gebhart/patrepeval huggingface dataset:
Computational Flow Optimization of Rotary Blood Pump Components (1995)

In an effort to improve and automate the fluid dynamic design of rotary blood pumps, a coupled computational fluid dynamics (CFD) shape optimization methodology has been developed and implemented. This program couples a finite element flow simulation with a gradient-based optimization routine to modify automatically the shape of an initial candidate blood path, according to a variety of desired fluid dynamic criteria, including shear stress, vorticity/circulation, and viscous dissipation. Preliminary results have led to both intuitive and nonintuitive transformations of the initial blood flow paths for both internal and external flows. This application of computer design optimization offers the ability to explore a much broader design space much more efficiently than would be possible with traditional parametric methods. It is believed that this computer tool can assist developers of rotary blood pumps in designing blood-wetted components that minimize thrombosis and hemolysis while simultaneously providing maximum flow performance.
Loss of Daxx, a promiscuously interacting protein, results in extensive apoptosis in early mouse development (1999)

The mammalian Daxx gene has been identified in a diverse set of yeast interaction trap experiments. Although a facilitating role for Daxx in Fas-induced apoptosis has been suggested, Daxx's physiologic function remains unknown. To elucidate the in vivo role of Daxx, we have generated Daxx-deficient mice. Surprisingly, rather than a hyperproliferative disorder expected from the loss of a pro-apoptotic gene, mutation of Daxx results in extensive apoptosis and embryonic lethality. These findings argue against a role for Daxx in promoting Fas-induced cell death and suggest that Daxx either directly or indirectly suppresses apoptosis in the early embryo.
Physical Mechanism of Chaos in Thyristors and Coupled-Transistor Structures (1995)

Electronic chaos in thyristors was observed by ac signal excitation of the anode of thyristors. The origin of this chaotic phenomenon was revealed by detailed measurement of the p-base potential, measurement with a coupled-transistor structure and the results of SPICE simulation. Chaos was generated by the return-mapping nature in the variation of the p-base potential. Chaotic behavior in a thyristor was also reproduced in the experimental coupled-transistor structure and in the results of SPICE simulation.
SOP Integration and Codesign of Antennas (2004)

The successful deployment of wireless systems requires the integration of small, cost-effective antennas while preserving a reasonable electrical performance in the required bandwidth. This paper begins with a short overview of the most important antenna characteristics, and then uses these to describe the minimum requirements and fundamental performance-size limits for electrically small integrated antennas. The performance-size tradeoff is further illustrated by the design of a planar integrated antenna for WLAN. Codesign guidelines are given to avoid parasitic coupling between the integrated antenna and RF circuits. A concluding comparison is made between on-chip and on-package integration of a small antenna for microwave and millimeter wave systems.
ChemInform Abstract: Studies Towards Understanding the Mechanism of the Unusual Rearrangement of Certain 5‐Propargyloxyindoles. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Mathematical model of the effects of government intervention and rehabilitation of prostitution (2018)

In the United States, prostitution is considered illegal in all but one state; Nevada allows some legal activities in exchange for substantial guidelines. In 2010, approximately 43,600 females were arrested for prostitution. Numerous intervention programs were established in order to obstruct the lifestyle of a prostitute (PRP, Project ROSE, etc.). There are many documentations and programs that share their forethought on prostitution; however, few target prostitution directly. To determine the dynamics of prostitution, this paper constructs a four-class compartmental model that focuses on the effectiveness of government intervention and rehabilitation of prostitutes mathematically. The basic reproductive number, [Formula: see text], helps to discover the threshold values for the dynamics of prostitution to become both prevalent or absent in society. This paper predominately observes government intervention to curtail a prostitution prevalent society. Various parameters and variables help to define and indicate the dynamics of prostitution to construct viable simulations. Successful prostitution interaction prevention deemed essential in prostitution prevention; however, government intervention corresponding with successful rehabilitation competitively challenges prostitution interaction prevention in reducing basic reproductive values.
Single cell viability observation in cell dielectrophoretic trapping on a microchip (2014)

We reported a microfluidic integrated dielectrophoretic (DEP) device for single MCF-7 cell trapping and studied the different effects of applied electric field on the viability of the trapped cell. The cell remained alive when DEP voltage was 3 V. Above 3 V, cell viability significantly decreased when increasing stimulation time. At 8 V, the cell was rapidly lysed by the electric field. The high transmembrane potential induced was found to be the major cause of cell damage. The obtained results indicated that an operational electric field below than 2 kV/cm was safe for cell viability when using DEP for cell manipulation.
Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder (2014)

Studies of genomic copy number variants (CNVs) have identified genes associated with autism spectrum disorder (ASD) and intellectual disability (ID) such as NRXN1, SHANK2, SHANK3 and PTCHD1. Deletions have been reported in PTCHD1 however there has been little information available regarding the clinical presentation of these individuals. Herein we present 23 individuals with PTCHD1 deletions or truncating mutations with detailed phenotypic descriptions. The results suggest that individuals with disruption of the PTCHD1 coding region may have subtle dysmorphic features including a long face, prominent forehead, puffy eyelids and a thin upper lip. They do not have a consistent pattern of associated congenital anomalies or growth abnormalities. They have mild to moderate global developmental delay, variable degrees of ID, and many have prominent behavioral issues. Over 40% of subjects have ASD or ASD-like behaviors. The only consistent neurological findings in our cohort are orofacial hypotonia and mild motor incoordination. Our findings suggest that hemizygous PTCHD1 loss of function causes an X-linked neurodevelopmental disorder with a strong propensity to autistic behaviors. Detailed neuropsychological studies are required to better define the cognitive and behavioral phenotype.
Expression of the c‐Ha‐ras and neu oncogenes in DMBA‐induced, anti‐estrogen‐treated rat mammary tumors (1988)

Dimethylbenzanthracene (DMBA)-induced rat mammary tumors were analyzed for the structure and expression of the oncogenes c-Ha-ras and neu and the effects of anti-estrogen treatment. Tumor samples were divided into 3 groups, the first consisting of untreated tumors, the second of anti-estrogen (toremifene)-treated unresponsive (growing) tumors, and the third of toremifene-treated responsive (regressing) tumors. DNA and RNA derived from normal tissues of the same experimental animals were also analyzed. In Southern blot analysis of genomic DNAs, 2 tumors out of 23 contained a new Xbal site in the Ha-ras gene, indicating a point mutation in the second nucleotide of codon 61. Both of these tumors belonged to the group that had not received toremifene. No amplifications of the Ha-ras or the neu genes were observed. Although greatly variable, the levels of Ha-ras mRNA were highest in untreated tumors, lower in toremifene-treated, unresponsive tumors and even lower in toremifene-treated, regressing tumors, corresponding approximately to the levels detected in normal liver and uterus of untreated animals. Expression of the neu mRNA was variable and considerably lower than that of Ha-ras mRNA. It was similar in all 3 groups and somewhat elevated than in several non-malignant control tissues. Localization of c-Ha-ras expression by in situ hybridization revealed a relatively even distribution of the mRNA throughout the mammary tissue. The results suggest that mechanisms other than activation of the c-Ha-ras or neu genes are important for progression and regression of DMBA-induced rat mammary carcinomas.
Short Chain Branching Distribution of Amorphous Ethylene Copolymers (1999)

A new method is proposed to characterize the short chain branching distribution (SCBD) for amorphous ethylene copolymers. SCBD controls many important properties for polyethylenes. It was well known, for example, that at equal density or crystallinity, the optical clarity measured by % haze with different short chain distributions could be different by more than an order of magnitude. The recently introduced metallocene catalysts are capable of producing very homogeneous copolymers at densities heretofore near impossible. These developments re-emphasized the need for rapid assessments of SCBD. Dynamic mechanical analysis was carried out on a series of low crystallinity ethylene copolymers including very low density and ultralow density polyethylenes (VLDPE and ULDPE) and ethylene vinyl acetate (EVA). The beta relaxation linewidth when normalized for mole fraction of the comonomer, was found to correlate with the short chain branching distribution obtained by temperature rising elution fractionation (TREF). The proposed method for assessing SCBD is applicable for totally amorphous systems where TREF analysis loses its fractionation ability. Results on an ethylene propylene rubber system will be used to illustrate this point.
Additive manufacturing of lightweight mirrors (Conference Presentation) (2018)

Additive manufacturing offers new routes to lightweight optics inaccessible by conventional methods by providing a broader range of reconciled functionality, form factor, and cost. Predictive lattice design combined with the ability to 3D print complex structures allows for the creation of low-density metamaterials with high global and local stiffness and tunable response to static and dynamic loading. This capacity provides a path to fabrication of lightweight optical supports with tuned geometries and mechanical properties. Our approach involves the simulation and optimization of lightweight lattices for anticipated stresses due to polishing and mounting loads via adaptive mesh refinement. The designed lattices are 3D printed using large area projection microstereolithography (LAPuSL), coated with a metallic plating to improve mechanical properties, and bonded to a thin (1.25 mm) fused silica substrate. We demonstrate that this lightweight assembly can be polished to a desired flatness using convergent polishing, and subsequently treated with a reflective coating. *This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 within the LDRD program. LLNL-ABS-738806.
СО2 Adsorbents Deposited on Silicon Carbide (2020)

Adsorbents for the absorption of CO2 (Li2ZrO3, Li4SiO4, CaSiO3, MgO, and Li2O) are synthesized and deposited on silicon carbide. The adsorbents are effective in the range of medium (300–400°C) and high (450–750°C) temperatures, have a high capacity for the dynamic absorption of CO2, and an enhanced rate of absorption.
Spectral signatures and optic coefficients of surface and reservoir rocks at COIL, CO 2 , and Nd:YAG laser wavelengths (2004)

Approximately 40 different reservoir and surface rock samples were lased using high power COIL (&lambda; = 1.315 &mu;m), CO<sub>2</sub> (&lambda; = 10.6 &mu;m) and Nd:YAG (&lambda; = 1.06 &mu;m) lasers. Spectrum of the samples in the wavelength region from 0.35 to 15.387 &mu;m was obtained. The objectives of this research are to make a detailed study of the spectral properties and optic signatures of rock samples, including reservoir rocks collected from a depth of more that 8,000 ft, in order to predict the energy absorbed when a laser hits a rock. The optical coefficients [extinction/reflection (E), scattering (S), absorption (K) and emission (F)] of these rocks are critically investigated against rock chemistry, grain size, mode of occurrence, porosity, cementing matrix and rock textures, and total organic content. This research, initiated for the petroleum industry, develops a relationship between reflectance and rock properties that are commonly known and used as correlation parameters for other reservoir characterization uses. Our results show that: (1) More than 25% of the COIL and Nd:YAG laser energy is reflected and/or scattered by rocks with more than 85% SiO<sub>2</sub> content. (2) Surface and reservoir sandstones have almost the same spectral features and hence similar optic coefficients. (3) Rocks with high porosity have greater reflection coefficients (at the COIL and Nd:YAG wavelengths) compared to those having lower porosity. (4) The reflectance at the CO<sub>2</sub> laser wavelength (10.6 &mu;m) is not a function of porosity or grain size.
Integrating Culture-Based Antibiotic Resistance Profiles with Whole-Genome Sequencing Data for 11,087 Clinical Isolates (2019)

Abstract Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.
Eco-Friendly High-Sensitive Piezoelectrets for Force Myography (2022)

Piezoelectrets (or ferroelectrets) are polarized cellular polymers exhibiting outstanding piezoelectric activity. Recently, a new manufacturing route has been introduced by combining 3-D-printed elastomeric soft grids and bulk fluorinated ethylene propylene (FEP) thin films to build an artificial ferroelectret sandwich exhibiting outstanding <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${d} _{{33}}$ </tex-math></inline-formula> coefficients. In this work, a similar approach is taken, however, replacing the environmentally harmful fluorinated polymer FEP by eco-friendly polylactic acid (PLA). The goal of this study is thereby threefold: 1) to investigate the temporal charge stability of PLA films charged at 25 °C and 80 °C, respectively; 2) to determine the stability of the piezoelectric activity when assembled as ferroelectret; and 3) to study the applicability of this easy assembled eco-friendly sensors for force myography (FMG). The surface potential of the PLA films was recorded over 180 days and showed promising stability. Because of the high flexibility of the spacer material, a large piezoelectric <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${d} _{{33}}$ </tex-math></inline-formula> coefficient of up to 2850pC/N was recorded directly after charging and stabilized at about 1500pC/N after <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\approx 50$ </tex-math></inline-formula> days under ambient environmental conditions. The FMG was conducted using four similar ferroelectrets placed on a human forearm. The generated signal shapes and magnitudes of the sensors can be clearly distinguished from each other using simple machine learning algorithms known as support vector machine (SVM) with a classification accuracy (CA) of 89.5%. This work can be regarded as a milestone for these sensors to be accepted in the field of human–machine interfaces (HMIs) as an eco-friendly alternative to the conventional piezoelectric sensors.
Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems (2021)

CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expand the targeting scope of Cas12a, we screen nine Cas12a orthologs that have not been demonstrated in plants, and identify six, ErCas12a, Lb5Cas12a, BsCas12a, Mb2Cas12a, TsCas12a and MbCas12a, that possess high editing activity in rice. Among them, Mb2Cas12a stands out with high editing efficiency and tolerance to low temperature. An engineered Mb2Cas12a-RVRR variant enables editing with more relaxed PAM requirements in rice, yielding two times higher genome coverage than the wild type SpCas9. To enable large-scale genome engineering, we compare 12 multiplexed Cas12a systems and identify a potent system that exhibits nearly 100% biallelic editing efficiency with the ability to target as many as 16 sites in rice. This is the highest level of multiplex edits in plants to date using Cas12a. Two compact single transcript unit CRISPR-Cas12a interference systems are also developed for multi-gene repression in rice and Arabidopsis. This study greatly expands the targeting scope of Cas12a for crop genome engineering.
Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains (2013)

Vol. 12 (2013) 651–663 DOI.10.1074/mcp.A112.023135, Page 1488, 2013 Page 651 Dr. Yang's first name was misspelled. The correct spelling is shown above.
Machine Learning of Protein Interactions in Fungal Secretory Pathways (2016)

In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker's yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities.
The clinical promise of biomarkers of synapse damage or loss in Alzheimer’s disease (2020)

A number of emerging biomarkers are able to measure synapse injury and loss in the brain and may correlate with cognitive function in AD. These biomarkers hold promise both for use in diagnostics and in the measurement of therapeutic successes.
Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi (2018)

The secretion of small Fe-binding molecules called siderophores is an important microbial strategy for survival in Fe-limited environments. Siderophore production is often regulated by quorum sensing (QS), a microbial counting technique that allows organisms to alter gene expression based on cell density. However, the identity and quantities of siderophores produced under QS regulation are rarely studied in the context of their roles in Fe uptake. We investigated the link between QS, siderophores, and Fe uptake in the model marine organism <i>Vibrio harveyi</i> where QS is thought to repress siderophore production. We find that <i>V. harveyi</i> uses a single QS- and Fe-repressed gene cluster to produce both cell-associated siderophores (amphiphilic enterobactins) as well as several related soluble siderophores, which we identify and quantify using liquid chromatography-coupled (LC)-MS as well as tandem high-resolution MS (LC-HR-MS/MS). Measurements of siderophore production show that soluble siderophores are present at ∼100× higher concentrations than amphi-enterobactin and that over the course of growth <i>V. harveyi</i> decreases amphi-enterobactin concentrations but accumulates soluble siderophores. <sup>55</sup>Fe radio-tracer uptake experiments demonstrate that these soluble siderophores play a significant role in Fe uptake and that the QS-dictated concentrations of soluble siderophores in stationary phase are near the limit of cellular uptake capacities. We propose that cell-associated and soluble siderophores are beneficial to <i>V. harveyi</i> in different environmental and growth contexts and that QS allows <i>V. harveyi</i> to exploit "knowledge" of its population size to avoid unnecessary siderophore production.