Miracle-dz/UniFAR-FTUs huggingface dataset:
Bcl-2 protein expression and p53 gene mutation in chronic lymphocytic leukemia: correlation with in vitro sensitivity to chlorambucil and purine analogs.

BACKGROUND AND OBJECTIVE Bcl-2 oncogenic protein expression plays a major role in blocking the apoptotic mechanism. p53 gene mutations have also been suggested to account for the chlorambucil resistance in CLL. Thus we studied the relationship between bcl-2 protein expression, p53 gene mutations and in vitro drug sensitivity in CLL. METHODS Fifty-three samples from untreated CLL patients in early disease stages were tested in vitro for chemosensitivity to chlorambucil (CLB), fludarabine (FAMP) and 2-chlorodeoxyadenosine (2-CDA) using the MTT assay. Intracellular bcl-2 protein expression was evaluated by flow cytometry analysis. p53 gene mutations were detected by using polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) analysis. RESULTS The median LD50 values were 1.55 microM, 4.41 microM and 58.2 microM for 2-CDA, FAMP and CLB, respectively. About 23%, 41% and 11% of samples were defined as being sensitive to FAMP, 2-CDA and CLB, respectively, when samples were clustered for LD50 threshold values corresponding to the plasmatic levels of the drug. No statistically significant difference in bcl-2 protein expression was noted between sensitive and resistant samples for each drug. A p53 gene mutation was detected in 4 of the 30 cases studies and all of them were among samples resistant to CLB. INTERPRETATION AND CONCLUSIONS Bcl-2 expression is not an indicator of in vitro response to drugs in CLL; similarly, although the four cases showing a p53 gene mutation were associated with CLB resistance, drug resistant samples were also observed in the group of patients showing wild type p53, suggesting multiple mechanisms of drug resistance in CLL.
Review: Plasma renin and the incidence of cardiovascular disease

Whether renin is involved in the onset of coronary heart disease (CHD) remains unclear. A case-control study in 1972, suggesting a causal association between renin and CHD, has now been followed by three prospective studies. One was based on 1,717 hypertensive subjects in a Work-Site Program in New York. The main results showed an increased risk of CHD the higher the renin level. A second study in occupational groups in North West London, UK, recruited 803 white men not selected according to blood pressure, and found no association. A possible exception was in the minority of those with similar blood pressure levels to participants in the Work-Site Program, in whom the incidence of CHD was higher according to the renin level, but not significantly so. The third study was in Framingham Offspring and included 3,532 participants also not selected according to blood pressure. As in the UK study, there was no clear association between renin and risk of CHD in all participants, or in this study in those with raised blood pressure. The authors considered their results consistent with those of the UK study in finding “no association of renin with overall risk of CHD”. Besides the three epidemiological studies, dealing explicitly with renin, other studies in which it has been one of several variables considered have also not found convincing evidence of its involvement in CHD. There is, therefore, little support for the hypothesis that high renin levels increase the risk of CHD, with the possible but uncertain exception of those with raised blood pressure.
Family Structure and Adolescent Substance Use: An International Perspective

ABSTRACT Background: Numerous studies indicate that family structure is a key correlate of adolescent substance use. Yet there are some important limitations to this research. Studies have been conducted mainly in the United States, with relatively few studies that have compared family structure and youth substance use across nations. There is also a lack of recognition of the complexity of family types prevalent in contemporary global society. Moreover, there remains a need to consider personal, interpersonal, and macro-level characteristics that may help account for the association between family structure and youth substance use. Objective: This study uses data from 37 countries to examine several models that purport to explain the association between family structure and substance use. Methods: The data are from the 2005–2006 WHO-sponsored Health Behaviour in School-Aged Children (HBSC) (n = 193,202). Multilevel models, including linear, probit, and structural equation models (SEMs), were used to test several hypotheses. Results: The results suggest that time spent with friends largely accounted for the association between specific types of family structures and frequency of alcohol use and getting drunk, but that cannabis use was negatively associated with living with both biological parents irrespective of other factors.
Two Phase Non-Rigid Multi-Modal Image Registration Using Weber Local Descriptor-Based Similarity Metrics and Normalized Mutual Information

Non-rigid multi-modal image registration plays an important role in medical image processing and analysis. Existing image registration methods based on similarity metrics such as mutual information (MI) and sum of squared differences (SSD) cannot achieve either high registration accuracy or high registration efficiency. To address this problem, we propose a novel two phase non-rigid multi-modal image registration method by combining Weber local descriptor (WLD) based similarity metrics with the normalized mutual information (NMI) using the diffeomorphic free-form deformation (FFD) model. The first phase aims at recovering the large deformation component using the WLD based non-local SSD (wldNSSD) or weighted structural similarity (wldWSSIM). Based on the output of the former phase, the second phase is focused on getting accurate transformation parameters related to the small deformation using the NMI. Extensive experiments on T1, T2 and PD weighted MR images demonstrate that the proposed wldNSSD-NMI or wldWSSIM-NMI method outperforms the registration methods based on the NMI, the conditional mutual information (CMI), the SSD on entropy images (ESSD) and the ESSD-NMI in terms of registration accuracy and computation efficiency.
Emergence and Plasmid Analysis of Klebsiella pneumoniae KP01 Carrying blaGES-5 from Guangzhou, China

ABSTRACT Klebsiella pneumoniae strain KP01 carrying blaGES-5 was identified from a patient in Guangzhou, China. High-throughput sequencing assigned blaGES-5 to a 28.5-kb nonconjugative plasmid, pGES-GZ. A 13-kb plasmid backbone sequence on pGES-GZ was found to share high sequence identities with plasmids from Gram-negative nonfermenters. A novel class 1 integron carrying a gene cassette array of orf28-orf28-blaGES-5 was identified on pGES-GZ, within which orf28 encoded a hypothetical protein possibly correlated to fosfomycin resistance.
Image Pattern Similarity Index and Its Application to Task-Specific Transfer Learning

SUMMARY A quantized index for evaluating the pattern similarity of two di ﬀ erent datasets is designed by calculating the number of correlated dictionary atoms. Guided by this theory, task-speciﬁc biometric recognition model transferred from state-of-the-art DNN models is realized for both face and vein recognition.
Loss of neurogenesis in Hydra leads to compensatory regulation of neurogenic and neurotransmission genes in epithelial cells

Hydra continuously differentiates a sophisticated nervous system made of mechanosensory cells (nematocytes) and sensory–motor and ganglionic neurons from interstitial stem cells. However, this dynamic adult neurogenesis is dispensable for morphogenesis. Indeed animals depleted of their interstitial stem cells and interstitial progenitors lose their active behaviours but maintain their developmental fitness, and regenerate and bud when force-fed. To characterize the impact of the loss of neurogenesis in Hydra, we first performed transcriptomic profiling at five positions along the body axis. We found neurogenic genes predominantly expressed along the central body column, which contains stem cells and progenitors, and neurotransmission genes predominantly expressed at the extremities, where the nervous system is dense. Next, we performed transcriptomics on animals depleted of their interstitial cells by hydroxyurea, colchicine or heat-shock treatment. By crossing these results with cell-type-specific transcriptomics, we identified epithelial genes up-regulated upon loss of neurogenesis: transcription factors (Dlx, Dlx1, DMBX1/Manacle, Ets1, Gli3, KLF11, LMX1A, ZNF436, Shox1), epitheliopeptides (Arminins, PW peptide), neurosignalling components (CAMK1D, DDCl2, Inx1), ligand-ion channel receptors (CHRNA1, NaC7), G-Protein Coupled Receptors and FMRFRL. Hence epitheliomuscular cells seemingly enhance their sensing ability when neurogenesis is compromised. This unsuspected plasticity might reflect the extended multifunctionality of epithelial-like cells in early eumetazoan evolution.
Object-oriented implementation of CA/LGCA modelling applied to the spread of epidemics

The authors have applied the CA/LGCA ("cellular automata"/"lattice gas cellular automata") methodology to develop and analyse models of spread of epidemics of infectious diseases. Object-oriented analysis and design of the computer models has been performed using the Unified Modelling Language (UML). All required algorithms and data structures have been coded in C++.
A privacy preserving web recommender system

In this paper we propose a recommender system that helps users to navigate though the Web by providing dynamically generated links to pages that have not yet been visited and are of potential interest. To this end, traditional recommender systems use Web Usage Mining (WUM) techniques in order to automatically extract knowledge from Web usage data. Thanks to WUM techniques we are able to classify users and adaptively provide useful recommendations. The drawback of a user classification approach is that it makes the system prone to privacy breaches.Our contribution here is πSUGGEST, a privacy enhanced recommender system that allows for creating serendipity recommendations without breaching users privacy. We will show that our system does not provide malicious users with any mean to track or detect users activity or preferences.
INFLUENCE OF NONPRESTRESSED REINFORCEMENT ON THE STRENGTH OF UNBONDED PARTIALLY PRESTRESSED CONCRETE MEMBERS

An ivestigation of the stress in the prestresing tendons at ultimate in unbonded partially prestressed concrete beams is described with particular emphasis on the effects of nonprestressed bonded reinforcement. Load tests on 6 rectangular section unbonded beams are reported. It is shown that the presence of bonded nonprestressed reinforcement has a marked influence on the flexural behavior of unbonded beams and the related increase of stress in the prestressed steel at ultimate. Test results are compared with predictions from 2 relevant design codes, and some limitations in the application of these codes to unbonded partially prestressed concrete construction are identified.
Face recognition based on improved projection dictionary pair learning algorithm

This paper presents an improved projection dictionary pair learning (DPL) algorithm, namely the C-DPL algorithm. The algorithm combines the fastness of DPL algorithm dictionary training and the discriminant strongness of collaborative representation classification (CRC) algorithm. Compared with DPL algorithm, C-DPL algorithm has achieved better recognition in face recognition. Experiments on the ORL datasets showed that the recognition rate of C-DPL is at least 0.7% higher than that of DPL at different training ratios; on the Yale datasets, the recognition rate of C-DPL is at least 1.01% higher than that of DPL at different training ratios; the validity and superiority of C-DPL algorithm are verified. On the Extended YaleB datasets, the recognition rate of C-DPL is 0.9% higher than that of DPL, indicating that C-DPL has good robustness to light change.
Feature Selection for Wireless Sensor Networks

– In a wireless sensor network, appropriate use of resources can be achieved by choosing the most relevant sensors that are important to the current context. By applying feature selection to determine the optimal sensor locations, the number of sensors can be reduced and great savings (in term of power, hardware, and transmission channel) can be achieved without degrading the decision process. This paper presents the use of BFFS (Bayesian Approach for Feature Selection), a filter based feature selection method, for optimum sensor location selection. The virtue of the method is that the selection of features is purely based on the data distribution and thus is unbiased towards a specific model. The strength of this framework is demonstrated by experiments on activity recognition with the use of a Self-Organising-Map.
Low Molecular Weight SBR Effect on Properties of Silica-Filled SBR Compounds

Influence of low molecular weight styrene-butadiene rubber (liquid SBR) on properties of a silica-filled styrene-butadiene rubber (SBR) compounds was studied. Viscosity of the silica-filled SBR compound decreased by adding the liquid SBR. The crosslink density decreased and the cure rate became slower as the liquid SBR content increased. The modulus and tensile strength decreased while the elongation at break became longer by increasing the liquid SBR content. The abrasion losses were nearly the same irrespective of the liquid SBR content. This might be due to the improvement of silica dispersion by adding the liquid SBR. Considering the experimental results, it was believed that addition of small amount of the liquid SBR (less than 5 phr) was desirable to improve properties of silica-filled SBR compounds.
Cognitive impairment as marker of diffuse brain abnormalities in early relapsing remitting multiple sclerosis

Objectives: To establish the frequency of cognitive impairment in a population based sample of patients with recently diagnosed relapsing-remitting multiple sclerosis (RRMS), and to determine the relation between cognitive abnormalities and the extent of macroscopic and microscopic tissue damage revealed by magnetic resonance imaging (MRI) and magnetisation transfer (MT) imaging. Methods: 58 patients with RRMS consecutively diagnosed in the previous six months in Aquitaine and 70 healthy controls underwent a battery of neuropsychological tests. Lesion load and atrophy indices (brain parenchymal fraction and ventricular fraction) were measured on brain MRI. MT ratio (MTR) histograms were obtained from lesions, normal appearing white matter (NAWM), and normal appearing grey matter (NAGM). Gadolinium enhanced lesions were counted. Results: 44 RRMS patients could be individually matched with healthy controls for age, sex, and education. Patients performed worse in tests of verbal and spatial memory, attention, information processing speed, inhibition, and conceptualisation. Measures of attention and information processing speed were correlated with lesion load, mean NAWM MTR, and the peak location of the NAGM MTR histogram in the patients. Multivariate regression analysis showed that lesion load and mean NAWM MTR were among the MR indices that were most significantly associated with impairment of attention and information processing speed in these early RRMS cases. Conclusions: Cognitive impairment appears to be common in the early stages of RRMS, mainly affecting attention, information processing speed, memory, inhibition, and conceptualisation. The severity of these deficits reflects the extent of the lesions and the severity of tissue disorganisation outside lesions.
A New Bayesian Method to Identify the Environmental Factors That Influence Recent Migration

We present a new multilocus genotype method that makes inferences about recent immigration rates and identifies the environmental factors that are more likely to explain observed gene flow patterns. It also estimates population-specific inbreeding coefficients, allele frequencies, and local population FST's and performs individual assignments. We generate synthetic data sets to determine the region of the parameter space where our method is and is not able to provide accurate estimates. Our simulation study indicates that reliable results can be obtained when the global level of genetic differentiation (FST) is >1%, the number of loci is only 10, and sample sizes are of the order of 50 individuals per population. We illustrate our method by applying it to Pakistani human data, considering altitude and geographic distance as explanatory factors. Our results suggest that altitude explains better the genetic data than geographic distance. Additionally, they show that southern low-altitude populations have higher migration rates than northern high-altitude ones.
Merocel versus Nasopore for Nasal Packing: A Meta-Analysis of Randomized Controlled Trials

Objective To compare the clinical outcomes, including efficacy and complications, of Merocel versus Nasopore as a nasal packing material after nasal surgery. Methods Relevant randomized controlled trials were identified from electronic databases (The Cochrane Library, PubMed, EMBASE, China National Knowledge Infrastructure and Chinese Biomedical Database). Conference proceedings and references from identified trials and review articles were also searched. Outcome measures were pain during nasal packing, pain and bleeding upon packing removal, pressure sensation, nasal blockage, formation of synechiae, mucosal healing, and patients' general satisfaction. Results Seven randomized controlled trials met criteria for analysis. Compared with Merocel, Nasopore significantly reduced patients' subjective symptoms including in situ pain (pain experienced while packing is in place), nasal pressure, pain and bleeding during packing removal, and increased patients' general satisfaction with nasal packing. There were no significant differences in nasal obstruction, adhesion and mucosal healing between the Merocel and Nasopore groups. Conclusions Preliminary evidence suggests that Nasopore may be superior to Merocel as a nasal packing material with regard to in situ pain, pain and bleeding upon removal, pressure, and general satisfaction and does not differ from Merocel in terms of nasal obstruction, tissue adhesion, and long-term mucosal healing.
Generation of mice with a conditional null fraser syndrome 1 (Fras1) allele

Summary: Fraser syndrome (FS) is an autosomal recessive disease characterized by skin lesions and kidney and upper airway malformations. Fraser syndrome 1 (FRAS1) is an extracellular matrix protein, and FRAS1 homozygous mutations occur in some FS individuals. FRAS1is expressed at the epithelial‐mesenchymal interface in embryonic skin and kidney. blebbed mice have a null Fras1 mutation and phenocopy human FS. Like humans with FS, they exhibit a high fetal and neonatal mortality, precluding studies of FRAS1 functions in later life. We generated conditional Fras1 null allele mice. Cre‐mediated generalized deletion of this allele generated embryonic skin blisters and renal agenesis characteristic of blebbed mice and human FS. Targeted deletion of Fras1 in kidney podocytes circumvented skin blistering, renal agenesis, and early death. FRAS1 expression was downregulated in maturing glomeruli which then became sclerotic. The data are consistent with the hypothesis that locally produced FRAS1 has roles in glomerular maturation and integrity. This conditional allele will facilitate study of possible role for FRAS1 in other tissues such as the skin. genesis 50:892–898, 2012. © 2012 Wiley Periodicals, Inc.
The plant cell wall in the feeding sites of cyst nematodes

Plant parasitic cyst nematodes (genera Heterodera and Globodera) are serious pests for many crops. They enter the host roots as migratory second stage juveniles (J2) and migrate intracellularly toward the vascular cylinder using their stylet and a set of cell wall degrading enzymes produced in the pharyngeal glands. They select an initial syncytial cell (ISC) within the vascular cylinder or inner cortex layers to induce the formation of a multicellular feeding site called a syncytium, which is the only source of nutrients for the parasite during its entire life. A syncytium can consist of more than hundred cells whose protoplasts are fused together through local cell wall dissolutions. While the nematode produces a cocktail of cell wall degrading and modifying enzymes during migration through the root, the cell wall degradations occurring during syncytium development are due to the plants own cell wall modifying and degrading proteins. The outer syncytial cell wall thickens to withstand the increasing osmotic pressure inside the syncytium. Furthermore, pronounced cell wall ingrowths can be formed on the outer syncytial wall at the interface with xylem vessels. They increase the surface of the symplast-apoplast interface, thus enhancing nutrient uptake into the syncytium. Processes of cell wall degradation, synthesis and modification in the syncytium are facilitated by a variety of plant proteins and enzymes including expansins, glucanases, pectate lyases and cellulose synthases, which are produced inside the syncytium or in cells surrounding the syncytium.
Figure Metadata Extraction from Digital Documents

Academic papers contain multiple figures (information graphics) representing important findings and experimental results. Automatic data extraction from such figures and classification of information graphics is not straightforward and a well studied problem in document analysis cite{4275059}. Also, very few digital library search engines index figures and/or associated metadata (figure caption) from PDF documents. We describe the very first step in indexing, classification and data extraction from figures in PDF documents - accurate automatic extraction of figures and associated metadata, a nontrivial task. Document layout, font information, lexical and linguistic features for figure caption extraction from PDF documents is considered for both rule based and machine learning based approaches. We also describe a digital library search engine that indexes figure captions and mentions from 150K documents, extracted by our custom built extractor.