Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative array storage layouts for regular scientific programs

This thesis concerns techniques for using hierarchical storage formats such as Morton layout as an alternative storage layout for regular scientific programs operating over dense two-dimensional arrays. Programming languages with support for two-dimensional arrays use one of two linear mappings from two-dimensional array indices to locations in the machine’s one-dimensional address space: rowmajor or column-major. Unfortunately, a wrong choice of one of these two layouts can lead to very poor spatial locality if an array is not traversed in the order in which it is stored. Although a simple loop interchange transformation may resolve the situation, such a transformation may not always be valid due to actual dependencies or dependencies assumed by conservative compiler analyses. An attractive strategy is to store elements in such a way that both row-major and column-major traversals offer good spatial locality. Hierarchically-blocked non-linear storage layouts, such as Morton ordering have been proposed as a compromise between row-major and column-major layouts. Morton layout offers some spatial locality whether traversed row-wise or column-wise. The contributions of the thesis are: • An experimental exploration of performance issues of Morton layout using a suite of microbenchmark kernels on several hardware platforms. • We show that the performance of the basic Morton scheme can be improved by aligning the base address of Morton arrays to the largest significant size in the memory hierarchy, namely page size. • We show that unrolling the loops with strength reduction reduces address calculation overhead associated with the usage of Morton layouts and significantly improves performance of basic Morton scheme. • We discuss the design issues for implementing a prototype compiler to support Morton layout in large scientific programs including required transformations. The optimisations we propose here enable Morton layout to be a promising alternative to conventional array layouts. Further, we support our claims through experimental results using selected benchmark kernels on several hardware platforms.
A large-vocabulary continuous speech recognition system for Hindi

In this paper we present two new techniques that have been used to build a large-vocabulary continuous Hindi speech recognition system. We present a technique for fast bootstrapping of initial phone models of a new language. The training data for the new language is aligned using an existing speech recognition engine for another language. This aligned data is used to obtain the initial acoustic models for the phones of the new language. Following this approach requires less training data. We also present a technique for generating baseforms (phonetic spellings) for phonetic languages such as Hindi. As is inherent in phonetic languages, rules generally capture the mapping of spelling to phonemes very well. However, deep linguistic knowledge is required to write all possible rules, and there are some ambiguities in the language that are difficult to capture with rules. On the other hand, pure statistical techniques for base and generation require large amounts of training data that are not readily available. We propose a hybrid approach that combines rule-based and statistical approaches in a two-step fashion. We evaluate the performance of the proposed approaches through various phonetic classification and recognition experiments.
Optimization of Envelope Tracking Power Amplifier for Base-Station Applications

We have proposed two methods of enhancing efficiency of an envelope tracking power amplifier (ET PA) from an interlock operation. The first is the utilization of sinking current. The sinking current is a critical efficiency reduction factor since it is a wasted power. To reduce the sinking current, the gate bias of the power amplifier (PA) is increased so that the sinking current is delivered to the PA and is utilized for amplification. The other one is the RF input shaping method. The input signal of ET PAs is a modulated RF signal, and the signal does not guarantee fully saturated operation of the PA at all power levels due to $g_{ m}$ nonlinearity of a device. To obtain the maximum efficiency for all of the envelope voltage, we have found the optimum RF input conditions and applied it to the input of the PA. To verify the methods, the proposed ET PA is implemented using a Cree CGH40045 GaN HEMT. For a long-term evolution 5-MHz signal with 6.5-dB peak-to-average power ratio, the PA delivers power-added efficiency of 58.76% with 40.14-dBm output power at 889 MHz.
Actin, its associated proteins and metastasis.

In this short article we have overviewed the effect of transformation on AAPs. We have not dealt with molecules indirectly associated with actin which are modified by transformation, such as the catenins, cadherins, vinculin, and integrins [Tsukita et al., 1993], although their relationship with and importance to the transformed phenotype cannot be overemphasised. Similarly, alterations in polyphosphoinositide metabolism that occur in transformed cells may also promote or induce alterations in the microfilament cytoskeleton via interactions with proteins such as gelsolin, alpha-actinin, and MARCKS [Bretscher, 1993]. At present, there are no clear-cut rules regarding the effect that oncogenesis has on AAPs, since the expression level of one oncogenically modified AAP can vary from one tumour to another, even within the same type of tumour [Yamamoto et al., 1993]. This apparent inconsistency may well be because we are "playing with an incomplete pack of cards" [Pollard, 1993], or it may reflect this highly complex control mechanism in which any perturbation of the normal expression levels of actin/AAPs unbalances the delicate equilibrium which controls normal cell behaviour [Bray and Vasiliev, 1989]. For example, it is possible that oncogenically induced alterations to actin isoform expression [Lin et al., 1985] exert a downstream effect on actin-associated protein expression. Oncogenically induced actin based cell movements may be activated by alterations to either a single AAP or a synergistic functional unit of these molecules [Shapland et al., 1993; Vandekerckhove et al., 1990]. (ABSTRACT TRUNCATED AT 250 WORDS)
Microbiomarkers in inflammatory bowel diseases: caveats come with caviar

The largest numbers of commensal bacteria reside within our intestinal tract, with an increasing density from mouth to anus. Recently, a new estimate for the total number of bacteria (3.8×1013) in the 70 kg ‘reference man’ was reported.1 For human cells, the same authors revised past estimates to 3.0×1013 cells, out of which approximately 90% belong to the haematopoietic lineage. Hence, the widely cited 10:1 ratio of bacteria versus human cells received an update, showing that the number of bacteria in the body is actually of the same order as the number of human cells, and that the cumulative bacterial mass is about 200 g. Still, this large number of bacteria highlights their importance in maintaining health and metabolism. Different parts of the intestinal tract have different functions, tissue structure varies accordingly and gradients exist for several physicochemical parameters such as nutrients, pH or oxygen levels.2 Consequently, microbiota composition varies along the gut, but also between luminal and mucosa-attached communities of the same intestinal segment, and even along the crypt-villus axis in the epithelium. Thus, host–microbiota interactions are likely regionally specific and the local crosstalk determines intestinal function and physiology. Probably each human individual carries its own ‘microbial fingerprint’ (especially when considering genomic variation within the bacterial species’ populations), which is why forensic scientists started to exploit the use of this non-human organ.3 Recent large-scale analyses of population-based cohorts with >1000 samples validated that body mass index, age at sampling and gender are important covariates that need to be included in microbiome association analyses.4 In sum, Falony et al identified 18 covariates, including stool consistency, dietary factors and blood traits, cumulatively explaining 7.7% of the total variation in the gut microbiota, leaving 92.3% of the interindividual microbial variation unexplained. In a …
Validity of Single Question for Screening Intimate Partner Violence among Urban Latina Women

OBJECTIVE The purpose of this study was to test the validity of a single violence question compared with revised Conflict Tactics Scales (CTS2) as an initial tool which can be easily used in community-based health care settings to detect IPV in Latina women. DESIGN AND SAMPLE The study was conducted using secondary analyses of the baseline data from a culturally tailored HIV risk prevention project SEPA. A total of 657 Mexican and Puerto-Rican women aged 18-40, who reported sexual activities were interviewed. MEASURES We used data regarding sociodemographic factors, Latino acculturation, a single violence question of "Did your partner hit or hurt you in any way? " and the CTS2 measuring intimate partner violence. RESULTS Using the CTS2 as a gold standard, the sensitivity and specificity of a single question for screening partner physical violence was 45.9% and 94.7%, respectively. The positive likelihood ratio of a single question for physical violence was 8.59. The sensitivity, specificity, and likelihood ratio of a single question for screening psychological aggression were 17.9%, 98.5%, and 11.89, respectively. CONCLUSION While a single question used in our study needs further improvement for desirable sensitivity, it may be usable as an initial question for detecting IPV.
The reductive hotspot hypothesis: an update.

The mitochondrial free radical theory of aging is seriously challenged by the finding that mutant mtDNA never becomes abundant in vivo, a result disputed only in experiments using novel PCR variants whose quantitative accuracy is widely doubted. However, evidence continues to mount that mitochondria are the crucial site of free radical damage in vivo, most notably that mice lacking the nonmitochondrial isoforms of superoxide dismutase are healthy. It is thus important to determine whether a low level of mutant mtDNA could have serious systemic effects. This possibility exists because of the observed mosaic distribution of mutant mtDNA: some cells (or muscle fiber segments) lack any aerobic respiration. Such cells are presumed to satisfy their ATP needs by glycolysis. In vitro, however, NADH recycling by transmembrane pyruvate/lactate exchange does not suffice: cells only survive if they can up-regulate the plasma membrane oxidoreductase (PMOR). The PMOR's physiological electron acceptor is unknown. It was proposed recently (de Grey, A. D. N. J. (1998) J. Anti-Aging Med. 1(1), 53–66) that a prominent in vivo acceptor from these mitochondrially mutant cells may be oxygen, forming extracellular superoxide. The mosaic (“hotspot”) distribution of this superoxide would limit its dismutation by extracellular superoxide dismutase; it may thus reduce transition metals leading to oxidation of circulating material, such as LDL. This would raise systemic oxidative stress, greatly amplifying the damage done by the originating mitochondrially mutant cells. This model, now known as the “reductive hotspot hypothesis,” has recently gained much indirect experimental support; several direct tests of it are also feasible.
The effects of root angle on root growth and yield of wheat in the Australian cereal belt

Genetic variation in seminal root angle exists in wheat. It has been suggested that narrow root angles contribute to adaptation to summer–dominant rainfall zones and wide angles are important in the Mediterranean climates of southern Australia. This hypothesis was tested by measuring root angles in wheat and examining its relationship with yield and root distribution. Root angles of 52 genotypes, defined as the angle subtending the first pair of seminal roots of 14-day old seedlings, were measured in a root box. Field experiments were conducted in successive years to measure the depth and distribution of roots. The importance of root angle to yield over a wider range of sites was assessed by an analysis of yield variation among the 52 varieties in 12 years of breeding trials. Root angle varied significantly from 56? to 113? and there was no consistent difference between genotypes from South Australia (mean ? SEM = 82 ? 2.9? ) and Queensland (82 ? 5.4? ); genotypes from Western Australia had a slightly wider angle (90 ? 2.2? ). In the two field trials, maximum depth of rooting did not differ significantly among the genotypes. Narrow root angle was weakly associated with more roots at 60 to 70 cm, but there was no relationship with yield. Within breeding trials, varieties with narrow root angles tended to produce slightly higher (c. 5%) yields, but this occurred in all states. The hypothesis that root angle is associated with adaptation to different parts of the cereal zone was not supported.
Bile Stress Response in Listeria monocytogenes LO28: Adaptation, Cross-Protection, and Identification of Genetic Loci Involved in Bile Resistance

ABSTRACT Bile is one of many barriers that Listeria monocytogenes must overcome in the human gastrointestinal tract in order to infect and cause disease. We demonstrated that stationary-phase cultures of L. monocytogenes LO28 were able to tolerate concentrations of bovine, porcine, and human bile and bile acids well in excess of those encountered in vivo. Strain LO28 was relatively bile resistant compared with other clinical isolates of L. monocytogenes, as well as with Listeria innocua, Salmonella enterica serovar Typhimurium LT2, and Lactobacillus sakei. While exponential-phase L. monocytogenes LO28 cells were exquisitely sensitive to unconjugated bile acids, prior adaptation to sublethal levels of bile acids or heterologous stresses, such as acid, heat, salt, or sodium dodecyl sulfate (SDS), significantly enhanced bile resistance. This adaptive response was independent of protein synthesis, and in the cases of bile and SDS adaptation, occurred in seconds. In order to identify genetic loci involved in the bile tolerance phenotype of L. monocytogenes LO28, transposon (Tn917) and plasmid (pORI19) integration banks were screened for bile-sensitive mutants. The disrupted genes included a homologue of the capA locus required for capsule formation in Bacillus anthracis; a gene encoding the transcriptional regulator ZurR; a homologue of an Escherichia coli gene, lytB, involved in isoprenoid biosynthesis; a gene encoding a homologue of the Bacillus subtilis membrane protein YxiO; and a gene encoding an amino acid transporter with a putative role in pH homeostasis, gadE. Interestingly, all of the identified loci play putative roles in maintenance of the cell envelope or in stress responses.
HLA involvement in nevirapine-induced dermatological reaction in antiretroviral-treated HIV-1 patients

114 Journal of Pharmacology and Pharmacotherapeutics | April-June 2011 | Vol 2 | Issue 2 asthmatics at Shiraz University of Medical Sciences. Iran: Ahvaz University of Medical sciences; School of Nursing and Midwifery; 1997. 6. Miranzadeh Omran H. Patient opinion about MDI use. Iran: Golestan University of Medical Sciences; 1997. 7. Farhadi K, Atai P. Difficulties with MDI use among asthmatics, bronchial asthma and influence of education. Iran: Kordestan University of Medical Sciences; 2001. 8. Scherer YK, Bruce S. Knowledge, attitudes and self-efficacy and compliance with medical regimen, number of emergency department visits, and hospitalization in adults with asthma. Heart Lung 2001;30:250-7. 9. Becker MH, Maiman LA. Sociobehavioral determinants of compliance with health and medical recommendations. Med Care 1975;13:10-24. 10. Scherer YK, Bruce S. Knowledge, attitudes and self-efficacy and compliance with medical regimen, number of emergency department visits, and hospitalization in adults with asthma. Heart Lung 2001;30:250-7.
Clinical Use of Growth Factors in the Improvement of Skin Wound Healing

To discuss the normal mechanism of wound healing (WH), the role of growth factors (GF) in prec-linical and clinical studies and its importance in the healing of abnormal wound therapy. For search, we used the PUBMED and LILACS database, and the following descriptors: skin, wound healing, growth factor and clinical trials. We also prioritized the analysis of the Clinical Trials in the previous 10 years. Although there are many studies being conducted in the pre-clinical phase, we see that there are few studies in the clinical phase. 274 studies were identified, and 58 were selected. After tissue injury, repair occurs through coordinated biological actions that are healing. The importance of the study of healing in the skin is not only because of its anatomical location, easy access and exposure, but also because of its vital function. There is accumulating evidence that the process of healing after injury may be mediated by several GF. However, may this class of molecules even act effectively on the clinical response of this pathological condition? Many preclinical studies (in vitro and in vivo) reinforce the importance and efficacy of GF in the regeneration of damaged skin. Furthermore, recent studies have reported the use in adjuvant or not, of GF in clinical treatment to improve WH in humans. Therefore, we conclude that it seems to be effective by the use of GF in adjuvant or not in WH. However, it still seems to be necessary to carry out more clinical trials in phase I and II.
Oxygen and carbon dioxide mass balance for the estuarine – intertidal marsh complex of five rivers in the southeastern

We measured dissolved O2 concentrations, pCO2 values, and respiratory rates in five estuaries of the southeastern U.S. in October 1995 and July 1996. In the low-salinity sections of the coastal plain rivers, dissolved O2 saturation states were typically only 50%, while pCO2 values were over 4,000 matm. Respiratory rates measured concurrently in estuarine water averaged 8 and 23 mmol m23 d21 in October 1995 and July 1996, but they showed little variability either within or among the five estuaries. Benthic chamber incubations in the adjacent intertidal marshes indicated fluxes of 30–40 mmol m22 d21 and 50–120 mmol m22 d21 for O2 and total dissolved inorganic carbon (DIC), respectively. For the Satilla River estuary, simple calculations revealed that neither respiratory activity in estuarine waters and sediments nor any other within-estuary process (not including the intertidal marsh system) was sufficient to account for the observed O2 concentrations and pCO2 values. Dissolved oxygen concentrations in four other southeastern U.S. estuaries fit the same general pattern as the Satilla, and likewise, within-estuary processes could not explain observed gas concentrations. Measured O2 concentrations, pCO2 values, pelagic respiratory rates, and benthic fluxes were used to construct a mass-balance model, focusing on the influence of the extensive intertidal marshes on O2 and CO2 mass balance and water–atmosphere gas exchange in the five estuaries. Results indicate that respiratory activity in the sediments and overlying water of the marshes during high tide leaves a signal that is funneled back to the estuary during ebb tide and can account for the estuarine gas concentrations and fluxes. Both experimental and modeling approaches argue that the intertidal marshes of the southeastern U.S. export considerable amounts of inorganic respiratory products to the estuaries and that ‘‘outwelling’’ of organic matter to the estuaries is a minor process by comparison. The DIC exported to the coastal ocean, however, is only a small fraction of the total gas mass flow between the marsh, estuary, and atmosphere. Early recognition of coastal intertidal marshes as highly productive ecosystems led to the hypothesis that marshes contribute significant amounts of organic carbon to estuaries and the coastal ocean (Teal 1962; Odum 1968, 1980). This hypothesis, based primarily on the coastal marshes of Georgia, was further supported by observations of estuarine oxygen deficits (Ragotzkie 1959; Pomeroy et al. 1972; Frankenberg 1975; Frankenberg and Shimmel 1975). The outwelling hypothesis was later challenged, at first because there were insufficient supporting data (Nixon 1980) and later because new data and more detailed models of estuaries did not reveal large fluxes of organic matter from marshes (Woodwell et al. 1977; Wiegert et al. 1981; Chalmers et al. 1985; Childers et al. 1993). For example, the model of Wiegert et al. (1981) suggested a net export of about 25% of
Crime and Morality - The Significance of Criminal Justice in Post-Modern Culture

Preface M. Tonry. Foreword to the Translation. 1. Morality, Criminal Justice and Criminal Events. 2. Morality and Criminal Justice Policy. 3. Morality and Victims. 4. Victimalization of the Sexually Abused Child. 5. The De-victimalization of the Prostitute. 6. Solidarity or Virtuousness: Rorty versus MacIntyre. 7. Criminality and Liberalism: Some Closing Comments. References.
Molecular phytogeny and typing of blackflies (Diptera: Simuliidae) that serve as vectors of human or bovine onchocerciasis

Abstract. A subregion of the mitochondrial large subunit (16s) rRNA gene was amplified by polymerase chain reaction (PCR) from nine species of blackflies (Diptera: Simuliidae) which serve as natural or experimental vectors of human or bovine Onchocerca parasites. PCR products from each species of blackfly were tested by directed heteroduplex analysis (DHDA), and their genotypes established according to diagnostic banding patterns of the heteroduplex products. Three alleles of mitochondrial 16s rRNA were found to exist in members of the Simulium (Ewardsellum) damnosum sensu lato complex from West Africa, and two alleles were found in the Neotropical Simulium (Psilopelmia) ochraceum Walker complex and the Simulium (Simulium) metallicum Bellardi complex. Different single alleles were detected in Austrosimulium bancrofti, in English S. (S.)noelleri and in two North American laboratory vectors: Simulium (Psilozia) vittatum Zetterstedt and S. (S.)decorum Walker. Phylogenetic analysis of 16s sequences indicated that blackflies from West Africa and the Americas formed distinct clades. Neotropical onchocerciasis vectors were found to be more closely related to Nearctic and Palaearctic non‐vector Simulium species than to the African vectors of onchocerciasis.