one hand, and dominant ideologies and institutions in society, on the other hand, are to be found a long way back in German history. The German welfare state is a typical representative of the ‘conservative welfare regime’ type according to the typology of Esping-Andersen (1990). It has been influenced throughout its historical development – as can be shown for all welfare states of this type – by the Catholic church and political Catholicism. This, and the experience of
Characterization of the VIER F-BOX PROTEINE Genes from Arabidopsis Reveals Their Importance for Plant Growth and Development[W]

E3 ubiquitin ligases (E3s) target proteins for degradation by the 26S proteasome. In SKP1/CDC53/F-box protein–type E3s, substrate specificity is conferred by the interchangeable F-box protein subunit. The vast majority of the 694 F-box proteins encoded by the Arabidopsis thaliana genome remain to be understood. We characterize the VIER F-BOX PROTEINE (VFB; German for FOUR F-BOX PROTEINS) genes from Arabidopsis that belong to subfamily C of the Arabidopsis F-box protein superfamily. This subfamily also includes the F-box proteins TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) proteins and EIN3 BINDING F-BOX proteins, which regulate auxin and ethylene responses, respectively. We show that loss of VFB function causes delayed plant growth and reduced lateral root formation. We find that the expression of a number of auxin-responsive genes and the activity of DR5:β-glucuronidase, a reporter for auxin reponse, are reduced in the vfb mutants. This finding correlates with an increase in the abundance of an AUXIN/INDOLE-3-ACETIC ACID repressor. However, we also find that auxin responses are not affected in the vfb mutants and that a representative VFB family member, VFB2, cannot functionally complement the tir1-1 mutant. We therefore exclude the possibility that VFBs are functional orthologs of TIR1/AFB proteins.
Double‐stranded DNA‐induced localized unfolding of HCV NS3 helicase subdomain 2

The NS3 helicase of the hepatitis C virus (HCV) unwinds double‐stranded (ds) nucleic acid (NA) in an NTP‐dependent fashion. Mechanistic details of this process are, however, largely unknown for the HCV helicase. We have studied the binding of dsDNA to an engineered version of subdomain 2 of the HCV helicase (d2ΔNS3h) by NMR and circular dichroism. Binding of dsDNA to d2ΔNS3h induces a local unfolding of helix (α3), which includes residues of conserved helicase motif VI (Q460RxxRxxR467), and strands (β1 and β8) from the central β‐sheet. This also occurs upon lowering the pH (4.4) and introducing an R461A point mutation, which disrupt salt bridges with Asp 412 and Asp 427 in the protein structure. NMR studies on d2ΔNS3h in the partially unfolded state at low pH map the dsDNA binding site to residues previously shown to be involved in single‐stranded DNA binding. Sequence alignment and structural comparison suggest that these Arg–Asp interactions are highly conserved in SF2 DEx(D/H) proteins. Thus, modulation of these interactions by dsNA may allow SF2 helicases to switch between conformations required for helicase function.
Interface Automata with Complex Actions-Extended Version Shahram

Many formalisms use interleaving to model concurrency. To describe some system behaviours appropriately, we need to limit interleaving. For example, in component-based systems, we wish to limit interleaving to force the inputs to a method to arrive together in order. In Web services, the arrival of XML messages consisting of multiple simple parts should not be interleaved with the behaviour of another component. We introduce interface automata with complex actions (IACA), which add complex actions to de Alfaro and Henzinger’s interface automata (IA). A complex action is a sequence of actions that may not be interleaved with actions from other components. The composition and refinement operations are more involved in IACA compared to IA, and we must sacrifice associativity of composition. However, we argue that the advantages of having complex actions make it a useful formalism. We provide proofs of various properties of IACA and discuss the use of IACA for modelling Web services.
What Is Qualitative Research?

The defining nature and characteristics of qualitative research are surveyed in this article, which identifies key distinctions between method and methodology. The authors note that qualitative research is primarily concerned understanding human beings' experiences in a humanistic, interpretive approach. Issues of research design differences between quantitative and qualitative research are traced with an emphasis on identifying diverse methodologies, including those focusing on analysis of text, and diverse forms of data collection along with criteria for evaluating qualitative research.
Full catastrophe living : using the wisdom of your body and mind to face stress, pain, and illness

FULL CATA STROPHE LIV ING: USING THE W ISDOM OF YOUR BODY A ND MIND TO FA CE STRESS, PA IN, A ND ILLNESS To read Full Catastrophe Living : Using the W isdom of Your Body and Mind to Face Stress, Pain, and Illness eBook, please click the link under and download the ebook or get access to additional information which might be related to Full Catastrophe Living: Using the Wisdom of Your Body and Mind to Face Stress, Pain, and Illness book.
INTERIOR-POINT METHODS FOR NONCONVEX NONLINEAR PROGRAMMING: JAMMING AND COMPARATIVE NUMERICAL TESTING

The paper considers a current example of W¨ achter and Biegler which is shown not to converge for the standard primal-dual interior-point method for nonlinear program- ming. Three possible solutions to the problem are derived and discussed, including shifting slack variables, a trust region method, and a modified barrier method. The paper then compares LOQO, a line-search interior-point code, with SNOPT, a sequential-quadratic- programming code, and NITRO, a trust-region interior-point code on a large test set of nonlinear programming problems. Specific types of problems which can cause LOQO to fail are identified.
Unsupervised induction of dependency structures using Probabilistic Bilexical Grammars

Unsupervised parsing induction has attracted a significant amount of attention over the last few years. However, current systems exhibit a degree of complexity that can shy away newcomers to the field. We challenge the need for such complexity and present a straightforward weak-EM based system. The results we obtained are close to state-of-the-art ones while still making it extremely simple to experiment with different sub-components. We use a k-best parser, an inductor for Probabilistic Bilexical Grammars (PBGs) [1] and a simple treebank builder. Since our algorithm is independent of the PBG inductor, it overlaps with other models from the literature such as Dependency Model with Valence [2]. Our algorithms are fully fleshed and easily reproducible. We experiment in 8 languages that inform intuitions in training- size dependent parameterization.
Primal decomposition based decentralized weighted sum rate maximization with QoS constraints for interfering broadcast channel

We propose a decentralized beamforming design for weighted sum rate maximization with quality-of-service constraints based on primal decomposition of the corresponding centralized problem. The considered system consists of multiple coordinated multi-antenna base stations (BS) serving multiple users each with multiple receive antennas. The considered rate maximization problem is known to be NP-hard and as such intractable in practice. The problem is separated into downlink receive beamformer and transmit precoder design problems. The transmit precoder design problem is further decoupled between the interfering base stations by primal decomposition with respect to the caused inter-cell interference per BS. Particular emphasis is given to signaling requirements and rate of convergence.
ANCA-negative pauci-immune renal vasculitis: histology and outcome.

BACKGROUND Pauci-immune renal vasculitis with focal glomerular necrosis and crescent formation is usually associated with anti-neutrophil cytoplasmic antibodies (ANCAs). However, ANCA's are absent in up to 10% of cases, which constitutes a rarely studied variant of renal vasculitis. METHODS This retrospective multicentre cohort study analyzed the presenting features, renal histology and outcome in 20 patients with pauci-immune crescentic necrotizing renal vasculitis in whom indirect immunofluorescence did not detect ANCA. RESULTS Renal histology revealed a high percentage of active glomerular lesions (50%), mainly cellular crescents, 28% of them with glomerular necrosis. Chronic tissue damage with glomerulosclerosis (21%) and diffuse interstitial fibrosis (40%) was already present at diagnosis, more prominent than in historical PR3-positive patients. Infiltrates of polymorphonuclear neutrophils in glomerular capillary loops were observed in 40% of all biopsies, mainly in necrotic lesions. The subsets of interstitially infiltrating leukocytes similar to ANCA-associated disease. Microscopic polyangiitis was diagnosed in 17 patients, Wegener's granulomatosis in two and renal-limited vasculitis in one. The patients median disease extent index (DEI) of 5 (range 4-11) reflected a systemic vasculitis. ANCA-negative vasculitis was not associated with infection or malignancy. Renal outcome was correlated to DEI (P = 0.032) and serum creatinine at diagnosis (P = 0.04). The mortality rate was high (35%) and closely related to age above 65 years at diagnosis (P = 0.014). Conclusions. The histological findings and prognosis in ANCA-negative renal vasculitis are comparable with those of ANCA-positive disease. Our data underline the importance of the exact diagnosis in an active vasculitic disease process even in the absence of ANCAs.