Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term storage of Campylobacter pylori

A reproducible method for long-term storage of Campylobacter pylori has been previously described. We cultured 10 strains of C. pylori in brucella broth that was supplemented with 10% fetal bovine serum. After incubation for 24 h, 10% glycerol and an additional 10% fetal bovine serum were added to the cultures, which when then held in storage at -70 degrees C. After 6 months, each of the strains remained viable. This technique, therefore, represents an excellent method for long-term storage of C. pylori isolates.
Self-Adjusting Heaps

In this paper we explore two themes in data structure design: amortized computational complexity and self adjustment. We are motivated by the following observations. In most applications of data structures, we wish to perform not just a single operation but a sequence of operations, possibly having correlated behavior. By averaging the running time per operation over a worst-case sequence of operations, we can sometimes obtain an overall time bound much smaller than the worst-case time per operation multiplied by the number of operations. We call this kind of averaging amortization.Standard kinds of data structures, such as the many varieties of balanced trees, are specifically designed so that the worst-case time per operation is small. Such efficiency is achieved by imposing an explicit structural constraint that must be maintained during updates, at a cost of both running time and storage space. However, if amortized running time is the complexity measure of interest, we can guarantee efficiency withou.
Evolved Cellular Mechanisms to Respond to Genotoxic Insults: Implications for Radiation-Induced Hematologic Malignancies

Human exposure to ionizing radiation is highly associated with adverse health effects, including reduced hematopoietic cell function and increased risk of carcinogenesis. The hematopoietic deficits manifest across blood cell types and persist for years after radiation exposure, suggesting a long-lived and multi-potent cellular reservoir for radiation-induced effects. As such, research has focused on identifying both the immediate and latent hematopoietic stem cell responses to radiation exposure. Radiation-associated effects on hematopoietic function and malignancy development have generally been attributed to the direct induction of mutations resulting from radiation-induced DNA damage. Other studies have illuminated the role of cellular programs that both limit and enhance radiation-induced tissue phenotypes and carcinogenesis. In this review, distinct but collaborative cellular responses to genotoxic insults are highlighted, with an emphasis on how these programmed responses impact hematopoietic cellular fitness and competition. These radiation-induced cellular programs include apoptosis, senescence and impaired self-renewal within the hematopoietic stem cell (HSC) pool. In the context of sporadic DNA damage to a cell, these cellular responses act in concert to restore tissue function and prevent selection for adaptive oncogenic mutations. But in the contexts of whole-tissue exposure or whole-body exposure to genotoxins, such as radiotherapy or chemotherapy, we propose that these programs can contribute to long-lasting tissue impairment and increased carcinogenesis.
Haplotype analysis of the H63D, IVS2+4t/c, and C282Y polymorphisms of the HFE gene reveals rare events of intragenic recombination

Objective: Two missense mutations of the HFE gene, one (C282Y) being a major gene for hereditary hemochromatosis and the other (H63D) playing a minor role in this disease, are carried by different haplotypes. Among other sequence variants of HFE, IVS2+4t/c polymorphism has been reported as a possible splicing mutation or risk modifier. Our aims were to identify sequence variants possibly associated with iron overload in our population, to study the intragenic haplotypes of the HFE gene, and to evaluate the role of IVS2+4t/c in hyperferritinemia.
Characterization of arsenic-induced cytotoxicity in liver with stress in erythrocytes and its reversibility with Pleurotus florida lectin

Arsenic is one of the most hazardous substances in the environment known to cause toxicity in multiple organs. Cell adhesion, morphological alterations, cell proliferation, terminal deoxyuridine triphosphate nick-end labeling (TUNEL) and caspase-3/CPP32 fluorometric protease assay were important biomarkers to assess apoptosis in cells. This study aimed to evaluate arsenic-induced apoptosis in the hepatocytes of rat and its protective efficacy with coadministration of ascorbic acid (AA) and Pleurotus florida lectin (PFL) individually. Results of the present study also showed that arsenic caused cytotoxicity by elevating morphological alterations, TUNEL-positive nuclei, caspase-3 activity and DNA damage and reducing cell adhesion and cell proliferation in a time-dependent manner. The apoptosis in hepatocytes was reverted to normal value after coadministration of mushroom lectin in arsenic-exposed rat. The study provided significant evidence that PFL has antiapoptotic property against arsenic-induced toxicity. The beneficial effect of PFL was proportional to its duration of exposure. Retard activities of superoxide dismutase and catalase, enhanced lipid peroxidation as well as protein carbonyl in erythrocytes caused by arsenic could also be maintained toward normalcy by supplementation of AA and PFL. These antioxidative effects were exhibited in a time-dependant manner. In rat, treatment with AA and PFL prevented alteration of plasma enzyme activities caused by arsenic. The results concluded that treatment with PFL has significant role in protecting animals from arsenic-induced erythrocytic damage. This finding might be of therapeutic benefit in people suffering from chronic exposure to arsenic from natural sources, a global problem especially relevant to millions of people on the Indian subcontinent.
Meaningful Life Experiences for Elderly Persons

50 elderly persons from two settings were assessed for objective purpose scores as well as the sources of meaningful experiences. The noninstitutionalized elders felt younger than their institutionalized peers, reported more meaningful life events, and had higher Purpose-In-Life scores, but did not differ from each other with respect to the events in life that were most meaningful. The categories that evolved were Love and Marriage, Births, Career/Education, Separations/Divorce, Accidents/ Illnesses/Deaths, Other/Miscellaneous Pursuits, and Major Purchases. No meaningful experiences (except Accidents/Illnesses/Deaths) were reported by either group after the age of 40 yr. The lack of meaningful experience in the second half of life is addressed with respect to consequences for both institutionalized and noninstitutionalized elderly.
Biology and Molecular Markers of Malignant Gonadal Germ Cell Tumors

5 Original Publications 8 Abbreviations 9 Introduction 10 Review of the Literature 11 1. Germ cells 11 1.1 Inner cell mass and embryonic stem cells 11 1.2 Factors essential for maintenance of pluripotency and self-renewal 11 1.3 Development and migration of germ cells 14 2. Gonadal development 16 2.1 Ovarian differ entiation 17 2.2 Testicular differentiation 18 3. GATA transcription factors in gonadal development and physiology 19 4. Estrogen receptors in gonadal development and physiology 21 5. Gonadal Germ Cell Tumors 23 5.1 Germ cell tumor development 24 5.2 Testicular dysgenesis syndrome 25 5.3 Clinicopathological characteristics of gonadal germ cell tumors 26 5.4 Serum and tissue tumor markers 26 5.5 Treatment and survival of gonadal germ cell tumor patients 28 Aims of the Study 29 Patients, Samples and Methods 29 1. Malignant ovarian germ cell tumor patients (I, II, III) 30 2. Tissue samples (I–V) 30 2.1. Human malignant ovarian germ cell tumor samples 30 2.2. Human fetal testicular, testicular CIS and tumor samples 30 3. Human germinoma-derived cell line (II, III, V) 31 4. Immunohistochemistry (I–IV) 31 5. Western blotting (V) 32 6. Semi-quantitative RT-PCR (III, V) 32 7. Stimulation of NCC-IT cells with estradiol (III) 33 8. Cell transfection and siRNA (V) 33 9. Flow cytometric analysis (III, V) 33 10. Statistical analysis (II, III) 34 Results and Discussion 34 1. Biology of gonadal germ cell tumors 34 1.1 Pluripotency and self-renewal in ovarian germ cell tumors (II, IV) 34 1.2 CIS and fetal origin of testicular germ cell tumors (IV) 35 1.3 Function of GATA-4 in fetal testicular and CIS cells (IV) 37 1.4 Estrogen signalling pathway in MOGCTs (III, V) 38 2. Diagnosis and prognosis of gonadal germ cell tumors 40 2.1 Diagnostic tools for gonadal germ cell tumors (I, II, IV) 40 2.2 Prognostic tools for malignant ovarian germ cell tumors (II) 42 3. Clinical significance of the studies 44 Conclusions and Future Perspectives 44 1.1 Conclusions 44 1.2 Future perspectives 45 Acknowledgments 46 References 47
Enhanced Classification via Clustering Techniques using Decision Tree for Feature Selection

Information overload has raggedly increased as a result of the advances in the aspect of storage capabilities and data collection in previous years. The growth seen in the number of observation has partly cause a collapse in analytical method but the increases in the number of variable associated with each observation has grossly collapse it. The number of variables that are measured on each observation.is referred to as the dimension of the data, and a major problem of dataset containing high dimensions is that, there exist only few “important” measured variables for understanding the fundamental occurrences of interest. Hence, dimension reduction of the original data prior to any modeling of the data is of great necessity today. In this paper, a précis of K-Means, Expectation Maximization and J48 decision tree classifier is presented with a framework on the performance measurement of base classifiers with and without feature reduction. A performance evaluation was carried out based on F-Measure, Precision, Recall, True Positive Rate, False Positive Rate, ROC Area and Time taken to build model. The experiment revealed that the reduced dataset yielded improved results than the full dataset after performing classification via clustering. General Terms Data mining, Intrusion detection, features reduction, and classification algorithms.
Enzymatic activities of Ura2 and Ura1 proteins (aspartate carbamoyltransferase and dihydro‐orotate dehydrogenase) are present in both isolated membranes and cytoplasm of Saccharomyces cerevisiae

Computational analysis predicted three potential hydrophobic transmembrane α‐helices within the Ura2 multidomain protein of Saccharomyces cerevisiae, the C‐terminal subdomain of which catalyses the second step of uridine‐monophosphate biosynthesis by its L‐aspartate carbamoyltransferase activity (EC 2.1.3.2). The fourth step of pyrimidine biosynthesis is catalysed by dihydro‐orotate dehydrogenase (Ura1 protein; EC 1.3.99.11), which was similarly characterized as a peripheral membrane protein. Ex situ, the activities of the investigated enzymes were associated both with isolated yeast membranes, fractionated by differential centrifugation to remove intact nuclei, and with soluble cytoplasmic proteins. Copyright © 2002 John Wiley & Sons, Ltd.
Formulas for Discrete Time LQR, LQG, LEQG and Minimax LQG Optimal Control Problems

Abstract The purpose of this paper is to provide a unified presentation of the formulas arising in the discrete-time finite-horizon linear Linear Quadratic Regulator problem, the Linear Quadratic Gaussian problem, the Linear Exponential of Quadratic Gaussian problem, and the minimax Linear Quadratic Gaussian problem. For these classes of optimal control problems, the paper presents formulas for optimal policies and optimal cost. This allows for a comparison between these different optimal control problems.
NAT 1 polymorphisms and cancer risk : a systematic review and meta-analysis

Purpose: To investigate the association between the N-acetyltransferase 1 (NAT1) slow and rapid acetylation phenotypes with cancer risk based on a meta-analysis. Methods: Previously published case-control studies were retrieved from PubMed, Embase, and Web of Science. Odds ratios (ORs) with 95% confidence intervals (CIs) were determined to assess the relationship between NAT1 polymorphisms and cancer risk. Results: A total of 73 studies (24874 cases and 30226 controls) were included in this meta-analysis. No significant association was identified between NAT1 polymorphisms (slow acetylation versus rapid acetylation genotypes: OR = 0.978, 95% CI = 0.927-1.030, P < 0.001 for heterogeneity, I2 = 45.5%) and cancer risk, whereas a significantly reduced risk of pancreatic cancer was identified in individuals with NAT1 slow acetylation genotype (OR = 0.856, 95% CI = 0.7330.999, P =0.509 for heterogeneity, I2 = 0). When the NAT1 slow acetylation genotype was analysed on the basis of stratified analyses of ethnicity, a significantly reduced risk of head and neck cancers was found among Asian (OR=0.281, 95% CI = 0.127-0.622). When the NAT1 slow acetylation genotype was analysed on the basis of stratified analyses of source of control, only significantly reduced risks of colorectal cancer (OR = 0.882, 95% CI = 0.7980.974, P = 0.212 for heterogeneity, I2 = 22.9) and pancreatic cancer (OR=0.856, 95% CI = 0.733-0.999, P = 0.509 for heterogeneity, I2 = 0) were found among hospital-based studies. Conclusions: No significant association between the NAT1 polymorphisms and the risk of cancer was found except for pancreatic cancer.
Decrease of the Number of Opioid Receptors and of the Responsiveness to Morphineduring Neuronal Differentiation Induced by 17β-Estradiol in Estrogen Receptor-Transfected Neuroblastoma Cells (SK-ER3)

Estrogens modulate the density of opioid receptors in selected brain areas; however, it is not clear whether they exert such an effect directly on the cells which express the opioid receptors. Therefore, we analyzed the binding of [3H]-diprenorphine in human neuroblastoma cells stably transfected with the estrogen receptor cDNA (SK-ER3 cell line). A 16-hour exposure of these cells with 1 nM 17β-estradiol induces a progressive morphological differentiation which appears clearly established 6 days after the suspension of the treatment. The binding of [3H]-diprenorphine was then measured immediately after the exposure to 17β-estradiol (16 h) as well as 6 days later. The results shows that the number of opioid receptors in SK-ER3 cells is unaffected at 16 h but appears significantly reduced at 6 days. This effect is blocked by the estrogen antagonist ICI-182780, and is coincident to a decrease of the inhibitory effect of morphine on cyclic AMP accumulation. Binding experiments performed using selective ligands suggest that the µ subclass of opioid receptors is down-regulated by estradiol in SK-ER3 cells.
Multivariate Classifi cation for Qualitative Analysis

Introduction . 83 Principles of classifi cation . 84 The classes . 84 Main categories of classifi cation methods . 85 Validation and variable selection procedures . 87 Evaluation of classifi cation performances . 88 Classifi cation methods . 94 Nearest mean classifi er and K-nearest neighbors . 94 Discriminant analysis . 95 Partial least squares-discriminant analysis (PLS-DA) . 97 Soft independent modeling of class analogy (SIMCA) . 97 Artifi cial neural networks . 98 Support vector machines . 100 Classifi cation and regression trees . 100 New classifi ers . 102 Conclusions . 102 Nomenclature . 102
FR4 Laser Scanner With Dynamic Focus

An electromagnetically actuated optical scanner made using standard printed circuit board technology with integrated dynamic focusing feature is presented. Dynamic focus is achieved with an independently controlled plunger machined on the flame retardant-4 (FR4) platform. Integration of a laser diode and lens, torsional scanner, and the plunger for dynamic focus adjustment on FR4 platform greatly improves the form factor of the device for imaging applications. A peak-to-peak mechanical scan angle of 50deg is achieved. The dynamic focus control allows for shifting the beam waist location from 80 mm up to 650 mm.
Enabling Applications for RDMA : Distributed Compilation Revisited

Remote Direct Memory Access (RDMA) traditionally aimed at improving high-performance computing applications and storage-area networks because CPU cycles and memory bus load can be reduced significantly by applying the zero-copy and direct data-placement techniques offered by RDMA. With the advent of iWARP, the RDMA technology is now available to the ubiquitous TCP/IP infrastructure and, thus, becomes interesting and relevant for legacy applications. In this paper, we present the conversion of the distributed C/C++ compiler distcc from sockets to the RDMA interface, and investigate the implications of using asynchronous and one-sided versus two-sided communication, RDMA-style buffer management, and notification mechanisms. We have designed a distcc extension that takes full advantage of asynchronous one-sided RDMA operations. By introducing a connection manager, we improve the communication efficiency and increase the scalability of distcc. Our tests with the RDMA-enabled distcc use a software-only iWARP implementation called SoftRDMA, which offers RDMA communication using conventional Ethernet adapters. The ideas and approach presented in this paper can be generalized to a wide range of applications.
Doping of ceria surfaces with lanthanum: a DFT + U study

In this paper we use density functional theory corrected for on-site Coulomb interactions (DFT + U) to study the defects formed in the ceria (111) and (110) surfaces doped with La. To describe consistently the defect formed with substitutional La3 + doping at a Ce4 + site we use DFT and DFT + U, with U = 5 eV for Ce 4f states and U = 7 eV for O 2p states. When La3 + substitutes on a Ce3 + site, an defect state, with an oxygen hole, is formed at both surfaces, but only with the DFT + U approach. The formation energy of an oxygen vacancy in a structure with two La dopants in their most stable distribution is reduced over the undoped surfaces but remains positive. Formation of an oxygen vacancy results in the appearance of a reduced Ce3 + cation and a compensated oxygen hole, instead of compensation of both oxygen holes, which is typical of metal oxides doped with lower valence cations. We tentatively suggest that the key role in the formation of this unusual defect is played by cerium and arises from the ease with which cerium can be reduced, as compared to other metal oxides. Experimental confirmation of these results is suggested.
Disease prevalence in women attending the STD clinic in Mumbai (formerly Bombay), India

Our objectives were to determine the prevalence of Neisseria gonorrhoeae and its association with other STD causing organisms. Three hundred and thirty-six consecutive women (female sex workers (FSWs) and married contacts), attending a sexually transmitted disease (STD) clinic in Mumbai, were screened for N. gonorrhoeae, Chlamydia trachomatis and Trichomonas vaginalis. Per speculum examination was performed and clinical signs were recorded. Symptoms perceived by the women were also recorded. The mean age for married contacts, FSWs and gonorrhoea-positive women was 27.9, 29.7 and 27.5, respectively. 9.7% of the women were positive for N. gonorrhoeae, 23.2% were chlamydia-positive and 5.9% had trichomoniasis. N. gonorrhoeae was isolated more frequently from FSWs as compared to the married contacts. The prevalence of HIV was significantly higher among women with multiple sex partners (FSWs) (P < 0.001). Gonococcal infection is significantly associated with the presence of HIV. A significant association between sexual habits and prevalence of gonorrhoea, trichomoniasis and HIV was observed. The prevalence of gonorrhoea over 1988 to 1996 remained approximately the same.
Number Processing and Calculation – Normative Data from Healthy Adults

Despite the high incidence of numerical deficits in neurological patients, little attention has been paid to the development of diagnostic tools. In fact, most of the published reports on acquired numerical disorders, whether single case or group studies, do not refer to standardised measures of performance providing little, if any, control data specifically collected for the examination. In this study we present data of 282 healthy controls of different age groups and educational levels in a new battery of Number Processing and Calculation (NPC). The NPC battery includes a total of 35 tasks, assessing different counting abilities, various aspects of number comprehension (such as parity and magnitude judgements), numerical transcoding, calculation, arithmetic reasoning and conceptual knowledge. Special attention is paid to the assessment of different calculation abilities, including simple fact retrieval, rule based processing, mental calculation and written calculation in all four operations. Moreover, text problem solving is assessed as well as the understanding of arithmetic principles. Thus, the NPC battery differs from the EC 301 battery proposed by Deloche et al., 1994 (Dellatolas, Deloche, Basso, & Claros-Salinas, 2001) and allows a more fine grained diagnosis which is relevant for planning targeted interventions. The battery is easy to administer and does not require special materials or equipment.
Health Care Expenditures, Hospitalizations, and Productivity Associated With Cancer in US Employer Settings

Objective:To assess outcomes of health care expenditures, hospitalizations, and productivity among employed persons with cancer in the United States from 2004 to 2008. Methods:Agency for Healthcare Research and Quality's Medical Expenditure Panel Survey data were used in this retrospective cross-sectional study of employed adults aged 18 years or older with any diagnosis of malignant neoplasms. Multivariate regression analyses assessed the study's outcomes according to prominent cancer types and other factors. Results:Overall, 3.31 million employed persons had cancer annually, incurring productivity losses of approximately 33.4 million disability days. Women's cancers and melanoma were associated with higher burdens of illness relative to other forms. Conclusions:This nationally representative investigation found that disability days in employed persons with cancer equates to 20% of health care expenditures. Resources present within small organizational settings may be especially important to consider when implementing programs to prevent and cure cancer.
A voice activity detection system based on FPGA

In this paper, we present a FPGA-based voice activity detection system. DoV (Degree of Voicing) and QSNR (Quantile Signal-to-Noise Ratio) are used as parameters of the VAD algorithm of the proposed system. All VAD system functions are implemented using a dedicated parallel architecture, including signal capturing, DoV processing module and QSNR processing module. The system uses several DPRAMs (Dual Port RAMs) inside the FPGA as parallel buffers in which speech data and the intermediate result are stored, to speed up processing. The functional modules process data in parallel using those buffers. The sampling rate of the proposed system is 16 KHz, and the resolution of each sample is 16 bits. The system can generate the VAD result every 15 ms. The proposed system can be used in speech processing such as speech coding and speech recognition.