gebhart/patrepeval huggingface dataset:
Improved Greedy Algorithms for Learning Graphical Models (2015)

We propose new greedy algorithms for learning the structure of a graphical model of a probability distribution, given samples drawn from the distribution. While structure learning of graphical models is a widely studied problem with several existing methods, greedy approaches remain attractive due to their low computational cost. The most natural greedy algorithm would be one which, essentially, adds neighbors to a node in sequence until stopping; it would do this for each node. While it is fast, simple and parallel, this naive greedy algorithm has the tendency to add non-neighbors that show high correlations with the given node. Our new algorithms overcome this problem in three different ways. The recursive greedy algorithm iteratively recovers the neighbors by running the greedy algorithm in an inner loop, but each time only adding the last added node to the neighborhood set. The second forward-backward greedy algorithm includes a node deletion step in each iteration that allows non-neighbors to be removed from the neighborhood set which may have been added in the previous steps. Finally, the greedy algorithm with pruning runs the greedy algorithm until completion and then removes all the incorrect neighbors. We provide both analytical guarantees and empirical performance for our algorithms. We show that in graphical models with strong non-neighbor interactions, our greedy algorithms can correctly recover the graph, whereas the previous greedy and convex optimization-based algorithms do not succeed.
Influence of Mg2+ on cardiac performance, intracellular free Mg2+ and pH in perfused hearts as assessed with 31P nuclear magnetic resonance spectroscopy. (1993)

The cellular bioenergetic responses of isolated perfused working rat hearts to alterations in hemodynamic function caused by acute exposure to elevated levels of extracellular magnesium ions ([Mg2+]o) were examined using 31P nuclear magnetic resonance (31P NMR) spectroscopy. Results showed that in hearts working against 90 cm H2O afterload, an increase in [Mg2+]o from 1.2 to 4.8 mM reduced the heart rate by 35%, while coronary flow was increased by 38%. Unexpectedly, despite the pronounced bradycardia, the rate-pressure product was reduced only slightly (from 2.36 x 10(4) to 2.08 x 10(4) mm Hg/min) due to a significant increase (36%) in systolic pressure. In addition, cardiac output actually increased by 23%, owing to a > 100% increase in stroke volume, indicating that the performance of the heart was improved and suggesting that the efficiency of the heart was improved as well. In a separate series of experiments, 31P NMR measurements performed on hearts perfused in the Langendorff mode revealed that elevated levels of [Mg2+]o increase phosphocreatine (PCr) levels by 23% (from 9.2 to 11.3 mM), while Pi levels declined by a corresponding amount. Perfusion of hearts in the working mode with elevated [Mg2+]o was also observed to increase PCr levels from 6.3 to 9.0 mM, while ATP levels declined by 17%. Measurement of the chemical shift difference between Pi and PCr and that between the alpha and beta phosphate resonances of ATP were used to determine intracellular pH and the cytosolic levels of free Mg2+ ([Mg2+]i), respectively. These results showed that acute exposure of hearts, perfused in either the working or Langendorff mode, to increased levels of [Mg2+]o increased intracellular pH by 0.12-0.13 units, while free Mg2+ nearly doubled to a level of 1.1-1.2 mM. The latter observation may suggest that acute variations in the level of [Mg2+]o can influence a multitude of cellular processes requiring Mg2+ as an essential cofactor. Using the above data and assuming equilibrium of the creatine kinase reaction, the levels of ADP, cytosolic phosphorylation potential ([ATP]/[ADP][Pi]) and free energy change from ATP hydrolysis (-delta G/delta E) were also calculated. Results obtained illustrate that in the presence of elevated [Mg2+]o, ADP levels declined by 33-48%, the cytosolic phosphorylation potential increased from 41 to 112 mM-1 and -delta G/delta E increased from 56.7 to 59.3 kJ/mol. These changes are not completely accountable by the known bradycardia and vasodilatory effects of elevated [Mg2+]o and strongly argue for a direct action of [Mg2+]o on the myocyte as well.(ABSTRACT TRUNCATED AT 400 WORDS)
Learning microarchitectural behaviors to improve stimuli generation quality (2011)

Microarchitectural information regarding various aspects of instruction execution can help processor-level stimuli generators more easily reach verification goals. While many such aspects are based on common microarchitectural concepts, their specific manifestations are highly design-specific. We propose using an automatic method for acquiring such microarchitectural knowledge and integrating it into the stimuli generator. We start by extracting microarchitectural data from simulation traces. This data is fed to a decision tree learning algorithm that produces rules for microarchitectural behavior of instructions; these rules are then integrated into the testing knowledge of the stimuli generator. This testing knowledge can provide users with the ability to better control the microarchitectural behavior of generated instructions, leading to higher quality test cases. Experimental results on the POWER7 processor showed that our proposed method can improve the microarchitectural coverage of the design.
Transthyretin is a metallopeptidase with an inducible active site (2012)

TTR (transthyretin) was found recently to possess proteolytic competency besides its well-known transport capabilities. It was described as a cryptic serine peptidase cleaving multiple natural substrates (including β-amyloid and apolipoprotein A-I) involved in diseases such as Alzheimer's disease and atherosclerosis. In the present study, we aimed to elucidate the catalytic machinery of TTR. All attempts to identify a catalytic serine residue were unsuccessful. However, metal chelators abolished TTR activity. Proteolytic inhibition by EDTA or 1,10-phenanthroline could be reversed with Zn2+ and Mn2+. These observations, supported by analysis of three-dimensional structures of TTR complexed with Zn2+, led to the hypothesis that TTR is a metallopeptidase. Site-directed mutagenesis of selected amino acids unambiguously confirmed this hypothesis. The TTR active site is inducible and constituted via a protein rearrangement resulting in ~7% of proteolytically active TTR at pH 7.4. The side chain of His88 is shifted near His90 and Glu92 establishing a Zn2+-chelating pattern HXHXE not found previously in any metallopeptidase and only conserved in TTR of humans and some other primates. Point mutations of these three residues yielded proteins devoid of proteolytic activity. Glu72 was identified as the general base involved in activation of the catalytic water. Our results unveil TTR as a metallopeptidase and define its catalytic machinery.
Stromal derived factor-1 mediates the lung regenerative effects of mesenchymal stem cells in a rodent model of bronchopulmonary dysplasia (2017)

The therapeutic benefits of MSCs in neonatal HILI are in part mediated by SDF-1, through anti-inflammatory and angiogenesis promoting mechanisms. Therapies directly targeting this chemokine may provide a novel strategy for the treatment of BPD.
Materialized View Selection for Multidimensional Datasets (1998)

Echocardiography is widely available in most cardiac centers, plays a key role in both the diagnosis and management of IE, is often the first-hand imaging modality, and should be performed immediately when mitral regurgitation is suspected. In addition, it is helpful during therapy and after surgery to assess valve morphology and function, complications, and heart function. In particular, transthoracic echocardiography is useful to detect new silent complications, monitor vegetation size, assess perivalvular abscess formation, pseudoaneurysm, intracardiac fistula and valvular perforation, as well as examine the embolic risk. In addition, echocardiographic outcomes differences among cardiovascular outcomes assessment of the MitraClip percutaneous therapy for heart failure patients with functional mitral regurgitation (COAPT) like and non COAPT-like patients have shown that non COAPT-like patients had higher left ventricular (LV) dimensions and overall contractility therefore, differences in clinical outcomes have been underestimated. Mitral transcatheter edge-to-edge repair (MTEER) is an established therapeutic approach for mitral regurgitation (MR). Recurrence of MR after TEER with MitraClip is a concern due to increased patients' hospital readmission rate and increasing hospital costs. However, little is known about clinical, valvular, or ventricular parameters that may impact postinterventional course and recurrence of MR after TEER. While individual long-term echocardiographic outcomes of functional vs degenerative MR have been described, there is little data on follow-up echocardiographic outcomes comparing functional vs degenerative MR.
Gastrointestinal Tract as a Target Organ for Orally Administered Insulin (2006)

The intestine is not considered to be a classic target tissue for insulin. Recent in vitro and in vivo experiments suggest that intestinal as well as systemic effects are observed following oral administration of insulin. Local effects include enhancement of intestinal growth, cell maturation, enzyme expression, gut adaptation after intestinal resection and reduction of intestinal permeability. Systemic effects, at least in animal models, include favorable effects on blood glucose and lipid profile and on the prevention of autoimmunity and attenuating the atherosclerotic process.
VÎ³9/VÎ´2 T cell activation induced by bacterial low molecular mass compounds depends on the 1-deoxy-d-xylulose 5-phosphate pathway of isoprenoid biosynthesis (1999)

Isopentenyl diphosphate (IPP), an important precursor of isoprenoid biosynthesis in prokaryotic and eukaryotic organisms, has been shown to activate Vgamma9/Vdelta2 T cells, the major subset of human gammadelta T cells. The biosynthesis of IPP has been first described as the acetate/mevalonate pathway. Recently, 1-deoxy-D-xylulose 5-phosphate (DOXP) and 2-C-methyl-D-erythritol 4-phosphate have been shown to be key metabolites in the DOXP pathway also leading to the formation of IPP in some eubacteria such as Escherichia coli. Here we report that the low molecular mass fraction of extracts from bacteria using the DOXP pathway induces Vgamma9/Vdelta2 T cell activation, while analogous preparations from bacteria using the classical mevalonate pathway fail to do so. Addition of 1-deoxy-D-xylulose potentiates the ability of E. coli extracts to activate Vgamma9/Vdelta2 T cells. As the amounts of IPP present in the bacterial preparations are not sufficient to induce significant Vgamma9/Vdelta2 T cell activation, our data suggest that compounds other than IPP associated with the DOXP pathway are responsible for Vgamma9/Vdelta2 T cell activation.
Δ‐Myrtoxin‐Mp1a is a Helical Heterodimer from the Venom of the Jack Jumper Ant that has Antimicrobial, Membrane‐Disrupting, and Nociceptive Activities (2017)

Abstract Δ‐Myrtoxin‐Mp1a (Mp1a), a 49‐residue heterodimeric peptide from the venom of Myrmecia pilosula, comprises a 26‐mer A chain and a 23‐mer B chain connected by two disulfide bonds in an antiparallel arrangement. Combination of the individual synthetic chains through aerial oxidation remarkably resulted in the self‐assembly of Mp1a as a homogenous product without the need for directed disulfide‐bond formation. NMR analysis revealed a well‐defined, unique structure containing an antiparallel α‐helix pair. Dual polarization interferometry (DPI) analysis showed strong interaction with supported lipid bilayers and insertion within the bilayers. Mp1a caused non‐specific Ca 2+ influx in SH‐SY5Y cells with a half maximal effective concentration (EC 50 ) of 4.3 μ m . Mp1a also displayed broad‐spectrum antimicrobial activity, with the highest potency against Gram‐negative Acinetobacter baumannii (MIC 25 n m ). Intraplantar injection (10 μ m ) in mice elicited spontaneous pain and mechanical allodynia. Single‐ and two‐chain mimetics of Mp1a revealed functional selectivity.
Differential behaviors of Staphylococcus aureus and Escherichia coli type II DNA topoisomerases (1996)

Staphylococcus aureus gyrA and gyrB genes encoding DNA gyrase subunits were cloned and coexpressed in Escherichia coli under the control of the T7 promoter-T7 RNA polymerase system, leading to soluble gyrase which was purified to homogeneity. Purified gyrase was catalytically indistinguishable from the gyrase purified from S. aureus and did not contain detectable amounts of topoisomerases from the E. coli host. Topoisomerase IV subunits GrlA and GrlB from S. aureus were also expressed in E. coli and were separately purified to apparent homogeneity. Topoisomerase IV, which was reconstituted by mixing equimolar amounts of GrlA and GrlB, had both ATP-dependent decatenation and DNA relaxation activities in vitro. This enzyme was more sensitive than gyrase to inhibition by typical fluoroquinolone antimicrobial agents such as ciprofloxacin or sparfloxacin, adding strong support to genetic studies which indicate that topoisomerase IV is the primary target of fluoroquinolones in S. aureus. The results obtained with ofloxacin suggest that this fluoroquinolone could also primarily target gyrase. No cleavable complex could be detected with S. aureus gyrase upon incubation with ciprofloxacin or sparfloxacin at concentrations which fully inhibit DNA supercoiling. This suggests that these drugs do not stabilize the open DNA-gyrase complex, at least under standard in vitro incubation conditions, but are more likely to interfere primarily with the DNA breakage step, contrary to what has been reported with E. coli gyrase. Both S. aureus gyrase-catalyzed DNA supercoiling and S. aureus topoisomerase IV-catalyzed decatenation were dramatically stimulated by potassium glutamate or aspartate (500- and 50-fold by 700 and 350 mM glutamate, respectively), whereas topoisomerase IV-dependent DNA relaxation was inhibited 3-fold by 350 mM glutamate. The relevance of the effect of dicarboxylic amino acids on the activities of type II topoisomerases is discussed with regard to the intracellular osmolite composition of S. aureus.
&lt;i&gt;Effects of Moisture on the Fundamental Mechanical Properties of the Biomass Flow Models&lt;/i&gt; (2020)

<b>Abstract.</b> The effects of moisture on biomass flow characteristics are known to be significant. However, the degree and origin of such changes are not well understood. This knowledge gap exists partly because of the lack of quantitative data on the fundamental mechanical properties of bulk biomass. Cubical triaxial tester (CTT) is a true triaxial tester with a flexible pressure application membrane that minimizes the interference of the test device with the mechanical responses of a specimen. It has been shown that the test data collected with CTT enables the interrogation of mechanical behavior bulk solids based on first principles. Different fundamental mechanical properties of bulk ground biomass will be determined using a CTT. By examining the change in mechanical properties with respect to the differences in the moisture level of milled corn stover and Douglas fir, this study aims to elucidate the effect of moisture on the bulk mechanical behavior of ground biomass with a focus on flowability.
Supplementary Document 1 from Development and Validation of a Gene Profile Predicting Benefit of Postmastectomy Radiotherapy in Patients with High-Risk Breast Cancer: A Study of Gene Expression in the DBCG82bc Cohort (2023)

&lt;p&gt;Development of the DBCG-RT profile including description of Lasso method, selection of genes, and definition of index cut-off.&lt;/p&gt;
An FPGA implementation of NIST 256 prime field ECC processor (2013)

In this paper, we propose a new Application Specific Instruction-set (ASIP) ECC processor based on Redundant Signed Digit representation with a novel Iterative-Recursive Karatsuba multiplier. The results of Vertix-5 FPGA implementation with full CLB based design is presented in this paper. The processor performs point multiplication for NIST recommended curve P256 and is based on an extended NIST reduction scheme. Our processor performs single point multiplication where points are represented in affine coordinates within 6.67 ms and runs at maximum frequency of 66.3 MHz. The design of our processor is entirely based on CLB blocks as opposed to other FPGA implementations.
Targeting the SUMO pathway primes all- trans -retinoic acid-induced differentiation of non promyelocytic Acute Myeloid Leukemias (2018)

Abstract Differentiation therapies using All- trans -retinoic acid (ATRA) are highly efficient at treating Acute Promyelocytic Leukemia (APL), a minor subtype of Acute Myeloid Leukemias (AML). However, their efficacy, if any, is very limited in the case of non-APL AMLs. We report here that the inhibition of SUMOylation, a post-translational modification related to ubiquitinylation, restores the pro-differentiation and anti-proliferative activities of retinoids in non-APL AMLs. Controlled inhibition of SUMOylation with pharmacological inhibitors (2-D08 or anacardic acid), or via overexpression of SENP desumoylases, strongly enhances the ATRA-induced expression of key genes involved in differentiation, proliferation and apoptosis in non-APL AML cells. This activates ATRA-induced terminal myeloid differentiation and reduces cell proliferation and viability, including in AML cells resistant to chemotherapeutic drugs. Conversely, enhancement of SUMOylation by overexpressing the SUMO-conjugating enzyme Ubc9 dampens the expression of ATRA-responsive genes and prevents differentiation. Thus, inhibition of the SUMO pathway is a promising strategy to sensitize non-APL AML patients to retinoids and improve the treatment of this poor prognosis cancer, which has not significantly changed over the past 40 years.
Table S4 from Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer (2023)

&lt;p&gt;Raw data and heat maps for metabolomics of cell lines and tumors.&lt;/p&gt;
Leaky-mode assisted fluorescence extraction: application to fluorescence enhancement biosensors (2008)

Efficient recovery of light emitted by fluorescent molecules by employing photonic structures can result in high signal-to-noise ratio detection for biological applications including DNA microarrays, fluorescence microscopy and single molecule detection. By employing a model system comprised of colloidal quantum dots, we consider the physical basis of the extraction effect as provided by photonic crystals. Devices with different lattice symmetry are fabricated ensuring spectral and spatial coupling of quantum dot emission with leaky eigenmodes and the emission characteristics are studied using angle-resolved and angle-integrated measurements. Comparison with numerical calculations and lifetime measurements reveals that the enhancement occurs via resonant redirection of the emitted radiation. Comparison of various lattices reveals differences in the enhancement factor with a maximum enhancement factor approaching 220. We also demonstrate the first enhanced extraction biosensor that allows for over 20-fold enhancement of the fluorescence signal in detection of the cytokine TNF-alpha by a fluorescence sandwich immunoassay.
Three-dimensional lithographical fabrication of microchannels (2005)

With the rapid development of microfluidic systems, there is high demand for fabrication methods for the fluidic components that can be used to realize complex three-dimensional (3-D) geometries, high integration levels, full compatibility with sensing and controlling circuits, and possess batch fabrication capability. In this paper, we propose and demonstrate such a method based on a novel 3-D lithography technique. The method employs commercially available photoresist and standard lithography facilities. Single-level microchannels with micron-size cross sections up to 1.2 mm in length, as well as multilevel channels with unique 3-D structures, have been fabricated using the proposed method. This method allows direct postintegration of microchannels with previously fabricated integrated circuits without etching, bonding or additional material deposition except resist spin coating. Using this method, the fabrication of microchannels can be greatly simplified, and many unique 3-D topologies beyond the ability of current techniques can be obtained.
Applications of 3D X-Ray Microscopy for Advanced Package Development (2011)

This paper describes the utilization of non-destructive imaging using 3D x-ray microscopy for package development and failure analysis. Four case studies are discussed to explain our methodology and its impact on our advanced packaging development effort. Identifying and locating failures embedded deep inside the package, such as a solder fatigue failure within a flip chip package, without the need for physical cross-sectioning is of substantial benefit because it preserves the package for further analysis. Also of utility is the ability to reveal the structural details of the package while producing superior quality 2D and volumetric images. The technique could be used not only for analysis of defects and failures, but also to characterize geometries and morphologies during the process and package development stage.
Measurement of the azimuthal anisotropy of and mesons in PbPb collisions at sNN=5.02TeV (2021)

The second-order Fourier coefficients (v 2 ) characterizing the azimuthal distributions of (1S) and (2S) mesons produced in PbPb collisions at s NN = 5.02 TeV are studied. The mesons are reconstructed in their dimuon decay channel, as measured by the CMS detector. The collected data set corresponds to an integrated luminosity of 1.7 nb -1 . The scalar product method is used to extract the v 2 coefficients of the azimuthal distributions. Results are reported for the rapidity range |y| < 2.4, in the transverse momentum interval 0 < p T < 50 GeV/c, and in three centrality ranges of 10-30%, 30-50% and 50-90%.
Chloroplast Gene Expression: Regulation at Multiple Levels (2005)

SummaryThe plastid DNA of higher plants contains genes that primarily encode photosynthetic proteins or products required for their synthesis. Expression of plastid genes resembles prokaryotic gene expression in many aspects, reflecting the plastid’s probable origin as prokaryotic endosymbionts. Early theories suggested that plastid gene expression, like that of prokaryotes, was regulated principally at the level of transcription initiation, although further research led to competing theories regarding the relative importance of regulation at different levels. It is becoming apparent that regulation of transcription initiation is an important, but not exclusive, mechanism for control of plastid gene expression. Post-transcriptional control of transcript abundance has also emerged as an important level of regulation, with identification of nuclear-encoded factors that mediate processing, stabilization, and degradation of plastid transcripts. Translation initiation and elongation can also be specifically regulated, as can post-translational mechanisms affecting protein turnover. Thus, plastid gene expression is regulated by a combination of mechanisms that operate at multiple levels. Most of the regulatory factors affecting plastid gene expression are nuclear-encoded, illustrating the regulatory role that the nucleus plays in the control of plastid function. This allows plastid differentiation to be coordinated with the tissue-specific and developmental program of the plant. At the same time, transcription of certain nuclear-encoded plastid-localized proteins requires a plastid-generated signal; thus, expression of nuclear and plastid genes is controlled by bidirectional signaling between the two compartments. Elucidation of the mechanisms controlling the coordinated expression of the two genomes will remain a fruitful area of investigation for many years to come.