gebhart/patrepeval huggingface dataset:
The design and analysis of binary variable traits in common garden genetic experiments of highly fecund species to assess heritability (2015)

Abstract Many biologically important traits are binomially distributed, with their key phenotypes being presence or absence. Despite their prevalence, estimating the heritability of binomial traits presents both experimental and statistical challenges. Here we develop both an empirical and computational methodology for estimating the narrow-sense heritability of binary traits for highly fecund species. Our experimental approach controls for undesirable culturing effects, while minimizing culture numbers, increasing feasibility in the field. Our statistical approach accounts for known issues with model-selection by using a permutation test to calculate significance values and includes both fitting and power calculation methods. We illustrate our methodology by estimating the narrow-sense heritability for larval settlement, a key life-history trait, in the reef-building coral Orbicella faveolata . The experimental, statistical and computational methods, along with all of the data from this study, were deployed in the R package multiDimBio.
Optical memories in digital computing (1979)

High capacity optical memories with relatively-high data-transfer rate and multiport simultaneous access capability may serve as basis for new computer architectures. Several computer structures that might profitably use memories are: a) simultaneous record-access system, b) simultaneously-shared memory computer system, and c) parallel digital processing structure.
Serologic detection ofBrachyspira (Serpulina) hyodysenteriaeinfections (2001)

Swine dysentery (SD) caused by the intestinal spirochete Brachyspira hyodysenteriae is an economically important disease in pig-producing countries throughout the world. To date, no specific serologic assay is commercially available for the diagnosis of pigs with SD. Several serologic techniques have been identified in the past; however, these tests have all used either whole-cell proteins or lipopolysaccharide (LPS) as the antigen. Whole-cell antigens are plagued with false-positive reactions due to cross-reactivity with common proteins shared with other spirochetes. LPS antigens produce fewer false-positives; however, false-negatives may result due to LPS components being serogroup-specific. Generally, these techniques are useful for detecting infected herds, but are unreliable for the detection of individual infected pigs. In order to develop improved serologic tests it will be necessary to identify suitable diagnostic antigens, in particular immunogenic cell-surface structures which are specific to B. hyodysenteriae but common amongst different strains of the species. Recently, we identified and cloned a 30-kDa outer membrane lipoprotein (BmpB) which is specific to B. hyodysenteriae and is recognized by experimentally and naturally infected pigs. In this review we summarize the available serologic tests for SD, and speculate on the use of recombinant BmpB as an antigen for future development of an improved serologic test for SD diagnosis.
Trap Inlaid Cationic Hybrid Composite Material for Efficient Segregation of Toxic Chemicals from Water (2022)

Abstract Metal‐based oxoanions are potentially toxic pollutants that can cause serious water pollution. Therefore, the segregation of such species has recently received significant research attention. Even though several adsorbents have been employed for effective management of chemicals, their limited microporous nature along with non‐monolithic applicability has thwarted their large‐scale real‐time application. Herein, we developed a unique anion exchangeable hybrid composite aerogel material (IPcomp‐6), integrating a stable cationic metal–organic polyhedron with a hierarchically porous metal–organic gel. The composite scavenger demonstrated a highly selective and very fast segregation efficiency for various hazardous oxoanions such as, HAsO 4 2− , SeO 4 2− , ReO 4 − , CrO 4 2− , MnO 4 − , in water, in the presence of 100‐fold excess of other coexisting anions. The material was able to selectively eliminate trace HAsO 4 2− even at low concentration to well below the As V limit in drinking water defined by WHO.
CuMF_SGD: Fast and Scalable Matrix Factorization (2016)

Matrix factorization (MF) has been widely used in e.g., recommender systems, topic modeling and word embedding. Stochastic gradient descent (SGD) is popular in solving MF problems because it can deal with large data sets and is easy to do incremental learning. We observed that SGD for MF is memory bound. Meanwhile, single-node CPU systems with caching performs well only for small data sets; distributed systems have higher aggregated memory bandwidth but suffer from relatively slow network connection. This observation inspires us to accelerate MF by utilizing GPUs's high memory bandwidth and fast intra-node connection. We present cuMF_SGD, a CUDA-based SGD solution for large-scale MF problems. On a single CPU, we design two workload schedule schemes, i.e., batch-Hogwild! and wavefront-update that fully exploit the massive amount of cores. Especially, batch-Hogwild! as a vectorized version of Hogwild! overcomes the issue of memory discontinuity. We also develop highly-optimized kernels for SGD update, leveraging cache, warp-shuffle instructions and half-precision floats. We also design a partition scheme to utilize multiple GPUs while addressing the well-known convergence issue when parallelizing SGD. On three data sets with only one Maxwell or Pascal GPU, cuMF_SGD runs 3.1X-28.2X as fast compared with state-of-art CPU solutions on 1-64 CPU nodes. Evaluations also show that cuMF_SGD scales well on multiple GPUs in large data sets.
AdRoit is an accurate and robust method to infer complex transcriptome composition (2021)

Bulk RNA sequencing provides the opportunity to understand biology at the whole transcriptome level without the prohibitive cost of single cell profiling. Advances in spatial transcriptomics enable to dissect tissue organization and function by genome-wide gene expressions. However, the readout of both technologies is the overall gene expression across potentially many cell types without directly providing the information of cell type constitution. Although several in-silico approaches have been proposed to deconvolute RNA-Seq data composed of multiple cell types, many suffer a deterioration of performance in complex tissues. Here we present AdRoit, an accurate and robust method to infer the cell composition from transcriptome data of mixed cell types. AdRoit uses gene expression profiles obtained from single cell RNA sequencing as a reference. It employs an adaptive learning approach to alleviate the sequencing technique difference between the single cell and the bulk (or spatial) transcriptome data, enhancing cross-platform readout comparability. Our systematic benchmarking and applications, which include deconvoluting complex mixtures that encompass 30 cell types, demonstrate its preferable sensitivity and specificity compared to many existing methods as well as its utilities. In addition, AdRoit is computationally efficient and runs orders of magnitude faster than most methods.
Tests of Isotopic Separation Efficiency of Palladium Packed Columns (2008)

The isotopic effect of palladium has been applied in different ways to separate hydrogen isotopes for many years. At Savannah River Site palladium deposited on kieselguhr (Pd/k) is used in a thermal cycling absorption process (TCAP) to purify tritium for over ten years. The need to design columns for different throughputs and the desire to advance the performance of TCAP created the need to evaluate different column designs and packing materials for their separation efficiency. In this work, columns with variations in length, diameter and metal foam presence were tested using an isotope displacement method. A simple computer model was also developed to calculate the number of theoretical separation stages based on the test results. The effects of column diameter, metal foam presence and gas flow rate were identified.
Interobserver Variability in CT and MR Staging of Lung Cancer (1993)

Although interobserver agreement rates are good for determining T and N classification in patients with lung cancer, variability in image interpretation is frequent, even among experienced observers.
Formation of Insulated-Gate Bipolar Transistor Highly Activated Anodes via Nickel Silicidation With Dopant Segregation (2015)

We propose a low-temperature nickel silicidation with a dopant segregation approach to form shallow anode profiles in thin wafer insulated-gate bipolar transistors (IGBTs). The process provides an anode with a boron peak concentration of 3×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">19</sup> /cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> after annealing at 400 °C. The silicidation results in a NiSi phase with a strong interface roughness, independent of the polishing process after grinding. The devices exhibit characteristics comparable with the state-of-the-art IGBTs in terms of voltage drop (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CE,ON</sub> ), which indicates that a higher anode activation was achieved at low temperature in comparison with the reference samples, since the anode is <;27% of its initial thickness. Devices that underwent chemical mechanical planarization exhibit higher V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CE,ON</sub> than those without, possibly due the increase of surface roughness.
Iterative Learning Control Applications to High Power Microwave Tubes (2012)

In this paper, we present a “smart” high-peak power microwave tube, by implementing iterative learning control methodologies to control a repetitively-pulsed, high-power, backward wave oscillator. The learning control algorithm is used to drive the error between the actual output and its desired value to zero. The desired output may be a given power level, a given frequency, or a combination of both. The learning control methodology is then experimentally verified.
Dissolution of Pre-Existing Platelet Thrombus by Synergistic Administration of Low Concentrations of Bifunctional Antibodies against β3 Integrin (2011)

Most antithrombotic approaches target prevention rather than the more clinically relevant issue of resolution of an existing thrombus. In this study, we describe a novel and effective therapeutic strategy for ex vivo clearance of pre-existing platelet thrombus by the combination of two bifunctional platelet GPIIIa49-66 ligands that target different parts of the arterial thrombus. We produced an additional GPIIIa49-66 agent (named APAC), which homes to activated platelets. Like our previously described SLK (which targets newly deposited fibrin strands surrounding the platelet thrombus), APAC destroys platelet aggregates ex vivo in an identical fashion with 85% destruction of platelet aggregates at 2 hours. The combined application of APAC and SLK demonstrated a ~2 fold greater platelet thrombus dissolution than either agent alone at a low concentration (0.025 µM). Platelet-rich clot lysis experiments demonstrated the time required for 50% platelet-rich fibrin clot lysis (T(50%)) by APAC (95 ± 6.1 min) or SLK (145 ± 7.1 min) was much longer than that by combined APAC + SLK (65 ± 7.6 min) at the final concentration of 0.025 µM (APAC + SLK vs APAC, p<0.05; APAC + SLK vs SLK, p<0.01). Thus these low concentrations of a combination of both agents are likely to be more effective and less toxic when used therapeutically in vivo.
Postoperative opioid cessation rates based on preoperative opioid use (2019)

Chronic preoperative opioid use increases the risk of chronic postoperative use, but an opioid-free period before surgery decreases this risk compared with continuous preoperative use Cite this article: <i>Bone Joint J</i> 2019;101-B:1570-1577.
Enhancement in the Critical Current Density of C-Doped MgB2 Wire Using a Polyacrylic Acid Dopant (2012)

C-doped MgB2 wires were fabricated from a polyacrylic acid (PAA) using a conventional in-situ PIT technique. The effects of the PAA content on the lattice parameter, microstructure, critical temperature (Tc) and critical current density (Jc) were examined. With increasing PAA content, the amount of MgO in the sample increased but the crystallinity, a-axis lattice parameter, and Tc of MgB2 wires decreased, indicating that the C that decomposed from PAA during heat treatment had substituted for B. All doped samples exhibited a higher Jc than the undoped sample at high magnetic field, and the Jc(B) property improved with increasing PAA content: for the 7 wt% doped sample, the Jc was approximately 3-times higher than that of the pristine sample (1.28 kA/cm2 vs. 3.43 kA/cm2) at 5 K and 6.6 T. The improved Jc(B) of the doped sample was attributed to the decreased grain size, enlarged lattice distortion and increased C doping level.
Data from miR-130a Deregulates PTEN and Stimulates Tumor Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;H-RasV12 oncogene has been shown to promote autophagic cell death. Here, we provide evidence of a contextual role for H-RasV12 in cell death that is varied by its effects on miR-130a. In E1A-immortalized murine embryo fibroblasts, acute expression of H-RasV12 promoted apoptosis, but not autophagic cell death. miRNA screens in this system showed that miR-130a was strongly downregulated by H-RasV12 in this model system. Enforced expression of miR-130a increased cell proliferation in part via repression of PTEN. Consistent with this effect, miR-130a overexpression in human breast cancer cells promoted Akt phosphorylation, cell survival, and tumor growth. In clinical specimens of multiple human cancers, expression of miR-130 family members correlated inversely with PTEN expression. Overall, our results defined miR-130a as an oncogenic miRNA that targets PTEN to drive malignant cell survival and tumor growth. &lt;i&gt;Cancer Res; 77(22); 6168–78. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Thermomechanical Topology Optimization of Three-Dimensional Heat Guiding Structures for Electronics Packaging (2022)

Abstract Heterogeneous and complex electronic packages may require unique thermomechanical structures to provide optimal heat guiding. In particular, when a heat source and a heat sink are not aligned and do not allow a direct path, conventional thermal management methods providing uniform heat dissipation may not be appropriate. Here we present a topology optimization method to find thermally conductive and mechanically stable structures for optimal heat guiding under various heat source-sink arrangements. To exploit the capabilities, we consider complex heat guiding scenarios and three-dimensional (3D) serpentine structures to carry the heat with corner angles ranging from 30 deg to 90 deg. While the thermal objective function is defined to minimize the temperature gradient, the mechanical objective function is defined to maximize the stiffness with a volume constraint. Our simulations show that the optimized structures can have a thermal resistance of less than 32% and stiffness greater than 43% compared to reference structures with no topology optimization at an identical volume fraction. The significant difference in thermal resistance is attributed to a thermally dead volume near the sharp corners. As a proof-of-concept experiment, we have created 3D heat guiding structures using a selective laser melting technique and characterized their thermal properties using an infrared thermography technique. The experiment shows the thermal resistance of the thermally optimized structure is 29% less than that of the reference structure. These results present the unique capabilities of topology optimization and 3D manufacturing in enabling optimal heat guiding for heterogeneous systems and advancing the state-of-the-art in electronics packaging.
Fabrication of Fresnel zone plates by holography in the extreme ultraviolet region (2008)

Fabrication of Fresnel zone plates (FZPs) with nanometer scale resolution is one of the major challenges in lithographic fabrication. The authors present a holographic approach to create FZPs where the interference pattern between a spherical beam and a plane wave is recorded to obtain the FZP structure. The spherical beam is obtained by diffraction from a circular aperture (pinhole) in a semiopaque membrane which is illuminated by a spatially coherent extreme ultraviolet beam. The beam transmitted by the membrane serves as the reference plane wave. The resulting pattern gives rise to a FZP with outermost zone width comparable to the dimension of the circular aperture. Fabrication and test results of a FZP obtained with this method are presented. The technique offers a solution to the pattern-placement problem encountered in serial ZP writing techniques as well as high resolution potential.
Retroviruses of wild and cultured fish (2011)

Retroviruses comprise a large group of enveloped RNA viruses which have been found in a wide range of vertebrate species including fish. To date a number of fish retrovirus genomes have been partially or completely sequenced. Phylogenetic analysis and genome organization indicate a high diversity of fish retroviruses as well as some unique structural features that have not been found in any other retroviruses. Piscine retroviruses comprise both exogenous and endogenous viruses; most of them are associated with proliferative diseases. Because several of these proliferative diseases have a seasonal trend, they provide an excellent model for studying tumor development and regression. The aim of this work was to review the best-described fish retroviruses.
Abstract 5618: Multi-armed myxoma virus has therapeutic potential for treatment of multiple myeloma (2022)

Abstract Oncolytic viruses (OV) selectively replicate in and lyse tumor cells and provide stimulation to the immune system, representing a promising therapeutic option in development to treat cancers that do not respond well to treatment with immune checkpoint inhibitors. Myxoma virus (MYXV) is a member of the Pox family of double stranded DNA viruses and infects cancer cell lines of humans and other species. The genome of MYXV is relatively large and is amenable to engineering for expression of transgenic proteins, making it an excellent oncolytic virus for introduction of immunomodulatory proteins. We generated MYXV carrying IL-12 and decorin. IL-12 is an immune modulator that activates T- and NK-cells. Cellular responses to decorin include tumor cell intrinsic signaling effects, tumor matrix modulation, and inhibition of the TGF-beta pathway. We demonstrate the activity of multi-armed MYXV against human and mouse multiple myeloma (MM) cancer cell lines. Efficacy and mechanism of action of multi-armed myxoma virus was also demonstrated in vivo via syngeneic and xenograft models. Multi-armed MYXV represents a promising therapeutic option for MM patients that do not respond well to immunotherapy. Citation Format: Ana L. de Matos, Rachel Dutcher, Lina S. Franco, Lino E. Torres-Dominguez, Heather Hrach, Mario Abrantes, Wazir Abdullahi, Zachary Tacner, Dillon McCrite, Nicole Grigiatis, Jack St. Peter, Leslie L. Sharp. Multi-armed myxoma virus has therapeutic potential for treatment of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5618.
Plasmodium falciparum Regulatory Subunit of cAMP-Dependent PKA and Anion Channel Conductance (2008)

Malaria symptoms occur during Plasmodium falciparum development into red blood cells. During this process, the parasites make substantial modifications to the host cell in order to facilitate nutrient uptake and aid in parasite metabolism. One significant alteration that is required for parasite development is the establishment of an anion channel, as part of the establishment of New Permeation Pathways (NPPs) in the red blood cell plasma membrane, and we have shown previously that one channel can be activated in uninfected cells by exogenous protein kinase A. Here, we present evidence that in P. falciparum-infected red blood cells, a cAMP pathway modulates anion conductance of the erythrocyte membrane. In patch-clamp experiments on infected erythrocytes, addition of recombinant PfPKA-R to the pipette in vitro, or overexpression of PfPKA-R in transgenic parasites lead to down-regulation of anion conductance. Moreover, this overexpressing PfPKA-R strain has a growth defect that can be restored by increasing the levels of intracellular cAMP. Our data demonstrate that the anion channel is indeed regulated by a cAMP-dependent pathway in P. falciparum-infected red blood cells. The discovery of a parasite regulatory pathway responsible for modulating anion channel activity in the membranes of P. falciparum-infected red blood cells represents an important insight into how parasites modify host cell permeation pathways. These findings may also provide an avenue for the development of new intervention strategies targeting this important anion channel and its regulation.
Transparent ceramic photo-optical semiconductor high power switches (2023)

A photoconductive semiconductor switch according to one embodiment includes a structure of sintered nanoparticles of a high band gap material exhibiting a lower electrical resistance when excited by light relative to an electrical resistance thereof when not exposed to the light. A method according to one embodiment includes creating a mixture comprising particles, at least one dopant, and at least one solvent; adding the mixture to a mold; forming a green structure in the mold; and sintering the green structure to form a transparent ceramic. Additional system, methods and products are also presented.
High-Volume Performance Test Framework using Big Data (2015)

The inherent issues with handling large files and complex scenarios cause the data-driven approach [1] to be rarely used for performance tests. Volume and scalability testing of enterprise solutions typically requires custom-made test frameworks because of the complexity and uniqueness of data flow. The generation, transformation and transmission of large sets of data pose a unique challenge for testing a highly transactional back-end system like the IBM Sterling Order Management (OMS). This paper describes a test framework built on document-oriented NoSQL database, a design that helps validate the functionality and scalability of the solution simultaneously. This paper also describes various phases of planning, development, and testing of the OMS solution that was executed for a large retailer in Europe to test an extremely high online sales scenario. An out-of-the-box configuration of the OMS with the feature support for database sharding was used to drive scalability. The exercise was a success, and it is the world's largest IBM Sterling Order Management benchmark in terms of sales order volume, to date.
Expression of prostate‐specific membrane antigen (PSMA), increases cell folate uptake and proliferation and suggests a novel role for PSMA in the uptake of the non‐polyglutamated folate, folic acid (2009)

These findings implicate PSMA in both the metabolism of polyglutamated folates, and in the uptake of monoglutamated folates. Under conditions of LF or PF levels, PSMA gives cells expressing it a proliferative advantage.