gebhart/patrepeval huggingface dataset:
Failure Propagation Modeling Based on Contracts Theory (2015)

Previous approaches to fault and failure modeling are based on adding explicit models of faults/failures, and failure propagation to behavioral and architectural modes. This adds a lot of overhead (extra work), and also, is a cause of creating inconsistencies, especially by obtaining a mismatch between failures and violation of requirements or specifications. Instead of creating separate models for failures, the idea here is to exploit the fundamental definition of failures as violation of requirement or specification. We assume that the systems functionality is specified using a set of requirements, and in particular, requirements structured according to contracts theory. Instead of creating separate models for failure propagation, we exploit the structuring of requirements obtained when the system is specified using contracts theory. The use of contracts theory establishes a formal framework for how traceability links between requirements themselves and to the architecture are specified. It is further explained how fault and failure propagation models in the form of Bayesian Networks are obtained. One particular challenge is the modeling of faults/failure and their propagation when fault management mechanisms have been implemented. Therefore this area is covered in some extra depth.
Detection of Nuclease Activity in Semisolid and Broth Cultures1 (1969)

A method for the detection of deoxyribonuclease activity in semisolid agar cultures was investigated. When cultures were overlaid with an acridine orangedeoxyribonucleate-agar (ADA) mixture, incubated for 1 to 3 hr, and observed under ultraviolet light, clear halos developed around colonies that produced deoxyribonuclease. A variation of the method for use with broth cultures involved impregnation of filter-paper discs with a small portion of the culture and overlaying the discs with the ADA mixture. This alteration has the advantage that the test tube cultures are easily heat-treated prior to assay to determine the heat resistance of the enzyme.
Identification of growth factor conditions that reduce ex vivo cord blood progenitor expansion but do not alter human repopulating cell function in vivo. (2005)

The use of minimal cytokine stimulation and simultaneous assessment of CFU and SRC indicate that hematopoietic progenitors and in vivo-detected repopulating cells are differentially responsive to TPO; CFU expand in response to TPO but SRC do not. In addition, our study suggests that TPO can functionally replace IL-3+IL-6+G-CSF for CFU expansion of ex vivo cultured CB Lin-CD34+CD38- hematopoietic stem cells.
Compact high-power diode laser pump modules for intersatellite communications (2003)

High reliable diode laser pump modules are essential for free-space optical telecommunications. Besides the reliability, low mass and small dimensions, radiation-hardness and low power-consumption are requirements to be met for space applications. A diode laser module suited for pumping Nd:YAG lasers for optical intersatellite links has been developed. The module consists of two diode laser bars overlaid by a polarization beam splitter to increase the system’s reliability. Each diode laser bar consists of six emitters. If the integrated photodiode detects the failure of one bar, the second, substitute bar is switched on and can fully sustain all module functions. To equalize the beam quality of the diode laser bar, a pair of micro step mirrors is used for each bar. The laser beam is focussed on the entrance of a d=200 &mu;m, NA=0.22 fiber. Both the coupling efficiency and the accuracy of the mounting of the diode laser components have been analyzed by raytracing. Passive cooling has been chosen because liquid chilling systems are unsuitable for space applications. To evaluate the effects of different heat sink materials and to predict the temperature drop over the module, a 3D finite element analysis for the steady-state temperature distribution of the module has been performed. The optical output power of the module described above amounts to 2,8 W with one bar operating derated to 0.5x maximum current, and the whole unit fits in a housing of 78 x 50 x 24 mm. Further developments will lead to a more compact design and a smaller fiber diameter.
Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D (2021)

Protein N-terminal acetyltransferase D (NatD, NAA40) that specifically acetylates the alpha-N-terminus of histone H4 and H2A has been implicated in various diseases, but no inhibitor has been reported for this important enzyme. Based on the acetyl transfer mechanism of NatD, we designed and prepared a series of highly potent NatD bisubstrate inhibitors by covalently linking coenzyme A to different peptide substrates via an acetyl or propionyl spacer. The most potent bisubstrate inhibitor displayed an apparent <i>K</i><sub>i</sub> value of 1.0 nM. Biochemical studies indicated that bisubstrate inhibitors are competitive to the peptide substrate and noncompetitive to the cofactor, suggesting that NatD undergoes an ordered Bi-Bi mechanism. We also demonstrated that these inhibitors are highly specific toward NatD, displaying about 1000-fold selectivity over other closely related acetyltransferases. High-resolution crystal structures of NatD bound to two of these inhibitors revealed the molecular basis for their selectivity and inhibition mechanism, providing a rational path for future inhibitor development.
B Cell Abnormalities in Systemic Lupus Erythematosus and Lupus Nephritis—Role in Pathogenesis and Effect of Immunosuppressive Treatments (2019)

Abnormalities in B cells play pivotal roles in the pathogenesis of systemic lupus erythematosus (SLE) and lupus nephritis (LN). Breach in central and peripheral tolerance mechanisms generates autoreactive B cells which contribute to the pathogenesis of SLE and LN. Dysregulation of B cell transcription factors, cytokines and B cell-T cell interaction can result in aberrant B cell maturation and autoantibody production. These immunological abnormalities also lead to perturbations in circulating and infiltrating B cells in SLE and LN patients. Conventional and novel immunosuppressive medications confer differential effects on B cells which have important clinical implications. While cyclophosphamide and mycophenolate mofetil (MMF) showed comparable clinical efficacy in active LN, MMF induction was associated with earlier reduction in circulating plasmablasts and plasma cells. Accumulating evidence suggests that MMF maintenance is associated with lower risk of disease relapse than azathioprine, which may be explained by its more potent and selective suppression of B cell proliferation. Novel therapeutic approaches targeting the B cell repertoire include B cell depletion with monoclonal antibodies binding to cell surface markers, inhibition of B cell cytokines, and modulation of costimulatory signals in B cell-T cell interaction. These biologics, despite showing improvements in serological parameters and proteinuria, did not achieve primary endpoints when used as add-on therapy to standard treatments in active LN patients. Other emerging treatments such as calcineurin inhibitors, mammalian target of rapamycin inhibitors and proteasome inhibitors also show distinct inhibitory effects on the B cell repertoire. Advancement in the knowledge on B cell biology has fueled the development of new therapeutic strategies in SLE and LN. Modification in background treatments, study endpoints and selective recruitment of subjects showing aberrant B cells or its signaling pathways when designing future clinical trials may better elucidate the roles of these novel therapies for SLE and LN patients.
Bradykinin B1receptor expression and function on T lymphocytes in active multiple sclerosis (1999)

The authors demonstrate that B1 receptors are upregulated by T lymphocytes during the course of MS and that signaling through this receptor with a B1 agonist can negatively regulate T-cell migration in vitro.
Multicolor immunofluorescence and flow cytometry utilizing cascade blue to purify murine hematopoietic stem cells from fetal liver and bone marrow (1999)

Despite the fact that the CB antibody conjugate has a tendency to adhere specifically to a B cell subpopulation in bone marrow, we nevertheless could purify stem cells by using CB for the detection and elimination of lineage positive cells. Isolated stem cells from mouse fetal liver (Lin-CD34(+)Sca-1(+)c-Kit(high)) and adult bone marrow (Lin-CD34(-/low)Sca-1(+)c-Kit(+)) were transplanted into lethally irradiated mice, and the sorted stem cells had the ability to efficiently repopulate all mature hematopoietic lineages in recipient mice.
Forces at flange–web connections in T-beams (1984)

The flanges of T- and I-beams are subjected, near their junctions with the web, to three in-plane forces: N x , N y , and N xy , where x and y are horizontal axes parallel and normal to the beam axis. The finite element method is used to study the variation of these forces in T-beams under point or line load. It is concluded that forces N x and N xy can be determined for design purposes using conventional engineering beam theory. Force N y , on the other hand, cannot be determined by available closed-form solutions. Based on a detailed parametric study, a simplified procedure is proposed for determining N y . Key words: beams (supports), connections, finite element, flanges, loads (forces), T-beams, webs (supports).
A GALS FFT processor with clock modulation for low-EMI applications (2010)

With the growth in complexity of digital CMOS circuits, the steep current fluctuations introduced by numerous transistors switching with clock signals are proven to be a significant source of electromagnetic interference (EMI). In recent years the reduction in EMI noise from high speed digital ICs has already gained intensive research attention. In this paper the pausible clocking based globally asynchronous locally synchronous (GALS) design with phase and frequency modulation on the locally generated clocks is proposed as a systematic solution to EMI reduction. As a practical example, a 64-point Radix-2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> pipelined GALS FFT processor was implemented using the IHP 130nm CMOS technology for low-EMI applications. The on-chip measurements demonstrate 13dB attenuation at the clock fundamental frequency and more than 20dB attenuation at higher clock harmonics, in comparison with the synchronous design.
Incident "Quick Clearance" Legislation: Will It Effectively Reduce Congestion? (2007)

Innovative incident management strategies have been sought by transportation professionals to minimize the impacts of incidents on traffic operation and safety. More agencies will move to adopt these strategies as information becomes available regarding how well these tools can mitigate the current traffic problems faced in every major metropolitan area of the United States. Some current “quick clearance” strategies, such as “Steer It and Clear It” legislation in South Carolina, which requires driver(s) of the involved vehicle(s) in a minor incident to move vehicles promptly from the traveled roadway prior to the arrival of the first responders, can potentially reduce the duration of an incident. The research detailed in this paper endeavored to measure the benefit of the Steer It and Clear It law on one particular freeway network in South Carolina. A simulation analysis, using a microscopic traffic simulation platform PARAMICS, suggested that by implementing the Steer It and Clear It legislation that resulted in reduced incident clearance time, the total traffic delay can be reduced by 11 percent for minor incidents with one lane blocked. This reduced delay in turn resulted in an average cost savings of $1,682 per incident, which is significant when considering the number of minor incidents occurring on a daily basis in large metropolitan areas. Besides affecting congestion and its associated problems, reducing the incident duration through the Steer It and Clear It law can also improve the safety of road users and incident response personnel.
Phase II study of the combination carboplatin plus celecoxib in heavily pre-treated recurrent ovarian cancer patients (2011)

NCT01124435 (ClinicalTrials.gov Identifier) and 935/03 (study ID numbers).
Acoustics and oceanographic observations collected during the QPE Experiment by Research Vessels OR1, OR2 and OR3 in the East China Sea in the Summer of 2009 (2010)

This document describes data, sensors, and other useful information pertaining to the ONR sponsored QPE field program to quantify, predict and exploit uncertainty in observations and prediction of sound propagation. This experiment was a joint operation between Taiwanese and U.S. researchers to measure and assess uncertainty of predictions of acoustic transmission loss and ambient noise, and to observe the physical oceanography and geology that are necessary to improve their predictability. This work was performed over the continental shelf and slope northeast of Taiwan at two sites: one that was a relatively flat, homogeneous shelf region and a more complex geological site just shoreward of the shelfbreak that was influenced by the proximity of the Kuroshio Current. Environmental moorings and ADCP moorings were deployed and a shipboard SeaSoar vehicle was used to measure environmental spatial structure. In addition, multiple bottom moored receivers and a horizontal hydrophone array were deployed to sample transmission loss from a mobile source and ambient noise. The acoustic sensors, environmental sensors, shipboard resources, and experiment design, and their data, are presented and described in this technical report.
Detection of Prostate Cancer with a Blood-Based Assay for Early Prostate Cancer Antigen (2005)

Prostate-specific antigen lacks specificity for prostate cancer, so the identification and characterization of a unique blood-based marker for the disease would provide for a more accurate diagnosis, reducing both unnecessary biopsies and patient uncertainty. We previously identified a novel biomarker for prostate cancer, early prostate cancer antigen (EPCA). EPCA antibodies positively stained the negative biopsies of men who, as much as 5 years later, were diagnosed with prostate cancer. The goal of this study was to determine whether EPCA antibodies could be used in a clinically applicable plasma-based immunoassay to specifically detect prostate cancer. Using an EPCA-based ELISA, the protein was measured in the plasma of 46 individuals, including prostate cancer patients, healthy individuals, other cancer patients, spinal cord injury victims, and patients with prostatitis. With a predetermined cutoff value of 1.7 absorbance at 450 nm, only the prostate cancer population, as a whole, expressed plasma-EPCA levels above the cutoff. Statistical analysis showed a significant difference in EPCA levels between the prostate cancer population and each of the other groups, specifically the healthy donors (P < 0.0001), bladder cancer patients (P = 0.03), and spinal cord injury patients (P = 0.001). Sensitivity of the EPCA assay for prostate cancer patients was 92% whereas the overall specificity was 94%. Specificity for the healthy donors was 100%. Although larger trials are required, this initial study shows the potential of EPCA to serve as a highly specific blood-based marker for prostate cancer. EPCA, when coupled with prostate-specific antigen, may help reduce the number of both unnecessary biopsies and undetected prostate tumors.
Preoperative management of spontaneous cerebrospinal fluid rhinorrhea with acetazolamide (2018)

This is the first study to report the use of acetazolamide therapy as a primary treatment option for spontaneous CSF rhinorrhea. This therapy enabled surgery to be avoided in 31.3% of patients. This would indicate that in the absence of other contraindications for delaying repair, a trial of acetazolamide therapy could be considered as an initial option in the management of isolated spontaneous CSF rhinorrhea.
Applications of rank-reduction to ECG analysis (2002)

The authors demonstrate application of SVD-based subspace techniques to electrocardiography. SVD, a high resolution spectrum estimation tool, is used to decompose the ECG data matrix into orthogonal subspaces. Due to the energy-preserving orthogonal transformations in the SVD, these subspaces correspond to the signal and noise components contained in the ECG data. Projection of the data onto the desired subspace eliminates the noise and the unwanted signal components.
Targeting mitochondrial biogenesis to overcome drug resistance to MAPK inhibitors (2016)

Targeting multiple components of the MAPK pathway can prolong the survival of patients with BRAFV600E melanoma. This approach is not curative, as some BRAF-mutated melanoma cells are intrinsically resistant to MAPK inhibitors (MAPKi). At the systemic level, our knowledge of how signaling pathways underlie drug resistance needs to be further expanded. Here, we have shown that intrinsically resistant BRAF-mutated melanoma cells with a low basal level of mitochondrial biogenesis depend on this process to survive MAPKi. Intrinsically resistant cells exploited an integrated stress response, exhibited an increase in mitochondrial DNA content, and required oxidative phosphorylation to meet their bioenergetic needs. We determined that intrinsically resistant cells rely on the genes encoding TFAM, which controls mitochondrial genome replication and transcription, and TRAP1, which regulates mitochondrial protein folding. Therefore, we targeted mitochondrial biogenesis with a mitochondrium-targeted, small-molecule HSP90 inhibitor (Gamitrinib), which eradicated intrinsically resistant cells and augmented the efficacy of MAPKi by inducing mitochondrial dysfunction and inhibiting tumor bioenergetics. A subset of tumor biopsies from patients with disease progression despite MAPKi treatment showed increased mitochondrial biogenesis and tumor bioenergetics. A subset of acquired drug-resistant melanoma cell lines was sensitive to Gamitrinib. Our study establishes mitochondrial biogenesis, coupled with aberrant tumor bioenergetics, as a potential therapy escape mechanism and paves the way for a rationale-based combinatorial strategy to improve the efficacy of MAPKi.
Water content and size of spore components determined by laser diffractometry (1987)

For the first time laser diffractometry was used to obtain the refractive index distribution within individual cells in an aqueous environment, allowing accurate determination of their compartmental water content. For bacterial spores the results demonstrated the existence of a dehydrated protoplast surrounded by a less dehydrated integument, thus accounting for the extreme heat resistance of the spores. In contrast, the presence of a dry wall surrounding a water-rich protoplast was shown in fungal spores.
Mos proto-oncogene function during oocyte maturation in Xenopus. (1996)

The function of the Xenopus c-mos proto-oncogene product (Mos(xe)) has been investigated during oocyte maturation. Experiments with a new antibody able to immunoblot Mos(xe) demonstrated the time course of MAP kinase (MAP K) activation in oocytes paralleled Mos(xe) accumulation, and in activated eggs the deactivation of MAP K paralleled the degradation of Mos(xe). Ablation of Mos synthesis by microinjection of antisense oligodeoxynucleotides abolished activation of MAP K by progesterone, but microinjection of GST-Mos fully restored both MAP K activation and germinal vesicle breakdown (GVBD). The Mos(xe) level at metaphase of Meiosis I (MI) was 2 - 3-fold less than that at metaphase of Meiosis II (MII), but MAP K activation was maximal at metaphase in both MI and MII. In the transition between MI and MII, both cyclin B and Mos(xe) levels rapidly declined in the presence of cycloheximide and injection of exogenous GST-Mos(xe) did not prevent degradation of either protein, although MAP K was activated. Microinjection of GST-Mos(xe) into oocytes was able to activate MAP K before GVBD and H1 kinase activation, and microinjection of constitutively-activated thiophosphorylated MAP K induced de novo synthesis of Mos(xe) before H1 kinase activation, suggesting the existence of a positive feedback loop between MAP K and Mos(xe) accumulation.
Flow regulation of collecting duct endothelin-1 production (2010)

Collecting duct (CD) endothelin-1 (ET-1) is an important autocrine inhibitor of CD Na(+) reabsorption. Salt loading is thought to increase CD ET-1 production; however, definitive evidence of this, as well as understanding of the mechanisms transducing this effect, is lacking. Tubule fluid flow increases in response to Na(+) loading; hence, we studied flow modulation of CD ET-1 production. Three days of a high-salt diet increased mouse and rat inner medullary CD (IMCD) ET-1 mRNA expression. Acute furosemide infusion increased urinary ET-1 excretion in anesthetized rats. Primary cultures of mouse or rat IMCD detached in response to flow using a closed perfusion chamber, consequently a CD cell line (mpkCCDcl4) was examined. Flow increased ET-1 mRNA at shear stress rates exceeding 1 dyne/cm(2), with the maximal effect seen between 2 and 10 dyne/cm(2). Induction of ET-1 mRNA was first evident after 1 h, and most apparent after 2 h, of flow. Inhibition of calmodulin or dihydropyridine-sensitive Ca(2+) channels did not alter the flow response; however, chelation of intracellular Ca(2+) or removal of extracellular Ca(2+) largely prevented flow-stimulated ET-1 mRNA accumulation. Downregulation of protein kinase C (PKC) using phorbol 12-myristate 13-acetate, or PKC inhibition with calphostin C, markedly reduced flow-stimulated ET-1 mRNA levels. Flow-stimulated ET-1 mRNA accumulation was abolished by inhibition of phospholipase C (PLC). Taken together, these data indicate that flow increases CD ET-1 production and this is dependent on extracellular and intracellular Ca(2+), PKC, and PLC. These studies suggest a novel pathway for coupling alterations in extracellular fluid volume to CD ET-1 production and ultimately control of CD Na(+) reabsorption.
Magnetically Aligned Bicelles To Study the Orientation of Lipophilic Ligands in Membrane Bilayers (2008)

Magnetically aligned bicelles were used as a model membrane to study the orientation and dynamic properties of two cannabinoids (Delta (8)-THC and Me-Delta (8)-THC) using (31)P and (2)H NMR. The uniform alignment of the bicelles allowed us to obtain well resolved deuterium spectra from a solution NMR spectrometer. The preferred orientations of Delta (8)-THC and Me-Delta (8)-THC were calculated on the basis of the measurements of individual quadrupolar splittings. Our results agree with previous experiments using multilamellar membranes as well as with molecular dynamics simulation data described here. In conjunction with our earlier report using small and fast tumbling bicelles, the present work of well aligned bicelles shows that bicelle preparations can provide either pseudoisotropic or anisotropic NMR spectra to study the conformation, orientation, and dynamic properties of ligands in membrane bilayers. Such data are of critical value for understanding the interactions of lipophilic drug molecules with membrane proteins.
Coherentπ0photoproduction on the deuteron up to 4 GeV (1999)

The differential cross section for ${}^{2}\mathrm{H}(\ensuremath{\gamma},d){\ensuremath{\pi}}^{0}$ has been measured at deuteron center-of-mass angles of 90\ifmmode^\circ\else\textdegree\fi{} and 136\ifmmode^\circ\else\textdegree\fi{}. This work reports the first data for this reaction above a photon energy of 1 GeV, and permits a test of the apparent constituent counting rule and reduced nuclear amplitude behavior as observed in elastic ed scattering. Measurements were performed up to a photon energy of 4.0 GeV, and are in good agreement with previous lower energy measurements. Overall, the data are inconsistent with both constituent-counting rule and reduced nuclear amplitude predictions.