Miracle-dz/UniFAR-FTUs huggingface dataset:
Netbus: A Transparent Mechanism for Remote Device Access in Virtualized Systems

Virtual Machine Monitors (VMMs) (e.g., Xen and VMWare) support the creation and execution of multiple virtual machines (VMs) on the same platform, and they enforce the isolation properties necessary to make the underlying shared platform resources appear exclusive to each VM. Toward these ends, VMMs export virtual instances of physical resources to VMs and they offer secure methods for sharing them. For I/O devices, such methods include time-sharing, space-sharing, and exclusive use. This paper argues the importance of VMMlevel support for transparent access to remote devices. By decoupling device locations from the VMs that access them, we enable device consolidation, flexibility in VM configurations and seamless VM migration. By enabling virtual device migration, such support will make it easier to develop the load balancing methods envisioned for next generation datacenters. VMM-level support for access to remote devices provides complete transparency in accessing remote vs. local devices, at a level of abstraction not visible to guest operating systems. Specifically, since the hypervisors or VMMs that control the hardware platform already virtualize the platform’s physical resources, it becomes possible to extend their perplatform methods for device virtualization into remoting methods that make the physical locations of devices entirely transparent to guest operating systems. Toward this end, this paper briefly describes a new abstraction termed Netbus, which provides VMs with transparent access to remote devices. For full description, please refer to [1]. To support seamless VM migration, it describes virtual device migration mechanism built using Netbus, which not only enables a VM to continuously access its IO devices, including remotely after migration, but also, to seamlessly hot-swap devices, to replace remote with local devices whenever indicated or necessary, without any noticiable downtime. Netbus currently targets LAN-centric environments Client user
A method for determining optimal decomposition scale in wavelet threshold de-noising

While taking wavelet transforms to signal de-noising in signal processing field, determining signal decomposition scale is the key factor for wavelet threshold de-noising. By using the Mallat algorithm to dyadic wavelet decomposition, the sequence length decays with 2 powers to the increase of decomposition. Therefore a method to determine the optimal decomposition scale based on small sample of white noise verification is proposed in this paper. Finally, simulation results indicate that the above method is effective.
Liver disease in pediatric patients with cystic fibrosis is associated with glutathione S‐transferase P1 polymorphism

Liver disease in patients with cystic fibrosis (CF) is inconstant and has not yet been clearly related to any specific risk factor. While the expression of cystic fibrosis transmembrane conductance regulator (CFTR) is restricted to the biliary epithelium in the liver, recent findings indicate that CFTR modulates reduced glutathione (GSH) transport and that CFTR dysfunction creates an imbalance in the antioxidant defense. Among liver detoxifying enzymes, the glutathione S‐transferases (GSTs) play a key role in the protection against oxidative stress. Because oxidative injury contributes to the development of liver disease, we hypothesized that 2 members of the GST superfamily, GSTM1 and GSTP1, which are expressed in the biliary epithelium, could influence the hepatic status in patients with CF. The potential impact of GSTM1 and GSTP1 gene polymorphisms was assessed in 106 children with CF (mean age, 11.5 years). Based on polymerase chain reaction/restriction fragment length polymorphism analysis, we found that the frequency of GSTP1‐Ile105/Ile105 genotype was significantly higher in patients with CF with liver disease than in those without (P < .03). Among the youngest patients, aged 6 years, GSTP1‐Ile105/Ile105 genotype was associated with a 8‐fold increase in the risk of liver disease compared with other GSTP1 genotypes (P = .002). No association between the GSTM1 genotype and liver status was documented. In conclusion, GSTP1‐Ile105‐encoding allele contributes to hepatic dysfunction in CF. Identification of this polymorphism may have prognostic value and prompt early treatment in patients with CF with an increased risk of liver disease.
Distinct microRNA expression signatures are associated with melanoma subtypes and are regulated by HIF1A

The complex genetic changes underlying metastatic melanoma need to be deciphered to develop new and effective therapeutics. Previously, genome‐wide microarray analyses of human melanoma identified two reciprocal gene expression programs, including transcripts regulated by either transforming growth factor, beta 1 (TGFβ1) pathways, or microphthalmia‐associated transcription factor (MITF)/SRY‐box containing gene 10 (SOX10) pathways. We extended this knowledge by discovering that melanoma cell lines with these two expression programs exhibit distinctive microRNA (miRNA) expression patterns. We also demonstrated that hypoxia‐inducible factor 1 alpha (HIF1A) is increased in TGFβ1 pathway‐expressing melanoma cells and that HIF1A upregulates miR‐210, miR‐218, miR‐224, and miR‐452. Reduced expression of these four miRNAs in TGFβ1 pathway‐expressing melanoma cells arrests the cell cycle, while their overexpression in mouse melanoma cells increases the expression of the hypoxic response gene Bnip3. Taken together, these data suggest that HIF1A may regulate some of the gene expression and biological behavior of TGFβ1 pathway‐expressing melanoma cells, in part via alterations in these four miRNAs.
Inhibition of protein synthesis: a mechanism of amebicide action of emetine and other structurally related compounds.

SYNOPSIS New amebicides usually have been discovered by empirical screening procedures while other drugs, such as emetine, were adopted after their clinical efficacy was demonstrated. Emetine, puromycin, and cycloheximide are amebicides recently shown to act as inhibitors of protein synthesis in animal cells; the present study was designed to determine the general relationship of this mode of action to amebicidal activity. Our results indicate that amebicides structurally related to emetine inhibit protein synthesis in Entamoeba histolytica. It seems likely that the lethality of many amebicides may be attributed to specific effects on macromolecular synthesis in E. histolytica.
Randomness-optimal unique element isolation, with applications to perfect matching and related problems

In this paper, we precisely characterize the randomness complexity of the unique element isolation problem, a crucial step in the RNC algorithm for perfect matching due to Mulmuley, Vazirani \& Vazirani[21] and in several other applications. Given a set $S$ and an unknown family $\cal F \subseteq$ $2^{S}$ with $|\cal F| \leq$ $Z$, we present a scheme to assign polynomially bounded weights to the elements of $S$, using only $O(\log Z + \log |S|)$ ransom bits, such that the minimum weight set in $\cal F$ is unique with high probability. This generalizes and improves the results of Mulmuley, Vazirani \& Vazirani who give a scheme which uses $O(S \log S)$ random bits independent of $Z$. We also prove a matching lower bound for the randomness complexity of this problem. This new weight assignment scheme yields a randomness-efficient $RNC^{2}$ algorithm for perfect matching which uses $O(\log Z + \log n)$ random bits where $Z$ is any given upper bound on the number of perfect matchings in the input graph. This generalizes the result of Grigoriev \& Karpinski[11] who present an $NC^{3}$ algorithm when $Z$ is polynomially bounded and also gives an improvement on the running time in this case. The worst-case randomness complexity of our algorithm is $O(n \log (m/n))$ random bits, as opposed to the previous bound of $O(m \log n)$ bits. Our technique also gives randomness-efficient solutions for several problems in which the unique element isolation tool is used, such as $RNC$ algorithms for variants of matching and basic problems on linear matroids such as matroid intersection and matroid matching. We also obtain a randomness-efficient alternative to the random reduction from $SAT$ to $USAT$, the language of uniquely satisfiable formulas, due to Valiant and Vazirani[32]. This reduction can be derandomized in the case of languages in $F ew P$ to yield new proofs of the results $F ew P \subseteq \oplus P$ and $F ew P \subseteq C_{=} P$.
Dye Adsorption on Nanocomposite

This article focuses carbon nanotube as adsorbent material for toxic contaminants. Carbon nanotube is an emerging adsorbent materials for the removal of pollutants from wastewaters. Carbon nanotube-based nanocomposites have adsorption capability towards toxic contaminants including dyes. Adsorption of dyes on nanotube depends on various parameters such as dye concentration, contact time, temperature, pH, etc. Functionalization of nanotube has enhanced the dye adsorption efficiency owing to functional groups on the surface, relative to neat nanotubes. In addition, nanocomposites have been designed for enhanced dye removal efficiency of these materials. It is evident that carbon nanotube-based nanocomposite nanosorbents have fine potential for the removal of dyes from aqueous solution. These are cost effective and environmental friendly materials. New functional carbon nanotube-based nanosorbents must be designed for efficient commercial dye removal applications.
A Machine Learning Approach to Predict Turning Points for Chaotic Financial Time Series

In this paper, a novel approach to predict turning points for chaotic financial time series is proposed based on chaotic theory and machine learning. The nonlinear mapping between different data points in primitive time series is derived and proven. Our definition of turning points produces an event characterization function, which can transform the profile of time series to a measure. The RBF neural network is further used as a nonlinear modeler. We discuss the threshold selection and give a procedure for threshold estimation using out-of sample validation. The proposed approach is applied to the prediction problem of two real-world financial time series. The experimental results validate the effectiveness of our new approach.
Evaluation of the PAX8/PPARG translocation in follicular thyroid cancer with a 4-color reverse-transcription PCR assay and automated high-resolution fragment analysis.

BACKGROUND Molecular testing of thyroid malignancies, in combination with cytologic and histologic examination, is becoming increasingly attractive as a tool for refining traditional morphologic diagnosis. The molecular changes associated with follicular thyroid carcinoma (FTC) are point mutations in RAS oncogenes or the presence of PAX8/PPARG (paired box 8/peroxisome proliferator-activated receptor gamma) rearrangement. METHODS We developed and validated a clinical assay for the detection of PAX8/PPARG rearrangements that uses a 4-color reverse-transcription PCR (RT-PCR) assay and high-resolution fragment analysis. RESULTS The RT-PCR assay is applicable for detecting the various described fusion transcripts of PAX8/PPARG in formalin-fixed, paraffin-embedded thyroid tissue and in fine-needle aspirate biopsy washes from thyroid nodules. The analytical sensitivity of the assay is 1 abnormal cell in a background of 100-10 000 translocation-negative cells. A comparison of the RT-PCR assay with dual-fusion fluorescence in situ hybridization showed an overall concordance of 95%. With this assay, we obtained a prevalence for the PAX8/PPARG rearrangement in FTC of 62% (13 of 21 cases), compared with a 5% prevalence (3 of 55) for other follicular cell-derived neoplasms. CONCLUSIONS The introduction of this assay into clinical practice could provide useful information for the diagnosis and possibly for the prognosis and treatment of thyroid cancer in the future.
Fast Parallel Algorithms for Sparse Multivariate Polynomial Interpolation over Finite Fields

The authors consider the problem of reconstructing (i.e., interpolating) a t-sparse multivariate polynomial given a black box which will produce the value of the polynomial for any value of the arguments. It is shown that, if the polynomial has coefficients in a finite field $GF[q]$ and the black box can evaluate the polynomial in the field $GF[q^{\ulcorner 2\log_{q}(nt)+3 \urcorner}]$, where n is the number of variables, then there is an algorithm to interpolate the polynomial in $O(\log^3 (nt))$ boolean parallel time and $O(n^2 t^6 \log^2 nt)$ processors.This algorithm yields the first efficient deterministic polynomial time algorithm (and moreover boolean $NC$-algorithm) for interpolating t-sparse polynomials over finite fields and should be contrasted with the fact that efficient interpolation using a black box that only evaluates the polynomial at points in $GF[q]$ is not possible (cf. [M. Clausen, A. Dress, J. Grabmeier, and M. Karpinski, Theoret. Comput. Sci., 1990, to appear]). This algorithm, tog.
A Trimodal Dialogue Corpus : Speech , Gesture , and Sketching

To build computer interfaces around human-human interaction, human dialogues must be studied in more detail, from the perspective of ultimately building computer programs that can participate. Pure speech corpora, such as S WITCHBOARD (Godfrey et al., 1992), have greatly contributed towards the development of speech user interfaces. The next generation of multimodal user interfaces requires the development of corpora that include not only speech, but also non-verbal modes of communication, including gesture and sketching. Such corpora will help us understand how to interpret these modalities individually and how they interact with each other.
Full-Chip Routing Considering Double-Via Insertion

As the technology node advances into the nanometer era, via-open defects are one of the dominant failures due to the copper cladding process. To improve via yield and reliability, redundant-via insertion is a highly recommended technique proposed by foundries. Traditionally, double-via insertion is performed at the postlayout stage. The increasing design complexity, however, leaves very limited space for postlayout optimization. It is thus desirable to consider the double-via insertion at both the routing and postrouting stages. In this paper, we present a new full-chip gridless routing system considering double-via insertion for yield enhancement. To fully consider double vias, the router applies a novel two-pass, bottom-up routability-driven routing framework and features a new redundant-via aware detailed maze routing algorithm (which could be applied to both gridless and grid-based routing). We also propose a graph-matching based post-layout double-via insertion algorithm to achieve a higher insertion rate. In particular, the algorithm is optimal for grid-based routing with up to three routing layers and the stacked-via structure. Experiments show that our methods significantly improve the via count, number of dead vias, double-via insertion rates, and running times.
RTFM (Read the Factual Mails) - Augmenting Program Comprehension with Remail

The advent of globalization has led to the adoption of distributed software development as a common practice. One of its drawbacks-the absence of impromptu meetings-is tackled with other communication means, such as emails, instant messaging, or forums. Mailing lists have proven to be effective for enabling developers' collaboration and coordination: Being asynchronous, emails can evade time zone barriers, being public, mailing lists maintain developers' awareness, being recorded, email archives offer information on system evolution. Emails can provide information about a task, clarify implementation details, or reveal hidden connections among entities, always within the clear context of a discussion. As a result, we argue that emails might help program comprehension. We devised Remail, an Eclipse plug in to integrate email communication in the IDE. It allows developers to seamlessly handle code entities and emails concerning the source code. Discussions relevant to chosen entities can be retrieved easily, thus providing an updated and effective form of complementary documentation. We present design and implementation of Remail, and illustrate, through a number of scenarios, how it can augment program comprehension.
Protocols.io: Virtual Communities for Protocol Development and Discussion

The detailed know-how to implement research protocols frequently remains restricted to the research group that developed the method or technology. This knowledge often exists at a level that is too detailed for inclusion in the methods section of scientific articles. Consequently, methods are not easily reproduced, leading to a loss of time and effort by other researchers. The challenge is to develop a method-centered collaborative platform to connect with fellow researchers and discover state-of-the-art knowledge. Protocols.io is an open-access platform for detailing, sharing, and discussing molecular and computational protocols that can be useful before, during, and after publication of research results.
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms. They can be easily coamplified with orthologous mtDNA by using conserved universal primers; however, this is especially problematic for DNA barcoding, which attempts to characterize all living organisms by using a short fragment of the mitochondrial cytochrome c oxidase I (COI) gene. Here, we study the effect of numts on DNA barcoding based on phylogenetic and barcoding analyses of numt and mtDNA sequences in two divergent lineages of arthropods: grasshoppers and crayfish. Single individuals from both organisms have numts of the COI gene, many of which are highly divergent from orthologous mtDNA sequences, and DNA barcoding analysis incorrectly overestimates the number of unique species based on the standard metric of 3% sequence divergence. Removal of numts based on a careful examination of sequence characteristics, including indels, in-frame stop codons, and nucleotide composition, drastically reduces the incorrect inferences of the number of unique species, but even such rigorous quality control measures fail to identify certain numts. We also show that the distribution of numts is lineage-specific and the presence of numts cannot be known a priori. Whereas DNA barcoding strives for rapid and inexpensive generation of molecular species tags, we demonstrate that the presence of COI numts makes this goal difficult to achieve when numts are prevalent and can introduce serious ambiguity into DNA barcoding.
Die Morphologie (f): Targeted Lexical Acquisition for Languages other than English

We examine standard deep lexical acquisition features in automatically predicting the gender of noun types and tokens by bootstrapping from a small annotated corpus. Using a knowledge-poor approach to simulate prediction in unseen languages, we observe results comparable to morphological analysers trained specifically on our target languages of German and French. These results describe further scope in analysing other properties in languages displaying a more challenging morphosyntax, in order to create language resources in a language-independent manner.
Rapid quantification of human ABCA1 mRNA in various cell types and tissues by real-time reverse transcription-PCR.

BACKGROUND The ABCA1 gene encodes for a member of subfamily A of the ATP-binding cassette transporters that plays an important role in cellular export of cholesterol and phospholipids; therefore, quantification of the ABCA1 mRNA is critical in many studies related to its expression and regulation by metabolic factors, nutritional status, and new antiatherogenic drug candidates. We developed a rapid, sensitive, specific, and reproducible real-time reverse transcription-PCR (RT-PCR) method for detection and quantification of ABCA1 transcripts in total RNA isolated from cultured human cells and tissues. METHODS To quantify ABCA1 mRNA, we generated a calibration curve from serial dilutions of in vitro-transcribed RNA corresponding to an amplified ABCA1 cDNA 205-bp fragment (homologous calibrator). Two pairs of fluorescent hybridization probes were used to detect the ABCA1 and porphobilinogen deaminase (PBGD) mRNAs; the latter served as an internal control. PCR was performed as real-time amplification of ABCA1 mRNA in 100 ng of total RNA isolated from various human tissues, and cultured cells were calculated from the calibration curve. In addition, normalized values of target (ABCA1/PBGD ratio) were calculated. RESULTS Using this method, we quantified ABCA1 transcripts in various human tissue samples as well as in monocytes, THP-1 cells, fibroblasts, and adipocytes. We demonstrated ABCA1 mRNA up-regulation during human adipocyte and monocyte differentiation. In addition, we examined the effect of cholesterol loading and deloading on ABCA1 expression in monocytes, THP-1 cells, and fibroblasts. CONCLUSIONS Our RT-PCR assay allows the specific and highly reproducible detection and quantification of minute amounts of human ABCA1 mRNA. This new method is more accurate, more informative, and less laborious than the classic RT-PCR methods and Northern blot; it therefore could simplify all studies on ABCA1 mRNA expression.
Pain Relief, Prescription Drugs, and Prosecution: A Four-State Survey of Chief Prosecutors

The experience of having to suffer debilitating pain is far too common in the United States, and many patients continue to be inadequately treated by their doctors. Although many physicians freely admit that their pain management practices may have been somewhat lacking, many more express concern that the prescribing of heightened levels of opioid analgesics may result in closer regulatory scrutiny, criminal investigation, or even criminal prosecution. Although several researchers have examined the regulatory environment and the threat of sanction or harm it poses to physicians and patients, few have examined the likelihood of investigation or prosecution stemming from the aggressive use of opioids in physician-directed pain management. Accordingly, in an effort to assess whether the fear of prosecution is realistic and, if so, what factors contribute to its likelihood, we surveyed chief prosecutors in four states about their knowledge, opinions, and attitudes concerning opioids and the prosecution of physicians stemming from the treatment of patients who were either terminally ill or suffering from chronic noncancer pain.