Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of host response to bacterial infection using error model based gene expression microarray experiments

A key step in the analysis of microarray data is the selection of genes that are differentially expressed. Ideally, such experiments should be properly replicated in order to infer both technical and biological variability, and the data should be subjected to rigorous hypothesis tests to identify the differentially expressed genes. However, in microarray experiments involving the analysis of very large numbers of biological samples, replication is not always practical. Therefore, there is a need for a method to select differentially expressed genes in a rational way from insufficiently replicated data. In this paper, we describe a simple method that uses bootstrapping to generate an error model from a replicated pilot study that can be used to identify differentially expressed genes in subsequent large-scale studies on the same platform, but in which there may be no replicated arrays. The method builds a stratified error model that includes array-to-array variability, feature-to-feature variability and the dependence of error on signal intensity. We apply this model to the characterization of the host response in a model of bacterial infection of human intestinal epithelial cells. We demonstrate the effectiveness of error model based microarray experiments and propose this as a general strategy for a microarray-based screening of large collections of biological samples.
Assessment of recurrence of non-small cell lung cancer after therapy using CT and Integrated PET/CT.

INTRODUCTION Non-small cell lung cancer (NSCLC) has become the leading cause of cancer-related deaths in Poland. Follow-up of patients with NSCLC is aimed at early detection of local recurrence, metastatic process, treatment-related complications or second primary lung cancer. We investigated the diagnostic accuracy of FDG-PET-CT in the detection of recurrence of NSCLC after treatment. MATERIAL AND METHODS Seventy-two NSCLC patients (19 females, 56 males), stage I to IV, who had undergone surgery and/ /or radiation therapy, occasionally associated with chemotherapy, were retrospectively included in our study. Chest radiographs and thoracic computed tomography (CT) were performed to localize the abnormality prior to PET-CT. All the patients underwent CT and PET-CT in the period from January 2008 until January 2012. All PET images were interpreted in conjunction with thoracic CT. PET-CT and CT diagnoses were correlated with pathological diagnoses. RESULTS Forty-five patients had recurrent tumour. Tumour recurrence was observed more often in men than in women and also in case of neoplastic cell emboli in lymphatic or blood vessels. In three patients second primary lung cancer was diagnosed. False positive diagnosis of relapse based on PET-CT was obtained in 4 patients, mainly due to inflammatory lesions. The accuracy of PET-CT for diagnosis of recurrence was 94.4% (95% CI 91; 100). CONCLUSIONS FDG PET-CT was the best method to differentiate recurrent bronchogenic carcinoma from inflammatory lesions, especially at post-therapeutic sites. It has been shown that PET-CT is more accurate method than CT in recurrent NSCLC. PET-CT results had a further impact on the clinical management and treatment planning.
Association of Chronic Kidney Disease With Cerebral Microbleeds in Patients With Primary Intracerebral Hemorrhage

Background and Purpose— To investigate the relationship between chronic kidney disease (CKD) and MRI-defined cerebral microbleeds (CMB), a harbinger of future intracerebral hemorrhage (ICH), among patients with a recent history of primary ICH. Methods— Using data from a predominantly black cohort of patients with a recent ICH-enrolled in an observational study between September 2007 and June 2011, we evaluated the association between CKD (defined as estimated low glomerular filtration rate<60 mL/min per 1.73 m2) and CMB on gradient-echo MRI. Multivariable models were generated to determine the contribution of CKD to the presence, number, and location of CMB. Results— Of 197 subjects with imaging data, mean age was 59 years, 48% were women, 73% were black, 114 (58%) had ≥1 CMBs, and 52 (26%) had CKD. Overall, CKD was associated with presence of CMB (adjusted odds ratio, 2.70; 95% confidence interval [CI], 1.10–6.59) and number of CMB (adjusted relative risk, 2.04; 95% CI, 1.27–3.27). CKD was associated with CMB presence (adjusted odds ratio, 3.44; 95% CI, 1.64–7.24) and number (adjusted relative risk, 2.46; 95% CI, 1.11–5.42) in black patients, but not CMB presence (adjusted odds ratio, 3.00; 95% CI, 0.61–14.86) or number (adjusted relative risk, 1.03; 95% CI: 0.22–4.89) in non-Hispanic white patients (interactions by race were statistically not significant). Conclusions— CKD is associated with a greater presence and number of CMB in ICH patients, particularly in patients of black race. Future studies should assess whether low estimated glomerular filtration rate may be a CMB risk marker or potential therapeutic target for mitigating the development of CMB.
A model for handling approximate, noisy or incomplete labeling in text classification

We introduce a Bayesian model, BayesANIL, that is capable of estimating uncertainties associated with the labeling process. Given a labeled or partially labeled training corpus of text documents, the model estimates the joint distribution of training documents and class labels by using a generalization of the Expectation Maximization algorithm. The estimates can be used in standard classification models to reduce error rates. Since uncertainties in the labeling are taken into account, the model provides an elegant mechanism to deal with noisy labels. We provide an intuitive modification to the EM iterations by re-estimating the empirical. distribution in order to reinforce feature values in unlabeled data and to reduce the influence of noisily labeled examples. Considerable improvement in the classification accuracies of two popular classification algorithms on standard labeled data-sets with and without artificially introduced noise, as well as in the presence and absence of unlabeled data, indicates that this may be a promising method to reduce the burden of manual labeling.
Distributive Equations of Fuzzy Implications Based on Continuous Triangular Conorms Given as Ordinal Sums

Recently, the distributive equations of fuzzy implications based on t -norms or t-conorms have become a focus of research. The solutions to these equations can help people design the structures of fuzzy systems in such a way that the number of rules is largely reduced. This paper studies the distributive functional equation I(x,S<sub>1</sub>(<i>y</i>,<i>z</i>))=<i>S</i><sub>2</sub>(<i>I</i>(<i>x</i>,<i>y</i>),<i>I</i>(<i>x</i>,<i>z</i>)), where <i>S</i><sub>1</sub> and <i>S</i><sub>2</sub> are two continuous t -conorms given as ordinal sums, and <i>I</i>:[0,1]<sup>2</sup>→ [0,1] is a binary function which is increasing with respect to the second place. If there is no summand of <i>S</i><sub>2</sub> in the interval [<i>I</i>(1,0),<i>I</i>(1,1)], we get its continuous solutions directly. If there are summands of <i>S</i><sub>2</sub> in the interval [<i>I</i>(1,0),<i>I</i>(1,1)], by defining a new concept called feasible correspondence and using this concept, we describe the solvability of the distributive equation above and characterize its general continuous solutions. When <i>I</i> is restricted to fuzzy implications, it is showed that there is no continuous solution to this equation. We characterize its fuzzy implication solutions, which are continuous on (0,1] × [0,1].
Evolutionary responses to environmental change: trophic interactions affect adaptation and persistence

According to recent reviews, the question of how trophic interactions may affect evolutionary responses to climate change remains unanswered. In this modelling study, we explore the evolutionary dynamics of thermal and plant–herbivore interaction traits in a warming environment. We find the herbivore usually reduces adaptation speed and persistence time of the plant by reducing biomass. However, if the plant interaction trait and thermal trait are correlated, herbivores can create different coevolutionary attractors. One attractor has a warmer plant thermal optimum, and the other a colder one compared with the environment. A warmer plant thermal strategy is given a head start under warming, the only case where herbivores can increase plant persistence under warming. Persistence time of the plant under warming is maximal at small or large thermal niche width. This study shows that considering trophic interactions is necessary and feasible for understanding how ecosystems respond to climate change.
Duration-dependent effects of the BDNF Val66Met polymorphism on anodal tDCS induced motor cortex plasticity in older adults: a group and individual perspective

The brain derived neurotrophic factor (BDNF) Val66Met polymorphism and stimulation duration are thought to play an important role in modulating motor cortex plasticity induced by non-invasive brain stimulation (NBS). In the present study we sought to determine whether these factors interact or exert independent effects in older adults. Fifty-four healthy older adults (mean age = 66.85 years) underwent two counterbalanced sessions of 1.5 mA anodal transcranial direct current stimulation (atDCS), applied over left M1 for either 10 or 20 min. Single pulse transcranial magnetic stimulation (TMS) was used to assess corticospinal excitability (CSE) before and every 5 min for 30 min following atDCS. On a group level, there was an interaction between stimulation duration and BDNF genotype, with Met carriers (n = 13) showing greater post-intervention potentiation of CSE compared to Val66Val homozygotes homozygotes (n = 37) following 20 min (p = 0.002) but not 10 min (p = 0.219) of stimulation. Moreover, Met carriers, but not Val/Val homozygotes, exhibited larger responses to TMS (p = 0.046) after 20 min atDCS, than following 10 min atDCS. On an individual level, two-step cluster analysis revealed a considerable degree of inter-individual variability, with under half of the total sample (42%) showing the expected potentiation of CSE in response to atDCS across both sessions. Intra-individual variability in response to different durations of atDCS was also apparent, with one-third of the total sample (34%) exhibiting LTP-like effects in one session but LTD-like effects in the other session. Both the inter-individual (p = 0.027) and intra-individual (p = 0.04) variability was associated with BDNF genotype. In older adults, the BDNF Val66Met polymorphism along with stimulation duration appears to play a role in modulating tDCS-induced motor cortex plasticity. The results may have implications for the design of NBS protocols for healthy and diseased aged populations.
Four Rice Genes Encoding NADP Malic Enzyme Exhibit Distinct Expression Profiles

In plants, the NADP malic enzymes (NADP-MEs) are encoded by small gene families. These NADP-ME gene families are relatively well described in C4 plants but not well studied in C3 plants. In this study, we investigated the NADP-ME gene family in a model C3 monocot plant (rice, Oryza sativa) based on its recently released genomic DNA sequence. We found that the rice NADP-ME family is composed of four members, one plastidic NADP-ME and three cytosolic versions. Although the rice NADP-ME genes identified share a high degree of similarity with one another, one cytosolic NADP-ME (OscytME3) contains several unique amino acid substitutions within highly conserved amino acid regions. Phylogenetic analysis showed that OscytME3 might be derived from a different evolutionary branch than the other three rice genes. Expression analysis of the four rice NADP-ME genes indicated that each had a different tissue-specific and developmental profile, although all four responded to stress stimuli.
SaberLDA: Sparsity-Aware Learning of Topic Models on GPUs

Latent Dirichlet Allocation (LDA) is a popular tool for analyzing discrete count data such as text and images, which are required to model datasets and a large number of topics, e.g., tens of thousands of topics for industry scale applications. Although distributed CPU systems have been used to address this problem, they are slow and resource inefficient. GPU-based systems have emerged as a promising alternative because of their high computational power and memory bandwidth. However, existing GPU-based LDA systems can only learn thousands of topics, because they use dense data structures, and have linear time complexity to the number of topics. In this article, we propose SaberLDA, a GPU-based LDA system that implements a sparsity-aware algorithm to achieve sublinear time complexity to learn a large number of topics. To address the challenges introduced by sparsity, we propose a novel data layout, a warp-based sampling kernel, an efficient sparse matrix counting method, and a fine-grained load balancing strategy. SaberLDA achieves linear speedup on 4 GPUs and is 6–10 times faster than existing GPU systems in thousands of topics. It can learn 40,000 topics from a dataset of billions of tokens in two hours, which was previously only achievable using clusters of tens of CPU servers.
Synthesis of lta type zeolites from georgian clinoptilolite

Generally, the microporous structure of synthetic zeolite is affected by the nature of used reactants and their pretreatments, as well as by composition of the reaction mixture. Our recent investigation of hydrothermal transformation of natural Georgian clinoptilolite demonstrated possibility of preparation of zeolites with high silicon content (mordenite-like materials) without organic template, directly from aged gels having suitable chemical composition and prepared by acid treatment of raw material. The aim of present work was preparation of zeolites with high aluminium content on the same basis without organic templates. The study tested possibility of synthesis of the LTA type zeolites in following steps: treatment of the natural clinoptilolite ((Na 3.3 K 1.15 Ca 0.75 Mg 0.25 [Me] 0.55 )(A l7.0 Si 29.3 O 72 )22.5H 2 O, where Me = Cu, Zn, Ba, etc.) in HCl water solution; gel preparation by suspension in NaOH solution; its hydrothermal crystallization to the sodalite structure (SOD) with Si/Al=1, and then re-crystallization of the sodalite into the NaA zeolite (LTA). Chemical elemental analyses confirm a good accordance with the UPAC SOD and LTA chemical formulas for prepared materials having nearly monocationic composition (Na – 78 % SOD and 89 % LTA). In XRD patterns there are no additional peaks from zeolitic or other impurities, prepared materials have high crystallinity, their FTIR spectra are typical for SOD and LTA structures, developed zeolitic crystal microporous structure is confirmed by comparatively high averaged value of water adsorption capacity (0.08 cm 3 /g for SOD, and of 0.24 cm 3 /g for LTA at p/p S = 0.4). SEM images show uniform LTA micrometric crystallites (average diameter 4 μm) with fairly narrow distribution of sizes produced by lasting (> 10 h) low temperature crystallization, as well as nanoscale spherical zeolites (0.2 μm) and fibrous aggregates (0.08 μm) produced at low temperature, that can be used for preparation of composite and hierarchical structures for various catalytic and adsorptive applications.
Institutional experience of paediatric high-grade central nervous system tumours: an analysis of 74 patients and review of the literature

Aim of the study Although the survival for children with certain central nervous system (CNS) tumour types has improved through current surgical and adjuvant treatment modalities, the prognosis of many high-grade tumours remains poor despite aggressive treatment. The aim of this study is to analyse patients with high-grade brain tumours in our institution to determine the histopathology, clinical characteristics, treatment modalities, and survival. Material and methods A total of 74 patients with a diagnosis of high-grade brain tumour were analysed. There were a total of 31 patients with embryonal tumours, 27 patients with high-grade glial tumours, 12 patients with brain stem gliomas and 4 patients with other high-grade brain tumours. Results There were 48 (65%) boys and 26 (35%) girls (ratio: 1.85) with a median age of 99.7 months (range = 2-204 months). The median follow-up period was 19 months (range = 1-204 months). Tumour recurrence was observed in 38 patients (51.4%). The overall survival rate and event-free survival rate of our patients were 27% and 19.5%, respectively. Conclusions Pediatric high-grade CNS tumours have a very aggressive behaviour and a significant number of children eventually succumb to disease despite multimodal treatment. There is a need of more effective therapeutic approaches for these tumours with poor prognosis. The future improvement in childhood high-grade brain tumour management depends on a better understanding of the molecular genetics and biology of brain tumours.
Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks

This paper discusses fast parallel algorithms for evaluating several centrality indices frequently used in complex network analysis. These algorithms have been optimized to exploit properties typically observed in real-world large scale networks, such as the low average distance, high local density, and heavy-tailed power law degree distributions. We test our implementations on real datasets such as the Web graph, protein-interaction networks, movie-actor and citation networks, and report impressive parallel performance for evaluation of the computationally intensive centrality metrics (betweenness and closeness centrality) on high-end shared memory symmetric multiprocessor and multithreaded architectures. To our knowledge, these are the first parallel implementations of these widely-used social network analysis metrics. We demonstrate that it is possible to rigorously analyze networks three orders of magnitude larger than instances that can be handled by existing network analysis (SNA) software packages. For instance, we compute the exact betweenness centrality value for each vertex in a large US patent citation network (3 million patents, 16 million citations) in 42 minutes on 16 processors, utilizing 20GB RAM of the IBM p5 570. SNA packages on the other hand cannot handle graphs with more than hundred thousand edges
Medication continuation and compliance: a comparison of patients treated with clozapine and haloperidol.

BACKGROUND This study compares medication continuation and regimen compliance with the atypical antipsychotic medication clozapine versus the conventional antipsychotic haloperidol. METHOD Data from a 15-site double-blind, randomized clinical trial (N = 423) were used to compare patients with DSM-III-R schizophrenia assigned to clozapine or haloperidol in terms of duration of participation while taking the randomly assigned study drug (continuation) and the proportion of prescribed pills that were taken (compliance). Multiple regression analysis was used to determine the relationship of baseline characteristics and measures of clinical change to continuation for the entire sample and for patients assigned to each medication. RESULTS Patients assigned to clozapine continued taking the study drug for a mean of 35.5 weeks as compared with only 27.2 among patients assigned to haloperidol (F = 4.45, df = 1,422; p = .0001). No differences were found between the groups in the proportion of prescribed pills that were returned at any timepoint. Among patients assigned to haloperidol, poorer continuation was associated with being older and greater continuation with receiving public support. Among patients on clozapine treatment, continuation was poorer among African American patients and greater among patients who showed reduced clinical symptoms and akathisia. Continuation with clozapine was greater even after adjusting for these factors. CONCLUSION Continuation with medication is greater with clozapine than haloperidol and is partly explained by greater symptom improvement and reduced side effects. No differences were found in regimen compliance.
The childbearing experience during a natural disaster.

OBJECTIVE To gain insight into the needs of pregnant women during Hurricane Katrina. DESIGN Grounded theory using semistructured interviews. SETTING Participants were recruited with flyers. Interviews were conducted in a location preferred by the participant. PATIENTS/PARTICIPANTS Eleven participants were interviewed. All were pregnant during the storm, lived in an area affected by Hurricane Katrina prior to the storm, were between the ages of 18 and 49, and spoke English. METHODS Qualitative interviews were performed and recorded, transcribed, and reviewed to organize the women's thoughts into categories. RESULTS The core category was disruption of life during pregnancy, and four additional subcategories were destruction of normalcy, uncertainty, loss of expectations, and coping with disruption. CONCLUSION The women relied on family and friends for support. Life in New Orleans for months after the storm was difficult due to unreliable information. Health care professionals that interact with pregnant women should move toward use of electronic medical records and educate women about coping with stress during pregnancy.
THE THREE TYPES OF ACUTE HAEMATOGENOUS OSTEOMYELITIS A Clinical and Vascular Study

1. The three age types of acute haematogenous osteomyelitis are conditioned in their respective clinical features by the differing nature of their vascular bone pattern. 2. In the infant the condition causes severe and often permanent epiphysial damage and joint infection, a large involucrum but only transient damage to the shaft and metaphysis. 3. In the child the condition is responsible for extensive cortical damage with involucrum formation, but, except for some stimulation of growth, permanent damage to the growth cartilage and to joints is exceptional. Chronicity of the disease is rare if treatment has been effective. 4. In the adult acute osteomyelitis of the long bones is rare. It causes very frequent joint infection; the cortex is absorbed instead of sequestrating. The whole of the bone is invaded and frequently leaves chronic infection in the bone marrow. 5. The vascular characteristics of the bones in each age group and their relation to the onset of infection are described. 6. Some general directives for management based on these facts are suggested.
The Emerging Role of microRNAs in Schizophrenia and Autism Spectrum Disorders

MicroRNAs (miRNAs) are small non-coding RNAs conserved throughout evolution whose perceived importance for brain development and maturation is increasingly being understood. Although a plethora of new discoveries have provided novel insights into miRNA-mediated molecular mechanisms that influence brain plasticity, their relevance for neuropsychiatric diseases with known deficits in synaptic plasticity, such as schizophrenia and autism, has not been adequately explored. In this review we discuss the intersection between current and old knowledge on the role of miRNAs in brain plasticity and function with a focus in the potential involvement of brain expressed miRNAs in the pathophysiology of neuropsychiatric disorders.