gebhart/patrepeval huggingface dataset:
Toxicity of metal-contaminated sediments from the upper clark fork river, montana, to aquatic invertebrates and fish in laboratory exposures (1994)

Abstract Sediments of the upper Clark Fork River, from the Butte and Anaconda area to Milltown Reservoir (230 km downstream), are contaminated with As, Cd, Cu, Pb, Mn, and Zn primarily from mining activities. The toxicity of pore water from these sediments was determined using Daphnia magna (48-h exposure), rainbow trout (96-h exposure), and Microtox®. However, pore-water data from these exposures were questionable because of changes in the toxicity of pore-water samples after 5 to 7 d of storage. Whole-sediment tests were conducted with Hyalella azteca (28-d exposure), Chironomus riparius (14-d exposure), rainbow trout (Oncorhynchus mykiss) 21- to 28-d exposure and Daphnia magna (2- to 22-d exposure). Sediment samples from Milltown Reservoir and the Clark Fork River were not generally lethal to test organisms. However, both reduced growth and delayed sexual maturation of amphipods were associated with exposure to elevated concentrations of metals in sediments from the reservoir and river. Relative sensitivity (most sensitive to least sensitive) of organisms in whole-sediment toxicity tests was: Hyalella azteca &amp;gt; Chironomus riparius &amp;gt; rainbow trout &amp;gt; Daphnia magna. Relative sensitivity (most sensitive to least sensitive) of the three end points evaluated with Hyalella azteca was: length &amp;gt; sexual maturation &amp;gt; survival. The lack of lethal effects on organisms may be related to temporal differences in sediment, acid-volatile sulfide, or organic carbon.
Incidence and Prevention of Cardiac Tamponade Complicating Ablation for Atrial Fibrillation (2005)

Cardiac tamponade complicating catheter ablation of atrial fibrillation (AF) occurs in approximately 1% of pulmonary vein isolation (PVI), and up to 6% of linear ablation procedures. We reviewed 348 consecutive AF ablation (including repeat) procedures over 1 year, which all included PVI, with additional linear lesions at the mitral isthmus in 73%, and cavotricuspid isthmus (CTI) in 76%. An irrigated-tip ablation catheter was used, with power limited to 25-35 W for PVI and 45-60 W for linear lesions. Tamponade occurred in seven men and three women (2.9% of the population) during the creation of linear ablation lesions. Mechanical perforations occurred in two patients, and "popping" during radiofrequency (RF) energy delivery at the mitral isthmus in six, and at the CTI in two patients. Peak RF power was significantly higher in patients with than without tamponade (53 +/- 4 W vs 48 +/- 7 W; P = 0.02), and was greater than 48 W in all cases of "popping." In the following year, RF power for linear ablation was limited to </=42 W. Among 398 procedures, tamponade occurred in four patients (1.0%; P = 0.047 vs first year), three from "popping" and one from mechanical trauma. Procedural success rate remained the same despite reduction of power. Risk of tamponade was highest during linear ablation, mainly associated with high energy delivery and "popping." Reducing the energy limited, though did not eliminate this complication.
Hydrazine reduction of transition metal oxides: I n s i t u characterization using x-ray photoelectron spectroscopy (1986)

Among the first row transition metal oxides from V2O5 to ZnO, CuO was found to be the most easily reduced by hydrazine. CuO surfaces exposed to hydrazine at ∼10−6 Torr could be reduced to the metallic state at room temperature. Reduction kinetics, continuously measured at the surface using in situ x-ray photoelectron spectroscopy (XPS) at hydrazine pressures of 6×10−3 Torr and temperatures from 295 to 381 K, indicated that the reaction was first order with respect to CuO. The kinetics of this reaction, as monitored by the rate of change of the shakeup feature which accompanies the CuO spectrum at 943 eV, proceeded with a measured activation energy of 35±4 kJ/mol and a preexponential factor of 103.3±0.7/s. In situ XPS observations of reduced copper surfaces at temperatures of 295 K indicated that two types of adsorption occurred: (i) an irreversible component which could not be removed by extended vacuum pumping and provided a N:Cu atomic ratio of 0.28 and (ii) a reversible component which increased the measured N:Cu ratio to ∼0.60 at hydrazine pressures up to 0.5 Torr. Gas phase and adsorbed species were readily discernible based on the values of their observed N 1s photoemission peaks at 406 and 400 eV, respectively. While the pressure of hydrazine over metallic copper could significantly increase the measured N:Cu ratio, the N ls spectrum could not be used to distinguish between the various adsorbed components which yielded only a single peak spectrum at a binding energy of ∼400 eV. This value is in agreement with that found by previous investigators (M.H. Matloob and M. W. Roberts, J. Chem. Soc. Faraday Trans. 1 1977, 1393) who suggested that hydrazine was molecularly adsorbed at these conditions.
Drive optimisation of a pulsatile Total Artificial Heart (2011)

Drive optimisation of a pulsatile Total Artificial Heart Total Artificial Hearts (TAHs) are required for the therapy of terminal heart diseases as heart transplants are only a limited option due to the available number of donor hearts. For implantation TAHs have to meet constraints regarding its dimensions, weight, perfusions and electrical losses. An innovative linear driven TAH is presented, which meets all constraints except weight. Therefore the geometry of the linear drive is optimised to reduce its weights while simultaneously limiting the electrical losses as much as possible. In order to calculate the losses, this paper introduced a combined calculation chain consisting of FEM simulations and analytical equations. Based on this chain the linear drive is optmised by the method of parameter variations. The results yield a hierachic order of parameters which are most suitable for the weight reduction of the drive for low losses. By this the weight of the linear drive is reduced by 25%. As the allowable loss limit is not exceeded yet, room for further weight reduction achieved by an optimisation of the axial geomtry parameters is given.
SF3B1 and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia (2011)

Background: The somatic genetic basis of chronic lymphocytic leukemia, a common and clinically heterogeneous leukemia occurring in adults, remains poorly understood. Methods: We obtained DNA samples from leukemia cells in 91 patients with chronic lymphocytic leukemia and performed massively parallel sequencing of 88 whole exomes and whole genomes, together with sequencing of matched germline DNA, to characterize the spectrum of somatic mutations in this disease. Results: Nine genes that are mutated at significant frequencies were identified, including four with established roles in chronic lymphocytic leukemia (TP53 in 15% of patients, ATM in 9%, MYD88 in 10%, and NOTCH1 in 4%) and five with unestablished roles (SF3B1, ZMYM3, MAPK1, FBXW7, and DDX3X). SF3B1, which functions at the catalytic core of the spliceosome, was the second most frequently mutated gene (with mutations occurring in 15% of patients). SF3B1 mutations occurred primarily in tumors with deletions in chromosome 11q, which are associated with a poor prognosis in patients with chronic lymphocytic leukemia. We further discovered that tumor samples with mutations in SF3B1 had alterations in pre–messenger RNA (mRNA) splicing. Conclusions: Our study defines the landscape of somatic mutations in chronic lymphocytic leukemia and highlights pre-mRNA splicing as a critical cellular process contributing to chronic lymphocytic leukemia.
Internal Combustion Engine Cylinder Volume Trace Deviation (2018)

&lt;div&gt;Heat release analysis is a widely used cylinder pressure-based method for evaluating combustion in engine development, and it is also being investigated as a means to control engine combustion. Heat release analysis has been shown to be sensitive to errors in the calculated cylinder volume, but despite this one of the most common assumptions is that the cylinder volume is nominal and can be calculated solely by the geometrical relations among the measures of the engine components. During engine operation, the components surrounding the combustion chamber are exposed to thermal forces, pressure forces, and mass forces from the reciprocating components. Due to these forces, the components will deform and the volume of the combustion chamber will deviate from its ideal volume. The volume will also be affected by the production tolerances of the engine. This article investigates the validity of the assumption of nominal cylinder volume in a heavy-duty engine context and considers the effect of production variations, static distortion of the cylinder liner, and dynamic deformation of the cylinder and crank mechanism. A detailed plant model was used to show that there was a significant deviation from nominal cylinder volume. In the crank angle domain around top dead center, the cylinder volume could deviate as much as 6% due to static distortion and dynamic deformation. Production tolerances were found to give an additional ±2% deviation. Based on the plant model study, a virtual sensor (VS) was developed to enable better cylinder volume estimation. The complexity of the VS was limited to enable the VS to be used in an embedded system. The VS decreased the cylinder volume error from static distortion and dynamic deformation to below 0.4%. Because the VS does not account for the effect of production variations, these variations will define the accuracy of the VS.&lt;/div&gt;
Nanoporous low-? polyimide films prepared from poly(amic acid)s with grafted poly(methylmethacrylate)/poly(acrylamide) side chains (2003)

Copolymers of poly[N,N′-(1,4-phenylene)-3,3′4,4′-benzophenonetetra-carboxylic amic acid] (PAmA) with grafted poly(methylmethacrylate) (PMMA) and poly(acryamide) (PAAM) side chains (PMMA-g-PAmA and PAAM-g-PAmA, respectively) were synthesized by thermally-induced graft copolymerization of methylmethacrylate (MMA) and acrylamide (AAM) with the ozone-pretreated PAmA in N-methyl-2-pyrrolidone (NMP) solutions. The graft copolymers were characterized by elemental analysis, X-ray photoelectron spectroscopy (XPS), thermogravimetric (TG) analysis, and differential scanning calorimetry (DSC). Nanoporous low dielectric constant (low-κ) polyimide (PI) films were obtained by thermal imidization of the PAmA graft copolymers under reduced argon pressure, followed by thermal decomposition of the side chains in air. The nanoporous PI films were characterized by density, scanning electron microscopy (SEM) and dielectric constant measurements. Nanoporous PI films with porosities in the range 4–15% and pore sizes in the range 30–60 nm were obtained. Dielectric constants as low as 2.3 and 2.5 were obtained for the nanoporous PI films prepared from the PMMA-g-PAmA and PAAM-g-PAmA copolymers, respectively.
Regulatory T cells induce a privileged tolerant microenvironment at the fetal‐maternal interface (2005)

The mechanisms underlying immune tolerance during pregnancy are poorly understood. In this regard, Treg seem to play an important role in mediating maternal tolerance to the fetus. We proposed a crucial role of T regulatory cells (Treg) in avoiding immunological rejection of the fetus after observing diminished number and function of Treg in abortion-prone mice. We further confirmed the protective role of Treg during pregnancy by transferring pregnancy-induced Treg into abortion-prone mice, which prevented rejection. Here, we analyzed the mechanisms involved in Treg-mediated protection. As expected, Treg therapy prevented abortion, while expanding the peripheral and thymic Treg population. Surprisingly, the decidual levels of the Th1 cytokines IFN-gamma and TNF-alpha were not diminished after therapy. Interestingly, the mRNA levels of leukemia inhibitory factor, TGF-beta and heme oxygenase-1 at the fetal-maternal interface were dramatically up-regulated after Treg transfer, while the levels of indolamine 2,3-dioxygenase remained unchanged. Our data suggest that Treg treatment can not prevent T cell infiltration or high Th1 levels but is able to create a privileged tolerant microenvironment at the fetal-maternal interface, further shedding light onto the molecular mechanisms involved in pregnancy tolerance.
Characterization of Xylan Utilization and Discovery of a New Endoxylanase in Thermoanaerobacterium saccharolyticum through Targeted Gene Deletions (2012)

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C(5) and C(6) sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of β-xylosidase xylD slowed the growth of T. saccharolyticum on birchwood xylan and led to an accumulation of short-chain xylo-oligomers, no other single deletion, including the deletion of the previously characterized endoxylanase XynA, had a phenotype distinct from that of the wild type. This result indicates a multiplicity of xylanase enzymes which facilitate xylan degradation in T. saccharolyticum. Growth on xylan was prevented only when a previously uncharacterized endoxylanase encoded by xynC was also deleted in conjunction with xynA. Sequence analysis of xynC indicates that this enzyme, a low-molecular-weight endoxylanase with homology to glycoside hydrolase family 11 enzymes, is secreted yet untethered to the cell wall. Together, these observations expand our understanding of the enzymatic basis of xylan hydrolysis by T. saccharolyticum.
Microfluidic Cell Sorter (μFCS) for On‐chip Capture and Analysis of Single Cells (2012)

A low-cost and rapid microfluidic cell sorter (μFCS) for circulating tumor cell (CTC) detection, culture and analyses is developed. Based on size separation and molecular characterization, μFCS efficiently enriches CTCs from unprocessed whole blood, allows on-chip culture and molecular profiling, and provides cell retrieval for subsequent analyses. The potential clinical application of the technology is demonstrated by capturing and genetically analyzing CTCs in tumor-bearing mice.
QIAD assay for quantitating a compound’s efficacy in elimination of toxic Aβ oligomers (2015)

Strong evidence exists for a central role of amyloid β-protein (Aβ) oligomers in the pathogenesis of Alzheimer's disease. We have developed a fast, reliable and robust in vitro assay, termed QIAD, to quantify the effect of any compound on the Aβ aggregate size distribution. Applying QIAD, we studied the effect of homotaurine, scyllo-inositol, EGCG, the benzofuran derivative KMS88009, ZAβ3W, the D-enantiomeric peptide D3 and its tandem version D3D3 on Aβ aggregation. The predictive power of the assay for in vivo efficacy is demonstrated by comparing the oligomer elimination efficiency of D3 and D3D3 with their treatment effects in animal models of Alzheimer´s disease.
Enhanced intramucosal cytotoxic lymphocyte gene expression in ulcerative colitis (1995)

: The histopathology of the mucosal lesions in ulcerative colitis suggests that cellular immune hyperactivity plays a role in the pathogenesis of ulcerative colitis. The role of colonic mucosal cytotoxic lymphocytes in ulcerative colitis is highly controversial. In vitro determinations of cytotoxic lymphocyte function vary according to the experimental conditions and target cells employed. Transcription of the cytotoxic molecules granzyme B and perforin are specific for activated cytotoxic lymphocytes. We investigated whether activated cytotoxic lymphocytes are present in ulcerative colitis lesions via identification of granzyme B, perforin, and interleukin 2 transcripts. RNA was extracted from endoscopic colonic biopsies taken from normal and ulcerative colitis patients. An aliquot was reverse transcribed, followed by gene amplification in the polymerase chain reaction. A competitive template was incorporated within the reaction permitting the quantitation of specific mRNA species. Granzyme B and perforin levels of reverse transcribed cDNAs (RT-cDNAs) were significantly elevated in active ulcerative colitis as compared to normal colonic tissues (p = 0.0081 and p = 0.0018, respectively) when calculated as a ratio with the RT-cDNA of the constitutively expressed gene GAPDH. Interleukin 2 mRNA measurements did not vary between normal and UC samples to a statistically significant degree. These data suggest heightened lymphocyte cytotoxic function within ulcerative colitis mucosal lesions.
The Superior Colliculus: Cell Types, Connectivity, and Behavior (2022)

The superior colliculus (SC), one of the most well-characterized midbrain sensorimotor structures where visual, auditory, and somatosensory information are integrated to initiate motor commands, is highly conserved across vertebrate evolution. Moreover, cell-type-specific SC neurons integrate afferent signals within local networks to generate defined output related to innate and cognitive behaviors. This review focuses on the recent progress in understanding of phenotypic diversity amongst SC neurons and their intrinsic circuits and long-projection targets. We further describe relevant neural circuits and specific cell types in relation to behavioral outputs and cognitive functions. The systematic delineation of SC organization, cell types, and neural connections is further put into context across species as these depend upon laminar architecture. Moreover, we focus on SC neural circuitry involving saccadic eye movement, and cognitive and innate behaviors. Overall, the review provides insight into SC functioning and represents a basis for further understanding of the pathology associated with SC dysfunction.
Analysis of concentration and temperature patterns on catalytic surfaces (1994)

A simple mathematical model for pattern formation on isothermal as well as nonisothermal catalytic surfaces is developed and analyzed. The model accounts for diffusion of the species, conduction of heat, convection from the fluid phase, and a bimolecular Langmuir–Hinshelwood type kinetic expression. The isothermal model is shown to exhibit stationary concentration patterns for typical sets of parameters. The nonisothermal model exhibits stationary temperature and concentration patterns only for near stoichiometric composition of the reactants (three equation model). The calculations show that these stationary patterns exist in regions near the ignition and extinction points and are most likely to form during ignition or extinction of the surface. It is also found that moving concentration and temperature patterns exist near the Hopf bifurcation point of the ignited homogeneous branch. The moving patterns predicted for realistic values of the transport and kinetic parameters are concentration patterns with almost constant temperature distribution on the surface. The typical size of the patterns and the period of oscillation are estimated in terms of the physicochemical parameters.
Velocity Saturation in Digital Microfluidics (2019)

In digital microfluidics, discrete droplets of fluid are made to move on an open surface with no microchannels. These systems are commonly operated by application of electrical driving forces to an array of electrodes. While these driving forces are well characterized, the dissipative forces opposing droplet movement have not been as thoroughly examined. In recognition of this deficit, we used force-velocity plots to characterize droplet movement in digital microfluidics, which was found to be consistent with a simple theoretical framework for understanding dissipation effects for droplets in two-plate, air-filled devices. Interestingly, in some conditions, a previously unreported ″velocity saturation″ effect was observed. When examined across a range of different liquids, the forces at which this saturation occurs seem to be lower for liquids with smaller surface tensions. Furthermore, when driven at forces that cause saturation, physical phenomena are observed that are akin to what has been reported for stationary droplets in the electrowetting literature. These phenomena are detrimental to device performance, leading to a new "force window" approach that delineates the optimum operation conditions for different liquids. We propose that these findings may be useful for a wide range of applications for experts and new users alike in this growing field.
Abstract 4709: Induction of enhanced tumor-specific immunity by Hsp90 targeted photodynamic therapy (Hsp90-PDT) combined with immune checkpoint inhibition (2017)

Abstract Background: Immunotherapy has become an emerging anti-cancer therapy, as immune checkpoint blockade with PD-1 or PD-L1 inhibition have been active against multiple cancer types. Nonetheless, there remain many non-responders, suggesting that combinations may improve activity, particularly combinations which can target tumors and have low toxicity. Methods &amp; Results: We have developed a novel Hsp90 targeted photodynamic therapy (Hsp90-PDT), which causes local anti-tumor responses. Hsp90-PDT can be combined with immune checkpoint blockade to generate potent anti-tumor effects. We synthesized well characterized PDT agent, verteporfin (VP) tethered to a HSP90 small molecule inhibitor, to create a Hsp90-PDT agent (Hsp90i-VP). We first compared the uptake of VP and Hsp90i-VP into the breast cancer cell lines (E0771-OVA) in vitro. Hsp90i-VP showed stronger incorporation than VP when the compounds were added 3μM or less in concentration. We next performed in vitro and vivo PDT with Hsp90i-VP and laser exposure (690 nm wavelength). Killing efficiency of VP and Hsp90i-VP was analyzed by MTT assay, which showed increased killing in a dose dependent manner for both photosensitizers (0-30µM) and laser (0-120J/cm2). Next, we treated E0771-OVA tumor-bearing C57BL/6 mice with Hsp90i-VP (25nmol/mouse) administration alone, laser irradiation (240J/cm2) alone, or the combination of Hsp90i-VP and laser. Suppression of the tumor growth was confirmed only in Hsp90i-VP and laser group. In addition, induction of tumor-specific immune response by PDT was confirmed by ELISA, where the elevation of anti-OVA antibody was seen only in PDT group. Furthermore, combination treatment of Hsp90-PDT and anti-PD-L1 mAbs was able to enhance cytotoxic T-cell response and suppress tumor growth significantly even with relatively PDT-resistant cell line. Conclusions: Hsp90-PDT showed a significant ability to induce antigen-specific immune response in both in vitro and in vivo. These results suggest that Hsp90-PDT can play an important role in anti-cancer immune therapy. Our future plan is to investigate the effect of local photodynamic therapy combined with various types of checkpoint inhibitor in breast cancer models. Citation Format: Kensuke Kaneko, Takuya Osada, Timothy A. Haystead, Michael A. Morse, Herbert K. Lyerly. Induction of enhanced tumor-specific immunity by Hsp90 targeted photodynamic therapy (Hsp90-PDT) combined with immune checkpoint inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4709. doi:10.1158/1538-7445.AM2017-4709