gebhart/patrepeval huggingface dataset:
2‐Chlorobenzoate Biodegradation by Recombinant Burkholderia cepacia under Hypoxic Conditions in a Membrane Bioreactor (2005)

The feasibility of applying bacterial hemoglobin technology to degrade 2-chlorobenzoate (2-CBA) through co-metabolism under hypoxic conditions in a membrane bioreactor (MBR) process has been studied in the laboratory. 2-chlorobenzoate removal and chloride release rates in the MBR system varied from 99 to 78% and 98 to 73%, respectively, depending on the operation conditions. Chemical oxygen demand (COD) removal efficiencies were more than 90% at food-to-microorganism ratios ranging from 0.32 to 0.62 g/g/d, and the observed yield was 0.13 to 0.20 g biomass/g COD. The bacterial cell-floc size-distribution analysis showed that there is a significant change in bacterial floc size due to high shear stress during operation of the MBR. To characterize growth kinetics of Burkholderia cepacia strain dinitrotoluene, a mathematical model that describes co-metabolic oxidation of 2-CBA in an MBR has been developed.
On the verification problem for weak memory models (2010)

We address the verification problem of finite-state concurrent programs running under weak memory models. These models capture the reordering of program (read and write) operations done by modern multi-processor architectures for performance. The verification problem we study is crucial for the correctness of concurrency libraries and other performance-critical system services employing lock-free synchronization, as well as for the correctness of compiler backends that generate code targeted to run on such architectures. We consider in this paper combinations of three well-known program order relaxations. We consider first the "write to read" relaxation, which corresponds to the TSO (Total Store Ordering) model. This relaxation is used in most hardware architectures available today. Then, we consider models obtained by adding either (1) the "write to write" relaxation, leading to a model which is essentially PSO (Partial Store Ordering), or (2) the "read to read/write" relaxation, or (3) both of them, as it is done in the RMO (Relaxed Memory Ordering) model for instance. We define abstract operational models for these weak memory models based on state machines with (potentially unbounded) FIFO buffers, and we investigate the decidability of their reachability and their repeated reachability problems. We prove that the reachability problem is decidable for the TSO model, as well as for its extension with "write to write" relaxation (PSO). Furthermore, we prove that the reachability problem becomes undecidable when the "read to read/write" relaxation is added to either of these two memory models, and we give a condition under which this addition preserves the decidability of the reachability problem. We show also that the repeated reachability problem is undecidable for all the considered memory models.
Carbon Mineralization by Aqueous Precipitation for Beneficial Use of CO2 from Flue Gas (2015)

The objective of this project was to demonstrate an innovative process to mineralize CO2 from flue gas directly to reactive carbonates and maximize the value and versatility of its beneficial use products. The program scope includes the design, construction, and testing of a CO2 Conversion to Material Products (CCMP) Pilot Demonstration Plant utilizing CO2 from the flue gas of a power production facility in Moss Landing, CA as well as flue gas from coal combustion. This final report details all development, analysis, design and testing of the project. Also included in the final report are an updated Techno-Economic Analysis and CO2 Lifecycle Analysis. The subsystems included in the pilot demonstration plant are the mineralization subsystem, the Alkalinity Based on Low Energy (ABLE) subsystem, the waste calcium oxide processing subsystem, and the fiber cement board production subsystem. The fully integrated plant was proven to be capable of capturing CO2 from various sources (gas and coal) and mineralizing it into a reactive calcium carbonate binder and subsequently producing commercial size (4ftx8ft) fiber cement boards. The final report provides a description of the “as built” design of these subsystems and the results of the commissioning activities that have taken place to confirm operability. The report also discusses the results of the fully integrated operation of the facility. Fiber cement boards have been produced in this facility exclusively using reactive calcium carbonate from captured CO2 from flue gas. These boards meet all US and China appropriate acceptance standards. Use demonstrations for these boards are now underway.
In‐line walkaway processing and integration (2003)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2003In‐line walkaway processing and integrationAuthors: Scott LeaneySergei TcherkashnevMark WheelerMuhammad IdreesAstley HastingsM. TouamiS. MekmoucheR. KasmiScott LeaneySchlumberger, Sergei TcherkashnevSchlumberger, Mark WheelerSchlumberger, Muhammad IdreesSchlumberger, Astley HastingsSchlumberger, M. TouamiSonatrach, S. MekmoucheSonatrach, and R. KasmiSonatrachhttps://doi.org/10.1190/1.1817782 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InReddit Permalink: https://doi.org/10.1190/1.1817782FiguresReferencesRelatedDetailsCited byCombining borehole and surface seismic data for velocity field estimation through slope tomographyGeophysical Journal International, Vol. 176, No. 3Joint slope tomography of borehole transmitted and surface seismic dataAdam Gosselet and Soazig Le Bégat7 December 2005 SEG Technical Program Expanded Abstracts 2003 ISSN (print):1052-3812 ISSN (online):1949-4645 Copyright: 2003 Pages: 2452 publication data© 2003 Copyright © 2003 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 03 Jan 2005 CITATION INFORMATION Scott Leaney, Sergei Tcherkashnev, Mark Wheeler, Muhammad Idrees, Astley Hastings, M. Touami, S. Mekmouche, and R. Kasmi, (2003), "In‐line walkaway processing and integration," SEG Technical Program Expanded Abstracts : 2203-2206. https://doi.org/10.1190/1.1817782 Plain-Language Summary PDF DownloadLoading ...
Temperature dependence of polariton lasing in a crystalline anthracene microcavity (2012)

The lasing threshold for crystalline anthracene sandwiched within an optical microcavity consisting of two dielectric Bragg reflectors (DBRs) is found to decrease by an order of magnitude as temperature is reduced from 300 to 12 K while maintaining an energy dispersion characteristic of the cavity polariton across the entire temperature range studied. The linear temperature dependence differs from a conventional organic semiconductor laser that shows practically no variation in threshold over the same temperature range. The two-dimensional Bose-Einstein condensate (BEC) critical density and its relation to the polariton lasing threshold is considered in the thermodynamic limit along with other temperature-dependent processes that are used to explain our observations.
Case Report: Hepatitis C Virus Activation in HIV-Infected Patients Initiating Highly Active Antiretroviral Therapy (2007)

We describe repeated episodes of hepatitis C (HCV) activation associated with initiation of highly active antiretroviral therapy (HAART) in two HIV/HCV coinfected individuals with undetectable serum HCV RNA. Both patients developed high HCV viremia (>1 million IU/mL) and elevations in aminotransferases >10 times upper limit of normal) within 4 months of starting HAART. This is the first report of clinically significant HCV activation in HCV-seropositive patients with initially undetectable HCV viremia. These observations suggest that flares of hepatitis C in the setting of the immune reconstitution inflammatory syndrome can occur even in those patients who have undetectable serum HCV levels prior to HAART initiation.
Identification of a specific sperm nuclei selenoenzyme necessary for protamine thiol cross‐linking during sperm maturation (2001)

ABSTRACT A 34 kD selenoprotein purified from rat testis was identified as a specific sperm nuclei glutathione peroxidase (snGPx) with similar properties to phospholipid hydroperoxide glutathione peroxidase (PHGPx). The determination of its primary structure by analysis of its first N‐terminal amino acids, database search, polymerase chain reaction, and sequencing of the cDNA showed that it differs from PHGPx in its N‐terminal sequence. This sequence, which is encoded for by an alternative exon in the first intron of the PHGPx gene, shows more than 50% homology to the protamine sequences and contains a nuclear localization signal. In rats, snGPx is highly expressed in the nuclei of the late spermatids where it is the only selenoprotein present. Its appearance coincides with the reorganization of DNA, which leads to highly condensed chromatin stabilized by cross‐linked protamine thiols. In selenium‐depleted rats where the concentration of snGPx had decreased to one‐third of the normal level, chromatin condensation was severely disturbed. We provided evidence that snGPx acts as a protamine thiol peroxidase responsible for disulfide cross‐linking by reduction of reactive oxygen species. Its dual function in chromatin condensation and the protection of sperm DNA against oxidation is necessary to ensure male fertility and sperm quality.
Epigenetic heredity: RNA‐mediated modes of phenotypic variation (2015)

In addition to the Mendelian mutations, several instances of heritable phenotypic variation have been reported. We have observed, in mice, a role for sperm RNAs in the induction of such stable phenotypic variation. When experimentally transferred by RNA microinjection into fertilized mouse eggs, the noncoding RNAs homologous in sequence to the target locus are efficient inducers of variation at the transcriptional level. Transmission of the phenotypic variation to progeny is highly efficient and independent of gender. Here, we have summarized these finding and how they relate to other reports of epigenetic variation.
Power/Performance/Thermal Design-Space Exploration for Multicore Architectures (2008)

Multicore architectures have been ruling the recent microprocessor design trend. This is due to different reasons: better performance, thread-level parallelism bounds in modern applications, ILP diminishing returns, better thermal/power scaling (many small cores dissipate less than a large and complex one), and the ease and reuse of design. This paper presents a thorough evaluation of multicore architectures. The architecture that we target is composed of a configurable number of cores, a memory hierarchy consisting of private L1, shared/private L2, and a shared bus interconnect. We consider a benchmark set composed of several parallel shared memory applications. We explore the design space related to the number of cores, L2 cache size, and processor complexity, showing the behavior of the different configurations/applications with respect to performance, energy consumption, and temperature. Design trade-offs are analyzed, stressing the interdependency of the metrics and design factors. In particular, we evaluate several chip floorplans. Their power/thermal characteristics are analyzed, showing the importance of considering thermal effects at the architectural level to achieve the best design choice.
IEEE Components, Packaging and Manufacturing Technology Society (2013)

Instructors Stephen Hall and Howard Heck Intel Corporation OVERVIEW: This one-day short course provides practicing design engineers an in-depth introduction into the fundamentals of signal integrity. It covers the practical and theoretical aspects necessary to design modern high-speed digital systems at the chip, package, and board levels. Attendees will learn from Stephen Hall and Howard Heck, two leading experts from Intel Corporation.
Assessing the Safety and Tolerability of Long‐Term Multi Day IVM Treatment for Alcohol Use Disorder (2015)

Alcohol use disorder (AUD) is a health crisis of unmet need. We propose that ivermectin (IVM), an FDA approved drug, can be repurposed to address this problem. Our group recently reported that long‐term (30 day) oral administration of IVM (10 mg/kg) significantly reduces murine ethanol intake without causing any overt signs of toxicity, suggesting that IVM represents a safe, tolerable, and effective agent for the treatment of AUDs. This first longer term study focused on an alcohol drinking paradigm that resulted in levels of alcohol intake that would more closely mimic the levels one would expect from someone drinking at a moderate level (i.e., social drinker). The current study extends this investigation and further assesses the safety and utility of multi‐day oral administration of IVM using a Drinking in the Dark (DID) paradigm, where animals in a very short period of time reach blood ethanol levels that are associated with “binge” drinking in humans. This was accomplished by investigating the effects of orally delivered IVM (10 mg/kg/day) in male alcohol preferring C57BL/6 over a 6 week (30 day, M‐F drinking) treatment period. We found that IVM significantly reduces ethanol intake and preference over the 6 week study without exerting any significant signs of toxicity, which was assessed using aspartate aminotransferase (AST) and alanine aminotransferase (ALT) liver enzyme level measurements. Histopathology assessments are currently ongoing. Taken together, findings, to date, continue to provide support for the development of of IVM for the treatment of AUD. Suport: Research grants SC CTSI NIH/NCRR/NCATS –UL1TR000130 (D.L. D.)
A variable step-size diffusion LMS algorithm with a quotient form (2020)

Abstract A new variable step-size strategy for the least mean square (LMS) algorithm is presented for distributed estimation in adaptive networks using the diffusion scheme. This approach utilizes the ratio of filtered and windowed versions of the squared instantaneous error for iteratively updating the step-size. The result is that the dependence of the update on the power of the error is reduced. The performance of the algorithm improves even though it is at the cost of added computational complexity. However, the increase in computational complexity can be minimized by careful manipulation of the update equation, resulting in an excellent performance-complexity trade-off. Complete theoretical analysis is presented for the proposed algorithm including stability, transient and steady-state analyses. Extensive experimental analysis is then done to show the performance of the proposed algorithm under various scenarios.
Microchip high-power radially pumped composite Yb:YAG laser (2001)

A novel design for a quasi-three level, microchip high-power laser is proposed. The design uses a Yb:YAG core surrounded byan undoped YAG region of slab shape that could be pumped from one or from both slab sides. Theoretical descriptions of thepumping optimization, pump-beam distribution, and output-to-input power characteristics are presented. The simulations showthat from a composite Yb:YAG chip, which consists of a Yb:YAG core of 2.0-mm diameter and l3.O-at.% Yb concentrationsurrounded by an undoped YAG slab of 5.0-mm width and 0.8-mm thickness, a TEMOO output beam of 100 W continuous-wavepower could be obtained. The expected optical-to-optical efficiency is 39%.Keywords: Quasi-four-level laser, Yb:YAG, diode-pumped solid-state laser, composite laser
SAW arrays using dendrimers and pattern recognition to detect volatile organics (1998)

chemical sensor arrays eliminate the need to develop a high-selectivity material for every analyte. The application of pattern recognition to the simultaneous responses of different microsensors enables the identification and quantification of multiple analytes with a small array. Maximum materials diversity is the surest means to create an effective array for many analytes, but using a single material family simplifies coating development. Here the authors report the successful combination of an array of six dendrimer films with mass-sensitive SAW (surface acoustic wave) sensors to correctly identify 18 organic analytes over wide concentration ranges, with 99.5% accuracy. The set of materials for the array is selected and the results evaluated using Sandia`s Visual-Empirical Region of Influence (VERI) pattern recognition (PR) technique. The authors evaluated eight dendrimer films and one self-assembled monolayer (SAM) as potential SAW array coatings. The 18 organic analytes they examined were: cyclohexane, n-hexane, i-octane, kerosene, benzene, toluene, chlorobenzene, carbon tetrachloride, trichloroethylene, methanol, n-propanol, pinacolyl alcohol, acetone, methyl isobutyl ketone, dimethylmethylphosphate, diisopropylmethylphosphonate, tributylphosphate, and water.
Supplementary Figure Legends, Table Legends from Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney (2023)

&lt;p&gt;Supplementary Figure Legends, Table Legends&lt;/p&gt;
Serum tumour markers CA 15-3, TPA, TPS, hCG β and TATI in the monitoring of chemotherapy response in metastatic breast cancer (2001)

The clinical utility of CA 15-3, polypeptide specific antigen (TPS), tissue polypeptide antigen (TPA), human chorionic gonadotropin (hCGbeta) and tumour-associated trypsin inhibitor (TATI) as indicators of chemotherapy response was assessed in advanced breast cancer. Serum was prospectively collected in one center before treatment (after the first course of chemotherapy) and at response evaluation from 57 patients taking part in a multicentre randomized trial comparing docetaxel with sequential methotrexate and 5-fluorouracil in the treatment of advanced breast cancer. The pretreatment levels of the serum markers were not predictors of the later response to treatment. Changes in the TPS level showed the strongest association with clinical response after the first course of chemotherapy and CA 15-3 at the best response evaluation. However, distinct mismatches occurred with every marker. The most problematic error was an increase in marker levels in patients with clinical responses, which might have caused interruption of therapy. This occurred in 8% and 17% of patients after the first course of chemotherapy and in 4% and 17% of patients at the best response evaluation with CA 15-3 and TPS, respectively. Moreover, after the first course of chemotherapy only 39% and 33% of the patients with progressive disease could be identified on the basis of increasing levels of CA 15-3 and TPS. respectively. Later, at clinical disease progression, TPA and TPS were found to be better indicators of disease progression than CA 15-3. In conclusion, changes in CA 15-3 or TPS levels usually correlate with clinical response, but owing to distinct discordances, they should not be used as sole indicators of response to chemotherapy in advanced breast cancer.
Observing Nanometre Scale Particles with Light Scattering for Manipulation Using Optical Tweezers (2008)

Nanometre-scale particles can be manipulated using optical tweezers, but cannot be directly observed. We present a simple method that nanoparticles can be directly observed using optical tweezers combined with dark field microscopy. A laser beam perpendicular to a tightly focused laser beam for trap illuminates specimen and does not enter objective, nanoparticles in focal plane all can be directly observed in dark field because of light scattering. It is implemented that the polystyrene beads of diameter 100nm can be directly observed and trapped.
4-Chloro-7-hydroxy-6-methyl-1,7-naphthyridin-8(7H)-one (2009)

The title compound, C(9)H(7)ClN(2)O(2), was prepared by reaction of methyl 4-chloro-3-(prop-1-yn-yl)picolinate with hydroxy-l-amine in MeOH/KOH solution. The two essentially planar mol-ecules which make up the asymmetric unit have almost identical geometries and and are linked into dimeric aggregates via pairs of O-H⋯O hydrogen bonds. These aggregates have almost perfect inversion symmetry; however, quite unusually, the inversion center of the dimer does not coincide with the crystallographic inversion center.
Quercitrin and quercetin 3-β-d-glucoside as chemical chaperones for the A4V SOD1 ALS-causing mutant (2017)

In many cases of familial amyotrophic lateral sclerosis (ALS), mutant forms of the Cu,Zn superoxide dismutase protein (SOD1) misfold and aggregate in motor neurons. Monomers of the normally homodimeric SOD1 have been found in patient tissue, presymptomatic mouse models of ALS, and in vitro misfolding assays which suggests that monomerization might be an early step in the pathological SOD1 misfolding pathway. In this study, we targeted the dimer interface with small molecules that might act as chemical chaperones to stabilize the native dimer and prevent downstream misfolding and aggregation. We performed a computational screen with a library of ~4400 drugs and natural compounds that were docked to two pockets around the SOD1 dimer interface. Of the resultant hits, seven were tested for misfolding and aggregation inhibition activity with A4V mutant SOD1. Quercitrin, quercetin-3-β-d-glucoside (Q3BDG), and, to a markedly lesser extent, epigallocatechin gallate (EGCG) were found to combat misfolding and aggregation induced by hydrogen peroxide, a physiologically relevant stress, as assessed by a gel-based assay and 8-anilinonaphthalene-1-suflonic acid (ANS) fluorescence. Isothermal titration calorimetry (ITC) and a colourimetric assay determined that these molecules directly bind A4V SOD1. Based on these findings, we speculate that quercitrin and Q3BDG may be potential therapeutic inhibitors of misfolding and aggregation in SOD1-associated ALS.
Nonalcoholic fatty liver disease prevalence and severity in Asian Americans from the national health and nutrition examination surveys 2017–2018 (2022)

Studies have examined nonalcoholic fatty liver disease (NAFLD) prevalence and severity in Asians; however, this is not well understood in Asian Americans (both East and South Asian Americans) as few studies have analyzed this population. We aimed to describe characteristics, prevalence of NAFLD, and its severity in Asian Americans in the National Health and Nutrition Examination Surveys (NHANES) from 2017 to 2018. Respondents 18 years and older with interview, laboratory testing, and transient elastography data were included. Other causes of liver disease were excluded. Controlled attenuation parameter (CAP) cutoff ≥ 274 dB/m, as published in the literature, defined NAFLD. Sensitivity analysis for CAP cutoffs ≥ 248 and ≥302 dB/m were performed. We found that 450 out of 3639 respondents were Asian Americans, and prevalence using CAP ≥ 274 dB/m was 43.23%. Using sensitivity analysis cutoffs of CAP ≥ 248 dB/m and CAP ≥ 302 dB/m, the prevalence was 57.38% and 28.03%, respectively. Compared with non-Asian Americans with NAFLD, Asian Americans with NAFLD had significantly lower body mass index (BMI) and less prevalent smoking history. Comorbidities, such as prediabetes, diabetes, and hypertension, were not significantly different between Asian and non-Asian Americans with NAFLD. Compared to non-Asian Americans with NAFLD, Asian Americans with NAFLD exhibited higher aminotransferases and triglycerides. Fibrosis assessed by transient elastography was not significantly different between Asian and non-Asian Americans with NAFLD. Despite decreased prevalence of BMI ≥ 30 kg/m<sup>2</sup> , Asian Americans experienced similar NAFLD prevalence with increased hepatocellular injury and triglyceridemia compared to non-Asian Americans. Fibrosis stages were similar to non-Asian Americans.
3D visualization of the stain-free buccal cells (2019)

The rotational view of the stain-free buccal cells with internal structures delineated from groupings of refractive index values.