gebhart/patrepeval huggingface dataset:
Abstract LB-145: Absence of pro-apoptotic protein Bax extended the life span of ku70−/− mice with accelerated aging phenotype (2011)

Abstract Bax is a proapoptotic Bcl-2 family protein. Previously, we found that Ku70 functions as a Bax inhibitor in the cell. Ku70 is 70 kDa protein expressed in the cytosol and nucleus, and Ku70 is required for the nonhomologous end-joining (NHEJ) pathway of DNA double strand break (DSB) repair in the nucleus. In the cytosol, Ku70 binds to Bax, and this interaction inhibits the cytotoxic activity of Bax. Ku70 null mice show a premature aging phenotype due to the absence of NHEJ-dependent DSB repair. We hypothesized that increased sensitivity to Bax-mediated cell death may contribute to the disease phenotype of Ku70 null mice. To determine our hypothesis, ku70−/−bax+/− and ku70−/−bax−/− mice were generated (all mice were on C57BL background). Interestingly, both ku70−/−bax+/− and ku70−/−bax−/− had a longer life spans than ku70−/− mice. The 50% mortality of ku70−/−, ku70−/−bax+/−, ku70−/−bax−/− was 21 weeks (n=36), 36 weeks (n=20), and 37 weeks (n=7) respectively. Some of these mutant mice developed T-lymphoma (ku70−/− (17%&amp;lt;), ku70−/−bax+/− (33%), and ku70−/−bax−/− (20%)). Ku70−/− MEFs (mouse embryonic fibroblasts) showed increased apoptosis sensitivity and accelerated cellular senescence during passage in comparison with wild type MEFs, as previously reported. ku70−/−bax+/− and ku70−/−bax−/− showed significantly higher survival in the apoptosis sensitivity test than ku70−/− MEFs. Cellular senescence of MEFs was analyzed including expressions of senescence associated β-galactosidase and phospho-γ H2AX. Bax deficiency did not show significant effects on the onset of cellular senescence of ku70−/− MEFs. The lung alveoli of ku70−/− mice were structurally normal (single alveolar cell layer); however, the lungs of ku70−/−bax+/− and ku70−/−bax−/− mice had abnormal multiple alveolar cell layers. The mechanism of this abnormal alveolar development is under investigation. We analyzed histology of several organs, blood cell count, and locomotion activities of these mutant mice. These data suggest that Bax-deficiency improved the overall health condition of Ku70 null mice. Previous studies demonstrated that p53 deletion was not able to extend the life span of Ku70 or Ku80 null mice due to increased cancer development (Li et al. 2009). In addition, p21 deletion was not able to extend the life span of Ku80 null mice even though p21 deletion significantly delayed cellular senescence of Ku80 null MEFs (Zhao et al, 2009). The present study suggests that increased Bax-mediated apoptosis rather than increased cellular senescence may be the major cause of the shortened life span of Ku70 null and NHEJ-defective mutant mice. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-145. doi:10.1158/1538-7445.AM2011-LB-145
Data from Low TCR Binding Strength Results in Increased Progenitor-like CD8<sup>+</sup> Tumor-Infiltrating Lymphocytes (2023)

&lt;div&gt;Abstract&lt;p&gt;T-cell receptor (TCR) binding strength to peptide-MHC antigen complex influences numerous T-cell functions. However, the vast diversity of a polyclonal T-cell repertoire for even a single antigen greatly increases the complexity of studying the impact of TCR affinity on T-cell function. Here, we determined how TCR binding strength affected the protein and transcriptional profile of an endogenous, polyclonal T-cell response to a known tumor-associated antigen (TAA) within the tumor microenvironment (TME). We confirmed that the staining intensity by flow cytometry and the counts by sequencing from MHC-tetramer labeling were reliable surrogates for the TCR-peptide-MHC steady-state binding affinity. We further demonstrated by single-cell RNA sequencing that tumor-infiltrating lymphocytes (TIL) with high and low binding affinity for a TAA can differentiate into cells with many antigen-specific transcriptional profiles within an established TME. However, more progenitor-like phenotypes were significantly biased towards lower affinity T cells, and proliferating phenotypes showed significant bias towards high-affinity TILs. In addition, we found that higher affinity T cells advanced more rapidly to terminal phases of T-cell exhaustion and exhibited better tumor control. We confirmed the polyclonal TIL results using a TCR transgenic mouse possessing a single low-affinity TCR targeting the same TAA. These T cells maintained a progenitor-exhausted phenotype and exhibited impaired tumor control. We propose that high-affinity TCR interactions drive T-cell fate decisions more rapidly than low-affinity interactions and that these cells differentiate faster. These findings illustrate divergent forms of T-cell dysfunction based on TCR affinity which may impact TIL therapies and antitumor responses.&lt;/p&gt;&lt;/div&gt;
The combined effects of reverberation and noise on speech intelligibility by cochlear implant listeners (2012)

The effect of reverberation on speech intelligibility by CI users was found to be larger than that by noise. The results from the present study highlight the importance of testing CI users in reverberant conditions, since testing in noise-alone conditions might underestimate the difficulties they experience in their daily lives where reverberation and noise often coexist.
Francisella tularensis type A Strains Cause the Rapid Encystment of Acanthamoeba castellanii and Survive in Amoebal Cysts for Three Weeks post Infection (2009)

Francisella tularensis, the causative agent of the zoonotic disease tularemia, has recently gained increased attention due to the emergence of tularemia in geographical areas where the disease has been previously unknown, and the organism's potential as a bioterrorism agent. Although F. tularensis has an extremely broad host range, the bacterial reservoir in nature has not been conclusively identified. In this study, the ability of virulent F. tularensis strains to survive and replicate in the amoeba Acanthamoeba castellanii was explored. We observe that A. castellanii trophozoites rapidly encyst in response to F. tularensis infection and that this rapid encystment phenotype (REP) is caused by factor(s) secreted by amoebae and/or F. tularensis into the co-culture media. Further, our results indicate that in contrast to LVS, virulent strains of F. tularensis can survive in A. castellanii cysts for at least 3 weeks post infection and that induction of rapid amoeba encystment is essential for survival. In addition, our data indicate that pathogenic F. tularensis strains block lysosomal fusion in A. castellanii. Taken together, these data suggest that the interactions between F. tularensis strains and amoeba may play a role in the environmental persistence of F. tularensis.
Microtubule-dependent effect of phorbol ester on the contractility of cytoskeleton of cultured fibroblasts. (1988)

The effect of the tumor promoter phorbol 12-myristate 13-acetate (PMA) upon the contractility of permeabilized cell models (cytoskeletons) of mouse fibroblasts was examined. Contraction was induced by incubation of cell models in a solution containing ATP and was assessed quantitatively by measuring alterations of the area of cell model projection on the substrate. Immunofluorescence microscopy was used to assess alterations of cytoskeleton morphology in the course of permeabilization and contraction. It was found that contractility of cell models from PMA-treated fibroblasts was considerably diminished as compared with the models from control fibroblasts. ATP induced only local contraction of certain zones of actin cortex in models from PMA-treated fibroblasts; it did not induce general contraction, characteristic of control models. Normal high contractility was characteristic of the models from the cells preincubated with PMA in combination with Colcemid. PMA is a specific activator of protein kinase C, one of the key enzymes of the membrane signal-transduction pathway. It is suggested that protein kinase C regulates contractility of actin cortex and that the pathway of this regulation has a microtubule-dependent stage blocked by Colcemid.
Surface Electromagnetic Waves at Seawater-Air and Seawater-Seafloor Interfaces (2022)

Underwater radio communication using surface electromagnetic waves propagating along the seawater-air and seawater-sea floor interfaces may provide a promising alternative to commonly used acoustic communication underwater. Here we present a detailed analytical and numerical consideration of TE and TM polarized surface electromagnetic wave properties. The resulting surface waves have propagation constants that permit communication ranges far longer than those of bulk propagation in the lossy media. We demonstrate theoretically and experimentally their ability to carry broadband radio signals over practical communication distances underwater. A 50 MHz radio signal was successfully carried along the sandy seabed over 7 m distance.
Cell-Cycle Control of Gene Expression in Budding and Fission Yeast (2005)

Cell-cycle control of transcription seems to be a universal feature of proliferating cells, although relatively little is known about its biological significance and conservation between organisms. The two distantly related yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have provided valuable complementary insight into the regulation of periodic transcription as a function of the cell cycle. More recently, genome-wide studies of proliferating cells have identified hundreds of periodically expressed genes and underlying mechanisms of transcriptional control. This review discusses the regulation of three major transcriptional waves, which roughly coincide with three main cell-cycle transitions (initiation of DNA replication, entry into mitosis, and exit from mitosis). I also compare and contrast the transcriptional regulatory networks between the two yeasts and discuss the evolutionary conservation and possible roles for cell cycle-regulated transcription.
A 1V 4 GHz-and-10 GHz transformer-based dual-band quadrature VCO in 0.18 &#x003BC;m CMOS (2007)

A notch-peak cancellation concept is introduced in transformer-based LC tanks to achieve a dual-band quadrature VCO. Fabricated in 0.18 μm CMOS process and operated at 1V supply, the QVCO prototype measures a stable dual-band operation from 3.27 GHz to 5.02 GHz and from 9.48 GHz to 11.36 GHz. At 4.2 GHz and 10 GHz, the QVCO measures phase noise at 1 MHz offset of -116.3 dBc/Hz and -112 dBc/Hz, and sideband rejection ratios (SBR) of 49 dB and 47 dB while drawing 6 mA and 10 mA, respectively. The QVCO occupies an active area of 0.88 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Plasticiser loss from plastic or rubber products through diffusion and evaporation (2019)

Abstract Polymers experience degradation during storage and service. One of the main degradation mechanisms of plasticised-polymer products is the loss of plasticiser, which leads to poorer mechanical properties and eventual contamination of the surrounding environment. This paper addresses the kinetics and predictions of plasticiser migration from polymers to a surrounding gas phase, an important issue for plastic and rubber products exposed to high service temperature conditions and during accelerated ageing and testing. The features and factors influencing the two migration-rate-limiting modes (plasticiser evaporation and diffusion), as well as migration issues related to bio-based plasticisers and plasticiser-biopolymer systems, are discussed.
Luminescent europium tetraazamacrocyclic complexes with wide range pH sensitivity (1998)

The complexes [EuL1]3+ and [EuL2] function as luminescent pH sensors over an extended pH range; two distinguishable pH switching ranges are observed: the delayed europium emission is switched on in acidic solution, whereas the fluorescence emission spectra show a pronounced pH dependence only in alkaline media.
Improvement of the depth resolution in depth-resolved wavenumber-scanning interferometry using multiple uncorrelated wavenumber bands (2013)

In this article, we provide a method to improve the depth resolution of wide-field depth-resolved wavenumber-scanning interferometry (DRWSI), because its depth resolution is limited by the range of the wavenumber scanning and mode hopping of the light source. An optical wedge is put into the optical path to measure the series of the wavenumber on time using a 2D spatial Fourier transform (FT) of the interferograms. Those uncorrelated multiple bands of the wavenumbers due to mode hopping of the diode laser can be synthesized into one band, to enlarge the range of the wavenumber scanning. A random-sampling FT is put forward to evaluate the distribution of frequencies and phases of the multiple surfaces measured. The benefit is that the depth resolution of the DRWSI is enhanced significantly with a higher signal-to-noise ratio. Because of its simplicity and practicability, this method broadens the way to employing multiple different lasers or lasers with mode hopping as the light sources in the DRWSI.
Structural and NMR investigations of the ternary adducts of twenty α-amino acids and selected dipeptides with a chiral, diaqua–ytterbium complex (2003)

A detailed investigation of the nature of the binding of each of the 20 common alpha-amino acids and various selected dipeptides to a chiral, diaqua-ytterbium complex in aqueous solution has been carried out. Analysis of the dipolar 1H NMR paramagnetic shifts suggests that the alpha-amino acids form a common chelated structure within a nine-coordinate mono-capped square antiprismatic coordination environment, with the amine N axially disposed. Crystal structures of nine chelated YbL1-amino acid adducts (Gly, Ala, Ser, Thr, Met) confirm this. The ternary complexes with dipeptides (e.g. Gly-Ala, Gly-Ser, Gly-Met, Gly-Asp, Gly-Asn, Gly-His, Ser-Met, Asp-Phe, His-Gly) also favour the terminal amine as the axial donor with the proximate amide group binding to generate a five-ring chelate. Evidence for chelation through side-chain functionality was found only in the case of N-terminal Asp. The chiral environment about the ytterbium ion upon amino acid binding has also been probed using near-IR circular dichroism spectroscopy.
Semi-Infinite Paths of the Two-Dimensional Radial Spanning Tree (2013)

We study semi-infinite paths of the radial spanning tree (RST) of a Poisson point process in the plane. We first show that the expectation of the number of intersection points between semi-infinite paths and the sphere with radius r grows sublinearly with r . Then we prove that in each (deterministic) direction there exists, with probability 1, a unique semi-infinite path, framed by an infinite number of other semi-infinite paths of close asymptotic directions. The set of (random) directions in which there is more than one semi-infinite path is dense in [0, 2π). It corresponds to possible asymptotic directions of competition interfaces. We show that the RST can be decomposed into at most five infinite subtrees directly connected to the root. The interfaces separating these subtrees are studied and simulations are provided.
Isolation and structure determination of Pachybasium cerebrosides which potentiate the antifungal activity of aculeacin. (1988)

A set of four cerebrosides was isolated from a Pachybasium species and purified by preparative reversed-phase HPLC. All four products displayed activity in a natural product screen aimed at detecting novel cell wall-active antifungal agents based on synergy with the known glucan synthetase inhibitor, aculeacin. Based on degradation studies, fast atom bombardment mass spectrometry and 13C and high field 1H NMR techniques, the structure of the major cerebroside was determined to be (4E,8E)-N-D-2'-hydroxy-(E)-3'- hexadecenoyl-1-O-beta-D-glucopyranosyl-9-methyl-4,8-sphingadiene. The other components were found to be the corresponding 2'-hydroxypalmitic acid analog with one less double bond and an analogous pair containing 2'-hydroxystearic acid with and without the 3' double bond.
Human induced pluripotent stem cell-derived cardiomyocytes as an electrophysiological model: Opportunities and challenges—The Hamburg perspective (2023)

Models based on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are proposed in almost any field of physiology and pharmacology. The development of human induced pluripotent stem cell-derived cardiomyocytes is expected to become a step forward to increase the translational power of cardiovascular research. Importantly they should allow to study genetic effects on an electrophysiological background close to the human situation. However, biological and methodological issues revealed when human induced pluripotent stem cell-derived cardiomyocytes were used in experimental electrophysiology. We will discuss some of the challenges that should be considered when human induced pluripotent stem cell-derived cardiomyocytes will be used as a physiological model.
Decreased Pulmonary Function in Asymptomatic Long Term Survivors After Busulfan-Based Myeloablative Allogeneic Hematopoietic Stem Cell Transplant (2013)

Pulmonary function post allogeneic hematopoietic stem cell transplant (HSCT) can be impaired by previous exposure to chemotherapy, infection, or graft versus host disease (GVHD). In this retrospective study, we analyzed 21 patients with hematologic malignancies who are long term transplant survivors with a median follow-up of 48 months who had received a related (60%) or unrelated (40%) HSCT conditioned with a busulfan-based regimen. Of 21 patients, 7 are of Caucasian and 14 non-Caucasian ethnicity. All patients had routine pulmonary function tests (PFTs) repeated within two years from transplant and none had underlying lung disease. To eliminate inter-lab variability, all PFTs were performed in the same laboratory. Survival rate at the time of analysis was 90%. We initially compared single parameters of PFTs including corrected diffusion limiting capacity of oxygen (DLCO), forced expiratory volume in one second (FEV1), forced vital capacity (FVC), FEV1/FVC ratio, and total lung capacity (TLC) obtained before and after transplant. Post transplant, all PFT parameters showed some degree of reduction compared to pre-transplant values. FEV1 and FEV1/FVC were significantly decreased (108 vs 92, P = .04 and 86 vs 80%, P = .04, respectively), with no difference between Caucasian and non-Caucasians. Overall, median values of corrected DLCO and TLC prior to and after transplant were only slightly reduced. However, in non-Caucasian patients a significant reduction of DLCO was observed (93%±31 vs 73%±11, P = .05). We analyzed intra-patient changes in DLCO and FEV1 values and no correlation was found between these parameters and the development of chronic GVHD. This study shows an overall decrease in pulmonary function in patients without apparent lung disease following a myeloablative busulfan-based HSCT. However, a higher risk of a reduced DLCO was noted only among non-Caucasian patients. At this time it is not known if this observation is due to genetic, biologic or environmental causes.
LPS alters pattern of sickness behavior but does not affect glutathione level in aged male rats (2016)

Behavioral symptoms of sickness, such as fever and motor activity are a coordinated set of changes that develop during infection. The aim of study was to compare the sickness behaviour (SB) in healthy old and young rats treated with pyrogenic dose of endotoxin and to check their glutathione level. Before experimentation male Wistar rats were selected according to standard body mass, motor activity, and white blood cells count. Intraperitoneal injection of lipopolysaccharide (LPS) from E. coli was used to provoke SB. The level of liver glutathione, interleukin (IL) -6, deep body temperature (Tb) and motor activity were measured. Glutathione level in old and young rats did not differ significantly. In both young and old rats LPS administration provoked fever (the mean value of Tb was 38.06 ± 0.01 °C in old rats, and 38.19 ± 0.06 °C in young rats). LPS injection affected night-time activity in both groups (12 h averages were 1.56 ± 0.40 counts in old LPS-treated rats vs 2.74 ± 0.53 counts in not-treated old rats and 3.44 ± 0.60 counts for young LPS-treated vs 4.28 ± 0.57 counts for young not-treated rats). The injection of LPS provoked an elevation of plasma IL-6 concentration (from values below the lowest detectable standard in not-treated groups of animals to 6322.82 ± 537.00 pg/mL in old LPS-treated rats and 7415.62 ± 451.88 pg/mL in young LPS-treated rats). Based on these data, we conclude that good health of aged rats prevents decrease in the glutathione level. Old rats are still able to develop SB in response to pyrogenic dose of LPS, although its components have changed pattern compared to young animals.
Plasma Etch in the Era of Atomic Scale Fidelity (2014)

In IC manufacturing, the ultimate goal is to produce the structures that are conceived and modeled by design engineers in the real world with high fidelity. The term “fidelity” is chosen deliberately to express that what is needed in the end is the highest possible degree to which a material structure matches the design intent. It includes but is not limited to statistical criteria such as accuracy and precision. Plasma etch plays a key role in obtaining structural fidelity in all three dimensions. Accuracy is obtained by control of proximity and 3D effects such as critical dimension (CD) loading, profile loading, aspect ratio dependent etching (ARDE), and selectivity. Precision, on the other hand, is obtained by means of wafer-to-wafer, chamber-to-chamber, and tool-to-tool matching. Atomic scale fidelity is required as we approach devices with a half pitch of 10 nm and below because the device dimensions and their allowed tolerances are of the same order of magnitude as the inter-atomic distances in the crystal lattice. This type of performance can be obtained when the material is removed layer by layer . Each step in the etch process uses the simplest possible chemistry to surgically target specific reactions at the wafer surface such as activation, removal, and passivation. We call this layer-by-layer etch with atomic fidelity atomic layer etch /1/ . We will introduce the framework of high productivity, production-worthy atomic layer etch and discuss the implications for hardware and process development. References: Kanarik, et al., Solid State Technology, 56 (2013) 14-17.
Evaluating the effects of alcohol and tobacco use on cardiovascular disease using multivariable Mendelian randomization (2019)

ABSTRACT Alcohol and tobacco use, two major modifiable risk factors for cardiovascular disease (CVD), are often consumed together. Using large publicly available genome-wide association studies (results from &gt; 940,000 participants), we conducted two-sample multivariable Mendelian randomization (MR) to simultaneously assess the independent effects of alcohol and tobacco use on CVD risk factors and events. We found genetic instruments associated with increased alcohol use, controlling for tobacco use, associated with increased high-density-lipoprotein-cholesterol (HDL-C), decreased triglycerides, but not with coronary heart disease (CHD), myocardial infarction (MI), nor stroke; and instruments for increased tobacco use, controlling for alcohol use, associated with decreased HDL-C, increased triglycerides, and increased risk of CHD and MI. Exploratory analysis found associations with HDL-C, LDL-C, and intermediate-density-lipoprotein metabolites. Consistency of results across complementary methods accommodating different MR assumptions strengthened causal inference, providing strong genetic evidence for the causal effects of modifiable lifestyle risk factors on CVD risk.