Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards malware inspired management frameworks

Scalability is a real challenge for network management due to the increase of the devices to be managed and their various locations. A potential solution is based on botnets basically used by attackers. To prove the efficiency of such a system, a model is needed. Since in a previous paper we propose an IRC botnet model, in this paper we introduce two kinds of P2P models, evaluate them and compare the three different models to determine a practicable solution for network management.
Stable Internet routing without global coordination

The Border Gateway Protocol (BGP) allows an autonomous system (AS) to apply diverse local policies for selecting routes and propagating reachability information to other domains. However, BGP permits ASes to have conflicting policies that can lead to routing instability. This paper proposes a set of guidelines for an AS to follow in setting its routing policies, without requiring coordination with other ASes. Our approach exploits the Internet's hierarchical structure and the commercial relationships between ASes to impose a partial order on the set of routes to each destination. The guidelines conform to conventional traffic-engineering practices of ISPs, and provide each AS with significant flexibility in selecting its local policies. Furthermore, the guidelines ensure route convergence even under changes in the topology and routing policies. Drawing on a formal model of BGP, we prove that following our proposed policy guidelines guarantees route convergence. We also describe how our methodology can be applied to new types of relationships between ASes, how to verify the hierarchical AS relationships, and how to realize our policy guidelines. Our approach has significant practical value since it preserves the ability of each AS to apply complex local policies without divulging its BGP configurations to others.
All-trans retinoic acid restores gap junctional intercellular communication between oral cancer cells with upregulation of Cx32 and Cx43 expressions in vitro

Objective: All-trans retinoic acid (ATRA) has been demonstrated to inhibit tumor growth by restoration of gap junctional intercellular communication (GJIC) via upregulation of connexin (Cx) expression in some solid tumors. However, the relationship between ATRA and GJIC remains unclear in oral squamous cell carcinoma (OSCC). The aim of this study was to investigate the effect of ATRA on the GJIC function of OSCC. Study design: We measured the effects of ATRA on the viability and cell cycle distribution of SCC9 and Tca8113 OSCC cells. The GJIC function was observed using the scrape-loading dye transfer technique, and the mRNA and protein levels of Cx32 and Cx43 were detected by qRT-PCR, Western blot, and immunofluorescence assays. Results: ATRA inhibited the growth of OSCC cells in a dose- and time-dependent manner (P <0.05) and caused cell cycle arrest. ATRA-treated cells showed a 2.69-fold and 2.06-fold enhancement of GJIC in SCC9 and Tca8113 cells, respectively (P <0.05). Moreover, ATRA induced upregulation of Cx32 and Cx43 at both the mRNA and protein levels in OSCC cells. Conclusion: Our results indicated that restoration of GJIC via enhanced Cx32 and Cx43 expression might serve as a novel mechanism for the anti-tumor effect of ATRA in OSCC. Key words:All-trans retinoic acid, oral squamous cell carcinoma, connexin, gap junctional intercellular communication.
Resistance to Bone Resorbing Effects of PTH in Black Women

Black women have a lower incidence of vertebral and hip fractures than white women, possibly due to differences in skeletal and mineral metabolism. One suggested mechanism is that blacks have decreased skeletal sensitivity to parathyroid hormone (PTH). To test this hypothesis, we infused h(1–34)PTH in healthy premenopausal black (n = 15) and white (n = 18) women over 24 h and measured serum and urine indices of bone turnover and calcium metabolism throughout the infusion. At baseline, the mean 25‐hydroxyvitamin D (25(OH)D) concentration was significantly lower in black women (46%). There were also nearly significant trends toward higher PTH and lower urinary calcium and pyridinoline levels in black women. During infusion, there were no racial differences in the mean (1–34)PTH levels achieved or in resultant elevations of serum calcium or 1,25‐dihydroxyvitamin D (1,25(OH)2D) levels. Endogenous parathyroid suppression (measured by (1–84)PTH levels) was also similar between blacks and whites. There was an initial decline in urinary calcium/creatinine in both groups with a greater reduction in black women early in the infusion period (p < 0.05 at 8 h). Furthermore, blacks had lower levels of urinary calcium/creatinine throughout the infusion (p < 0.05 group difference). Bone formation markers (carboxy‐terminal propeptide of type I procollagen and osteocalcin) decreased within 8 h and continued to decline throughout the infusion with no distinguishable racial differences (p < 0.05 time trend for both). The most dramatic difference between black and white women in response to PTH infusion was represented by the bone resorption markers. Three separate metabolites of bone resorption (cross‐linked N‐telopeptide of type I collagen, cross‐linked C‐telopeptide of type I collagen, and free pyridinoline) all showed substantially greater elevations in white (mean peak increments 399, 725, and 43%) compared with black women (mean peak increments 317, 369, and 17%) during the infusion (p < 0.05 group differences for all three variables). These data strongly suggest that blacks have decreased skeletal sensitivity to the acute resorptive effects of increased PTH. This finding indicates that calcium homeostasis may be accomplished in blacks (during times of relative calcium deficiency) by greater conservation of calcium from nonskeletal sources (most likely renal) with relative preservation of skeletal tissue. These differences in calcium economy could account, at least in part, for the increased bone mass and lower incidence of osteoporotic fractures in black women.
An Empirical Study on Learning to Rank of Tweets

Twitter, as one of the most popular micro-blogging services, provides large quantities of fresh information including real-time news, comments, conversation, pointless babble and advertisements. Twitter presents tweets in chronological order. Recently, Twitter introduced a new ranking strategy that considers popularity of tweets in terms of number of retweets. This ranking method, however, has not taken into account content relevance or the twitter account. Therefore a large amount of pointless tweets inevitably flood the relevant tweets. This paper proposes a new ranking strategy which uses not only the content relevance of a tweet, but also the account authority and tweet-specific features such as whether a URL link is included in the tweet. We employ learning to rank algorithms to determine the best set of features with a series of experiments. It is demonstrated that whether a tweet contains URL or not, length of tweet and account authority are the best conjunction.
Enhanced new production observed from the diurnal cycle of nitrate in an oligotrophic anticyclonic eddy

A diurnal study in an anticyclonic eddy provides the first evidence of nutrient dynamics consistent with the observed trends in solar radiation, oxygen concentration changes, and estimates of the eddy diffusive flux of nitrate from nitracline. A new production rate of 24 mmol C m−2 d−1 was determined from nitrate inventory changes at nM levels in the mixed layer using a liquid waveguide technique combined with eddy diffusion estimates across the base of the mixed layer from temporal changes in the vertical penetration of SF6. The new production supported by nitrate from deepening of the mixed layer after storm events is two times larger than that from the daily diffusive flux. Our results demonstrate that new production in the oligotrophic ocean can be enhanced by a supply of nitrate through the eddy turbulence‐induced diffusive flux and entrainment during storms.
Mutation analysis for Lustre programs: Fault model description and validation

Mutation analysis is usually used to provide an indication of the fault detection ability of a test set. It is mainly used for unit testing evaluation, but has also been extended for integration testing evaluation. This paper describes adaptation of mutation analysis to the Lustre programming language, including both unit and integration testing. This paper focuses on the fault model, which has been extended since our previous works. Validation of the fault model is presented.
Exome copy number variation detection: Use of a pool of unrelated healthy tissue as reference sample

An increasing number of bioinformatic tools designed to detect CNVs (copy number variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been published in the recent years. The idea of using a pool of unrelated healthy DNA as reference has previously been formulated but not thoroughly validated. As of today, the gold standard for CNV calling is still aCGH but there is an increasing interest in detecting CNVs by exome sequencing. We propose to design a metric allowing the comparison of two CNV profiles, independently of the technique used and assessed the validity of using a pool of unrelated healthy DNA instead of a matched healthy tissue as reference in exome‐based CNV detection. We compared the CNV profiles obtained with three different approaches (aCGH, exome sequencing with a matched healthy tissue as reference, exome sequencing with a pool of eight unrelated healthy tissue as reference) on three multiple myeloma samples. We show that the usual analyses performed to compare CNV profiles (deletion/amplification ratios and CNV size distribution) lack in precision when confronted with low LRR values, as they only consider the binary status of each CNV. We show that the metric‐based distance constitutes a more accurate comparison of two CNV profiles. Based on these analyses, we conclude that a reliable picture of CNV alterations in multiple myeloma samples can be obtained from whole‐exome sequencing in the absence of a matched healthy sample.
Effect of Culture Time on the Basal Expression Levels of Drug Transporters in Sandwich-Cultured Primary Rat Hepatocytes

Sandwich-cultured rat hepatocytes are used in drug discovery for pharmacological and toxicological assessment of drug candidates, yet their utility as a functional model for drug transporters has not been fully characterized. To evaluate the system as an in vitro model for drug transport, expression changes of hepatic transporters relative to whole liver and freshly isolated hepatocytes (day 0) were examined by real-time quantitative reverse transcription-polymerase chain reaction for 4 consecutive days of culture. No significant differences in transporter expression levels were observed between freshly isolated hepatocytes and whole liver. Two distinct mRNA profiles were detected over time showing 1) a more than 5-fold decline in levels of uptake transporters such as Na+-taurocholate cotransporting polypeptide (Ntcp), organic anion transporter (Oat) 2, organic anion-transporting polypeptide (Oatp) 1a1, Oatp1a4, and Oatp1b2 and 2) a greater than 5-fold increase of efflux transporters P-glycoprotein (P-gp), breast cancer resistance protein (Bcrp), and multidrug resistance-related proteins (Mrp) 1, 2, 3, and 4. In addition, protein levels and functional activities for selected transporters were also determined. Protein levels for Mrp2, Bcrp, P-gp, Ntcp, and Oatp1a4 corresponded to changes in mRNA. Functional activities of Oatps and Oct1 exhibited a 3- and 4-fold decrease on day 2 and day 4, respectively, relative to that on day 0, whereas a more than 10-fold reduction in Oat2 activity was observed. These results indicate that the cell culture conditions used herein did not provide an optimal environment for expression of all hepatic transporters. Significant time-dependent alterations in basal gene expression patterns of transporters were detected compared with those in liver or freshly isolated hepatocytes. Further work and new strategies are required to improve the validity of this model as an in vitro tool for in vivo drug transport or biliary clearance prediction.
The long-term temperature record from Markree Observatory, County Sligo, from 1842 to 2011

This study analysed long-term temperature patterns in the north-west of Ireland using a previously unexplored data-set from Markree Observatory, County Sligo. The Markree series extends back to 1842, making it one of the longest instrumental temperature records in Ireland and is renowned for holding the lowest recorded temperature for the island of Ireland, 198C on 16 January 1881. Despite its length, this record has been largely absent from past analyses of Ireland’s long-term temperature trends, rendering spatial coverage for the extended Irish climate chronology incomplete. Daily data stored in a variety ofthe historical archives were gathered and digitised and monthly records created. Calibrations to account for instrumentation, time of reading and exposure were applied where possible in order to standardise the record. Trends were subsequently investigated for seasonal averages of daily minimum, maximum and mean temperatures, and a comparison with previously published long Irish temperature records was carried out to situate the Markree record among the existing long-term series. Although the Markree series follows similar patterns to the other long-term temperature records, it displays more decadal variability,particularly in its minimum values which show a higher rate of late twentiethcentury warming compared to the other records. Due to its geographic location and surrounding topography shielding the site from direct ocean influences and prevailing south-westerly winds, Markree displays characteristic features of a more inland station (low minimum temperatures and large diurnal ranges) even though it is located only 7 km from the Atlantic Ocean. Such findings highlight the necessity of including the Markree data-set in future Irish climate change research.
Dispersed Mutations in Histone H3 That Affect Transcriptional Repression and Chromatin Structure of the CHA1 Promoter in Saccharomyces cerevisiae

ABSTRACT The histone H3 amino terminus, but not that of H4, is required to prevent the constitutively bound activator Cha4 from remodeling chromatin and activating transcription at the CHA1 gene in Saccharomyces cerevisiae. Here we show that neither the modifiable lysine residues nor any specific region of the H3 tail is required for repression of CHA1. We then screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, three of which are also temperature-sensitive mutants and four of which exhibit a sin− phenotype. Histone mutant levels were similar to that of wild-type H3, and the mutations did not cause gross alterations in nucleosome structure. One specific and strongly derepressing mutation, H3 A111G, was examined in depth and found to cause a constitutively active chromatin configuration at the uninduced CHA1 promoter as well as at the ADH2 promoter. Transcriptional derepression and altered chromatin structure of the CHA1 promoter depend on the activator Cha4. These results indicate that modest perturbations in distinct regions of the nucleosome can substantially affect the repressive function of chromatin, allowing activation in the absence of a normal inducing signal (at CHA1) or of Swi/Snf (resulting in a sin− phenotype).
Orbitally forced climate change in late mid-Eocene time at Blake Nose (Leg 171B): evidence from stable isotopes in foraminifera

Abstract Previous stable oxygen isotopic data from surface-dwelling foraminifera indicate that Eocene tropical sea surface temperatures (SSTs) were significantly lower than at present. Here we show that stable isotopic analyses (δ18O, δ13C) of the late mid-Eocene mixed-layer dweller Morozovella spinulosa are consistent with mid-Eocene mid-latitude SSTs close to, or slightly lower than modern temperatures at Blake Nose, western North Atlantic. In contrast, isotopic analyses of the benthic foraminifer, Nuttalides truempyi reveal a gradual fall in mean bottom-water temperatures from 8 to 7 °C over c. 500 ka years. These deep intermediate-water temperatures are significantly higher than modern ones and are similar to intermediate- and bottom-water temperatures recorded from earlier in Palaeogene and late Cretaceous time. Large shifts are seen in the δ18O and δ13C values of the planktonic foraminifers, of up to 1‰ and 2.6‰, respectively, that probably reflect temperature and nutrient fluctuations controlled by regional changes in upwelling intensity and runoff. The surface to benthos δ18O gradient decreases from 3‰ PDB to a minimum of c. 0.5‰ PDB over 400 ka, which could relate to the intensity of upwelling. Spectral analysis reveals precessional forcing in the foraminiferal δ18O records, which shows the direct influence of low-latitude insolation on surface-water stratification. Monsoonal wind systems may have forced the upwelling cycles and/or freshwater input. The benthic foraminifer δ18O record also contains the obliquity cycle, in addition to the precessional cycles, indicating the inheritance of mid- and high-latitude forcing to subtropical deep waters.
Characterization of micron‐sized Fe,Ni metal grains in fine‐grained rims in the Y‐791198 CM2 carbonaceous chondrite: Implications for asteroidal and preaccretionary models for aqueous alteration

Abstract— –The presence of apparently unaltered, micron‐sized Fe,Ni metal grains, juxtaposed against hydrated fine‐grained rim materials in the CM2 chondrite Yamato (Y‐) 791198 has been cited as unequivocal evidence of preaccretionary alteration. We have examined the occurrence, composition, and textural characteristics of 60 Fe,Ni metal grains located in fine‐grained rims in Y‐791198 using scanning electron microscopy (SEM) and electron microprobe analysis. In addition, three metal grains, prepared by focused ion beam (FIB) sample preparation techniques were studied by transmission electron microscopy (TEM). The metal grains are heterogeneously distributed within the rims. Electron microprobe analyses show that all the metal grains are kamacite with minor element contents (P, Cr, and Co) that lie either within or close to the range for other CM2 metal grains. X‐ray maps obtained by electron microprobe show S, P, and/or Ca enrichments on the outermost parts of many of the metal grains. Z‐contrast STEM imaging of FIB‐prepared Fe,Ni metal grains show the presence of a small amount of a lower Z secondary phase on the surface of the grains and within indentations on the grain surfaces. Energy‐filtered TEM (EFTEM) compositional mapping shows that these pits are enriched in oxygen and depleted in Fe relative to the metal. These observations are consistent with pitting corrosion of the metal on the edges of the grains and we suggest may be the result of the formation of Fe(OH)2, a common oxidation product of Fe metal. The presence of such a layer could have inhibited further alteration of the metal grains. These findings are consistent with alteration by an alkaline fluid as suggested by Zolensky et al. (1989), but the location of this alteration remains unconstrained, because Y‐791198 was recovered from Antarctica and therefore may have experienced incipient terrestrial alteration. However, we infer that the extremely low degree of oxidation of the metal is inconsistent with weathering in Antarctica and that alteration in an extraterrestrial environment is more probable. Although the presence of unaltered or incipiently altered metal grains in these fine‐grained rims could be interpreted as evidence for preaccretionary alteration, we suggest an alternative model in which metal alteration was inhibited by alkaline fluids on the asteroidal parent body.
Horizontal data partitioning in database design

In this paper the problem of horizontally partitioning data on a set of resources is considered.The main optimization parameter is the number of accesses performed by the application programs to different portions of data. The concepts which are required for the determination of relevant portions of data are defined and a methodology for determining the access parameters is proposed.The formulation of the general partitioning problem in 3 specific application environments is shown: distributed database design, file partitioning on a primary and a secondary memory and data distribution on different devices.It is shown that the analytical models of these specific applications use the parameters of the general formulation.
Simulated weathering of dinosaur tracks and the implications for their characterization

Digital models of the tracks of bipedal theropod and ornithopod dinosaurs, and the quadrupedal tracks of a sauropod, were computationally eroded to investigate the effects of erosion on the shapes, sizes, and diagnostic details of fossil tracks. Narrow and (or) angular details, such as claw marks, interdigital ridges, and internal ridges, are removed early in erosion, creating the potential for misidentification of eroded theropod tracks as those of ornithopods. However, with the erosion models presented here, all tracks retain their basic shapes as indicated by the relative constancy of their interdigital angles and by the relative constancy of their footlength:footwidth ratios. Surface lengths of tracks did not increase significantly with erosion, so that dinosaurian hip height and speed estimates derived from trackways would not be greatly in error if based on eroded surface tracks. Synthetic undertracks from the surface tracks were also produced using information from published physical models of trac.
Rhythmic Density Affects Listeners' Emotional Response to Microtiming

Microtiming has been assumed to be vital for the experience of groove, but past research presented conflicting results: some studies found that microtiming is irrelevant for groove, others reported that microtiming has a detrimental effect on the groove experience, yet others described circumstances under which microtiming has no negative impact on groove. The three studies in this paper aim at explaining some of these discrepancies by clarifying to what extent listeners' emotional responses to microtiming depend on the distribution of microtiming deviations across instrumental parts (voicing) or other moderating factors like tempo or rhythmic density. The studies use data from two listening experiments involving expert bass and drums duo recordings in swing and funk style. – Study A investigates the effect of fixed time displacements within and between the parts played by different musicians. Listeners (n = 160) reacted negatively to irregularities within the drum track, but the mutual displacement of bass vs. drums did not have an effect. – Study B develops three metrics to calculate the average microtiming magnitude in a musical excerpt. The experiment showed that listeners' (n = 160) emotional responses to expert performance microtiming aligned with each other across styles, when microtiming magnitude was adjusted for rhythmic density. This indicates that rhythmic density is a unifying moderator for listeners' emotional response to microtiming in swing and funk. – Study C used the data from both experiments in order to compare the effect of fixed microtiming displacements (from Study A) with scaled versions of the originally performed microtiming patterns (from Study B). It showed that fixed snare drum displacements irritated expert listeners more than the more flexible deviations occurring in the original performances. This provides some evidence that listeners' emotional response to microtiming deviations not only depends on the magnitude of the deviations, but also on the kind and origin of the microtiming patterns (fixed lab displacements vs. flexible performance microtiming).