gebhart/patrepeval huggingface dataset:
Complementary Description of the Middle Ordovician Trilobite Associations at Praha-Vokovice (2015)

Abstract The temporarily exposed rocks of the Dobrotivá Formation (Middle Ordovician, upper Darriwilian) accessible, due to lower water levels, in Džbán water reservoir (Praha-Vokovice area) have produced common fauna. The newly obtained trilobite-dominated fossil associations enable a more detailed discussion of faunal changes in the lower and lower-middle portions of the Dobrotivá Formation - a transition from the Placoparia Association to the newly recognized Degamella-Zeliszkella Association, dominated by mesopelagic forms.
The Haptoglobin-CD163-Heme Oxygenase-1 Pathway for Hemoglobin Scavenging (2013)

The haptoglobin- (Hp-) CD163-heme oxygenase-1 (HO-1) pathway is an efficient captor-receptor-enzyme system to circumvent the hemoglobin (Hb)/heme-induced toxicity during physiological and pathological hemolyses. In this pathway, Hb tightly binds to Hp leading to CD163-mediated uptake of the complex in macrophages followed by lysosomal Hp-Hb breakdown and HO-1-catalyzed conversion of heme into the metabolites carbon monoxide (CO), biliverdin, and iron. The plasma concentration of Hp is a limiting factor as evident during accelerated hemolysis, where the Hp depletion may cause serious Hb-induced toxicity and put pressure on backup protecting systems such as the hemopexin-CD91-HO pathway. The Hp-CD163-HO-1 pathway proteins are regulated by the acute phase mediator interleukin-6 (IL-6), but other regulatory factors indicate that this upregulation is a counteracting anti-inflammatory response during inflammation. The heme metabolites including bilirubin converted from biliverdin have overall an anti-inflammatory effect and thus reinforce the anti-inflammatory efficacy of the Hp-CD163-HO-1 pathway. Future studies of animal models of inflammation should further define the importance of the pathway in the anti-inflammatory response.
Nucleic acids useful for integrating into and gene expression in hyperthermophilic acidophilic Archaea (2023)

The present invention provides for a novel recombinant or isolated nucleic acid useful for integrating or being maintained in an Archaea or acidophilic hyperthermophilic eubacteria. The nucleic acid encodes a nucleotide sequence that is capable of stably integrating into the chromosome of a host cell, or being maintained as an extrachromosomal element in a host cell, that is an Archea, and a nucleotide sequence of interest. The present invention also provides for an Archaea host cell comprising the nucleic acid stably integrated into the chromosome or maintained episomally in the host cell, and a method of expressing the nucleotide sequence of interest in the host cell and/or directing glycosylation, multimerization, and/or membrane association or integration.
Estradiol and breast cancer risk. (2006)

Fifth AACR International Conference on Frontiers in Cancer Prevention Research, Nov 12-15, 2006

A144 

Background Estradiol levels have been associated with breast cancer risk in large cohort studies. We are conducting a Phase II chemoprevention study in which Letrozole, a potent selective non-steroidal aromatase inhibitor, is compared to placebo in postmenopausal women not using hormonal agents whose eligibility is determined only by estradiol level. This analysis explores the correlates of estradiol and established breast cancer factors among women screened for trial eligibility. Methods Screened subjects (postmenopausal women not using hormonal agents or osteoporosis medications) completed a self-administered questionnaire regarding reproductive history, hormone or SERM use, and family cancer history. Estradiol levels were measured using the double extraction technique (Esoterix Inc, Calabasas, CA) and stratified as highest quartile ≥0.9 ng/dL or lower. Crosstabular analyses and Chi-Square tests (0.05 level of significance) were performed on the overall cohort and by cancer status to explore potential differences between the two estradiol groups with regard to the following variables: age, BMI, type of menopause, family breast cancer history and Gail score, and previous hormone use. Results Our sample consisted of 324 postmenopausal women (amenorrhea ≥ 12 mo, ≥ 55 yrs with hysterectomy ± oophorectomy and/or documented FSH) with a mean age of 57.7 years (range 40-76) and mean BMI 27.2. The majority were Caucasian (96.7%), mean estradiol was 0.98 ng/dL (range 0.5-17.0) and 25.5% had an estradiol ≥ 0.9 ng/dL. 72.4% experienced natural menopause (27.5% surgical) and 28.9% had an oophorectomy. 33.5% were breast cancer survivors. For the overall cohort and for women without a breast cancer history the high estradiol group was significantly associated with younger age <57 (p=0.0025), BMI ≥ 26 (p=0.0080), natural menopause (p=0.0379), and no oophorectomy (p=0.0017). These relationships did not hold for women with a breast cancer history. No significant relationship was found between estradiol and family history or Gail score. Conclusion In our cohort of postmenopausal women considering enrollment in a Phase II chemoprevention trial, estradiol levels were related to BMI, younger age and natural menopause, and not to Gail score, which incorporates several hormonal risk factors. Estradiol level was not explored in this analysis for its potential as an independent risk predictor. However, other data suggest that it could supplement existing risk models. Issues in measurement of estradiol and other estrogens at postmenopausal levels and other potential confounders must be explored further in larger datasets. Our intervention trial will evaluate the effect of an aromatase inhibitor in postmenopausal women with higher estradiol levels.
The Jefferson Lab High Power THz User Facility (2005)

We describe a high power (100 Watt average, 10 MW peak) broadband THz facility based on emission from sub-picosecond bunches of relativistic electrons and the system that transports this beam in to a user laboratory.
Stability of Gyroscopic Systems (1999)

Flow-induced vibration of structures, A. Baja and C. Folley gyroelastic dynamics, G. D'Elenterio shape control and vibration suppression of elastic structures by means of fluid flow, A. Guran nonlinear oscillations of rotors, Y. Ishida dynamics of high-speed axially moving material systems, N. Perkins and S.-J. Hwang.
Particle Concentration and Characteristics near a Major Freeway with Heavy-Duty Diesel Traffic (2007)

This study presents the number, surface and volume concentrations, and size distribution of particles next to the 1-710 freeway during February through April 2006. 1-710 has the highest ratio (up to 25%) of heavy-duty diesel vehicles in the Los Angeles highway network. Particle concentration measurements were accompanied by measurements of black carbon, elemental and organic carbon, and gaseous species (CO, CO2). Using the incremental increase of CO2 over the background to calculate the dilution ratio, this study makes it possible to compare particle concentrations measured next to the freeway to concentrations measured in roadway tunnels and in vehicle exhaust. In addition to the effect of the dilution ratio on the measured particle concentrations, multivariate linear regressions showed that light and heavy organic carbon concentrations are positively correlated with the particle volume in the nucleation and accumulation modes, respectively. Solar radiation was also positively correlated with the particle surface concentration and the particle volume in the accumulation (40-638 nm) mode, presumably as a result of secondary particle formation. The methods developed in this study may be used to decouple the effect of sampling position, meteorology, and fleet operation on particle concentrations in the proximity of freeways, roadway tunnels, and in street canyons.
Distant regulatory effects of genetic variation in multiple human tissues (2016)

Abstract Understanding the genetics of gene regulation provides information on the cellular mechanisms through which genetic variation influences complex traits. Expression quantitative trait loci, or eQTLs, are enriched for polymorphisms that have been found to be associated with disease risk. While most analyses of human data has focused on regulation of expression by nearby variants (cis-eQTLs), distal or trans-eQTLs may have broader effects on the transcriptome and important phenotypic consequences, necessitating a comprehensive study of the effects of genetic variants on distal gene transcription levels. In this work, we identify trans-eQTLs in the Genotype Tissue Expression (GTEx) project data 1 , consisting of 449 individuals with RNA-sequencing data across 44 tissue types. We find 81 genes with a trans-eQTL in at least one tissue, and we demonstrate that trans-eQTLs are more likely than cis-eQTLs to have effects specific to a single tissue. We evaluate the genomic and functional properties of trans-eQTL variants, identifying strong enrichment in enhancer elements and Piwi-interacting RNA clusters. Finally, we describe three tissue-specific regulatory loci underlying relevant disease associations: 9q22 in thyroid that has a role in thyroid cancer, 5q31 in skeletal muscle, and a previously reported master regulator near KLF14 in adipose. These analyses provide a comprehensive characterization of trans-eQTLs across human tissues, which contribute to an improved understanding of the tissue-specific cellular mechanisms of regulatory genetic variation.
A Model for Computing Based on Information Search (2012)

While the initial file extract approach to the information search repository is a stop-gap measure, over time it should be embedded in the enterprise metadata repository. Even this short-term measure, however, will achieve the goal of creating a useful natural language interface that will allow staff to find the application, report, or spreadsheet that is directly relevant to their task. Often, such an approach also has the benefit of teaching people how to do a task better or allowing them to find information they would not even know they needed. Much of the approach described in this chapter is enabled by a concept called Web 2.0. With interactive metadata, the content is able to evolve and be maintained by the user community rather than relying solely on an administrator or team of programmers. Such a model for computing is far more sustainable and creates a more relevant set of business solutions.
Gene transduction in skin cells: Preventing cancer in xeroderma pigmentosum mice (2004)

UV radiation is the most common risk factor for skin cancer. Patients with the autosomal recessive DNA repair disorder xeroderma pigmentosum (XP) suffer high incidence of skin cancer after sunlight exposure. XP-mutant mice are attractive models to study this syndrome, as they, too, develop UV radiation-induced skin tumors, mimicking the human phenotype. Recombinant adenovirus carrying the human XPA gene was used for in vivo gene therapy in UVB-irradiated skin of such mice. Virus s.c. injection led to the expression of the XPA protein in basal keratinocytes and prevented deleterious effects in the skin, including late development of squamous cell carcinoma. Thus, efficient adenovirus gene delivery to the skin is a promising tool for reconstitution of specific DNA repair defects in XP patients.
On referring expressions in query answering over first order knowledge bases (2016)

A referring expression in linguistics is any noun phrase identifying an object in a way that will be useful to interlocutors. In the context of a query over a first order knowledge base K, constant symbols occurring in K are the artifacts usually used as referring expressions in certain answers to the query. In this paper, we begin to explore how this can be usefully extended by allowing a class of more general formulas, called singular referring expressions, to replace constants in this role. In particular, we lay a foundation for admitting singular referring expressions in certain answer computation for queries overK. An integral part of this foundation are characterization theorems for identification properties of singular referring expressions for queries annotated with a domain specific language for referring concept types. Finally, we apply this framework in the context of tractable description logic dialects, showing how identification properties can be determined at compile-time for conjunctive queries, and how off-the-shelf conjunctive query evaluation for these dialects can be used in query evaluations, preserving, in all cases, underlying tractability.
Distinct Inflammatory Gene Pathways Induced by Particles (2007)

The biologic response to particulate load after arthroplasty has not been fully characterized but is believed mediated by proinflammatory cytokines released from mononuclear cells in the periprosthetic region. To investigate the contribution of lymphocytes to expression of proinflammatory genes induced by metal particles, we compared gene expression of mononuclear cells in response to metal and polymethylmethacrylate particles using cDNA microarray profiling. Peripheral blood mononuclear cells and monocytes were stimulated with polymethylmethacrylate and titanium particles of clinically relevant sizes. Polymethylmethacrylate elicited a six- to 12-fold increase in gene expression of tumor necrosis factor alpha, interleukin 1alpha, interleukin 1beta, interleukin 6, and interleukin 8 in purified monocytes and unfractionated peripheral blood mononuclear cells. Although the effect of titanium on stimulation of purified monocytes was modest, stimulation of lymphocyte-containing peripheral blood mononuclear cells by titanium particles resulted in monocyte-derived proinflammatory cytokine expression. In contrast to polymethylmethacrylate, titanium particles stimulated increased expression of T lymphocyte-derived cytokines, including interleukin 2, interferon gamma, interleukin 9, and interleukin 22, in peripheral blood mononuclear cell cultures. The induction of T cell activation by titanium particles suggests lymphocytes may contribute to the inflammation that mediates osteolysis in patients with metallic particulate debris after total joint replacement.
Heterogeneity of Soluble Suppressor Factors in Rat Malignant Ascites (1988)

A study was undertaken to enumerate and partially characterize soluble factors generated by tumor-bearing animals capable of suppressing PHA-induced splenocyte proliferation. Sprague-Dawley rats were induced to form malignant ascites by the intraperitoneal injection of the Walker 256 carcinoma. Intact ascites suppressed splenocyte proliferation by 96%. Molecular sieving of the ascites by means of ultrafiltration (10-kilodalton particle cutoff) revealed suppressor activity to reside in both the ultrafiltrate and retentate. Further enumeration of suppressor factors was achieved by preparative polyacrylamide gel electrophoresis of the ascites ultrafiltrate and retentate. Five discrete bands of suppressor activity were resolved in the ultrafiltrate, three of which were heat-labile. Three discrete bands of suppressor activity were resolved in the retentate, none of which were heat-labile. This study underscores the complexity and heterogeneity of soluble factors elaborated in a cancer-bearing animal.
Biofilm penetration and disinfection efficacy of alkaline hypochlorite and chlorosulfamates (2001)

This study lends support to the theory that the penetration of antimicrobial agents into microbial biofilms is controlled by the reactivity of the antimicrobial agent with biofilm components. The finding that chlorine-based biocides can penetrate, but fail to kill, bacteria in biofilms should motivate the search for other mechanisms of protection from killing by antimicrobial agents in biofilms.
Economical routes to colloidal nanocrystals (2015)

A new precursor library yields high-quality quantum dots for device applications [Also see Report by Hendricks et al. ]
Physical, Behavioral, and Psychological Risk Factors for Chronic Fatigue Syndrome (1995)

In spite of the distinct epidemiologic features of chronic fatigue syndrome, its cause remains unknown and no risk factors for the illness have been identified. In order to better characterize CFS, we conducted a case-control study of well-defined CFS cases to identify physical, behavioral, and psychological factors related to the occurrence of CFS. The study, conducted in the metropolitan area surrounding Newark, New Jersey, USA, included 20 patients who fulfilled the CFS case definition and 20 matched controls. All subjects completed a self-administered questionnaire. The greatest difference between cases and controls was the reported level of stress from any of five sources in the 5 years prior to onset of illness (95% vs. 55%; P = 0.01 1). In addition, the risk of CFS was significantly related to the number of sources of stress, especially
A novel non-isolated high-gain dc-dc boost converter (2017)

In this paper, a novel interleaved boost converter topology is introduced. The proposed converter is based on a combination of two types of voltage multiplier cells (VMC): Dickson and Cockroft-Walton (CW) voltage multiplier. Connecting VMCs to an interleaved boost stage yields many benefits, including smaller ripples on the input current, reduced voltage stress across switches and capacitors, and high overall voltage gain. These advantages allow designers to design high gain dc-dc converters with low-rated and highly efficient semiconductor components. Moreover, the use of VMC can reduce the requirements of the required energy storage and also allow to design with smaller capacitors than the conventional boost converter. This paper presents the analysis of steady state voltage gain, the design of the converter, selection of the components, and simulation of the voltage and current stresses across switches and storage elements. Also, A 200 W prototype was implemented to convert 20 to 400 Vdc. The implementation details and major waveforms are included and illustrated.
Normalization and paraphrasing using symbolic methods (2003)

We describe an ongoing work in information extraction which is seen as a text normalization task. The normalized representation can be used to detect paraphrases in texts. Normalization and paraphrase detection tasks are built on top of a robust analyzer for English and are exclusively achieved using symbolic methods. Both grammar development rules and information extraction rules are expressed within the same formalism and are developed in an integrated way. The experiment we describe in the paper is evaluated and presents encouraging results.
MJ (2003)

While Java provides many software engineering benefits, it lacks a coherent module system and instead provides only packages (which are primarily a name space mechanism) and classloaders (which are very low-level). As a result, large Java applications suffer from unexpected interactions between independent components, require complex CLASSPATH definitions, and are often extremely complex to install and maintain. We have implemented a module system for Java called MJ that is implemented with class loaders, but provides a much higher-level interface. High-level properties can be specified in a module definition and are enforced by the module system as new modules are loaded. To experimentally validate the ability of MJ to properly handle the complex module inter-relationships found in large Java server systems, we replaced the classloader mechanisms of Apache Tomcat 4.1.18 [27] with 30 MJ modules. The modified Tomcat is functionally identical to the original, but requires no CLASSPATH definitions, and will operate correctly even if user code loads a different version of a module used by Tomcat, such as the Xerces XML parser [31]. Furthermore, by making a small change to the Java core libraries enabled by MJ, we obtained a 30% performance improvement in a servlet microbenchmark.
Centralized monitoring and fault localization for passive optical network (2013)

A real-time, centralized and cost efficient monitoring and fault localization system is presented. In this system, a superluminescent diode (SLED) is used as the monitoring signal and the signal is reflected by using different types of fiber Bragg gratings (FBGs); uniform and phase-shifted FBGs as branch identifiers. We demonstrate the enhancement of monitoring wavelength whereas for a distinct center wavelength, it represents the reflection spectrum of two types of FBG or two branches in the network. Thus, more optical network units (ONUs) can be monitored for the specific monitoring source with limited bandwidth. The system is capable to monitor up to 64 ONUs with BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-15</sup> .
Molecular characterization of angiomotin/JEAP family proteins: interaction with MUPP1/Patj and their endogenous properties (2007)

We have previously shown that MUPP1, which has an MRE domain and 13 PDZ domains, is expressed in epithelial cells and localize at tight junctions (TJs) and apical membranes. Using yeast two-hybrid screening, we found here that MUPP1 interacts with angiomotin (Amot), JEAP/Amot-like 1 and MASCOT/Amot-like 2, which we refer to as Amot/JEAP family proteins. PDZ2 and -3 were responsible for MUPP1's interaction with Amot and MASCOT, whereas only PDZ3 was responsible for its interaction with JEAP. All the Amot/JEAP family proteins also interacted with Patj, a close relative of MUPP1. The C-terminal PDZ-binding motives of the Amot/JEAP family were required for these interactions. We successfully generated specific antibodies for these proteins and analyzed the endogenous molecular properties of the family in parallel. Immunofluorescence microscopy of cultured epithelial cells showed that in subcellular distribution, the Amot/JEAP family proteins were indistinguishable; they were apparent at TJs as well as apical membranes, and mostly co-localized with MUPP1. They were also located at TJs in several mouse tissues, but each protein showed a distinct tissue distribution. In biochemical fractionation assays, the Amot/JEAP family behaved not as transmembrane but as peripheral membrane proteins. Unexpectedly, the PDZ-binding motives were not necessarily required for their localization to TJs, and dominant negative MUPP1 or Patj did not affect the localization of Amot/JEAP family proteins, suggesting that the interaction with MUPP1/Patj is not necessarily responsible for their proper subcellular distribution.
An Output-Capacitor-Free Synthesizable Digital LDO Using CMP-Triggered Oscillator and Droop Detector (2022)

This article presents a synthesizable digital low-dropout regulator (DLDO) that precludes the use of an output load capacitor. For efficient regulation, the DLDO consists of fine and coarse loops that have different load conditions to operate. The dual loops are made of typical standard cells to improve the synthesizability. In the coarse loop, a comparator (CMP)-triggered oscillator is employed to generate a high-frequency clock signal without concerning the metastability in the CMP. In order to achieve a fast response to a voltage droop caused by load–current variation, a droop detector and latch-based drivers are exploited that are capable of compensating for a voltage droop asynchronously. The prototype of the DLDO was fabricated in 28-nm CMOS technology. A range of supply voltage is from 0.5 to 1.0 V with a 50-mV dropout voltage. Depending on a supply voltage, a maximum load current and a quiescent current are measured as 160-to-480 mA and 7.7-to-241 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{A}$ </tex-math></inline-formula> , respectively. While a load current is increased from 20 to 450 mA with a 2-ns edge time, a 112-mV voltage droop and a 1.4-ns response time are achieved. Thanks to the synthesizability and the output-capacitor-free design, the DLDO occupies an 0.049-mm2 total area and offers 9.8-A/mm2 current density.