gebhart/patrepeval huggingface dataset:
Modelling of centralized concurrency control in a multi-system environment (1985)

The performance of multiple systems sharing a common data base is analyzed for an architecture with concurrency control using a centralized lock engine. The workload is based on traces from large mainframe systems running IBM's IMS database management system. Based on IMS lock traces the lock contention probability and data base buffer invalidation effect in a multi-system environment is predicted. Workload parameters are generated for use in event-driven simulation models that examine the overall performance of multi-system data sharing, and to determine the performance impact of various system parameters and design alternatives. While performance results are presented for realistic system parameters, the emphasis is on the methodology, approximate analysis technique and on examining the factors that affect multi-system performance.
Risk Factors Associated With Mortality Among Patients With COVID-19 in Intensive Care Units in Lombardy, Italy (2020)

In this retrospective cohort study of critically ill patients admitted to ICUs in Lombardy, Italy, with laboratory-confirmed COVID-19, most patients required IMV. The mortality rate and absolute mortality were high.
Shape Memory Alloy Actuator Design: CASMART Collaborative Best Practices (2011)

Upon examination of shape memory alloy (SMA) actuation designs, there are many considerations and methodologies that are common to them all. A goal of CASMART’s design working group is to compile the collective experiences of CASMART’s member organizations into a single medium that engineers can then use to make the best decisions regarding SMA system design. In this paper, a review of recent work toward this goal is presented, spanning a wide range of design aspects including evaluation, properties, testing, modeling, alloy selection, fabrication, actuator processing, design optimization, controls, and system integration. We have documented each aspect, based on our collective experiences, so that the design engineer may access the tools and information needed to successfully design and develop SMA systems. Through comparison of several case studies, it is shown that there is not an obvious single, linear route a designer can adopt to navigate the path of concept to product. SMA engineering aspects will have different priorities and emphasis for different applications.
A Unifying Theory of Security Metrics with Applications (2009)

This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its contents. In view of the transfer of copyright to the outside pub-lisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies (e.g., payment of royalties). Some re-ports are available at
Abstract AS15: DNA promoter hypermethylation of HIST1H2BB as a diagnostic and prognostic biomarker for ovarian cancer (2015)

Abstract Background: Until recently, epithelial ovarian cancers were thought to arise from the ovarian surface epithelial cells. However, recent studies suggest that the majority of high grade serous carcinomas (HGSCs) arise from lesions in the fallopian tubes. DNA promoter hypermethylation of certain genes is often an early event in tumorigenesis, and it can be detected in blood and other bodily fluids, making it a feasible biomarker strategy for early detection of tumors. Purpose of study: Therefore, we sought to determine the methylation profile of HGSCs as compared to fallopian tube epithelium. Using the Infinium HumanMethylation 450 Array, that permits to quantitatively assess over 450,000 methylation sites, within and outside of CpG islands and more than 20,000 genes per sample, at single-nucleotide resolution, we have obtained the genome-wide methylation profile of HGSC and fallopian tubal epithelium. We conducted a pilot study by comparing the global methylation in 12 HGSC tissue samples to 15 fallopian tube epithelium samples. In addition, we compared the methylation profile among long-term survivors (more than 5 years) and short-term survivors (2-3 years) of HGSCs. Results: Our results identified the HIST1H2BB promoter as the most differentially methylated region when comparing HGSC with normal fallopian tube samples. Furthermore, we also found that HIST1H2BB is differentially methylated in HGSC patients with long-term survival when compared to patients with short-term survival. Conclusions: Taken together, these results support the potential of HIST1H2BB promoter hypermethylation as a diagnostic and prognostic biomarker. Our findings could lead to the development of a biomarker for the diagnosis and/or prognosis of ovarian cancer and could contribute to the current understanding of the mechanisms of progression in ovarian cancer. Citation Format: Blanca L. Valle, Elisabetta Kuhn, David Sidransky, Rafael Guerrero-Preston. DNA promoter hypermethylation of HIST1H2BB as a diagnostic and prognostic biomarker for ovarian cancer [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS15.
S14‐95, a Novel Inhibitor of the JAK/STAT Pathway from a Penicillium Species. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Figure S2 from The MD Anderson Prostate Cancer Patient-derived Xenograft Series (MDA PCa PDX) Captures the Molecular Landscape of Prostate Cancer and Facilitates Marker-driven Therapy Development (2023)

&lt;p&gt;ETV1 rearrangement by RNA in situ hybridization in MDA PCa 177-B&lt;/p&gt;
Pd-Catalyzed Arylation of Acetone (2007)

Direct arylation of enolizable ketones by aryl electrophiles is a highly useful synthetic transformation, especially in the case of heteroarenes. Herein, the authors reported a simple microwave-assisted method for the preparation of various α-aryl- and -heteroarylacetones by a simple arylation of acetone silyl enol ether. This process is especially convenient for diversity synthesis, as the reaction requires only 15 min and is quite tolerant to the presence of functional groups.
Good News on the Conjugate Export Pump Cmrp in Human Liver and the Absence of Cmrp or Cmoat in Canalicular Membranes of Tr– Tr–Rat Hepatocytes (1996)

TR 0 TRmodel, the TR 0 rat, are characterized by a chronic conju-RAT HEPATOCYTES gated hyperbilirubinemia.TR 0 rats are defective in the Mayer R
Data-Driven Linear Quadratic Optimization for Controller Synthesis with Structural Constraints (2019)

For various typical cases and situations where the formulation results in an optimal control problem, the Linear Quadratic Regulator (LQR) approach and its variants continue to be highly attractive. In certain scenarios, it can happen that some prescribed structural constraints on the gain matrix would arise. Consequently then, the Algebraic Riccati Equation (ARE) is no longer applicable in a straightforward way to obtain the optimal solution. This work presents a rather effective alternative optimization approach based on gradient projection. The utilized gradient is obtained through a data-driven methodology, and then projected onto applicable constrained hyperplanes. Essentially, this projection gradient determines a direction of progression and computation for the gain matrix update with a decreasing functional cost; and then the gain matrix is further refined in an iterative framework. With this formulation, a data-driven optimization algorithm is summarized for controller synthesis with structural constraints. This data-driven approach has the key advantage that it avoids the necessity of precise modeling which is always required in the classical model-based counterpart; and thus the approach can additionally accommodate various model uncertainties. Illustrative examples are also provided in the work to validate the theoretical results.
Genetic Analysis of the Large Subunit of Yeast Transcription Factor IIE Reveals Two Regions with Distinct Functions (1997)

Biochemical analysis of proteins necessary for transcription initiation by eukaryotic RNA polymerase II (pol II) has identified transcription factor IIE (TFIIE) as an essential component of the reaction. To better understand the role of TFIIE in transcription, we isolated conditional alleles of TFA1, the gene encoding the large subunit of TFIIE in the yeast Saccharomyces cerevisiae. The mutant Tfa1 proteins fall into two classes. The first class causes thermosensitive growth due to single amino acid substitutions of the cysteines comprising the Zn-binding motif. The second mutant class is made up of proteins that are C-terminally truncated and that cause a cold-sensitive growth phenotype. The behavior of these mutants suggests that Tfa1p possesses at least two domains with genetically distinct functions. The mutations in the Zn-binding motif do not affect the mutant protein's stability at the nonpermissive temperature or its ability to associate with the small subunit of TFIIE. Our studies further determined that wild-type TFIIE can bind to single-stranded DNA in vitro. However, this property is unaffected in the mutant TFIIE complexes. Finally, we have demonstrated the biological importance of TFIIE in pol II-mediated transcription by depleting the Tfa1 protein from the cells and observing a concomitant decrease in total poly(A)+ mRNA.
Sample Size Reduction Method Based on Data Fusion for Freeways with Fixed Detectors (2015)

This research investigates the required minimum number of probe vehicles (PVs) necessary to report the real-time travel speed and travel time with the desired statistical accuracy for freeways equipped with fixed detectors. The field data used were collected from the Freeway Performance Measurement System from 7:00 to 10:00 a.m. on May 28, 2014, during a typical weekday. With corridor information and traffic volume data, this study uses VISSIM to create simulation scenarios to generate PV data and loop data for further analysis. Then the average relative errors of travel time by setting are compared with various PV percentages in traffic on different links. The least squares errors of the fused speed data are also compared with the PV and loop data. Through analysis, the study reaches the following results. When the probe sample size reaches a certain level (3% in the testing environment), the estimated errors are reduced gently with the increasing number of PVs. To ensure that the link is traversed by at least one PV in one sample interval, at least 5-min, 5- to 10-min, and 20- to 25-min sampling intervals are required when the PV percentages are 3%, 2%, and 1%, respectively. The fusion of PV data and loop data can increase the accuracy of estimation results. About 3% of PVs are sufficient to collect highly accurate data for general freeways; 2% is enough to obtain the same or higher accuracy for the same road with fixed detectors.
Calcium‐ and Voltage‐Gated Potassium (BK) Channel Activators in the 5β‐Cholanic Acid‐3α‐ol Analogue Series with Modifications in the Lateral Chain (2012)

Large conductance, calcium- and voltage-gated potassium (BK) channels regulate various physiological processes and represent an attractive target for drug discovery. Numerous BK channel activators are available. However, these agents usually interact with the ubiquitously distributed channel-forming subunit and thus cannot selectively target a particular tissue. We performed a structure-activity relationship study of lithocholic acid (LCA), a cholane that activates BK channels via the accessory BK β1 subunit. The latter protein is highly abundant in smooth muscle but scarce in most other tissues. Modifications to the LCA lateral chain length and functional group yielded two novel smooth muscle BK channel activators in which the substituent at C24 has a small volume and a net negative charge. Our data provide detailed structural information that will be useful to advance a pharmacophore in search of β1 subunit-selective BK channel activators. These compounds are expected to evoke smooth muscle relaxation, which would be beneficial in the pharmacotherapy of prevalent human disorders associated with increased smooth muscle contraction, such as systemic hypertension, cerebral or coronary vasospasm, bronchial asthma, bladder hyperactivity, and erectile dysfunction.
Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing (2015)

RNA cleavage by some endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5'-hydroxyl (5'-OH) and 2',3'-cyclic phosphate termini. To identify 5'-OH RNA fragments produced by these cleavage events, we exploited the unique ligation mechanism of Escherichia coli RtcB RNA ligase to attach an oligonucleotide linker to RNAs with 5'-OH termini, followed by steps for library construction and analysis by massively parallel DNA sequencing. We applied the method to RNA from budding yeast and captured known 5'-OH fragments produced by tRNA Splicing Endonuclease (SEN) during processing of intron-containing pre-tRNAs and by Ire1 cleavage of HAC1 mRNA following induction of the unfolded protein response (UPR). We identified numerous novel 5'-OH fragments derived from mRNAs: some 5'-OH mRNA fragments were derived from single, localized cleavages, while others were likely produced by multiple, distributed cleavages. Many 5'-OH fragments derived from mRNAs were produced upstream of codons for highly electrostatic peptides, suggesting that the fragments may be generated by co-translational mRNA decay. Several 5'-OH RNA fragments accumulated during the induction of the UPR, some of which share a common sequence motif that may direct cleavage of these mRNAs. This method enables specific capture of 5'-OH termini and complements existing methods for identifying RNAs with 2',3'-cyclic phosphate termini.
Diaryliodonium Tetrachloroplatinates(II): Recognition of a Trifurcated Metal-Involving μ3-I···(Cl,Cl,Pt) Halogen Bond (2021)

Synthesis and X-ray characterization of the four diaryliodonium tetrachloroplatinates(II) [Ar1Ar2I]2[PtCl4] (Ar1/Ar2 = Ph/Ph (1), 4-Cl-C6H4/2,4,6-(MeO)3C6H2 (2), 4-Me-C6H4/2,4,6-(MeO)3C6H2 (3), Ph/2,4,6-(MeO)3C6H2 (4)) allowed the deterimination of several types of unconventional halogen-bond (HaB) patterns. The first example of a metal-involved trifurcated four-center μ3-X···(X′,X′,M) HaB is represented by the metal-involving I···Pt HaB (the structure of 4) with iodonium cations acting as HaB donors, which is supported by two weak I···Cl HaB contacts. The structures of 1–3 display bifurcated three-center μ2-I···(Cl,Cl) HaBs with iodonium cations. DFT calculations were used to estimate the energetic features of the two types of HaB contacts. Molecular electrostatic potential (MEP) surfaces and noncovalent interaction plot index (NCIPlot) computational tools were used to evaluate the σ-holes and characterize the HaBs, respectively, in all structures.
Temperature-Induced Apparent Mass Changes Observed during Quartz Crystal Microbalance Measurements of Atomic Layer Deposition (2003)

The quartz crystal microbalance (QCM) is a valuable in situ probe of surface chemistry and film growth during atomic layer deposition (ALD). Unfortunately, the QCM is sensitive to both mass and temperature effects that complicate the interpretation of QCM measurements. To characterize the temperature effects, QCM measurements are performed at 170 °C in a hot-wall, ALD flow reactor using pulses of inert and other unreactive probe gases that simulate reactant dosing during ALD. The difference between the probe gas temperature and the QCM sensor temperature is shown to cause instantaneous positive or negative apparent mass transients during the gas pulse. In addition, there is a net apparent mass drift after the gas pulse. The apparent mass transients and apparent mass drifting can lead to misinterpretation of ALD surface chemistry and produce error in measured ALD growth rates. Temperature-induced apparent mass changes are shown to be affected by the temperature profile in the ALD flow reactor before the QCM sensor. Changes in the gas flux during the ALD dosing sequence, changes in the type of dosing gas, and adiabatic cooling of the dosing gas can also produce temperature-induced apparent mass changes. The temperature effects on the QCM sensor are also demonstrated during Al2O3 ALD growth using Al(CH3)3 and H2O. Experimental methods using unreactive probe gases, such as SF6, are developed to tune the temperature profile of the ALD flow reactor to minimize the temperature-induced apparent mass changes.
Photo-Mask for Wafer-Scale Fabrication of Two- and Three-Dimensional Photonic Crystal Structures (2006)

A methodology is presented for the batch fabrication of photonic crystal device structures across an entire wafer based on a Multi-Beam Interference Lithography (MBIL) photo-mask. The mask produces a pre-designed set of beams at various locations across a wafer to expose and record the desired two- and three-dimensional interference patterns.
Numerical modelling of plastic deformation and subsequent primary recrystallization in a polycrystalline volume element, based on a level set framework (2008)

International audience
Modelling parametric down-conversion yielding spectrally pure photon pairs (2016)

Pair creation by spontaneous parametric down-conversion (SPDC) has become a reliable source for single-photon states, used in many kinds of quantum information experiments and applications. In order to be spectrally pure, the two photons within a generated pair should be as frequency-uncorrelated as possible. For this purpose most experiments use narrow bandpass filters, having to put up with a drastic decrease in count rates. This article elaborates (theoretically and by numerical evaluation) the alternative method to engineer a setup such that the SPDC-generated quantum states are intrinsically pure. Using pulsed pump lasers and periodically poled crystals this approach makes bandpass filtering obsolete and allows for significantly higher output intensities and therefore count rates in the detectors. After numerically scanning all common wavelength regimes, polarisation configurations and three different non-linear crystals, we present a broad variety of setups which allow for an implementation of this method.
Markerless positional verification using template matching and triangulation of kV images acquired during irradiation for lung tumors treated in breath-hold (2018)

Lung tumors treated in breath-hold are subject to inter- and intra-breath-hold variations, which makes tumor position monitoring during each breath-hold important. A markerless technique is desirable, but limited tumor visibility on kV images makes this challenging. We evaluated if template matching + triangulation of kV projection images acquired during breath-hold stereotactic treatments could determine 3D tumor position. Band-pass filtering and/or digital tomosynthesis (DTS) were used as image pre-filtering/enhancement techniques. On-board kV images continuously acquired during volumetric modulated arc irradiation of (i) a 3D-printed anthropomorphic thorax phantom with three lung tumors (n = 6 stationary datasets, n = 2 gradually moving), and (ii) four patients (13 datasets) were analyzed. 2D reference templates (filtered DRRs) were created from planning CT data. Normalized cross-correlation was used for 2D matching between templates and pre-filtered/enhanced kV images. For 3D verification, each registration was triangulated with multiple previous registrations. Generally applicable image processing/algorithm settings for lung tumors in breath-hold were identified. For the stationary phantom, the interquartile range of the 3D position vector was on average 0.25 mm for 12° DTS + band-pass filtering (average detected positions in 2D = 99.7%, 3D = 96.1%, and 3D excluding first 12° due to triangulation angle = 99.9%) compared to 0.81 mm for band-pass filtering only (55.8/52.9/55.0%). For the moving phantom, RMS errors for the lateral/longitudinal/vertical direction after 12° DTS + band-pass filtering were 1.5/0.4/1.1 mm and 2.2/0.3/3.2 mm. For the clinical data, 2D position was determined for at least 93% of each dataset and 3D position excluding first 12° for at least 82% of each dataset using 12° DTS + band-pass filtering. Template matching + triangulation using DTS + band-pass filtered images could accurately determine the position of stationary lung tumors. However, triangulation was less accurate/reliable for targets with continuous, gradual displacement in the lateral and vertical directions. This technique is therefore currently most suited to detect/monitor offsets occurring between initial setup and the start of treatment, inter-breath-hold variations, and tumors with predominantly longitudinal motion.
Supplementary Figures and Legends from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer (2023)

&lt;p&gt;Supplementary figures and figure legends for S1-7&lt;/p&gt;
Mutation of colocalized residues of the pore helix and transmembrane segments S5 and S6 disrupt deactivation and modify inactivation of KCNQ1 K+ channels (2005)

KCNQ1 (Kv 7.1) alpha-subunits and KCNE1 beta-subunits co-assemble to form channels that conduct the slow delayed rectifier K+ current (IKs) in the heart. Mutations in either subunit cause long QT syndrome (LQTS), an inherited disorder of cardiac repolarization. Here, the functional consequences of the LQTS-associated missense mutation V310I and several nearby residues were determined. Val310 is located at the base of the pore helix of KCNQ1, two residues below the TIGYG signature sequence that defines the K+ selectivity filter. Channels were heterologously expressed in Xenopus laevis oocytes and currents were recorded using the two-microelectrode voltage-clamp technique. V310I KCNQ1 reduced IKs amplitude when co-expressed with wild-type KCNQ1 and KCNE1 subunits. Val310 was also mutated to Gly, Ala or Leu to explore the importance of amino acid side chain volume at this position. Like V310I, V310L KCNQ1 channels gated normally. Unexpectedly, V310G and V310A KCNQ1 channels inactivated strongly and did not close normally in response to membrane hyperpolarization. Based on a homology model of the KCNQ1 channel pore, we speculate that the side group of residue 310 can interact with specific residues in the S5 and S6 domains to alter channel gating. When volume of the side chain is small, the stability of the closed state is disrupted and the extent of channel inactivation is enhanced. We mutated putative interacting residues in S5 and S6 and found that mutant Leu273 and Phe340 channels also can disrupt close states and modify inactivation. Together these findings indicate the importance of a putative pore helix-S5-S6 interaction for normal KCNQ1 channel deactivation and confirm its role in KCNQ1 inactivation. Disturbance of these interactions might underly LQTS associated with KCNQ1 mutant channels.