gebhart/patrepeval huggingface dataset:
Signaling completion of a message transfer from an origin compute node to a target compute node (2023)

Signaling completion of a message transfer from an origin node to a target node includes: sending, by an origin DMA engine, an RTS message, the RTS message specifying an application message for transfer to the target node from the origin node; receiving, by the origin DMA engine, a remote get message containing a data descriptor for the message and a completion notification descriptor, the completion notification descriptor specifying a local memory FIFO data transfer operation for transferring data locally on the origin node; inserting, by the origin DMA engine in an injection FIFO buffer, the data descriptor followed by the completion notification descriptor; transferring, by the origin DMA engine to the target node, the message in dependence upon the data descriptor; and notifying, by the origin DMA engine, the application that transfer of the message is complete in dependence upon the completion notification descriptor.
Significance of the nitric oxide cascade in erectile function (2000)

In recent years, a significant body of experimental evidence has accumulated implicating nitric oxide as the central component of a novel signal transduction system that functions in the penis to mediate penile erection. The involvement of nitric oxide in erection physiology appears to be quite complex, involving multiple regulatory interactions: this gaseous molecule has been found to trigger several biochemical events that elicit erectile tissue responses, while a host of modulatory factors have been identified that influence its release and action in erectile tissue. Ongoing investigations in nitric oxide biology in other organ systems also suggest mechanisms which, while yet to be fully established in the penis, may operate significantly to determine the role of nitric oxide in this organ. Further elucidation of cellular and molecular interactions involving nitric oxide effects in the penis can be expected to reveal diverse targets that may serve as a basis for novel pharmacotherapeutic strategies for the future management of erectile dysfunction.
Practical implementation of robust MR-thermometry during clinical MR-guided microwave ablations in the liver at 1.5 T (2019)

Practical non-invasive equipment modifications and effective acquisition methods to achieve robust and reliable real-time MR thermometry for monitoring of clinical hepatic microwave ablations were implemented. These included selection of the microwave generator location (inside versus outside the MR scan room), the number of radiofrequency chokes added to the microwave generator's coaxial lines, and the use of copper wool to maximize their electrical grounding. Signal-to-noise ratio (SNR) of MR thermometry images of a small fluid-filled phantom acquired during activation of microwave antenna were used to evaluate image quality as a function of each modification. SNR measurements corresponding to both locations of the microwave generator were comparable and so it was located outside the MR scan room. For this location, addition of one RF choke on the power and four chokes on the sensor coaxial lines was found to be optimal, corresponding to a 68% increase in SNR. Furthermore, image quality strongly depended on the proper electrical grounding of the power and sensor lines. SNR ratio (relative to SNR of baseline images) during activation of microwave generator was found to be 0.49 ± 0.28 without adequate grounding, and 0.88 ± 0.08 with adequate grounding (p = 0.002, Student's t-test). These SNR measurements were sufficiently sensitive to detect issues related to equipment performance and hence formed part of the quality assurance testing performed prior to each clinical treatment. Incorporating these non-invasive approaches resulted in significant improvements to image quality and, importantly while maintaining the clinical integrity of the microwave system which is of paramount importance in a highly regulated healthcare environment.
On Losses of Performance in a Joint Source Channel Coder (2006)

A joint source channel coder (JSCC) for image transmission over an additive white Gaussian noise (AWGN) channel is presented, and analyzed with respect to the loss of performance due to practical limitations. It is shown how the non-optimality of dimensional changing mappings, and having a limited set of them, effects the overall performance of the system. From this analysis, an additional mapping is proposed
Gluing Ionic Liquids to Oxide Surfaces: Chemical Anchoring of Functionalized Ionic Liquids by Vapor Deposition onto Cobalt(II) Oxide (2017)

Ionic liquids (IL) hold a great potential as novel electrolytes for applications in electronic materials and energy technology. The functionality of ILs in these applications relies on their interface to semiconducting nanomaterials. Therefore, methods to control the chemistry and structure of this interface are the key to assemble new IL-based electronic and electrochemical materials. Here, we present a new method to prepare a chemically well-defined interface between an oxide and an IL film. An imidazolium-based IL, which is carrying an ester group, is deposited onto cobalt oxide surface by evaporation. The IL binds covalently to the surface by thermally activated cleavage of the ester group and formation of a bridging carboxylate. The anchoring reaction shows high structure sensitivity, which implies that the IL film can be adhered selectively to specific oxide surfaces.
Idelalisib in Waldenström macroglobulinemia: high incidence of hepatotoxicity (2016)

Waldenstrom macroglobulinemia (WM) is a rare B-cell lymphoma characterized by the accumulation of IgM-secreting lymphoplasmacytic cells.[1] Despite therapeutic advances, WM remains incurable, and n...
Evaluation of Perceived Threat Differences Posed by Filovirus Variants (2011)

In the United States, filoviruses (ebolaviruses and marburgviruses) are listed as National Institute of Allergy and Infectious Diseases (NIAID) Category A Priority Pathogens, Select Agents, and Centers for Disease Control and Prevention (CDC) Category A Bioterrorism Agents. In recent months, U.S. biodefense professionals and policy experts have initiated discussions on how to optimize filovirus research in regard to medical countermeasure (ie, diagnostics, antiviral, and vaccine) development. Standardized procedures and reagents could accelerate the independent verification of research results across government agencies and establish baselines for the development of animal models acceptable to regulatory entities, such as the Food and Drug Administration (FDA), while being fiscally responsible. At the root of standardization lies the question of which filovirus strains, variants, or isolates ought to be the prototypes for product development, evaluation, and validation. Here we discuss a rationale for their selection. We conclude that, based on currently available data, filovirus biodefense research ought to focus on the classical taxonomic filovirus prototypes: Marburg virus Musoke in the case of marburgviruses and Ebola virus Mayinga in the case of Zaire ebolaviruses. Arguments have been made in various committees in favor of other variants, such as Marburg virus Angola, Ci67 or Popp, or Ebola virus Kikwit, but these rationales seem to be largely based on anecdotal or unpublished and unverified data, or they may reflect a lack of awareness of important facts about the variants' isolation history and genomic properties.
The effect of complex stoichiometry in supramolecular chirality transfer to zinc bisporphyrin systems (2008)

The self-assembly of Zn-bisporphyrin tweezers induced by coordination to enantiopure 1,2-diaminocyclohexane features supramolecular chirality induction and inversion processes that are exclusively controlled by the stoichiometry of the assembled complexes.
Interactions Between Structural Remodeling and Hypertrophy in the Right Ventricle in Response to Pulmonary Arterial Hypertension (2019)

Pulmonary arterial hypertension (PAH) exerts substantial pressure overload on the right ventricle (RV), inducing RV remodeling and myocardial tissue adaptation often leading to right heart failure. The associated RV free wall (RVFW) adaptation involves myocardial hypertrophy, augmented intrinsic contractility, collagen fibrosis, and structural remodeling in an attempt to cope with pressure overload. If RVFW adaptation cannot maintain the RV stroke volume (SV), RV dilation will prevail as an exit mechanism, which usually decompensates RV function, leading to RV failure. Our knowledge of the factors determining the transition from the upper limit of RVFW adaptation to RV decompensation and the role of fiber remodeling events such as extracellular fibrosis and fiber reorientation in this transition remains very limited. Computational heart models that connect the growth and remodeling (G&R) events at the fiber and tissue levels with alterations in the organ-level function are essential to predict the temporal order and the compensatory level of the underlying mechanisms. In this work, building upon our recently developed rodent heart models (RHM) of PAH, we integrated mathematical models that describe volumetric growth of the RV and structural remodeling of the RVFW. The time-evolution of RV remodeling from control and post-PAH time points was simulated. The results suggest that the augmentation of the intrinsic contractility of myofibers, accompanied by an increase in passive stiffness of RVFW, is among the first remodeling events through which the RV strives to maintain the cardiac output. Interestingly, we found that the observed reorientation of the myofibers toward the longitudinal (apex-to-base) direction was a maladaptive mechanism that impaired the RVFW contractile pattern and advanced along with RV dilation at later stages of PAH. In fact, although individual fibers were more contractile post-PAH, the disruption in the optimal transmural fiber architecture compromised the effective contractile function of the RVFW, contributing to the depressed ejection fraction (EF) of the RV. Our findings clearly demonstrate the critical need for developing multiscale approaches that can model and delineate relationships between pathological alterations in cardiac function and underlying remodeling events across fiber, cellular, and molecular levels.
First dual-vessel high-repeat GoM 4D survey shows development options at Holstein Field (2008)

In the Gulf of Mexico (GoM), loop and eddy currents can cause large errors in 4D shot and receiver locations between baseline and repeat streamer surveys, which invariably lead to poor data quality. In a recent 4D acquisition, a dual-vessel 3D acquisition method addressed the repeatability problem and showed reliable time-lapse measurements over Holstein Field. The time-lapse seismic data show time shifts up to 6 ms over depleting sands and amplitude changes over swept and compacted sands. This 4D information has improved understanding of the field and can support optimal placement of injection and production wells.
LaPO4 Nanoparticles Doped with Actinium-225 that Partially Sequester Daughter Radionuclides (2011)

Nanoscale materials have been envisioned as carriers for various therapeutic drugs, including radioisotopes. Inorganic nanoparticles (NPs) are particularly appealing vehicles for targeted radiotherapy because they can package several radioactive atoms into a single carrier and can potentially retain daughter radioisotopes produced by in vivo generators such as actinium-225 ((225)Ac, t(1/2) = 10 d). Decay of this radioisotope to stable bismuth-209 proceeds through a chain of short-lived daughters accompanied by the emission of four α-particles that release >27 MeV of energy. The challenge in realizing the enhanced cytotoxic potential of in vivo generators lies in retaining the daughter nuclei at the therapy site. When (225)Ac is attached to targeting agents via standard chelate conjugation methods, all of the daughter radionuclides are released after the initial α-decay occurs. In this work, (225)Ac was incorporated into lanthanum phosphate NPs to determine whether the radioisotope and its daughters would be retained within the dense mineral lattice. Further, the (225)Ac-doped NPs were conjugated to the monoclonal antibody mAb 201B, which targets mouse lung endothelium through the vasculature, to ascertain the targeting efficacy and in vivo retention of radioisotopes. Standard biodistribution techniques and microSPECT/CT imaging of (225)Ac as well as the daughter radioisotopes showed that the NPs accumulated rapidly in mouse lung after intravenous injection. By showing that excess, competing, uncoupled antibodies or NPs coupled to control mAbs are deposited primarily in the liver and spleen, specific targeting of NP-mAb 201B conjugates was demonstrated. Biodistribution analysis showed that ∼30% of the total injected dose of La((225)Ac)PO(4) NPs accumulated in mouse lungs 1 h postinjection, yielding a value of % ID/g >200. Furthermore, after 24 h, 80% of the (213)Bi daughter produced from (225)Ac decay was retained within the target organ and (213)Bi retention increased to ∼87% at 120 h. In vitro analyses, conducted over a 1 month interval, demonstrated that ∼50% of the daughters were retained within the La((225)Ac)PO(4) NPs at any point over that time frame. Although most of the γ-rays from radionuclides in the (225)Ac decay chain are too energetic to be captured efficiently by SPECT detectors, appropriate energy windows were found that provided dramatic microSPECT images of the NP distribution in vivo. We conclude that La((225)Ac)PO(4)-mAb 201B conjugates can be targeted efficiently to mouse lung while partially retaining daughter products and that targeting can be monitored by biodistribution techniques and microSPECT imaging.
Do superconducting processors really need cryogenic memories? (2017)

Cryogenic, superconducting digital processors offer the promise of greatly reduced operating power for server-class computing systems. This is due to the exceptionally low energy per operation of Single Flux Quantum circuits built from Josephson junction devices operating at the temperature of 4 Kelvin. Unfortunately, no suitable same-temperature memory technology yet exists to complement these SFQ logic technologies. Possible memory technologies are in the early stages of development but will take years to reach the cost per bit and capacity capabilities of current semiconductor memory. We discuss the pros and cons of four alternative memory architectures that could be coupled to SFQ-based processors. Our feasibility studies indicate that cold memories built from CMOS DRAM and operating at 77K can support superconducting processors at low cost-per-bit, and that they can do so today.
A Testis-Specific Gene Encoding a Nuclear High-Mobility-Group Box Protein Located in Elongating Spermatids (1993)

A cDNA encoding a DNA-binding protein has been isolated by screening a mouse testicular expression cDNA library with a concatemer of a 12-bp putative protein-binding element present in the promoter of the testis-specific gene PGK-2. Sequence analysis of the isolated cDNA indicated the presence of an open reading frame that encodes a protein with two conserved DNA-binding motifs known as the high-mobility-group (HMG) boxes. Northern (RNA) blot analysis demonstrated that expression of the gene is restricted to the postpuberal testis. The DNA-binding activity and sequence specificity of the recombinant HMG protein were confirmed by DNA mobility shift assay using the initial concatemer of the PGK-2 promoter element as a probe as well as the wild-type or mutated versions of the 12-bp element within its natural sequence context. Immunocytochemical staining of adult testis sections with polyclonal antisera recognizing this recombinant HMG protein demonstrated that it is located predominantly in the nuclei of elongated spermatids at steps 9 and 10. These results suggest that this novel HMG box protein gene may be involved in the regulation of gene expression of the haploid male genome. The gene from which the cDNA was derived has been termed testis-specific HMG (tsHMG).
Characterization of Complementary DNA Encoding the Precursor for Gonadotropin-Releasing Hormone and Its Associated Peptide from a Teleost Fish (1991)

Reproductive maturity among male African cichlids Haplochromis burtoni is cued by a series of environmental and social interactions and is mediated physiologically by GnRH. A cDNA clone encoding the precursor for GnRH was isolated from this teleost. The molecular architecture of the predicted prohormone is analogous to that of the previously characterized mammalian forms; however, the predicted sequence of the associated peptide is strikingly different. Attempts to isolate a putative second precursor using low stringency hybridization were not successful despite evidence that a second related decapeptide exists in at least some teleost species.
Mobility Investigations on Strained 30-nm High-<inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> Metal Gate MOSFETs by Geometrical Magnetoresistance Effect (2015)

In this paper, we present mobility investigations of strained nMOS and pMOS short-channel transistors with dimensions down to 30-nm gate length. Using the geometrical magnetoresistance (MR) effect, carrier mobility of electrons and holes in the inversion channel of a recent state-of-the-art CMOS technology is presented from linear to saturation operation conditions. The MR effect allows for a more direct access to the carrier mobility compared with the conventional current/voltage and capacitance/voltage mobility derivation methods, in which series resistance, inversion charge density, and effective channel length are necessary to extract the mobility values of the short-channel devices. In another way, the MR effect can help to disentangle the performance gain of the strained state-of-the art devices to changes in channel mobility or device connection, e.g., series resistance effects.
Drug screening identifies tazarotene and bexarotene as therapeutic agents in multiple sulfatase deficiency (2023)

Multiple sulfatase deficiency (MSD, MIM #272200) results from pathogenic variants in the SUMF1 gene that impair proper function of the formylglycine-generating enzyme (FGE). FGE is essential for the posttranslational activation of cellular sulfatases. MSD patients display reduced or absent sulfatase activities and, as a result, clinical signs of single sulfatase disorders in a unique combination. Up to date therapeutic options for MSD are limited and mostly palliative. We performed a screen of FDA-approved drugs using immortalized MSD patient fibroblasts. Recovery of arylsulfatase A activity served as the primary readout. Subsequent analysis confirmed that treatment of primary MSD fibroblasts with tazarotene and bexarotene, two retinoids, led to a correction of MSD pathophysiology. Upon treatment, sulfatase activities increased in a dose- and time-dependent manner, reduced glycosaminoglycan content decreased and lysosomal position and size normalized. Treatment of MSD patient derived induced pluripotent stem cells (iPSC) differentiated into neuronal progenitor cells (NPC) resulted in a positive treatment response. Tazarotene and bexarotene act to ultimately increase the stability of FGE variants. The results lay the basis for future research on the development of a first therapeutic option for MSD patients.
Occidiofungin, an actin binding antifungal with in vivo efficacy in a vulvovaginal candidiasis infection (2018)

Abstract Current antifungal treatment options are plagued with rapidly increasing occurrence of resistance, high degree of toxicity and a limited spectrum of activity. The need to develop a novel antifungal with a unique target, wider spectrum of activity, and reduced toxicity to the host, is urgent. We have identified and characterized one such compound named occidiofungin that is produced by the soil bacterium Burkholderia contaminans MS14. This study identifies the primary cellular target of the antifungal, which was determined to be actin. Actin binding metabolites are generally characterized by their ability to inhibit polymerization or depolymerization of actin filaments, which presumably accounts for their severe toxicity. Occidiofungin, instead, has a subtler effect on actin dynamics that triggers apoptotic cell death. We were able to demonstrate the effectiveness of the antifungal in treating a vulvovaginal yeast infection in a murine model. This discovery puts occidiofungin in a unique class of actin-binding antifungal compounds with minimal reported toxicity to the host. The results of this study are important for the development of a novel class of antifungals that could fill the existing gap in treatment options for fungal infections. Author summary Widespread resistance to antifungal compounds currently in use has been alarming. Identification and development of a new class of antifungals with a novel cellular target is desperately needed. This study describes the assays carried out to determine the molecular target and evaluate efficacy of one such novel antifungal compound called occidiofungin. Occidiofungin modified with a functional alkyne group enabled affinity purification assays and localization studies in yeast. These studies led to the identification of the actin binding property of occidiofungin. Actin-binding by secondary metabolites often exhibit severe host toxicity, but this does not appear to be the case for occidiofungin. We have previously been able to administer occidiofungin to mice at concentrations in the range of 5 mg/kg without any serious complications. We were able to demonstrate the effectiveness of the antifungal in treating a vaginal fungal infection in a murine model. The results outlined in this manuscript establish that occidiofungin is an efficacious compound with a novel molecular target, putting it in a completely new class of antifungals.
A new approach for the estimation of the porosity in NMR (2011)

In this paper we describe a new approach for the estimation of the porosity and its uncertainty from Nuclear Magnetic Resonance relaxation measurements in porous media. The new approach is based on the Fourier transform of the measured data in √t domain. This approach was found to work reasonably well and had a smaller bias and variance in comparison to traditional methods of computing the porosity.
Preparation, properties, and some chemical reactions of phenaleno[1,9-bc]furan (1988)

The synthesis of hitherto unknown phenaleno[1,9-bc]furan (1), in 11% overall yield from 2-naphthol, has been achieved. Its 1H and 13C n.m.r. spectra have been fully assigned by means of heteronuclear 2D correlations. The furanoid moiety of (1) displays Diels–Alder diene reactivity in its reactions with benzyne, dimethyl acetylenedicarboxylate, and singlet oxygen. The furan ring of (1) also suffers oxidation by m-chloroperbenzoic acid and undergoes catalytic hydrogenation. This chemistry appears to be more characteristic of naphtho[1,2-c]furan than of naphtho[1,2-b]furan although both structural units co-exist in structure (1).
An Exceptionally Stable Ti Superoxide Radical Ion: A Novel Heterogeneous Catalyst for the Direct Conversion of Aromatic Primary Amines to Nitro Compounds (2001)

A matrix-bound superoxide radical anion, generated by treating Ti(OR)<sub>4</sub> (R=iPr, nBu) with H<sub>2</sub> O<sub>2</sub> , is a selective heterogeneous catalyst for the oxidation of anilines to the corresponding nitroarenes with 50 % aqueous H<sub>2</sub> O<sub>2</sub> [Eq. (1)]. Yields of 82-98 % are obtained, even with anilines bearing electron-withdrawing substituents (R=NO<sub>2</sub> , COOH).