Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying pitfalls in automatic parallelization of NAS parallel benchmarks

This paper provides an examination of OpenMP based auto-parallelizers and their limitations encountered during parallelization of NAS parallel benchmarks. It also elucidates the issues faced by the parallelizers during parallelization and the resolutions to overcome the problems. Compute-intensive loops are pinpointed using Gprof and the problematic loops within the hotspot area were recognized. Our work concentrates on identifying the pitfalls within the located hotspots and rendering solution in such cases. Analysis on measured speedup and its reasons are well illustrated. This paper underlines the need of a user-interactive environment that highlights the problems evoked during parallelization. It also underscores the obligation for minimal manual intervention concerning coding changes to resolve the problematic code section and make them amenable to parallelization.
Effect of PEG6000 on the In Vitro and In Vivo Transdermal Permeation of Ondansetron Hydrochloride from EVA1802 Membranes

The objective was to evaluate ethylene vinyl acetate (EVA) copolymer membranes with vinyl acetate content of 18% w/w (EVA1802) for transdermal delivery of ondansetron hydrochloride. The EVA1802 membranes containing selected concentrations (0, 5, 10 and 15% w/w) of PEG6000 were prepared, and subjected to in vitro permeation studies from a nerodilol-based drug reservoir. Flux of ondansetron from EVA1802 membranes without PEG6000 was 64.1 ± 0.6 μg/cm2·h, and with 10%w/w of PEG6000 (EVA1802-PEG6000-10) it increased to 194.9 ± 4.6 μg/cm2·h. However, with 15%w/w of PEG6000, EVA1802 membranes produced a burst release of drug which in turn decreased drug flux. The EVA1802-PEG6000-10 membrane was coated with an adhesive emulsion, applied to rat epidermis and subjected to in vitro permeation studies against controls. Flux of ondansetron from transdermal patch across rat epidermis was 111.7 ± 1.3 μg/cm2·h, which is about 1.3 times the required flux. A TTS was fabricated using adhesive-coated EVA1802-PEG6000-10 membrane and other TTS components, and subjected to in vivo delivery in human volunteers against a control. It was concluded from the comparative pharmacokinetic study that TTS of ondansetron, prepared with EVA1802-PEG6000-10 membrane, provided average steady-state plasma concentration on par with multiple-dosed oral tablets, but with a low percent of peak-to-trough fluctuation.
LMDS-based approach for efficient top-k local ligand-binding site search

In this work, we propose a LMDS-based binding-site search for improving the search speed of the Patch-Surfer method. Patch-Surfer is efficient in recognition of protein-ligand binding partners, further speedup is necessary to address multiple-user access. Futher speedup is realised by exploiting Landmark Multi-Dimensional Scaling (LMDS). It computes embedding coordinates for data points based on their distances from landmark points. When selecting the landmark points, we adopt two approaches--random and greedy selection. Our method approximately retrieves top-k results and the accuracy increases as we exploit more landmark points. Although two landmark selection approaches show comparable results, the greedy selection shows the best performance when the number of landmark points is large. Using our method, the searching time is reduced up to 99% and it retrieves almost 80% of exact top-k results. Additionally, LMDS-based binding-site search+ improves the retrieval accuracy from 80% to 95% while sacrificing the speedup ratio from 99% to 90% compared to Patch-Surfer.
Computer-aided detection of breast masses depicted on full-field digital mammograms: a performance assessment.

OBJECTIVES To investigate the feasibility of converting a computer-aided detection (CAD) scheme for digitised screen-film mammograms to full-field digital mammograms (FFDMs) and assessing CAD performance on a large database. METHODS The database included 6478 FFDM images acquired on 1120 females, with 525 cancer cases and 595 negative cases. The database was divided into five case groups: (1) cancer detected during screening, (2) interval cancers, (3) "high-risk" recommended for surgical excision, (4) recalled but negative and (5) negative (not recalled). A previously developed CAD scheme for masses depicted on digitised images was converted and re-optimised for FFDM images while keeping the same image-processing structure. CAD performance was analysed on the entire database. RESULTS The case-based sensitivity was 75.6% (397/525) for the current mammograms and 40.8% (42/103) for the prior mammograms deemed negative during clinical interpretation but "visible" during retrospective review. The region-based sensitivity was 58.1% (618/1064) for the current mammograms and 28.4% (57/201) for the prior mammograms. The CAD scheme marked 55.7% (221/397) and 35.7% (15/42) of the masses on both views of the current and the prior examinations, respectively. The overall CAD-cued false-positive rate was 0.32 per image, ranging from 0.29 to 0.51 for the five case groups. CONCLUSION This study indicated that (1) digitised image-based CAD can be converted for FFDMs while performing at a comparable, or better, level; (2) CAD detects a substantial fraction of cancers depicted on prior examinations, albeit most having been marked only on one view; and (3) CAD tends to mark more false-positive results on "difficult" negative cases that are more visually difficult for radiologists to interpret.
The Carter Administration's Policy toward Nicaragua: Imagesz, Goals, and Tactics

Academics and political activists alike have devoted a great deal of attention to U.S. policy toward Nicaragua in recent years. Oddly, current interest in that relationship has not resulted in many in-depth analyses of the Carter administration's actions despite every indication that they are far more interesting and puzzling than those of the Reagan administration. It is commonly argued that the Carter administration's foreign policies in general, and toward Central America in particular, were confused, incoherent, lacking in strategy, and inconsistent. ' Inconsistencies in policy toward Nicaragua included termination of aid in 1977 followed by the release of twelve million dollars in military aid in 1978; criticisms of human rights abuses by Anastasio Somoza and the National Guard in 1977 but praise for Somoza's performance in that area in 1978 and efforts to prevent the destruction of the National Guard; the encouragement of democratic
Insights into cell division using Listeria monocytogenes infections of PtK2 renal epithelial cells

The assembly of actin into a cleavage furrow is accompanied by disassembly of the interphase actin cytoskeleton. A variation of this actin filament disassembly/assembly cycle is seen during cell division in PtK2 cells infected with the intracellular pathogen, Listeria monocytogenes, where F‐actin associates with the bacteria either as a halo surrounding nonmoving bacteria, or as an array of filaments that encases the sides of moving baceteria and extends behind them like a tail. The moving Listeria are found both in the cytoplasm and in the distal ends of undulating filopodia. When infected cells enter mitosis, the distribution of moving and stationary bacteria changes. In the transition from prophase to metaphase, there is a decrease in the number of bacteria with tails of actin in the cytoplasm. The nonmoving bacteria surrounded with F‐actin are excluded from the mitotic spindle and moving bacteria are seldom seen in the cytoplasm during mitosis, although small thin filopodia cluster at the edges of the cells. After completion of cytokinesis, strong tail reformation first becomes obvious in the filopodia with Listeria moving back into the cytoplasm as the daughter cells spread. In summary, the disassembly and reassembly of actin tails extending from Listeria in dividing cells is a variation of the changes in actin organization produced by stress fiber and myofibril disassembly/assembly cycles during cell division. We suggest that the same unknown factors that regulate the disassembly/assembly of stress fibers and myofibrils during mitosis and post cytokinesis also affect the movement of Listeria inside mitotic cells. © 2012 Wiley Periodicals, Inc.
Prenatal Alcohol Exposure Increases Vulnerability to Stress and Anxiety‐Like Disorders in Adulthood

Children and adults with fetal alcohol spectrum disorder (FASD) have elevated rates of depression and anxiety disorders compared to control populations. The effects of prenatal alcohol exposure (PAE) on anxiety, locomotor activity, and hormonal reactivity in male and female rats tested on the elevated plus maze (EPM), a task commonly used to assess anxiety‐like behaviors in rodents, were examined. Pregnant dams were assigned to PAE, pair‐fed (PF), or ad libitum‐fed control (C) groups. At adulthood, half of all male (N= 60) and female (N= 60) PAE, PF, and C offspring were exposed to 10 days of chronic mild stress (CMS); the other half remained undisturbed. Animals were then tested on the EPM, and blood collected 30 min posttest for analysis of corticosterone (CORT), testosterone, estradiol, and progesterone. Overall, CMS exposure produced a significant anxiogenic profile. Moreover, CMS increased anxiety‐like behavior in PAE males and females compared to controls and eliminated the locomotor hyperactivity observed in nonstressed PAE females. CMS also increased post‐EPM CORT, testosterone, and progesterone levels in all groups, with CORT and progesterone levels significantly higher in PAE than in C females. By contrast, CMS selectively lowered estradiol levels in PAE and PF, but not C, females. CMS exposure reveals sexually dimorphic behavioral and endocrine alterations in PAE compared to C animals. Together, these data suggest the possibility that fetal reprogramming of hypothalamic–pituitary–adrenal (HPA) and –gonadal (HPG) systems by alcohol may underlie, at least partly, an enhanced susceptibility of fetal alcohol‐exposed offspring to depression/anxiety‐like disorders in adulthood.
Activation ratio of MMP‐2 and expression of MT1‐MMP are correlated in thymic epithelial tumours

Aims: To study the relationships between the activation of pro‐MMP‐2 and the mRNA levels of MT1‐MMP and TIMP‐2 in thymic tissues and thymic epithelial tumours. Methods: We examined the mRNA expressions of MMP‐2, MT1‐MMP and TIMP‐2 with real‐time reverse transcription‐polymerase chain reaction (RT‐PCR). The gelatinolytic activity and MMP‐2 activation ratio of thymic tissues, thymomas, and thymic carcinomas were determined with gelatin zymography. The cellular localisation of MMP‐2 was detected with film in situ gelatin zymography. We then examined the mRNA expression of MMP‐2 in the epithelial tumour cells or lymphocytes and stromal cells distant from the tumour (obtained from two invasive thymomas) using laser‐capture microdissection (LCM). Results: The mRNA levels of MMP‐2, MT1‐MMP and TIMP‐2 were significantly increased from thymic tissue, Stage I–II, III–IV thymomas to thymic carcinomas (p<0.005). They were also significantly increased from AB–B1 (lymphocyte rich and mixed types), B2–B3 (cortical and predominantly polygonal cells types) thymomas to thymic carcinomas (p<0.05). The MMP‐2 activation ratio also had the same tendency among the above groups (p<0.05) and was directly correlated to MT1‐MMP and TIMP‐2 mRNA expression (Spearman rank correlation: r = 0.8627, r = 0.8314; p<0.005). Film in situ zymography demonstrated that positive expression is mainly localised in tumour cell nests and adjacent stroma cells. LCM and real‐time RT‐PCR results comfirmed that the expression of MMP‐2 was higher in epithelial tumour cells than in lymphocytes and stromal cells. Conclusions: MMP‐2, MT1‐MMP and TIMP‐2 mRNA expression levels were correlated with clinical stages and histological subtypes of thymic epithelial tumours. The activation of pro‐MMP‐2 might be mediated by MT1‐MMP and TIMP‐2 up‐regulation.
The Contribution of Previous Episodes of Pain, Pain Intensity, Physical Impairment, and Pain-Related Fear to Disability in Patients with Chronic Mechanical Neck Pain

Objective The influence of physical and psychosocial variables on self-rated disability in patients with chronic mechanical neck pain has not been fully determined. This study examined the relationship of pain, physical impairment, and pain-related fear to disability in individuals with chronic mechanical neck pain. Design A cross-sectional study was conducted. Ninety-seven (n = 97) subjects (28 men, 69 women; mean age, 39.3 yrs) with chronic mechanical neck pain were prospectively recruited. Demographic information, duration of pain symptoms, pain intensity, pain-related fear, and cervical range of motion were collected on all subjects. Self-reported disability was measured with the Neck Disability Index. Correlation and regression analyses were performed to determine the association among the variables and to determine the proportions of explained variance in disability. Results Significant positive correlations existed between disability and previous history of neck pain (r = 0.45; P < 0.001), disability and pain intensity (r = 0.32, P = 0.01), and disability and kinesiophobia (r = 0.23, P = 0.02). In addition, a significant negative correlation existed between disability and cervical extension range of motion (r = −0.18, P = 0.04). Stepwise regression analyses revealed that previous neck pain episodes, intensity of neck pain, kinesiophobia, and cervical extension range of motion were significant predictors of disability (r 2 = 0.400; r 2 adjusted = 0.372; F = 14.64; P < 0.001). Conclusions This study found that previous episodes of neck pain, pain intensity, pain-related fear, and cervical extension range of motion explained 37.2% of the variability of self-report disability. Future longitudinal studies will help to determine the clinical implications of these findings.
Capitalism: Competition, Conflict, Crises

Neoclassical economical theory uses aspects of perfect functioning of markets as part of its basic assumptions and introduces imperfections as analysis proceeds forward. Many types of heterodox economics insist on dealing with imperfect competition but project backwards to a previous perfect state. In Capitalism, Anwar Shaikh demonstrates that most of the central propositions of economic analysis can be derived without any reference to hyperrationality, optimization, perfect competition, perfect information, representative agents or so-called rational expectations. These include the laws of demand and supply, the determination of wage and profit rates, technological change, relative prices, interest rates, bond and equity prices, exchange rates, terms and balance of trade, growth, unemployment, inflation, and long booms culminating in recurrent general crises. In every case, Shaikh's theory is applied to modern empirical patterns and contrasted with neoclassical, Keynesian, and Post Keynesian approaches to the same issues. The object of analysis is the economics of capitalism, and economic thought on the subject is addressed in that light. This is how the classical economists, as well as Keynes and Kalecki, approached the issue. Anyone interested in capitalism and economics in general can gain a wealth of knowledge from this ground-breaking text. Available in OSO:
Differential roles of metallothionein‐like proteins in cadmium uptake and elimination by the scallop Chlamys nobilis

Metallothionein‐like proteins (MTLPs) are important inducible ligands for Cd detoxification, but whether MTLPs are involved in Cd bioaccumulation remains unclear. The present study investigated the potential interrelationships between MTLP turnover and Cd biokinetics in the scallop Chlamys nobilis with or without dissolved Cd pre‐exposure. After Cd pre‐exposure, increased synthesis rate and standing stock concentration of MTLPs as well as increased dissolved Cd uptake rate, were found in C. nobilis. However, the level of newly sequestrated Cd by MTLPs in the pre‐exposed scallops was similar to that of the controls, indicating that MTLPs had no effect on Cd uptake from the dissolved phase. Instead, Cd uptake rate was positively related to the Cd binding rate of cellular debris and organelles. In addition, no significant difference was observed in the Cd dietary assimilation efficiency of the scallops, showing that MTLPs played a minimal role in Cd uptake from the dietary phase. Conversely, the Cd efflux rate constant decreased by 68 to 75% in the pre‐exposed scallops in comparison with that in the control. Correspondingly, progressive elevations of MTLP‐bound Cd and standing stock MTLP concentration were observed in the pre‐exposed individuals during the Cd elimination period. In the pre‐exposed scallops, the faster de novo MTLP synthesis could remobilize and recycle more Cd from other intracellular pools, effectively reducing the Cd elimination rate. The present study thus showed the differential roles of MTLPs in Cd uptake and elimination in the bivalves. Environ. Toxicol. Chem. 2011; 30:738–746. © 2011 SETAC
Women’s Participation in Agriculture and Gender Productivity Gap: The Case of Coffee Farmers in Southern Colombia and Northern Ecuador

This study examines the intra-household bargaining its impact on the productivity of coffee and other crops functions and on the gender productivity gap, using household-level data from 615 farmers in Colombia and Ecuador. The OLS estimates and the Oaxaca-Blinder (O-B) decomposition method corroborate the hypothesis that given a gain bargaining power through the distribution factor “female participation in the intra-household decision-making” would exacerbate household productivity and the gender gap as long this bargaining is not balanced and wives do not obtain fair benefits from agricultural activities. The results also confirm that differences in observed factors between female and male-headed households are the main reason for the gender gap.
"Safe zones" for miniscrew implant placement in different dentoskeletal patterns.

OBJECTIVE To assess the influence of different dentoskeletal patterns on the availability of interradicular spaces and to determine the safe zones for miniscrew implant placement. MATERIALS AND METHODS Periapical radiographs of 60 subjects with skeletal Class I, II, or III patterns were examined. For each interradicular site, the areas and distances at 3, 5, 7, 9, and 11 mm from the alveolar crest were measured. RESULTS In the maxilla, the greatest interradicular space was between the second premolar and the first molar. In the mandible, the greatest interradicular space was between the first and second molars, followed by the first and second premolars. Significant differences in interradicular spaces among the skeletal patterns were observed. Maxillary interradicular spaces, particularly between the first and second molars, in the subjects with skeletal Class II patterns, were greater than those in the subjects with skeletal Class III patterns. In contrast, in the mandible, interradicular spaces in the subjects with skeletal Class III patterns were greater than those in the subjects with skeletal Class II patterns. CONCLUSIONS For all skeletal patterns, the safest zones were the spaces between the second premolar and the first molar in the maxilla, and between the first and second premolars and between the first and second molars in the mandible.
Abscess formation due to Mycoplasma hominis infection after cesarean section

A 27‐year‐old female patient underwent cesarean section and a postoperative hematoma occurred at the site of the uterine incision. The patient underwent relaparotomy to remove the hematoma. Four days later she developed a fever of over 39°C and an abscess had formed at the site. Despite therapy with several antimicrobial agents, her fever persisted. Consequently, she underwent transvaginal abscess drainage, after which she promptly became afebrile. Mycoplasma hominis was considered to be the primary causative organism. There are two reasons that could explain why the wound infection became serious: (i) M. hominis is resistant to several antimicrobial agents that are usually used to treat obstetric infections; and (ii) a long time is required to identify the pathogen. In conclusion, M. hominis should be considered as a causative organism if an antimicrobial‐resistant infection occurs at the surgical site after a cesarean section.
Currents carried by monovalent cations through calcium channels in mouse neoplastic B lymphocytes.

Membrane currents through the Ca2+ channel were studied in a hybridoma cell line (MAb‐7B) constructed by fusion of S194 myeloma cells and splenic B lymphocytes from the mouse. The whole‐cell variation of the patch‐electrode voltage‐clamp technique was used. When [Ca2+]o = 2.5 mM, [Na+]o = 150 mM and [Na+]i = 155 mM, the current reversed from inward to outward at 20.9 +/‐ 2.4 mV (mean +/‐ S.D., n = 62). Both inward and outward currents showed voltage‐dependent inactivation with the same membrane potential dependence of steady‐state inactivation. The decay time constant of the current decreased from about 27 ms at ‐44 mV to a saturation value of 16 ms at about ‐20 mV, and remained at this value even when the current became outward. From the above results both the inward and outward currents were considered to flow through Ca2+ channels. The inward current showed no change when the external Na+ was replaced with Cs+ or tetraethylammonium and increased when [Ca2+]o was increased. Also, the reversal potential became more positive with increasing [Ca2+]o with a slope of 29 mV/decade change of [Ca2+]o. Effects of different divalent cations examined at 10 mM concentration showed the reversal potential to become more positive in the order of Mn2+, Sr2+ approximately equal to Ba2+ and Ca2+ whereas the relative maximum amplitudes of peak inward current were 1.0 for Ca2+, 1.24 for Sr2+, 0.99 for Ba2+ and 0.07 for Mn2+. When [Ca2+]o or [Mg2+]o was reduced by chelators, monovalent cations became capable of carrying inward current through the Ca2+ channel. These monovalent currents share common kinetic properties with the Ca2+ current, as judged from the steady‐state inactivation and the decay time constant of the current. The monovalent cation current was blocked by divalent cations in a voltage‐dependent manner. The half‐blocking concentrations of Ca2+ and Mg2+ at ‐45 mV were 2.0 X 10(‐6) M and 3.0 X 10(‐5) M respectively. The same voltage‐dependent binding mechanism can explain the outward current carried by monovalent cations at large positive potentials at normal Ca2+ concentrations. The suppression of the monovalent currents by Ca2+ and Mg2+ showed different voltage dependences. The suppression by Ca2+ increased and then decreased as the membrane potential was made negative, whereas the suppression by Mg2+ increased monotonically. This difference can be explained by considering the fact the Ca2+ is permeant and Mg2+ is impermeant through the Ca2+ channel.