gebhart/patrepeval huggingface dataset:
COX-2 mediates tumor-stromal prolactin signaling to initiate tumorigenesis (2019)

Tumor-stromal communication within the microenvironment contributes to initiation of metastasis and may present a therapeutic opportunity. Using serial single-cell RNA sequencing in an orthotopic mouse prostate cancer model, we find up-regulation of prolactin receptor as cancer cells that have disseminated to the lungs expand into micrometastases. Secretion of the ligand prolactin by adjacent lung stromal cells is induced by tumor cell production of the COX-2 synthetic product prostaglandin E2 (PGE2). PGE2 treatment of fibroblasts activates the orphan nuclear receptor NR4A (Nur77), with prolactin as a major transcriptional target for the NR4A-retinoid X receptor (RXR) heterodimer. Ectopic expression of prolactin receptor in mouse cancer cells enhances micrometastasis, while treatment with the COX-2 inhibitor celecoxib abrogates prolactin secretion by fibroblasts and reduces tumor initiation. Across multiple human cancers, COX-2, prolactin, and prolactin receptor show consistent differential expression in tumor and stromal compartments. Such paracrine cross-talk may thus contribute to the documented efficacy of COX-2 inhibitors in cancer suppression.
Electrical Breakdown of Ethylene Copolymers (1987)

co was found that the electric strength FB of ethylene co-polymers containing optimum content of halogen compouns copigher than that of LDPE over a wide temperature range from -196 to 90°C, and that their conduction current was suppressed at the higher fields. It is thought that the introductioned comonomers with halogen groups into polyethylene suppresses the electron acceleration due to an increase of the scattering of conduction electrons, leading to an increase of FB which is determined by the electron avalanche breakdown. However, the reason for a fall of FB with halogen content at high content level is not yet clear. A tentative explanation is presented: Existence of high halogen content in the amorphous part of the ethylene chain gives rise to some kind of defects which arise, for example, from locally brittle structures or stereo hindrance due to strong dipole-dipole interaction, leading to a decrease of FB.
Blue Gene/L compute chip: Memory and Ethernet subsystem (2005)

The Blue Gene®/L compute chip is a dual-processor system-on-a-chip capable of delivering an arithmetic peak performance of 5.6 gigaflops. To match the memory speed to the high compute performance, the system implements an aggressive three-level on-chip cache hierarchy. The implemented hierarchy offers high bandwidth and integrated prefetching on cache hierarchy levels 2 and 3 (L2 and L3) to reduce memory access time. A Gigabit Ethernet interface driven by direct memory access (DMA) is integrated in the cache hierarchy, requiring only an external physical link layer chip to connect to the media. The integrated L3 cache stores a total of 4 MB of data, using multibank embedded dynamic random access memory (DRAM). The 1,024-bit-wide data port of the embedded DRAM provides 22.4 GB/s bandwidth to serve the speculative prefetching demands of the two processor cores and the Gigabit Ethernet DMA engine. To reduce hardware overhead due to cache coherence intervention requests, memory coherence is maintained by software. This is particularly efficient for regular highly parallel applications with partitionable working sets. The system further integrates an on-chip double-data-rate (DDR) DRAM controller for direct attachment of main memory modules to optimize overall memory performance and cost. For booting the system and low-latency interprocessor communication and synchronization, a 16-KB static random access memory (SRAM) and hardware locks have been added to the design.
Patterns and Features of Families of Traveling Waves in Large-Scale Neuronal Networks (2008)

We study traveling wave solutions of a system of integro‐differential equations which describe the activity of large‐scale networks of excitatory neurons on spatially extended domains. The independent variables are the activity level u of a population of excitatory neurons, which have long range connections, and a recovery variable v. We have found a critical value of the parameter β ($\beta_* > 0$) that appears in the equation for v, at which the eigenvalues of the linearization of the system around the rest state $(u,v)=(0,0)$ change from real to complex. In contrast to previous studies which analyzed properties of traveling waves when the eigenvalues are real, we examine the range $\beta > \beta_*$, where the eigenvalues are complex. In this case we show that there is a range of parameters over which families of wave fronts and 1‐pulse and more general N‐pulse waves can coexist as stable solutions. In two space dimensions our numerical experiments show how single‐ring and multiring waves form in respon...
Inhibition of the RacGEF VAV3 by the small molecule IODVA1 impedes RAC signaling and overcomes resistance to tyrosine kinase inhibition in acute lymphoblastic leukemia (2021)

Aberrant RHO guanine nucleotide exchange factor (RhoGEF) activation is chief mechanism driving abnormal activation of their GTPase targets in transformation and tumorigenesis. Consequently, a small-molecule inhibitor of RhoGEF can make an anti-cancer drug. We used cellular, mouse, and humanized models of RAC-dependent BCR-ABL1-driven and Ph-like acute lymphoblastic leukemia to identify VAV3, a tyrosine phosphorylation-dependent RacGEF, as the target of the small molecule IODVA1. We show that through binding to VAV3, IODVA1 inhibits RAC activation and signaling and increases pro-apoptotic activity in BCR-ABL1-transformed cells. Consistent with this mechanism of action, cellular and animal models of BCR-ABL1-induced leukemia in Vav3-null background do not respond to IODVA1. By durably decreasing in vivo RAC signaling, IODVA1 eradicates leukemic propagating activity of TKI-resistant BCR-ABL1(T315I) B-ALL cells after treatment withdrawal. Importantly, IODVA1 suppresses the leukemic burden in the treatment refractory pediatric Ph<sup>+</sup> and TKI-resistant Ph<sup>+</sup> B-ALL patient-derived xenograft models better than standard-of-care dasatinib or ponatinib and provides a more durable response after treatment withdrawal. Pediatric leukemia samples with diverse genetic lesions show high sensitivity to IODVA1 ex vivo and this sensitivity is VAV3 dependent. IODVA1 thus spearheads a novel class of drugs that inhibits a RacGEF and holds promise as an anti-tumor therapy.
Variable volume piezometer for measurement of volumetric properties of materials under high pressure (2009)

A piezometer was designed to measure volume change of foods and other biomaterials as a function of pressure, and calibrated and tested up to 700 MPa at 25°C. The sensor was constructed from a polycarbonate tube, sealed with a plug on one end and a removable piston on the other. Samples were placed inside the tube. Upon pressurization, the piston displaced inside the tube, transmitting pressure to the sample; impedance in a magnet wire coil on the outside of the tube was measured to characterize volume change. Sensor calibration with water yielded a polynomial that characterized volume as a function of impedance. Sensor precision is 0.3% of measured volume; its resolution allows measurement of sub-microliter volume changes. Testing with ethanol and sucrose solutions yielded data within 1% of previously reported values. The sensor's applications include measurement of volumetric properties of liquid and solid biomaterials, and chemical reaction volumes.
Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum (2014)

Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent ~50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8,173 putative copy number variants and 3,336 presence/absence variants. While the majority of the SNPs (84%) detected were biallelic, a substantial number were tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome.
Inverted Silicon Nanopencil Array Solar Cells with Enhanced Contact Structures (2016)

Although three-dimensional nanostructured solar cells have attracted extensive research attention due to their superior broadband and omnidirectional light-harvesting properties, majority of them are still suffered from complicated fabrication processes as well as disappointed photovoltaic performances. Here, we employed our newly-developed, low-cost and simple wet anisotropic etching to fabricate hierarchical silicon nanostructured arrays with different solar cell contact design, followed by systematic investigations of their photovoltaic characteristics. Specifically, nano-arrays with the tapered tips (e.g. inverted nanopencils) are found to enable the more conformal top electrode deposition directly onto the nanostructures for better series and shunt conductance, but its insufficient film coverage at the basal plane would still restrict the charge carrier collection. In contrast, the low-platform contact design facilitates a substantial photovoltaic device performance enhancement of ~24%, as compared to the one of conventional top electrode design, due to the shortened current path and improved lateral conductance for the minimized carrier recombination and series resistance. This enhanced contact structure can not only maintain excellent photon-trapping behaviors of nanostructures, but also help to eliminate adverse impacts of these tapered nano-morphological features on the contact resistance, providing further insight into design consideration in optimizing the contact geometry for high-performance nanostructured photovoltaic devices.
Sparse multitask regression for identifying common mechanism of response to therapeutic targets (2010)

In this article, we propose a sparse, multitask regression model together with co-clustering analysis to explore the intrinsic grouping in associating the gene expression with phenotypic signatures. The global structure of association is captured by learning an intrinsic template that is shared among experimental conditions, with local perturbations introduced to integrate effects of therapeutic agents. We demonstrate the performance of our approach on both synthetic and experimental data. Synthetic data reveal that the multi-task regression has a superior reduction in the regression error when compared with traditional L(1)-and L(2)-regularized regression. On the other hand, experiments with cell cycle inhibitors over a panel of 14 breast cancer cell lines demonstrate the relevance of the computed molecular predictors with the cell cycle machinery, as well as the identification of hidden variables that are not captured by the baseline regression analysis. Accordingly, the system has identified CLCA2 as a hidden transcript and as a common mechanism of response for two therapeutic agents of CI-1040 and Iressa, which are currently in clinical use.
Digestive Responses to Fortified Cow or Goat Dairy Drinks: A Randomised Controlled Trial (2018)

Fortified milk drinks are predominantly manufactured from bovine (cow) sources. Alternative formulations include those prepared with hydrolysed bovine milk proteins or from alternate <i>bovidae</i> species, such as caprine (goat) milk. Currently, there is little data on protein digestive and metabolic responses following ingestion of fortified milk drinks. To examine the digestive and metabolic responses to commercially-available fortified milks, young adults (<i>n</i> = 15 males: 15 females), in a randomised sequence, ingested isonitrogenous quantities of whole cow-protein (WC), whole goat-protein (WG), or partially-hydrolysed whey cow-protein (HC), commercial fortified milks. Plasma amino acid (AA) and hormonal responses were measured at baseline and again at 5 h after ingestion. Paracetamol recovery, breath hydrogen, and subjective digestive responses were also measured. Postprandial plasma AA was similar between WC and WG, while AA appearance was suppressed with HC. Following HC, there was a negative incremental AUC in plasma branched-chain AAs. Further, HC had delayed gastric emptying, increased transit time, and led to exaggerated insulin and GLP-1 responses, in comparison to whole protein formulas. Overall, WC and WG had similar protein and digestive responses with no differences in digestive comfort. Contrastingly, HC led to delayed gastric emptying, attenuated AA appearance, and a heightened circulating insulin response.
Author response: SLC6A14, an amino acid transporter, modifies the primary CF defect in fluid secretion (2018)

Loss of an amino acid transporter and tissue depletion of nitric oxide worsens the intestinal function of CF mice, a finding that potentially explains variation in disease severity amongst CF individuals.
SPRAM with large thermal stability for high immunity to read disturbance and long retention for high-temperature operation (2006)

We investigate the effect of temperature on current-induced magnetization switching in SPRAM (spin-transfer torque RAM) consisting of MgO-barrier-based magnetic tunnel junctions (MTJs) with a synthetic ferrimagnetic recording layer (SyF) by comparing the MJTs to those with a single ferromagnetic recording layer. It is found that SPRAM using MTJs with a SyF has two advantages for high-temperature operation: 1) A thermal stability factor E/kBT as high as 64 at 150degC, which would ensure ten-year retention and ten-year immunity to read disturbance; and 2) an increase of the aspect ratio in the SyF, which leads to high coercivity HC, resulting in two stable states (ldquo0rdquo or ldquo1rdquo) at high temperature.
FM Laser Operation in SOA-Based Fiber Ring Lasers (2007)

We present methods for controlling both laser linewidth and lineshape via FM laser operation for tunable single frequency oscillated SOA-based fiber ring lasers, using either phase modulation, or amplitude modulation, or current modulation of SOA.
An Anti–Transforming Growth Factor β Antibody Suppresses Metastasis via Cooperative Effects on Multiple Cell Compartments (2008)

Overexpression of transforming growth factor beta (TGF-beta) is frequently associated with metastasis and poor prognosis, and TGF-beta antagonism has been shown to prevent metastasis in preclinical models with surprisingly little toxicity. Here, we have used the transplantable 4T1 model of metastatic breast cancer to address underlying mechanisms. We showed that efficacy of the anti-TGF-beta antibody 1D11 in suppressing metastasis was dependent on a synergistic combination of effects on both the tumor parenchyma and microenvironment. The main outcome was a highly significant enhancement of the CD8+ T-cell-mediated antitumor immune response, but effects on the innate immune response and on angiogenesis also contributed to efficacy. Treatment with 1D11 increased infiltration of natural killer cells and T cells at the metastatic site, and enhanced expression of coactivators (NKG2D) and cytotoxic effectors (perforin and granzyme B) on CD8+ T cells. On the tumor cells, increased expression of an NKG2D ligand (Rae1gamma) and of a death receptor (TNFRSF1A) contributed to enhanced immune cell-mediated recognition and lysis. The data suggest that elevated TGF-beta expression in the tumor microenvironment modulates a complex web of intercellular interactions that aggregately promote metastasis and progression. TGF-beta antibodies reverse this effect, and the absence of a major effect of TGF-beta antagonism on any one cell compartment may be critical for a good therapeutic window and the avoidance of autoimmune complications.
Current Density Distribution in Multiple YBCO Coated Conductors by Coupled Integral Equations (2009)

In this paper we present a new model to compute the current density distribution and the AC losses in multiple YBCO coated conductors by means of coupled integral equations implemented in a finite-element (FE) environment. The model considers the superconducting tapes as 1D objects and allows overcoming the problem of the mesh of conductors of large aspect ratio, typical of 2D implementations; as a result, it is also much faster. The interaction between the different conductors is taken into account by means of a coupling of the electromagnetic variables. The magnetic field distribution in the space between the conductors is computed by coupling the 1D model with a standard 2D magnetic model, which uses the computed current density distributions as sources for the magnetic field. Results are compared with those obtained with standard 2D implementations and with experimental results.
Ultrafast electron dynamics in two dimensional layered systems: two-photon photoemission studies of SnS2 (1997)

We performed femtosecond two-photon photoemission studies of SnS2, and measured the lifetime of electrons in the conduction band at different excitation energies. The lifetime is short (⩽ 60 fs) even at the conduction band minimum. In addition, the inverse lifetime shows a linear energy dependence. The experimental results are interpreted as due to the electron-plasmon interaction in layered two dimensional materials, which causes electron-hole recombination through the emission of a plasmon. These results are discussed in the context of the electron dephasing processes involved in the barrier crossing dynamics for electron transfer from physisorbed molecular donors at semiconductor surfaces (dye sensitization) under barrierless conditions.
Alternatives to conventional field evaluation for genetic selection for Fe‐efficiency of soybean (1986)

Abstract Breeding for improved Fe‐efficiency of soybean [Glycine max (L.) Merrill] has resulted in the identification of genotypes that exhibit little or no chlorosis when grown on calcareous soils in Iowa. Continued selection for even greater levels of Fe‐efficiency would be desirable to obtain parent lines that could facilitate the incorporation of Fe‐efficiency into high‐yielding cultivars. Two methods have been identified for inducing chlorosis in genotypes that do not have adequate symptoms in conventional field tests on calcareous soils. One method is used with soybeans grown on calcareous soil in the field. The main stems of plants to be evaluated are cut off above the cotyledonary or unifoliolate nodes during early vegetative development. The symptoms on the new leaves produced by plants after they have been cut off are more severe than on the leaves that develop on plants that are not cut off. The second method is a nutrient solution system designed to allow the evaluation of Fe‐efficiency. A good relationship between genotypic ratings derived from nutrient solution and field testing has been found. The major advantage of this system is that the severity of chlorosis can be controlled through the manipulation of nutrient concentrations.
Bombesin-related peptides induce calcium mobilization in a subset of human small cell lung cancer cell lines. (1987)

To examine the biochemical basis for growth factor-induced responses in human lung cancer cells, we used the quin2 technique to study the effect of the amphibian peptide bombesin and its congeners including mammalian gastrin-releasing peptide (GRP) on the intracellular free calcium level [Ca2+]i in small cell lung cancer cell lines. In five of eleven cell lines tested, Tyr4-bombesin or GRP elicited a rapid and transient increase in [Ca2+]i. The response was seen with as little as 1 nM ligand, was not affected by membrane depolarization, and derived in part from internal calcium stores. Desensitization to a second addition of active bombesin congeners occurs subsequent to initial addition of Tyr4-bombesin. Structure-activity analysis showed the carboxyl-terminal octapeptide was the active portion of the peptide. Analogs in which the carboxyl terminus was oxidized or deamidated were inactive. Ranatensin, litorin, alytesin, and GRP, but not physalaemin, were as active as Tyr4-bombesin. A monoclonal antibody to the carboxyl terminus of bombesin selectively blocked the increased [Ca2+]i elicited by Tyr4-bombesin. These studies suggest that bombesin congeners can act on some small cell lung cancer cell lines by a pathway utilizing increased [Ca2+]i.
Thermal Degradation and Fire Behavior of High Performance Polymers (2019)

High performance and high temperature polymers are a class of polymeric materials exhibiting high thermal stability and their resistance to fire makes them valuable assets for many applications. Those applications include as typical examples high temperature gas separation membranes, automotive and aerospace industry as well as the construction industry. The high performance polymers have been synthesized since the early 1960s, and have developed rapidly over the past few decades. Most high performance polymers comprise a highly aromatic backbone, linear chains, and strong inter-chain interactions. This review deals mostly with commercial polymeric materials. Studies regarding their thermal behavior, degradation mechanism and their reaction to fire have been synthetically combined in order to bring out potential insight concerning the effect of the thermal decomposition and thermal behavior on the fire properties of those polymers.
On the residual solvability of generalized free products of solvable groups (2011)

In this paper, we study the residual solvability of the generalized free product of solvable groups.
The Significance of Tread Element Flexibility to Thin Film Wet Traction (1975)

Abstract An analysis is presented for the action of individual tire tread elements on polished sections of pavement covered by thin fluid films. Tread element flexibility, wheel slip, and time‐dependent loading are incorporated. The effect of the lateral expansion of tread elements on groove closure is also studied.