Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithms and statistical methods for exact motif discovery

The motif discovery problem consists of uncovering exceptional patterns (called motifs) in sets of sequences. It arises in molecular biology when searching for yet unknown functional sites in DNA sequences. In this thesis, we develop a motif discovery algorithm that (1) is exact, that means it returns a motif with optimal score, (2) can use the statistical significance with respect to complex background models as a scoring function, (3) takes into account the effects of self-overlaps of motif instances, and (4) is efficient enough to be useful in large-scale applications. To this end, several algorithms and statistical methods are developed. First, the concepts of deterministic arithmetic automata (DAAs) and probabilistic arithmetic automata (PAAs) are introduced. We prove that they allow calculating the distributions of values resulting from deterministic computations on random texts generated by arbitrary finite-memory text models. This technique is applied three times: first, to compute the distribution of the number of occurrences of a pattern in a random string, second, to compute the distribution of the number of character accesses made by windowbased pattern matching algorithms, and, third, to compute the distribution of clump sizes, where a clump is a maximal set of overlapping motif occurrences. All of these applications are interesting theoretical topics in themselves and, in all three cases, our results go beyond those known previously. In order to compute the distribution of the number of occurrences of a motif in a random text, a deterministic finite automaton (DFA) accepting the motif’s instances is needed to subsequently construct a PAA. We therefore address the problem of efficiently constructing minimal DFAs for motif types common in computational biology. We introduce simple non-deterministic finite automata (NFAs) and prove that these NFAs are transformed into minimal DFAs by the classical subset construction. We show that they can be built from (sets of) generalized strings and from consensus strings with a Hamming neighborhood, allowing the direct construction of minimal DFAs for these pattern types. As a contribution to the field of motif statistics, we derive a formula for the expected clump size of motifs. It is remarkably simple and does not involve laborious operations like matrix inversions. This formula plays an important role in developing bounds for the expected clump size of partially known motifs. Such bounds are needed to obtain bounds for the p-value of a partially known motif. Using these, we are finally able to devise a branch-and-bound algorithm for motif discovery that extracts provably optimal motifs with respect to their p-values in compound Poisson approximation. Markovian text models of arbitrary order can be used as a background model (or null model). The algorithm is further generalized to jointly handle a motif and its reverse complement. An Open Source implementation is publicly available as part of the MoSDi software
Why are Exchange Rates so Smooth? A Household Finance Explanation

Empirical work on asset prices suggests that pricing kernels have to be almost perfectly correlated across countries. If they are not, real exchange rates are too smooth to be consistent with high Sharpe ratios in asset markets. However, the cross-country correlation of macro fundamentals is far from perfect. We reconcile these empirical facts in a two-country stochastic growth model with segmented markets. A large fraction of households either do not participate in the equity market or hold few equities, and these households drive down the cross-country correlation in aggregate consumption. Only a small fraction of households participate in international risk sharing by frequently trading domestic and foreign equities. These active traders are the marginal investors, who impute the almost perfect correlation in pricing kernels. In our calibrated economy, we show that this mechanism can quantitatively account for the excess smoothness of exchange rates in the presence of highly volatile stochastic discount factors.
The production of tissue inhibitors of metalloproteinases (TIMPs) in megakaryopoiesis: possible role of platelet‐ and megakaryocyte‐derived TIMPs in bone marrow fibrosis

We quantified tissue inhibitor of metalloproteinase (TIMP)‐1 and TIMP‐2 in serum and plasma in normal control subjects and patients with a low or high platelet count, using one‐step sandwich enzyme immunoassays. The serum levels of TIMP‐1 and TIMP‐2 were 101.1 ± 13.3 ng/ml, and 82.7 ± 26.3 ng/ml, respectively, in normal subjects. In patients with an elevated platelet count, such as in essential thrombocytosis, polycythaemia vera, and myelofibrosis, serum levels of TIMP‐1 and TIMP‐2 were 351.6 ± 200.9 ng/ml and 148.9 ± 84.0 ng/ml, respectively. Serum levels of TIMP‐1 and TIMP‐2 in patients with a low platelet count, such as in aplastic anaemia and idiopathic thrombocytopenic purpura, were 57.2 ± 25.8 ng/ml and 19.7 ± 7.68 ng/ml, respectively. The serum level of TIMP‐1 was significantly correlated with the platelet count in all subjects. The correlation between the serum level of TIMP‐2 and the platelet count was not as strong. The level of TIMP‐1 in platelet‐depleted plasma was not correlated with the platelet count.
Sequence-function relationships within the expanding family of prolactin, growth hormone, placental lactogen, and related proteins in mammals.

I. Introduction PRL PL, and GH are homologous proteins that are thought to have arisen from a common ancestral gene by two successive tandem duplications (Refs. 1–5; for review, see Ref. 6). PRL and GH are mainly secreted by the anterior pituitary of all vertebrates. The divergence of the PRL and GH lineage from the common ancestral gene has been located some 400 million years ago, which is in good agreement with the presence of distinct PRL and GH in fish (2, 3, 6, 7). PL is uniquely observed in mammals and is secreted in the placenta by syncytiotrophoblastic cells (for reviews, see Refs. 8–10). Initially, PLs were proposed to have evolved from the common PRL/GH precursor gene (1). Further cloning and analysis of PRL, GH, and PL genes from different species (chromosome carrier, gene size, splicing sites, sequence identity; see Refs. 6, 7, 11, and 12) have led to a reconsideration of this hypothesis, and it is now assumed that primate PLs evolved from the GH lineage while nonprimate PLs arose from the PRL.
Prenatal diagnosis of structural cardiac defects

Prenatal diagnosis of congenital heart defects has been possible now for over 25 years. This ability has extended from a few specialists to being within the scope of any sonographer engaged in routine obstetric evaluation of the low‐risk patient. However, the detection rate is widely varied. The recognition of major structural heart disease in fetal life has important implications for the child's future, so further efforts should be made to improve the success in diagnosis. © 2007 Wiley‐Liss, Inc.
Aggregate Installation Planning of Offshore Wind Farms

This paper addresses the problem of aggregated installation planning of offshore wind farms. The transport and installation of wind turbines at the wind farm is a complex planning problem, which has to take different operational constraints into account due to weather conditions and vessel availability. On a tactical level, the vessel allocation has to be planned months and years before the project will start. To this end, a mathematical model is proposed in this paper to deal with the aggregated installation planning problem. The objective is to minimize the total installation costs, which include the chartering costs as well as weather operation constraints for different vessel types. Key-Words: -Offshore wind farm, Aggregate planning, MixedInteger Linear Programming (MILP).
Nitric oxide‐mediated inhibition of NFκB regulates hyperthermia‐induced apoptosis

Ascertaining the upstream regulatory mechanisms of hyperthermia‐induced apoptosis is important to understand the role of hyperthermia in combined modality cancer therapy. Accordingly, we investigated whether (i) hyperthermia‐induced apoptosis is mediated through the nitric oxide (NO) signaling pathway and (ii) inhibition of post‐translational modification of IκBα and down regulation of NFκB‐DNA binding activity is an intermediate step in NO‐dependent apoptosis in MCF‐7 breast cancer cells. For hyperthermia treatment, the cells were exposed to 43°C. Intracellular NO levels measured by the fluorescent intensity of DAF‐2A and iNOS expression by immunobloting revealed an increased level of iNOS dependent NO production after 43°C. Apoptosis measured by Annexin V expression and cell survival by clonogenic assay showed a 20% increase in apoptosis after 43°C treatments. EMSA analysis showed a dose‐dependent inhibition of NFκB‐DNA binding activity. The hyperthermia‐mediated inhibition of NFκB was persistent even after 48 h. Inhibition of NO by L‐NAME rescued the NFκB‐DNA binding activity and inhibits heat‐induced apoptosis. Similarly, over‐expression of NFκB by transient transfection inhibits heat‐induced apoptosis. These results demonstrate that apoptosis upon hyperthermia exposure of MCF‐7 cells is regulated by NO‐mediated suppression of NFκB. J. Cell. Biochem. 106: 999–1009, 2009. © 2009 Wiley‐Liss, Inc.
Effects of methamphetamine, dopamine and noradrenaline administered into the nucleus accumbens of rats discriminating subcutaneous methamphetamine.

Since the nucleus accumbens has been hypothesized to centrally mediate the discriminative effects of psychomotor stimulants, the discriminative effects of methamphetamine (MA) as well as dopamine (DA) and noradrenaline (NA) were observed by intracerebral administration of these drugs into the nucleus accumbens in rats discriminating subcutaneous MA from saline. These rats were trained and maintained to discriminate between MA at 0.5 mg/kg, s.c. and saline under a fixed ratio 10 schedule for food reinforcement in a 2-lever operant chamber situation. Guide cannulae were implanted bilaterally into the nucleus accumbens. In the substitution tests, the drug was administered into the nucleus accumbens. MA at 10 micrograms per rat substituted for subcutaneous MA in 4 out of 5 rats but neither DA at 10-40 micrograms per rat (n = 7) nor NA at 10-40 micrograms per rat (n = 4) substituted for subcutaneous MA. On the other hand, the same drugs administered into the nucleus accumbens induced increased spontaneous motor activity as also observed in six other untrained rats. MA, DA or NA alone each at 10 micrograms per rat increased spontaneous motor activity. The discriminative effects of MA are considered to be mediated in the nucleus accumbens of rats. Although DA or NA alone administered into the nucleus accumbens showed similar increasing motor activity effects as those of MA, the discriminative effects of exogenous DA or NA alone administered into the same brain area were different from those of MA in the present experimental condition.
Determination of coronavirus 229E antibody by an immune‐adherence hemagglutination method

An immune‐adherence hemagglutination (IAHA) method for coronavirus 229E antibody determination has been developed both for diagnosis of recent infections and for detection of long‐past infections. Results have been compared with those obtained by complement fixation (CF), neutralization (Nt), and indirect hemagglutination (IHA) tests. The IAHA method has been shown to be as sensitive as the CF, Nt, and IHA tests in detecting cases of acute 229E infection. However, in a seroepidemiological survey of 343 healthy people of all ages, IAHA detected 229E antibody in 254 individuals (74.0%), Nt in 166 (48.3%), IHA in 89 (25.9%), and CF in 30 (8.7%). A study of the prevalence of coronavirus 229E IAHA antibody in the different age groups has shown that during the second decade of life nearly 100% of the population acquire this type of antibody, whereas only 50% are positive at the end of the first decade. In the older age groups, the high frequency of CF antibody (“marker” of recent infection) indirectly confirms the high rate of 229E reinfections and the nonprotective nature of IAHA antibody. CF titer ⩾ 1:8 in 90% of cases corresponded to IAHA titers ⩾ 1:64. However, sera with IAHA titers of ⩾ 1:128 were often CF‐negative. Recent 229E infections (or reinfections), as determined by the presence of CF antibody, were more frequent in April‐May than in October‐November. Three cases of acute infection showing 229E seroconversion (two adults and one child) were observed during the winter‐spring season. IAHA appears to be the test of choice for seroepidemiological surveys.
Simultaneous radioimmunoassay of plasma FSH, LH, progesterone, 17-hydroxyprogesterone, and estradiol-17 beta during the menstrual cycle.

Plasma levels of FSH, LH, progesterone (P), 17-hydroxy-progesterone (17-OHP), and estradiol-17β (E2) were measured daily by radioimmunoassay in eleven menstrual cycles from eleven normally menstruating women. The following criteria were used as indirect evidence for a normal ovulatory cycle: 1) mid-cycle LH peak, 2) luteal phase of 12–16 days duration, and 3) plasma progesterone above 5 ng/ml 5–8 days after the LH peak. Nine of eleven cycles studied were considered normal. A mid-cycle peak of E2 and 17-OHP was observed in every normal cycle studied. In one of the normal cycles, two peaks of plasma E2 occurred respectively on days 9 and 22. However, 17-OHP levels were low on day 9 and elevated on day 22. A gonadotropin surge occurred on day 22 followed by a normal luteal phase. The other two abnormal cycles studied either showed low levels of E2 and 17-OHP or a peak of only one of the two steroids. The data suggest that in women, there is a relationship between the steroids 17-OHP and E2, and the mid-cycle.
Occupational Assimilation as a Competitive Process

Insofar as Negroes and females compete with white males for jobs and are willing to accept wages below those demanded by white males, the incomes of the latter group will be adjusted downward by the competitive process. Regressions over detailed occupations of white male income on white male education, proportion Negro and proportion female for all occupations and within each major occupational level support this hypothesis, consistently indicating that white male income is negatively associated, net of education, with the proportion female and proportion Negro in an occupation. These cross-sectional results, augmented by a longitudinal analysis, suggest that discriminatory policies against females and Negroes are not due solely to prejudice but also to the attempts of occupational groups dominated by white males to avoid competition from minority workers.
Improvement in imaging diagnosis technique and modalities for solitary pulmonary nodules: from ground-glass opacity nodules to part-solid and solid nodules

SUMMARY With advances in CT technology and the popularity of low-dose CT as a device for lung cancer screening, the detection rate of sub-solid pulmonary nodules as well as solid nodules has been increased. Distinguishing solid from sub-solid features is an essential step in the CT evaluation of solitary pulmonary nodules (SPNs) because strategies for nodule characterization and guidelines for management are different for each category. In addition to conventional CT parameters, numerous novel concepts and modalities have been developed. Although there is currently no single effective method for differentiating malignant from benign nodules, growth rate measurement using volumetry, evaluation of tumor vascularity on dynamic helical CT, dual-energy CT and MRI and physiologic evaluation with PET/CT can all be useful for nodule characterization. New techniques such as tomosynthesis can improve detection over radiography alone. The purpose of this article is to enhance our understanding of the evidence-based strategies involved in diagnosing SPNs.
Sickle Cell Disease in Saudi Arabia: The Asian Haplotype

Recent developments in sickle cell disease were reviewed at a research meeting in Hofuf held in September 2003, having been postponed from fcMay 2003 because of events within the region. The meeting brought together speakers and researchers from all over the Kingdom along with visiting speakers from India, Nigeria, Greece, Bahrain, Sudan and Jamaica. Although the emphasis of the meeting was on recent advances, it was a timely reminder of the research opportunities posed by the Asian haplotype of the disease prevalent in the Eastern Province. The Asian haplotype refers to a variant of the DNA structure flanking the ß—globin locus (the site of the HbS gene), which is not encountered in African populations and appears to represent an independent occurrence of the HbS mutation. This haplotype is confined to peoples of the Eastern Province of Saudi Arabia and to India, and contrasts with African populations, where the HbS gene is associated with different DNA structures, named Benin, Senegal, and Bantu (or Central African Republic) after the places where they were first described. The interesting feature of the Asian haplotype is the extent to which it modifies the haematological and clinical expression of homozygous sickle cell (SS) disease. The DNA structure of the Asian haplotype was first recognized in Jamaica in an Indian family with SS disease1 who also had high levels of fetal haemoglobin (HbF). Early reports from the Eastern Province, especially from the ARAMCO facility in Dhahran reported unusually mild features in SS disease2-6 and near normal survival.7 The disease was characterized by high levels of HbF and most cases coincided with a-thalassaemia, both features believed to inhibit intravascular sickling. As a result, splenic architecture and splenic function persisted,8 minimizing the risk of pneumococcal septicaemia characteristic of African SS disease.9 Other features of clinical mildness included less frequent acute chest syndrome, leg ulceration and priapism,10 and less cumulative damage to neurological, pulmonary and renal function, which commonly contributes to death in African disease. The overall impression was of a disease process milder than that of African patients. However, serious pathology in association with the Asian haplotype has been described. Lack of splenic pathology might be expected to protect against acute splenic sequestration and chronic hypersplenism, but it is clear that these occur.11 There are insufficient data to determine whether the incidence is similar or less than in African disease. Priapism also occurs and can cause impotence, but its prevalence is unknown. It is also clear that bone From the Sickle Cell Trust (Jamaica) West Indies
TITLE : Dressing Materials for the Treatment of Pressure Ulcers in Patients in Long-Term Care Facilities : A Review of the Comparative Clinical Effectiveness and Guidelines

Pressure ulcers are regions of localized damage to the skin and underlying tissues that usually develop over bony prominences. They occur as a result of uninterrupted pressure exerted on the skin, soft tissues, muscle, and bone leading to the development of localized ischemia, followed by a cascade of processes resulting in necrosis. Areas of the body commonly predisposed to pressure ulcers include heels, hip, elbows, shoulders, back of the head, knees, thighs, and toes. Ulcer severity is assessed in a variety of ways, but the US National Pressure Ulcer Advisory Panel (NPUAP) staging system is the most commonly used. The NPUAP system includes a four-stage categorization, representing progressive severity from intact skin with nonblanchable redness of localized area in Stage I, to full thickness tissue loss with exposed bone in Stage IV.
Avaliação Empírica de Técnicas de Comparação Privada Aplicadas na Resolução de Entidades

A Resolução de Entidades com Preservação de Privacidade (REPP) consiste em identificar entidades que representam o mesmo objeto no mundo real, mantendo a privacidade dos dados. Nesse contexto, diferentes técnicas de comparação de dados privados vêm sendo utilizadas como, por exemplo, Filtros de Bloom. Contudo, o Filtro de Bloom, não apresenta uma boa precisão quando dados numéricos ou datas são comparados. Este trabalho tem por objetivo avaliar empiricamente se a Criptografia Assimétrica Homomórfica (CAH) pode melhorar a precisão da comparação envolvendo dados privados não textuais. Os resultados apontam que o uso de CAH para comparar dados não textuais pode melhorar a precisão da REPP.
Effects of Chronic Excess Salt Ingestion: Vascular Reactivity in Two Strains of Rats with Opposite Genetic Susceptibility to Experimental Hypertension

SELECTIVE inbreeding has resulted in the development of two strains of rats, one of which rapidly develops hypertension from the same high salt intake that is virtually ineffective in producing hypertension in the other strain.1' 2 This innate difference reflected the presence of a more general trait since it was manifest also after combined desoxycorticosterone-NaCl treatment as well as after unilateral renal artery compression without added dietary salt.3 This general trait is further indicated by the present work, in which the vascular responsiveness of these animals to vasopressor agents was tested. Among animals which were on a low salt regimen and were normotensive, the ones from the strain predisposed to develop hypertension from salt showed significantly higher vascular reactivity than did those from the strain resistant to this effect of salt. In addition to the experimental implications, these findings may have relevance in the problem of human essential hypertension. Most but not all 4 observers agree that in the established disease there is increased vascular reactivity. If vascular hyperreactivity antedates the development of established hypertension, it might play a role in the etiology or in the pathogenesis of the disease. There is some evidence to suggest that vascular hyperreactivity does precede the development of essential hypertension. For instance, it is well known that many patients with fixed hypertension have a history in their earlier years of labile blood pressures and periods of transient elevations under stress. Transi-
Competition or collaboration? A comparison of health services in the U.K.

Clinical Medicine 2010, Vol 10, No 5: 431‐3 ■ EDITORIALS Although devolution has had a major impact on the organisation of health services in the UK, there have always been differences between England, Scotland and Wales. Before the advent of the NHS in 1948 cooperative models of providing health services were more common, and more developed, in Wales than in England ‐ indeed it has been suggested that Bevan’s ideas on the NHS were based on his experiences with the Welsh miners’ welfare system. 1 In England the voluntary hospitals, including teaching hospitals such as St Bartholomew’s, St Thomas’ and Sheffield Royal Infirmary, provided a considerable proportion of hospital care, alongside the local authority and community hospitals. Voluntary hospitals, supported by charitable donations, were far less common in Wales and Scotland than England. Although the principles and basic structure were similar in the three countries when the NHS was introduced, differences remained. Until 1974, for example, teaching hospitals in Scotland were incorporated within the regional hospital boards in contrast to the independent boards of governors existing in England and Wales. When the three countries are compared differences in health status, and the underlying reasons for this, must be taken into account. Health in Scotland and Wales has always been worse than in England, associated with greater levels of deprivation. Infant mortality, often taken as an index of the health status of a country, demonstrates this (Table 1). Seventy years ago the rate was greater in Scotland than England and Wales. The differences have narrowed, now England has a higher rate than Wales or Scotland. Since devolution, differences in priorities and structure have become more evident. Previously there were differences in emphasis ‐ for example, fundholding, which became reasonably