Miracle-dz/UniFAR-FTUs huggingface dataset:
A Quantitative Analysis of the Performance and Scalability of Distributed Shared Memory

Scalable cache coherence protocols have become the key technology for creating moderate to large-scale shared-memory multiprocessors. Although the performance of such multiprocessors depends critically on the performance of the cache coherence protocol, little comparative performance data is available. Existing commercial implementations use a variety of different protocols, including bit-vector/coarse-vector protocols, SCI-based protocols, and COMA protocols. Using the programmable protocol processor of the Stanford FLASH multiprocessor, we provide a detailed, implementation-oriented evaluation of four popular cache coherence protocols. In addition to measurements of the characteristics of protocol execution (e.g., memory overhead, protocol execution time, and message count) and of overall performance, we examine the effects of scaling the processor count from 1 to 128 processors. Surprisingly, the optimal protocol changes for different applications and can change with processor count even within the same application. These results help identify the strengths of specific protocols and illustrate the benefits of providing flexibility in the choice of cache coherence protocol.
Structural characterization of an island aquifer via tidal methods

A set of water level time series collected along a transect through a sedimentary island aquifer was used to test the utility of various simple models of ocean tidal propagation in bounded one‐dimensional aquifers. Fourier spectra were calculated for the ocean tidal modes and compared with spectra measured in wells along the island transect. Other sources of fluctuation could be neglected. An observed spatial bias in the well responses (attenuations and lags) could not be modeled by a homogeneous aquifer theory. A theory involving composite heterogeneity accounted well for the spatial bias, yielding estimates of aquifer transmissivities and storage coefficients indicating a fivefold difference in hydraulic diffusivity along the transect. A lack of well locations toward one end of the transect reduced the statistical significance of this result, with correlations between regression parameters evident. At the same time, a second bias was seen involving the ratio of signal amplitude and lag with penetration distance into the aquifer, as observed in prior tidal studies. A brief set of numerical experiments showed that horizontal layering in aquifer properties was the most probable cause of this propagation bias. Application of these results to the island data set supported a conceptual stratigraphic model of a highly conductive, sloping stratum underlying a less conductive, superficial sand layer. This model is inconsistent with well logs along the island transect but is supported by additional off‐transect well logs. It was concluded that one‐dimensional tidal propagation models may be useful in inverse characterization of aquifers with macroscale hydrogeological structures, and that the analysis of measured propagation bias has the potential to yield extra information on aquifer properties in the vertical direction.
Violência urbana: uma análise comparativa da vitimização em São Paulo, Rio de Janeiro, Recife e Vitória

In the present article we reinterpret the routine activities model trying to incorporate some elements of rational choice model. The empirical analysis estimates the probability of victimization. The data base is a victimization survey conducted by FIA/USP and ILLANUD, in 2002. The survey was carried in Recife, Rio de Janeiro, Sao Paulo and Vitoria. We consider five categories of victimization: aggression, robbery, theft, burglary and auto theft. The more important factors to explain victimization are the proximity between the victim and the offender and the victim attractiveness. The comparison among cities shows that Recife is the capital with greater probability of victimization.
How Do We Want Others to Decide?

People who decide on behalf of others can be located at various geographical distances from their clients and constituents. Across five experiments, we examined the role distance plays in evaluations of these decision makers. Specifically, drawing on construal level theory, we examined how the type of information (aggregate or case-specific) that closer and more distant decision makers cited as the basis for their decisions influenced how they were evaluated. We found that people expressed more anger toward (Experiment 1) and were less enthusiastic about (Experiments 2 and 4) more distant decision makers who relied on case-specific (vs. aggregate) information. In addition, we found that people were less enthusiastic about decision makers who relied on case-specific (vs. aggregate) information when evaluators were in a higher-level (vs. lower-level) construal mind-set (Experiments 3 and 5). Implications for how decision makers can manage impressions are discussed.
THEORETICAL AND NUMERICAL COMPARISON OF SOME SAMPLING METHODS FOR MOLECULAR DYNAMICS

The purpose of the present article is to compare different phase-space sampling methods, such as purely stochastic methods (Rejection method, Metropolized independence sampler, Importance Sampling), stochastically perturbed Molecular Dynamics methods (Hybrid Monte Carlo, Langevin Dynamics, Biased Random Walk), and purely deterministic methods (Nose-Hoover chains, Nose-Poincare and Recursive Multiple Thermostats (RMT) methods). After recalling some theoretical convergence properties for the various methods, we provide some new convergence results for the Hybrid Monte Carlo scheme, requiring weaker (and easier to check) conditions than previously known conditions. We then turn to the numerical efficiency of the sampling schemes for a benchmark model of linear alkane molecules. In particular, the numerical distributions that are generated are compared in a systematic way, on the basis of some quantitative convergence indicators.
Low-temperature thermochronology: Resolving geotherm shapes or denudation histories?

Thermal histories derived from apatite fission-track data are remarkably consistent irrespective of tectonic setting and overall rate of cooling. Rapid cooling through the partial annealing zone is typically followed by slower cooling, and such histories can only be explained by systematic errors in the experimentally derived annealing rates used to determine the thermal histories, or a consistent geotherm shape characterized by a relatively low geothermal gradient in the uppermost crust. Differences between the cooling paths characterizing individual tectonic settings indicate that geotherm shape influences the cooling histories. This suggests that crustal geotherms, especially those in orogenic belts, are characterized by a shallow zone of high permeability, allowing the rapid transfer of heat by fluid advection, perhaps together with a near-surface zone affected by enhanced heat loss due to topographic effects. The influence of such controls on cooling histories must be considered prior to using thermochronology data to constrain denudation histories.
Transcriptome and proteome analyses of the molecular mechanisms underlying changes in oil storage under drought stress in Brassica napus L.

Rapeseed ( Brassica napus L.) is the second most important oilseed crop in edible vegetable oil and bioenergy; however, drought stress generally causes a decrease in rapeseed yield and oil content, especially during the reproductive stage. In our study, we measured the oil and protein contents and gibberellic acid (GA) and abscisic acid (ABA) levels in seeds that were acquired on the 30th, 40th, and 50th days after flowering under control and drought treatments. RNA and protein libraries were constructed from the stressed seeds to perform transcriptome and proteome analyses, respectively. Our results demonstrated that the oil content decreased due to four primary mechanisms: downregulation of fatty acid biosynthesis- associated genes and proteins; upregulation of fatty acid degradation- associated genes and proteins; en-hancement of protein storage due to changes in the abundances of relevant genes and proteins; and upregulation of Gly- Asp- Ser- Leu ( GDSL ) gene expression, potentially as the result of upregulating the GA biosynthesis gene GA20ox3 and downregulating the GA inactivating gene GA2ox3 and thus an increase in GA content. During seed maturation, oil storage change may also relate to increasing ABA content as the upregulation of two members of NCED6 (9- cis- epoxycarotenoid dioxygenase) gene family involved in ABA biosynthesis, and the upregulation of genes involved in ABA signal transduction. These results will help to establish a foundation for breeding ex-cellent varieties of rapeseed with high oil content for areas with frequent droughts to promote the supply of edible vegetable oil and biofuel.
Flow Near Groin‐Like Structures

This paper presents the results of an experimental study on the structure of turbulent flow near groin‐like structures. Based on experimental observations, the deflected flow has been analyzed using the model of the three‐dimensional turbulent boundary layer. The flow bounded by the separating stream line, the groin, and the adjacent bank has been analyzed by treating it as a shear layer in which the velocity profiles have been found to be similar. The amplified bed shear stress near the groin has also been analyzed using the similarity idea. Even though the majority of the present experiments were done with the thin‐plate groin, some observations were also made on a groin with a semicylindrical hose.
The impact of the North Atlantic Ocean on the Younger Dryas climate in northwestern and central Europe

The main results of multiproxy climate reconstructions for the Younger Dryas and experiments carried out with an atmospheric general circulation model are discussed. Quantitative temperature inferences for northwestern and central Europe show that winter conditions were remarkably extreme, with values of 20–30°C below that of today. Annual temperature ranges with a continental signature (30–34°C) were reconstructed for the entire study area. Compared with today, the greatest cooling was experienced in the seaboard area. The comparison of the climate reconstructions and simulation experiments indicates that sea-ice in the North Atlantic Ocean played a decisive role in the climate of the study area by cooling the surface air temperatures and by controlling the position of the storm track. Surface air circulation was westerly even during Younger Dryas winters. A slight northward shift of the mean Atlantic sea-ice margin during winter may explain the proposed subdivision of the Younger Drays into a phase of maximum cold and humidity succeeded by a less cold and relatively dry phase. © 1998 John Wiley & Sons, Ltd.
Phospholipase Cϵ Activates Nuclear Factor-κB Signaling by Causing Cytoplasmic Localization of Ribosomal S6 Kinase and Facilitating Its Phosphorylation of Inhibitor κB in Colon Epithelial Cells*

Phospholipase Cϵ (PLCϵ), an effector of Ras and Rap small GTPases, plays a crucial role in inflammation by augmenting proinflammatory cytokine expression. This proinflammatory function of PLCϵ is implicated in its facilitative role in tumor promotion and progression during skin and colorectal carcinogenesis, although their direct link remains to be established. Moreover, the molecular mechanism underlying these functions of PLCϵ remains unknown except that PKD works downstream of PLCϵ. Here we show by employing the colitis-induced colorectal carcinogenesis model, where ApcMin/+ mice are administered with dextran sulfate sodium, that PLCϵ knock-out alleviates the colitis and suppresses the following tumorigenesis concomitant with marked attenuation of proinflammatory cytokine expression. In human colon epithelial Caco2 cells, TNF-α induces sustained expression of proinflammatory molecules and sustained activation of nuclear factor-κB (NF-κB) and PKD, the late phases of which are suppressed by not only siRNA-mediated PLCϵ knockdown but also treatment with a lysophosphatidic acid (LPA) receptor antagonist. Also, LPA stimulation induces these events in an early time course, suggesting that LPA mediates TNF-α signaling in an autocrine manner. Moreover, PLCϵ knockdown results in inhibition of phosphorylation of IκB by ribosomal S6 kinase (RSK) but not by IκB kinases. Subcellular fractionation suggests that enhanced phosphorylation of a scaffolding protein, PEA15 (phosphoprotein enriched in astrocytes 15), downstream of the PLCϵ-PKD axis causes sustained cytoplasmic localization of phosphorylated RSK, thereby facilitating IκB phosphorylation in the cytoplasm. These results suggest the crucial role of the TNF-α-LPA-LPA receptor-PLCϵ-PKD-PEA15-RSK-IκB-NF-κB pathway in facilitating inflammation and inflammation-associated carcinogenesis in the colon.
Linking magma transport structures at Kīlauea volcano

Identifying magma pathways is important for understanding and interpreting volcanic signals. At Kīlauea volcano, seismicity illuminates subsurface plumbing, but the broad spectrum of seismic phenomena hampers event identification. Discrete, long‐period (LP) events dominate the shallow (5–10 km) plumbing, and deep (40+ km) tremor has been observed offshore. However, our inability to routinely identify these events limits their utility in tracking ascending magma. Using envelope cross‐correlation, we systematically catalog non‐earthquake seismicity between 2008 and 2014. We find that the LPs and deep tremor are spatially distinct, separated by the 15–25 km deep, horizontal mantle fault zone (MFZ). Our search corroborates previous observations, but we find broader band (0.5–20 Hz) tremor comprising collocated earthquakes and reinterpret the deep tremor as earthquake swarms in a volume surrounding and responding to magma intruding from the mantle plume beneath the MFZ. We propose that the overlying MFZ promotes lateral magma transport, linking this deep intrusion with Kīlauea's shallow magma plumbing.
A Proposed Approach for the Determination of the Bioequivalence Acceptance Range for Narrow Therapeutic Index Drugs in the European Union

The current regulatory criterion for bioequivalence of narrow therapeutic index (NTI) drugs in the European Union requires that the 90% confidence interval for the ratio of the population geometric means of the test product compared with the reference for area under the plasma concentration‐time curve (AUC), and in certain cases maximum plasma drug concentration (Cmax), to be included within the tighter acceptance range of 90.00–111.11%. As a consequence, sponsors need to recruit a higher number of subjects to demonstrate bioequivalence and this may be seen as increasing the burden for the development of generics. This “one‐size‐fits‐all” criterion is particularly questionable when the within‐subject variability of the reference product is moderate to high. As an alternative, we propose a further refined statistical approach where the acceptance range is narrowed based on the within‐subject variability of the reference product of the NTI drug, similar to the one used for widening the standard 80.00–125.00% acceptance range for highly variable drugs. The 80.00–125.00% acceptance range is narrowed, only if the within‐subject variability is lower than 30%, down to the current NTI acceptance range of 90.00–111.11% when the within‐subject variability is 13.93% or lower. Examples within the current European Medicines Agency list of NTI drugs show a considerable reduction in required sample size for drugs like tacrolimus and colchicine, where the predicted within‐subject variability is 20–30%. In these cases, this approach is less sample size demanding without any expected increase in the therapeutic risks, since patients treated with reference products with moderate to high within‐subject variability are frequently exposed to bioavailability differences larger than 10%.
Interferon enhances the susceptibility of virus-infected fibroblasts to cytotoxic T cells

Interferon (IFN) pretreatment of low-passage mouse embryonic fibroblasts (MEF) infected with lymphocytic choriomeningitis virus or vaccinia virus rendered these cells two to three times more susceptible to lysis by H-2 restricted, virus-specific cytotoxic T lymphocytes (CTL) than control, virus-infected MEF. The increased sensitivity to lysis correlated with increased expression of surface H-2 antigens, but not viral antigens. Continuous cell lines already highly sensitive to CTL-mediated lysis and already expressing high levels of surface H-2 antigens were unaffected by IFN pretreatment. These results suggest that IFN treatment, by increasing surface H-2 levels, may result in increased association of surface H-2 and virus antigens, leading to enhanced recognition and lysis by virus-specific CTL.
Demographic history and genetic structure in pre-Hispanic Central Mexico

Aridoamerica and Mesoamerica are two distinct cultural areas that hosted numerous pre-Hispanic civilizations between 2,500 BCE and 1,521 CE. The division between these regions shifted southward due to severe droughts ca. 1,100 years ago, allegedly driving demographic changes and population replacement in some sites in central Mexico. Here, we present shotgun genome-wide data from 12 individuals and 26 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity spanning the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the last 2,300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from an ancient unsampled ‘ghost’ population.
A phase 2 multicenter trial of ofatumumab and prednisone as initial therapy for chronic graft-versus-host disease

Standard initial therapy of chronic graft vs. host disease (cGVHD) with glucocorticoids results in suboptimal response. Safety and feasibility of therapy with ofatumumab (1000 mg IV on days 0 and 14) and prednisone (1 mg/kg/day) was previously established in our phase I trial (n 5 12). We now report the mature results of the phase II expansion of the trial (n 5 38). The overall NIH severity of cGVHD was moderate (63 % ) or severe (37 % ) with 74 % of all patients affected by the overlap subtype of cGVHD and 82 % by prior acute cGVHD. The observed 6 month clinician-reported and 2014 NIH-de ﬁ ned overall response rates (ORR 5 complete 1 partial response [CR/PR]) of 62.5 % (1-sided lower 90 % con ﬁ dence interval 5 51.5 % ) were not superior to pre-speci ﬁ ed historic benchmark of 60 % . Post-hoc comparison of 6 month NIH response suggested bene ﬁ t compared to more contemporaneous NIH-based benchmark of 48.6 % with frontline sirolimus/prednisone (CTN 0801 trial). Baseline cGVHD features (organ involvement, severity, initial immune suppression agents) were not signi ﬁ cantly associated with 6-month ORR. The median time to initiation of second-line therapy was 5.4 months (range 0.9-15.1 months). Failure-free survival (FFS) was 64.2 % (95 % CI 46.5-77.4 % ) at 6 months and 53.1 % (95 % CI 35.8-67.7 % ) at 12 months, whereas FFS with CR/PR at 12 months of 33.5 % exceeded a benchmark of 15 % in post-hoc analysis, and was associated with greater success in steroid discontinuation by 24 months (odds ratio 8 (95 % CI 1.21-52.7). This single-arm phase II trial demonstrated acceptable safety and potential ef ﬁ cacy of the upfront use of ofatumumab in combination with prednisone in cGVHD. This trial was registered at www.clinicaltrials. gov as #NCT01680965.
Behavioral Correlates of HPV Vaccine Acceptability in the 2007 Health Information National Trends Survey (HINTS)

The development of a prophylactic vaccine to prevent infection with oncogenic subtypes of human papillomavirus (HPV) is an important step in reducing cervical cancer incidence and mortality. However, national data indicate that only 37% of 13- to 17-year-old females have initiated the vaccine series. Prior studies have examined demographic, medical history, and psychosocial variables associated with parental HPV vaccine acceptability, although few have investigated the behavioral correlates of vaccine acceptability. The primary purpose of the current study is to report on national acceptability of the HPV vaccine among U.S. adults with female children in the household and to investigate the health behavior correlates of vaccine acceptability. Data were drawn from the 2007 Health Information National Trends Survey (HINTS). The study sample comprised 1,383 adults who reported having a female child under the age of 18 in their household (52% female, 59% white; mean age = 40 years). More than half (58%) reported they would have a daughter get the HPV vaccine, 25% were not sure, and 18% would not have a daughter vaccinated. Behavioral factors significantly associated with lower acceptance of the HPV vaccine included lack of physical activity in the past month (P = 0.002), past year use of complementary or alternative therapies (P = 0.021), and no history of smoking (P = 0.005). These results suggest that behavioral health factors may be associated with vaccine acceptability and further our understanding of how behavioral patterns may contribute to the uptake of new cancer prevention strategies. Cancer Epidemiol Biomarkers Prev; 19(2); 319–26
Probability of inducing given‐magnitude earthquakes by perturbing finite volumes of rocks

Fluid‐induced seismicity results from an activation of finite rock volumes. The finiteness of perturbed volumes influences frequency‐magnitude statistics. Previously we observed that induced large‐magnitude events at geothermal and hydrocarbon reservoirs are frequently underrepresented in comparison with the Gutenberg‐Richter law. This is an indication that the events are more probable on rupture surfaces contained within the stimulated volume. Here we theoretically and numerically analyze this effect. We consider different possible scenarios of event triggering: rupture surfaces located completely within or intersecting only the stimulated volume. We approximate the stimulated volume by an ellipsoid or cuboid and derive the statistics of induced events from the statistics of random thin flat discs modeling rupture surfaces. We derive lower and upper bounds of the probability to induce a given‐magnitude event. The bounds depend strongly on the minimum principal axis of the stimulated volume. We compare the bounds with data on seismicity induced by fluid injections in boreholes. Fitting the bounds to the frequency‐magnitude distribution provides estimates of a largest expected induced magnitude and a characteristic stress drop, in addition to improved estimates of the Gutenberg‐Richter a and b parameters. The observed frequency‐magnitude curves seem to follow mainly the lower bound. However, in some case studies there are individual large‐magnitude events clearly deviating from this statistic. We propose that such events can be interpreted as triggered ones, in contrast to the absolute majority of the induced events following the lower bound.