gebhart/patrepeval huggingface dataset:
Methods for saving and restoring register values across function calls (1991)

Abstract The method used to save and restore the values of registers across function calls can affect performance and influence the design of specific instructions. This paper describes the results of an experiment that empirically evaluated six different schemes for saving and restoring registers on CISC machines. The methods do not require special hardware or interprocedural analysis to be performed. The six schemes were logically divided into two classes. Three of the techniques do not require the compiler to perform data‐flow analysis, whereas the other three schemes do. Within each class one scheme delegates the responsibility of preserving the state of the registers to the calling function. The second scheme of each class delegates the responsibility of saving the registers to the function being called. In the third scheme of the two classes, the registers are partitioned into two disjoint sets. The calling function is responsible for preserving register values in one of the sets whereas the called function is responsible for the other set. For each class the third scheme is shown to produce the most effective code.
Forensic Analysis and Characterization of Burkholderia Isolates using Burkholderia SNP Genotyping Microarray: Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array (2012)

The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.
Advanced synchronization in Mac OS X: extending unix to SMP and real-time (2002)

Throughout the years, as Unix has grown and evolved so has computer hardware. The 4.4BSD-Lite2 distribution had no support for two features that are becoming more and more important: SMP and real-time processing.

With the release Mac OS X Apple has made extensive alterations to our kernel in order to support both SMP and real-time processing. These alterations affected both the BSD and Mach portions of our kernel, as well as shaping our driver system, IOKit.

These changes range from scheduling policies, enabling support for kernel preemption, altering locking hierarchies, and defining new serialization primitives, as well as designing a driver architecture that allows developers to easily make their drivers SMP and preemption safe.
Phase change random access memory cell with superlattice-like structure (2006)

A superlattice-like structure (SLL) incorporating two nonpromising phase change materials was applied to phase change random access memory (PCRAM) cell. A properly designed SLL structure could balance both the phase change speed and stability of a PCRAM. Moreover, SLL PCRAM cells exhibited lower programming current and fast working time of 5ns. The main reason for the excellent performances is due to the much lower thermal conductivity of the SLL material compared to that of bulk materials. The thermal conductivity of eight SLL layers cycle was found to be smaller than 30% of that of single layer material.
Apolipoprotein E Polymorphism: A New Genetic Marker of Hip Fracture Risk—The Study of Osteoporotic Fractures (1999)

Abstract Hip fractures are common and devastating events. The apolipoprotein E*4 (APOE) allele, associated with Alzheimer's disease, has also been associated with osteoporosis in hemodialysis patients. We prospectively studied 1750 women, age ≥65 years, who underwent measurements of hip and calcaneal bone mineral density (BMD), were typed for APOE and followed for ~7.0 years for the occurrence of fractures and falls. Women with at least one APOE*4 allele had an increased risk of hip fracture, relative hazard (RH) (95% confidence interval) = 1.90 (1.05–3.41) and wrist fracture, RH = 1.67 (1.01–2.77) compared with women without APOE*4, even after adjusting for age, cognitive function, falling, and BMD. The effect of APOE*4 on hip fracture was greatest among women with additional (≥3) other risk factors. Women with an APOE*4 allele were also likely to report a maternal history of fracture. The average number of falls per year did not differ by APOE*4: 0.46 for APOE*4 women and 0.41 for women without an APOE*4 allele. Women with an APOE*4 allele experienced greater weight loss which contributed to faster rates of bone loss. We conclude that women with the APOE*4 polymorphism are at substantially increased risk of hip and wrist fracture that is not explained by bone density, impaired cognitive function, or falling. Passible alternate explanations include an effect of APOE on vitamin K, bone turnover, or weight loss. The APOE polymorphism may be a candidate gene for hip fractures among community dwelling nondemented women.
Wall-Wetting Parameters Over the Operating Region of a Sequential Fuel-Injected SI Engine (1998)

&lt;div class="htmlview paragraph"&gt;In modern engine control applications, there is a distinct trend towards model-based control schemes. There are various reasons for this trend: Physical models allow deeper insights compared to heuristic functions, controllers can be designed faster and more accurately, and the possibility of obtaining an automated application scheme for the final engine to be controlled is a significant advantage. Another reason is that if physical effects can be separated, higher order models can be applied for different subsystems. This is in contrast to heuristic functions where the determination of the various maps poses large problems and is thus only feasible for low order models.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;One of the most important parts of an engine management system is the air-to-fuel control. The catalytic converter requires the mean air-to-fuel ratio to be very accurate in order to reach its optimal conversion rate. Disturbances from the active carbon filter and other additional devices have to be compensated. Emission-optimal warm-up strategies require the engine to be run slightly lean without misfires. All these tasks cannot be fulfilled with the feedback controller only but also need a very good feedforward strategy. Such a feedforward strategy usually inverts the known plant dynamics. One important part of the fuel dynamics is the wall-wetting dynamics, i.e., the fact that not all the fuel injected enters the cylinder during the following intake valve opening. First-order approximations of these dynamics are frequently used. Their advantage is that they are easy to implement in an inverse dynamic feedforward strategy and that the parameters can be determined quite simply. However, the wall-wetting dynamics are not sufficiently described by first-order approximations.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;New engine management systems increasingly are fitted with wide-range sensors. Due to a smaller time constant, these sensors allow the detection of higher-frequency phenomena and also yield quantitative information on the air-to-fuel ratio (lambda). Mounted closely to the exhaust valve, these sensors also allow a better identification of the wall-wetting dynamics.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A second-order model shows very good performance. It can be fitted into the frequency response measurements with a nonlinear optimization routine. The scheme for the parameter identification presented here does two things: It highlights certain problem areas which require special attention and it describes the parameter maps for the operating region at two different cylinders of an SI engine. Finally, some measurements taken on the cold engine are shown and interpreted.&lt;/div&gt;
DNA Sequencing Analysis of African <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> Virulence Gene ( <i>AXaVrg</i> ) DNA Marker (2018)

Abstract Global rice production is constrained by bacterial leaf blight (BLB) disease caused by Xanthomonas oryzae pv. oryzae ( Xoo ). BLB disease incidence in West Africa was between 70–85% and yield loss in farmers’ fields was in the range of 50–90% from 2005 to 2010. In the present study, African Xoo virulence gene OPP-17 2000 DNA marker was identified and purified using randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) products from 50 Xoo isolates. Genomic DNA of 50 Xoo isolates were analyzed using OPP-17 primer in RAPD-PCR during which African Xoo virulence gene OPP-17 2000 DNA marker was identified, purified, cloned, and sequenced. Cloning and DNA sequencing of African Xoo virulence gene OPP-17 2000 DNA generated a 1953 bp nucleotide sequence consequently tagged as AXaVrg -1953. BLAST homologous analysis of the AXaVrg- 1953 sequence provides comprehensive identification of the type II secretion genes and secreted proteins, type III secretion genes and secreted proteins in African Xoo virulence gene. Phylogenetic unweighted pairgroup method arithmetic (UPGMA) analysis revealed the African AXaVrg -1953 sequence was distinct from the other Xoo virulence gene sequences from China, Japan, Korea, Germany, and the United States. This information is potentially useful for effective management of BLB disease in West Africa.
The Biological Effectiveness of Neutrons: Implications for Radiation Protection (1992)

The radiobiology of neutrons has important societal implications. In nuclear facilities worldwide, several hundred thousand individuals are monitored as potentially receiving doses of neutrons, while there is increasing concern about the dose to which airline crew members are exposed, which includes a substantial neutron component. This represents an even larger number of individuals. The relative biological effectiveness (RBE) for neutrons varies with neutron energy. With cell killing as an endpoint, the maximum RBE occurs at about 300 to 400 keV, and falls off above and below this energy. For oncogenic transformation, the variation of effectiveness with energy is less marked. However, for some neutron energies and at some doses, there is a clear inverse dose-rate effect i.e. an increased rate of transformation with dose protraction, the magnitude of which depends on neutron energy, dose and dose rate. There is considerable uncertainty at the present time concerning the RBE of low energy 'soft' neutrons in the range 10 to 100 keV.
Frequency and epitope specificity of anti–factor VIII C1 domain antibodies in acquired and congenital hemophilia A (2017)

Several studies showed that neutralizing anti-factor VIII (anti-fVIII) antibodies (inhibitors) in patients with acquired hemophilia A (AHA) and congenital hemophilia A (HA) are primarily directed to the A2 and C2 domains. In this study, the frequency and epitope specificity of anti-C1 antibodies were analyzed in acquired and congenital hemophilia inhibitor patients (n = 178). The domain specificity of antibodies was studied by homolog-scanning mutagenesis (HSM) with single human domain human/porcine fVIII proteins and antibody binding to human A2, C1, and C2 domains presented as human serum albumin (HSA) fusion proteins. The analysis with HSA-fVIII domain proteins confirmed the results of the HSM approach but resulted in higher detection levels. The higher detection levels with HSA-fVIII domain proteins are a result of antibody cross-reactivity with human and porcine fVIII leading to false-negative HSM results. Overall, A2-, C1-, and C2-specific antibodies were detected in 23%, 78%, and 68% of patients with AHA (n = 115) and in 52%, 57%, and 81% of HA inhibitor patients (n = 63). Competitive binding of the human monoclonal antibody (mAb) LE2E9 revealed overlapping epitopes with murine C1-specific group A mAbs including 2A9. Mutational analyses identified distinct crucial binding residues for LE2E9 (E2066) and 2A9 (F2068) that are also recognized by anti-C1 antibodies present in patients with hemophilia. A strong contribution of LE2E9- and 2A9-like antibodies was particularly observed in patients with AHA. Overall, our study demonstrates that the C1 domain, in addition to the A2 and C2 domains, contributes significantly to the humoral anti-fVIII immune response in acquired and congenital hemophilia inhibitor patients.
Storage class memory based SSD performance in consideration of error correction capabilities and write/read latencies (2016)

The future storage class memory (SCM) can be comparable with NAND flash in terms of cost, and with DRAM from the perspective of speed. There are 3 primary memory technology candidates that match the target requirements for SCM: ReRAM, PCM, and MRAM. The future SCM-based solid state drive (SSD) shows advantages of high performance and low power consumption compared with NAND flash SSD. In this paper, SCM-only SSD performance with different SCM write/read latencies is analyzed for two workloads (write/read intensive). Next, impact of error-correcting code (ECC) capabilities on the SSD performance is also analyzed to consider the SSD reliability. Finally, the trade-off and the optimal relation of ECC capabilities and SCM latencies are analyzed to achieve the high-performance SCM-based SSD.
The Complement System Contributes to Functional Antibody-Mediated Responses Induced by Immunization with Plasmodium falciparum Malaria Sporozoites (2018)

Long-lasting and sterile homologous protection against malaria can be achieved by the exposure of malaria-naive volunteers under chemoprophylaxis to <i>Plasmodium falciparum</i>-infected mosquitoes (chemoprophylaxis and sporozoite [CPS] immunization). While CPS-induced antibodies neutralize sporozoite infectivity <i>in vitro</i> and <i>in vivo</i>, antibody-mediated effector mechanisms are still poorly understood. Here, we investigated whether complement contributes to CPS-induced preerythrocytic immunity. Sera collected before and after CPS immunization in the presence of active or inactive complement were assessed for the recognition of homologous NF54 and heterologous NF135.C10 sporozoites, complement fixation, sporozoite lysis, and possible subsequent effects on <i>in vitro</i> sporozoite infectivity in human hepatocytes. CPS immunization induced sporozoite-specific IgM (<i>P</i> < 0.0001) and IgG (<i>P</i> = 0.001) antibodies with complement-fixing capacities (<i>P</i> < 0.0001). Sporozoite lysis (<i>P</i> = 0.017), traversal (<i>P</i> < 0.0001), and hepatocyte invasion inhibition (<i>P</i> < 0.0001) by CPS-induced antibodies were strongly enhanced in the presence of active complement. Complement-mediated invasion inhibition in the presence of CPS-induced antibodies negatively correlated with cumulative parasitemia during CPS immunizations (<i>P</i> = 0.013). While IgG antibodies similarly recognized homologous and heterologous sporozoites, IgM binding to heterologous sporozoites was reduced (<i>P</i> = 0.023). Although CPS-induced antibodies did not differ in their abilities to fix complement, lyse sporozoites, or inhibit the traversal of homologous and heterologous sporozoites, heterologous sporozoite invasion was more strongly inhibited in the presence of active complement (<i>P</i> = 0.008). These findings demonstrate that CPS-induced antibodies have complement-fixing activity, thereby significantly further enhancing the functional inhibition of homologous and heterologous sporozoite infectivity <i>in vitro</i> The combined data highlight the importance of complement as an additional immune effector mechanism in preerythrocytic immunity after whole-parasite immunization against <i>Plasmodium falciparum</i> malaria.
Decoding gene regulation in the mouse embryo using single-cell multi-omics (2022)

Abstract Following gastrulation, the three primary germ layers develop into the major organs in a process known as organogenesis. Single-cell RNA sequencing has enabled the profiling of the gene expression dynamics of these cell fate decisions, yet a comprehensive map of the interplay between transcription factors and cis-regulatory elements is lacking, as are the underlying gene regulatory networks. Here we generate a multi-omics atlas of mouse early organogenesis by simultaneously profiling gene expression and chromatin accessibility from tens of thousands of single cells. We develop a computational method to leverage the multimodal readouts to predict transcription factor binding events in cis-regulatory elements, which we then use to infer gene regulatory networks that underpin lineage commitment events. Finally, we show that these models can be used to generate in silico predictions of the effect of transcription factor perturbations. We validate this experimentally by showing that Brachyury is essential for the differentiation of neuromesodermal progenitors to somitic mesoderm fate by priming cis-regulatory elements. The data set can be interactively explored at https://www.bioinformatics.babraham.ac.uk/shiny/shiny_multiome_organogenesis/
Polarization Imaging System for Colposcopy (2012)

The designed polarization adapter is incorporated into a colposcope provides illumination with polarized light and capturing of orthogonally polarized images, using liquid crystal retarder and polarizer. Pearson correlation analysis is used to characterize subsurface structures.
Three-Dimensional T1 Mapping for dGEMRIC at 3.0 T Using the Look Locker Method (2006)

The preliminary data presented here suggest that the 3DLL sequence provides accurate T1 values with sufficient in-plane resolution and allows full joint coverage in less than 10 minutes.
Magnetically Aligned Nanodomains: Application in High-Performance Ion Conductive Membranes (2014)

Polyelectrolyte-coated magnetic nanoparticles were prepared by decorating the surface of superparamagnetic iron oxide nanoparticles (SPIONs) with crosslinked chitosan oligopolysaccharide (CS). These positively charged particles (CS-SPIONs) were then added to a negatively charged polymer (Nafion), and cast into membranes under an applied magnetic field. TEM and SAXS measurements confirmed this process created aligned, cylindrical nanodomains in the membranes. This was also indirectly confirmed by proton conductivity values. The strong electrostatic interaction between chitosan and Nafion prevented oxygen permeability and water evaporation at elevated temperatures through the proton conductive channels. The resultant proton exchange membranes showed lower conduction dependency to relative humidity, which is highly desirable for hydrogen fuel cells. The fuel cell performance tests were performed on the designed polyelectrolyte membrane by hydrogen-oxygen single cells at elevated temperature (120 °C) and low relative humidity.
Charge Trapping &amp; NBTI in High k Gate Dielectric Stacks (2006)

Over recent years, there has been increasing research and development efforts to replace SiO2 with high dielectric constant (k) materials such as HfO2, HfSiO, Al2O3. An important transistor reliability issue is the threshold voltage stability under prolonged stressing. In this paper, we discuss two main causes of threshold voltage instability: charge trapping and negative bias temperature instability (NBTI) in high k gate dielectric stacks. Experimental and modeling studies for these threshold voltage instabilities are reviewed.
ChemInform Abstract: Diastereoselective Ritter Reactions of Chiral Secondary Benzylic Alcohols. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
1-deoxy-d-xylulose-5-phosphate reductoisomerases and method of use (2023)

The present invention relates to isolated DNA sequences which code for the expression of plant 1-deoxy-D-xylulose-5-phosphate reductoisomerase protein, such as the sequence presented in SEQ ID NO:1 which encodes a 1-deoxy-D-xylulose-5-phosphate reductoisomerase protein from peppermint (Mentha x piperita). Additionally, the present invention relates to isolated plant 1-deoxy-D-xylulose-5-phosphate reductoisomerase protein. In other aspects, the present invention is directed to replicable recombinant cloning vehicles comprising a nucleic acid sequence which codes for a plant 1-deoxy-D-xylulose-5-phosphate reductoisomerase, to modified host cells transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence of the invention.
On source-channel coding over Gaussian sensor networks for path planning (2014)

Path planning is an important component of mobile sensor and autonomous mobile systems. This paper studies inner and outer bounds for joint source-channel coding over Gaussian sensor networks, to drive power-distortion metrics for path planning problems for sensor data gathering. The Gaussian multiple access channel is considered for two source models. In the first setting, the underlying source is estimated with minimum mean squared error (MSE), while in the second, reconstruction of a random field is considered. The second problem simplifies to weighted MSE minimization over the sensor measurements. For both cases, we identify conditions for optimality of uncoded communication, beyond the known optimality results. For both problem settings, we derive inner and outer bounds of sensor power-distortion curve. Next, we consider optimal power allocation among sensors under a total weighted sum power constraint and obtain closed form characterizations of optimal total power versus distortion tradeoff. We numerically analyze the gap between outer and inner bounds for both total power and individual power constrained settings.
1-Ethyl-β-<i>N</i>-acetylglucosaminide increases hyaluronan production in human keratinocytes by being converted to <i>N</i>-acetylglucosamine via β-<i>N</i>-acetylglucosaminidase-dependent manner (2021)

Regulation of hyaluronan (HA) is important for the maintenance of epidermal homeostasis. Here, we examined the mechanism by which 1-ethyl-β-N-acetylglucosaminide (β-NAG2), a newly developed N-acetylglucosamine (NAG) derivative, increases HA production in cultured human epidermal keratinocytes. When keratinocytes were treated with β-NAG2, mRNA expression of HA synthase 3, which is responsible for HA production in human keratinocytes, was not influenced, but the intracellular level of UDP-NAG, a substrate used for HA synthesis, was increased. By using a synthetic substrate for β-N-acetylglucosaminidase (β-NAGase), keratinocytes were found to possess β-NAGase activity, and treatment of o-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino N-phenyl carbamate (PUGNAc), an inhibitor of β-NAGase, abolished the release of NAG from β-NAG2 in keratinocytes. Furthermore, PUGNAc attenuated the β-NAG2-induced intracellular UDP-NAG and HA production in keratinocytes. These results suggest that β-NAG2 is converted to NAG by endogenous β-NAGase in keratinocytes, and the resulting NAG is further metabolized to UDP-NAG and utilized for HA production.
Dimethyl Maleate (2001)

[624-48-6] C6H8O4 (MW 144.14) InChI = 1S/C6H8O4/c1-9-5(7)3-4-6(8)10-2/h3-4H,1-2H3/b4-3- InChIKey = LDCRTTXIJACKKU-ARJAWSKDSA-N (useful as a dienophile; dipolarophile; Michael acceptor; radical acceptor) Physical Data: bp 204–205 °C; d 1.152 g cm−3. Solubility: sol most ethers and methanol. Form Supplied in: colorless liquid; ≤4% impurity of dimethyl fumarate. Purification: distilled under reduced pressure. Handling, Storage, and Precautions: toxic, irritant. Store in a brown bottle; avoid exposure to light.