Miracle-dz/UniFAR-FTUs huggingface dataset:
Design Alternatives for Virtual Interface Architecture and an Implementation on IBM Netfinity NT Cluster

The Virtual Interface Architecture (VIA) specification has been developed to standardize user-level network interfaces that provide low-latency, high-bandwidth communications. Few hardware and software implementations of VIA exist. Since the VIA specification is flexible, different choices exist for implementing various components of VIA such as doorbells, address translation methods, and completion queues. Although previous studies have evaluated the overall performance of different VIA implementations, there has not been a comparative study on the performance of VIA components. In this paper, we evaluate and compare the performance of different implementations of essential VIA components. We discuss the pros and cons of each design approach and describe the required support for implementing each of them. Then, we discuss an experimental implementation of the Virtual Interface Architecture for the IBM SP Switch-Connected NT cluster, one of the newest clustering platforms available. We discuss different design issues involved in this implementation. In particular, we explain how the virtual-to-physical address translation is implemented efficiently with a minimum Network Interface Card (NIC) memory requirement. We show how caching the VIA descriptors on the NIC can reduce the communication latency. We also present an efficient scheme for implementing the VIA doorbells without any hardware support. We provide a comprehensive performance evaluation study and discuss the impact of several hardware improvements on the performance of our implementation. The performance of the implemented VIA surpasses that of other existing software implementations of the VIA and is comparable to that of a hardware VIA implementation. The peak measured bandwidth for our system is 101.4MBytes/s and the one-way latency for short messages is 18.2? s.
A 62dB SFDR, 500MSPS, 15mW Open-Loop Track-and-Hold Circuit

In this work, the design of an open-loop front-end track & hold (T&H) circuit is considered. Advantages of the presented circuit include low power-consumption, high-speed operation, simple reliable design, and ability to operate at low power-supplies. The major problem of open-loop circuits is their relatively poor linearity. In the presented design, high linearity is achieved by applying three linearization techniques: clock boosting (Abo and Gray, 1999), resistive source degeneration (Razavi, 2001), (Ouzounov et al., 2005) and cross-coupling (Ouzounov et al., 2005), (Voorman and Veenstra, 2000). As a result, a linearity corresponding to 10-bit accuracy is achieved. The final design in a 0.18mum CMOS process achieves an SFDR of 62 dB using a sample frequency of 500 MHz while consuming 15mW at a 1.8V power supply
A mixed-solvent strategy for efficient exfoliation of inorganic graphene analogues.

Layered two-dimensional (2D) nanomaterials such as graphene are a conceptually new class of materials that offers new access to low-dimensional physics. Besides wellknown graphene, inorganic graphene analogues (IGAs) such as layered transition metal dichalcogenides (e.g., MoS2 and WS2) [5–7] and boron nitride (BN) have been attracting rapidly increasing attention in the past few years. These IGAs were expected to exhibit unique properties and have great potential in applications like transistors, energy storage, thermal conductors, and topological insulators. Moreover, IGAs like MoS2 and WS2 have intrinsic band gap and high mobility, and may even compete with graphene in certain fields. However, investigations on IGAs have been significantly hindered by the practical difficulties in the preparation and assembly of these 2D nanomaterials. Only a few approaches to obtain few-layered IGAs have been reported. Mechanical exfoliation was first used to obtain layered IGAs from their bulk materials. Other approaches that are being explored include chemical synthesis and liquid exfoliation. Coleman et al. recently reported a surfactant-free liquid-exfoliation method which can produce few-layered nanosheets of IGAs dispersed in various organic solvents. Thermodynamic analysis suggested that, because of the high surface energy of IGAs, the best solvents are likely to have high boiling points. Using nonvolatile solvents makes it difficult to process IGAs into devices, due to the difficulties in the removal of solvent and the occurrence of aggregation during the slow solvent evaporation. To date, liquid exfoliation of layered MoS2 and WS2 in volatile solvent has met with very limited success. Herein we demonstrate a versatile and scaleable mixedsolvent strategy for liquid exfoliation of IGAs, including WS2, MoS2, and BN, in volatile solvents. By choosing solvents with appropriate composition, highly stable IGA suspensions can be obtained in low-boiling solvent mixtures, which can then be easily used in further applications. The dispersion of nanomaterials in liquids can be partially predicted by the theory of Hansen solubility parameters (HSP), which is a semi-empirical correlation developed to explain dissolution behavior. Three HSP parameters are used to describe the character of a solvent or material: dD, dP, and dH, which are the dispersive, polar, and hydrogen-bonding solubility parameters, respectively. The dissolution process is one of adaptation between the HSP parameters of solvents and solutes. The HSP distance Ra is used to evaluate the level of adaptation [Eq. (1)].
7-Ketocholesterol Is an Endogenous Modulator for the Arylhydrocarbon Receptor*

We have identified 7-ketocholesterol (7-KC) as an endogenous modulator that inhibits transactivation by the arylhydrocarbon receptor (AhR) through competitive binding against xenobiotic ligands. 7-KC binds AhR and displaces labeled dioxin (2,3,7,8-tetrachlorodibenzo(p)dioxin (TCDD)). IC50 is 5 × 10− 7 m in vivo and 7 × 10− 6 m in vitro. These figures are consistent with its concentration in human blood plasma and tissues. Association with 7-KC prevents AhR binding to DNA. 7-KC blocks the TCDD-mediated transactivation of stably expressed reporter gene constructs in T47-D cells as well as the expression of the endogenous CYP 1A1 gene in HepG2 cells and in primary porcine aortic endothelial cells. Injection of 7-KC to rats blocks the induction of CYP 1A1 messenger RNA and protein in endothelial cells from myocardial blood vessels. The differential sensitivity of mammalian species to toxic effects of AhR ligands, especially dioxin (TCDD), correlates with the expression of 7-hydroxycholesterol dehydrogenase, which synthesizes 7-KC from 7-hydroxycholesterol. The documented involvement of AhR ligands in cardiovascular diseases through lipid peroxidation and endothelium dysfunction can now be examined in the context of displacement of this protective modulator.
The III-Nitride Double Heterostructure Revisited: Benefits for Threshold Voltage Engineering of MIS Devices

GaN-based devices are seen as ideal candidates for power-switching applications. For the acceptance of GaN-based devices by module designers, obtaining enhancement-mode (e-mode) behavior in GaN-based heterostructure field-effect transistors (HFETs) has long been in the focus. Although the gate-injection approach appears to be the most promising one to achieve e-mode devices, using a double heterostructure in conjunction with a gate insulator has still its advantages, such as steeper turn-ON characteristics and lower leakage currents. An analytical expression to predict the threshold voltage Vth for a given double heterostructure device has not yet been derived. Moreover, neither an evaluation of the tradeoff between Vth and ON-state resistance Rds,ON has been performed to date. This paper addresses these two aspects. We will show an analytical expression for a metal-insulator-semiconductor double HFET (MIS-DHFET), which in certain cases is also valid for the gate-injection transistor. On the basis of this, we will discuss the actual influence of the Al concentration in the backbarrier on Vth. We will further employ technology computer aided design (TCAD) device simulations to evaluate the impact on Rds,ON when using MIS-DHFETs. It will be shown that by implementing a double heterostructure in MIS devices, it is possible to suppress the typically observed negative Vth-oxide thickness relationship while maintaining a constant Rds,ON.
Deoxycholic acid promotes the growth of colonic aberrant crypt foci

AKR/J mice are resistant to the tumorigenic properties of the colon carcinogen, azoxymethane (AOM). Following AOM exposure, limited numbers of preneoplastic lesions, referred to as aberrant crypt foci (ACF), are formed in the colon, and their progression to tumors rarely occurs. To determine whether genetic resistance can be overcome by exposure to a dietary tumor promoter, AOM‐exposed AKR/J mice were fed a diet containing 0.25% deoxycholic acid (DCA). DCA exposure was begun 1 wk prior to or 1 wk after tumor initiation with AOM. Mice placed on the DCA diet prior to AOM treatment developed a significantly higher multiplicity of ACF compared to AOM‐exposed mice fed a control diet (15.50 ± 0.96 vs. 6.17 ± 0.48, respectively; P < 0.05). When DCA exposure was begun after AOM treatment (post‐initiation), ACF formation was further enhanced (34.00 ± 1.22). Interestingly, increased numbers of ACF were associated with the presence of nuclear β‐catenin, assessed by immunohistochemistry. While ∼33% of ACF from mice exposed to DCA prior to AOM treatment contained positive nuclear β‐catenin staining, ∼77% of ACF from mice fed DCA after AOM were positive. Accumulation of nuclear β‐catenin was not associated with a loss of E‐cadherin from the plasma membrane, although loss of APC staining was a consistent feature of most AOM‐induced ACF, regardless of DCA exposure. These results demonstrate that exposure to DCA, an important digestive component, is sufficient to sensitize the resistant AKR/J colon to formation of high‐grade dysplasia, and that nuclear translocation of β‐catenin may play an important role in this process. © 2006 Wiley‐Liss, Inc.
Oral language, written language and language awareness

Ravid & Tolchinsky's paper draws a comprehensive picture of the fact that literacy is a lengthy developing process involving many linguistic factors which sometimes begins even before school age and lasts until adulthood. I very much appreciated the breadth and thoroughness of Ravid & Tolchinsky's paper and, in particular, the fact that they have taken the relationship between oral language and literacy into account. It seems to me that this is rarely the case in current linguistic theories and I would like to offer a few comments on some of the consequences that a serious approach to literacy development would have on the studies of both oral language and literacy, and on linguistic theories themselves as well.
Mosquito Saliva Serine Protease Enhances Dissemination of Dengue Virus into the Mammalian Host

ABSTRACT Dengue virus (DENV), a flavivirus of global importance, is transmitted to humans by mosquitoes. In this study, we developed in vitro and in vivo models of saliva-mediated enhancement of DENV infectivity. Serine protease activity in Aedes aegypti saliva augmented virus infectivity in vitro by proteolyzing extracellular matrix proteins, thereby increasing viral attachment to heparan sulfate proteoglycans and inducing cell migration. A serine protease inhibitor reduced saliva-mediated enhancement of DENV in vitro and in vivo, marked by a 100-fold reduction in DENV load in murine lymph nodes. A saliva-mediated infectivity enhancement screen of fractionated salivary gland extracts identified serine protease CLIPA3 as a putative cofactor, and short interfering RNA knockdown of CLIPA3 in mosquitoes demonstrated its role in influencing DENV infectivity. Molecules in mosquito saliva that facilitate viral infectivity in the vertebrate host provide novel targets that may aid in the prevention of disease.
In regard to: “In vivo strain analysis of the intact supraspinatus tendon by ultrasound speckles tracking imaging” (Journal of Orthopaedic Research, Vol. 29, No. 12, pp. 1931–1937, May 2011)

We read with great interest the recent article by Kim et al. in which an in vivo strain analysis was performed for the supraspinatus tendon using ultrasound speckle tracking. We believe strain tracking using ultrasound is a promising technique in a number of orthopedic applications, including research on shoulder, knee, and ankle functionality. However, strain tracking in 2D ultrasound images of the musculoskeletal system is challenging. Therefore, we would like to provide some remarks on the article by Kim et al. First, we would like to comment on the presentation of the strain tracking methodology. From the article, it is unclear to us how the strain calculations were performed. The article states that ‘‘the motion tracing program’’ was used, but does not provide sufficient details, references, or the origin of this program. From the descriptions, we think we can deduce that the GE EchoPac software was used (Fig. 1c). However, if the GE software was used, why do the authors state that ‘‘Recordings were exported as uncompressed AVI files and imported into Matlab for further analysis’’? Did they have a modified version of the software? In either case, commercial or home-made software, quite a few issues are unclear from the manuscript.
GestureChords: Transparency in gesturally controlled digital musical instruments through iconicity and conceptual metaphor

This paper presents GestureChords, a mapping strategy for chord selection in freehand gestural instruments. The strategy maps chord variations to a series of hand postures using the concepts of iconicity and conceptual metaphor, influenced by their use in American Sign Language (ASL), to encode meaning in gestural signs. The mapping uses the conceptual metaphors MUSICAL NOTES ARE POINTS IN SPACE and INTERVALS BETWEEN NOTES ARE SPACES BETWEEN POINTS, which are mapped respectively to the number of extended fingers in a performer’s hand and the abduction or adduction between them. The strategy is incorporated into a digital musical instrument and tested in a preliminary study for transparency by both performers and spectators, which gave promising results for the technique.
A multicenter, controlled trial of ursodiol for the treatment of primary biliary cirrhosis. UDCA-PBC Study Group.

BACKGROUND In primary biliary cirrhosis the hepatic lesions may result, at least in part, from the intracellular accumulation of potentially toxic endogenous bile acids. Preliminary work suggests that the administration of ursodiol (also called ursodeoxycholic acid), a hydrophilic bile acid without hepatotoxicity, leads to improvement in the condition of patients with primary biliary cirrhosis. METHODS We conducted a two-year, multicenter, double-blind trial to compare the efficacy of ursodiol with that of placebo. Patients with biopsy-proved primary biliary cirrhosis were randomly assigned to receive either ursodiol (13 to 15 mg per kilogram of body weight per day) (n = 73) or placebo (n = 73). Treatment failure was defined as a doubling of bilirubin levels to more than 70 mumol per liter or the occurrence of a severe complication (ascites or variceal bleeding) or an adverse reaction. RESULTS Treatment failed in 6 patients in the ursodiol group, as compared with 13 in the placebo group (P less than 0.01 by Cox regression model). A single patient in each group withdrew because of minor adverse effects. After two years of treatment, the proportion of patients with clinically overt disease decreased only in the ursodiol group (P less than 0.02). The patients treated with ursodiol had significant improvements in serum levels of bilirubin, alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, gamma-glutamyltransferase, cholesterol, and IgM (all P less than 0.001); the antimitochondrial-antibody titer (P less than 0.01); and the Mayo risk score (P less than 0.001). Follow-up analysis of 95 liver-biopsy specimens showed a significant improvement in the mean histologic score (P less than 0.002) and in all the characteristic histologic features except fibrosis only in the group given ursodiol. CONCLUSIONS Ursodiol is a safe and effective treatment for primary biliary cirrhosis.
Toll-Like Receptor 2-Dependent Inhibition of Macrophage Class II MHC Expression and Antigen Processing by 19-kDa Lipoprotein of Mycobacterium tuberculosis1

Mycobacterium tuberculosis (MTB) induces vigorous immune responses, yet persists inside macrophages, evading host immunity. MTB bacilli or lysate was found to inhibit macrophage expression of class II MHC (MHC-II) molecules and MHC-II Ag processing. This report characterizes and identifies a specific component of MTB that mediates these inhibitory effects. The inhibitor was extracted from MTB lysate with Triton X-114, isolated by gel electroelution, and identified with Abs to be MTB 19-kDa lipoprotein. Electroelution- or immunoaffinity-purified MTB 19-kDa lipoprotein inhibited MHC-II expression and processing of both soluble Ags and Ag 85B from intact MTB bacilli. Inhibition of MHC-II Ag processing by either MTB bacilli or purified MTB 19-kDa lipoprotein was dependent on Toll-like receptor (TLR) 2 and independent of TLR 4. Synthetic analogs of lipopeptides from Treponema pallidum also inhibited Ag processing. Despite the ability of MTB 19-kDa lipoprotein to activate microbicidal and innate immune functions early in infection, TLR 2-dependent inhibition of MHC-II expression and Ag processing by MTB 19-kDa lipoprotein during later phases of macrophage infection may prevent presentation of MTB Ags and decrease recognition by T cells. This mechanism may allow intracellular MTB to evade immune surveillance and maintain chronic infection.
Efficient Stochastic Scheduling for Simulation of Wind-Integrated Power Systems

Time-domain scheduling simulation is the most effective tool for predicting the operational costs in wind-integrated power systems, because it can represent the inter-temporal constraints that limit the balancing actions of the thermal plant, storage, and demand-side measures. High wind penetrations demand just-in-time commitment decisions that reflect the uncertainties in the wind infeed, so that it is desirable to generate the scheduling decisions using stochastic unit commitment (SUC) with rolling planning. However, the computational burden can make such methods impractical in long simulations. We present an efficient formulation of the SUC problem that is designed for use in scheduling simulations of single-bus power systems. Unlike traditional SUC techniques, the proposed formulation uses a quantile-based scenario tree structure that avoids the need for exogenous operating reserves. We compare the performance of various tree topologies in year-long simulations of a large system. Simple quantile-based trees give statistically significant cost improvements over fixed-quantile deterministic methods and compare favorably with trees based on Monte Carlo-generated scenarios.
Inhibition of MRP1/ABCC1, MRP2/ABCC2, and MRP3/ABCC3 by Nucleoside, Nucleotide, and Non-Nucleoside Reverse Transcriptase Inhibitors

Many drug interactions with drugs used for the therapy of human immunodeficiency virus (HIV) occur at the level of different cytochrome P450 isozymes. Increasing evidence suggests that antiretrovirals may also modify activity and expression of active drug transport systems. Such interactions may alter drug absorption, elimination, and also drug distribution and reach clinical importance if thereby access to the target site is affected. Beyond P-glycoprotein, the family of multidrug resistance-related proteins (MRP/ABCC) substantially contributes to the elimination of numerous drugs and their metabolites. Because the interaction of MRPs with non–HIV protease inhibitor antiretrovirals has not been studied thoroughly, we investigated whether important non-nucleoside reverse transcriptase inhibitors (NNRTI) (delavirdine, efavirenz, and nevirapine), nucleoside reverse transcriptase inhibitors (NRTI) (abacavir, emtricitabine, and lamivudine), and tenofovir as a nonnucleotide reverse transcriptase inhibitor can interact with MRP1, MRP2, and MRP3 in vitro. Inhibition of these ABC transporters was quantified by confocal laser-scanning microscopy using the 5-chloromethylfluorescein diacetate assay. With the exception of abacavir, which had no effect on MRP3, all the test compounds increased intracellular 5-chloromethylfluorescein fluorescence in a concentration-dependent manner, and this effect was observed in all the overexpressing cell lines but not in the parental cell line, indicating inhibition of MRP1, MRP2, and MRP3. In conclusion, the present study provides the first evidence for a significant and concentration-dependent inhibition of MRPs by NNRTI, NRTI, and tenofovir, which was most pronounced for delavirdine, efavirenz, and emtricitabine, suggesting that this might contribute to some of the known drug interactions impairing HIV therapy and also to the superior effectiveness of combination pharmacotherapy.
Differentiation and cytokinetic analyses of normal and neoplastic lymphoid cells in B and T cell malignancies of childhood

The labelling index (LI) of untreated B cell non‐Hodgkin's lymphoma (B NHL) in children was significantly higher (P< 0.002) than the LI of untreated T cell malignancies (median LI 27‐7% and 10 3%, respectively). In B NHL abdominal tumour material showed a significantly higher in vitro incorporation of tritiated thymidine (3H‐dT) than extra‐abdominal tumour material (P±0 01). Sequential immunological, cytochemical and cytokinetic studies revealed tumour cells in up to three marker‐defined subpopulations of lymphoid cells. In all 14 patients examined the LI of E−Ia+sIgM+ cells was higher than the LI of E+Ia+/‐ sIgM− cells; in all eight patients with Ia+ and la− tumour cells the former had a higher LI than the latter (P<0‐002).
Gene targeting in human somatic cells. Complete inactivation of an interferon-inducible gene.

The role, if any, of the human interferon-inducible 6-16 gene in the establishment of a cellular antiviral state is unknown. To address this problem, and as part of a wider investigation of homologous recombination (HR) and its applications in somatic cells, we have been using HR to disrupt the 6-16 gene in human cell lines [Itzhaki, J. E. & Porter, A. C. G. (1991) Nucleic Acids Res. 19, 3835-3842. ] We describe here the design and use of insertion and replacement-type targeting constructs based on a promoterless bacterial gpt gene that is activated by HR with the 6-16 gene. In HeLa cells, both targeting constructs underwent extrachromosomal HR with a cotransfected plasmid carrying the 6-16 gene. In a previously targeted clone derived from the fibrosarcoma cell line HT1080, the replacement construct underwent HR with either the modified or the unmodified 6-16 allele. The latter events generated doubly disrupted (6-16-/-) clones that failed to express any detectable 6-16 messenger RNA in response to interferon. Plaque assays of infected 6-16-/- cells showed that expression of the 6-16 gene was not required for the induction by interferon of an antiviral state against encephalomyocarditis virus, semliki forest virus or cocal virus.
Site Selection to Improve the Chinese Observation Network for Spacecraft Phase Referencing Imaging

Phase referencing imaging is a method newly used to determine the position of a spacecraft. But the bad (u, v) coverage formed by Chinese observation stations affects its real time performance due to the lack of stations. To improve the observation network, firstly, this paper established the relationship between the station configuration and the image obtained from the phase referencing technique. Then, two site selection schemes were proposed and corresponding simulations have been conducted. The results show that the new sites selected by our method can generate much better (u, v) coverage and the position deamination of the spacecraft with one minute observation is possible.