gebhart/patrepeval huggingface dataset:
The SARS-CoV-2 spike protein binds and modulates estrogen receptors (2022)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 as its primary infection mechanism. Interactions between S and endogenous proteins occur after infection but are not well understood. We profiled binding of S against >9000 human proteins and found an interaction between S and human estrogen receptor α (ERα). Using bioinformatics, supercomputing, and experimental assays, we identified a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit. In cultured cells, S DNA transfection increased ERα cytoplasmic accumulation, and S treatment induced ER-dependent biological effects. Non-invasive imaging in SARS-CoV-2-infected hamsters localized lung pathology with increased ERα lung levels. Postmortem lung experiments from infected hamsters and humans confirmed an increase in cytoplasmic ERα and its colocalization with S in alveolar macrophages. These findings describe the discovery of a S-ERα interaction, imply a role for S as an NRC, and advance knowledge of SARS-CoV-2 biology and coronavirus disease 2019 pathology.
T‐cell mediated immunity in murine malaria. I. Induction of T‐cell dependent proliferative responses to Plasmodium chabaudi (1984)

To investigate the mechanisms of cell mediated immunity to malaria, we studied different systems to measure specific activation of T lymphocytes by P. chabaudi antigens. Mice were primed by subcutaneous administration of parasite antigens followed by co-cultivation of lymphocytes taken from the draining lymph nodes in the presence of the priming antigen. A marked proliferative response was observed which was shown to be antigen specific, T-cell mediated and accessory cell dependent. Continuous T-cell lines were propagated in culture by repetitive restimulation in the presence of antigen and accessory cells, followed by expansion in a conditioned medium containing T-cell growth factors. These lines could be induced to proliferate to the priming antigen only in the presence of syngeneic accessory cells thus indicating that H-2 restriction operates in the recognition of plasmodium antigens by T cells. We also induced parasite specific T cells by the use of an in vitro primary 'education' system. Lymphocytes from unprimed mice were sensitized on parasite-fed macrophages and were then injected subcutaneously into each hind foot pad of syngeneic animals. This led to recruitment of antigen-reactive cells which were assayed in vitro by the ability of lymphocytes taken from the draining popliteal lymph nodes to proliferate in response to the sensitizing antigen. In vivo immunization with Plasmodium antigen fed macrophages also signalled antigen specific T cells that recruited reactive T cells in the draining lymph nodes.
Characterization of 4 Million Micro-Bump Interconnections at 7.6- $\mu \text{m}$ Pitch for 3-D Stacked 16 Million Pixel Image Sensor (2017)

We developed and reported on a 3-D stacked CMOS image sensor (CIS) with a massive number of micro-bump interconnections placed at a narrow pitch between silicon substrates that pushes the envelope of CIS functions. The resistances of the interconnections were measured to be less than one hundredth of an ohm per bump with a test structure. There were, however, a small number of defective micro bumps with much higher impedance among the four million interconnections of the sensor. We developed a method for distinguishing defective interconnections from other defects and evaluated all interconnection resistances in a short amount of time with additional circuits in the CIS with reduced variable factors by using a modified current flow mode. This method makes it possible not only to identify defective interconnections but also to measure their impedances with less fluctuation.
Palmitoylated Cysteine 192 Is Required for RhoB Tumor-suppressive and Apoptotic Activities (2005)

RhoA and RhoB share 86% amino acid sequence identity, yet RhoA promotes whereas RhoB suppresses malignant transformation. Amino acids 29, 100, 116, 123, 129, 140-143, 141, 146, 152, 154, 155, 173, 181, 183-187, 189, 190, 191, 192, and 193 in RhoB were mutated to the corresponding RhoA residues to determine those critical for RhoB tumor-suppressive activity. Of all the mutants made, only the cysteine 192 (one of two palmitoylation sites) and cysteine 193 (the prenylation site) point mutations abolish RhoB functions. In contrast, mutation of the other palmitoylation site, cysteine 189, did not affect RhoB functions. Moving cysteine 192 to position 190 did not affect RhoB function either. Mutation of cysteine 192 to glycine, alanine, or serine blocks the ability of RhoB to suppress transforming growth factor beta type II receptor, p2lwaf, and AP-1 promoter transcriptional activities. Furthermore, mutations of cysteines 192 and 193, but not 189, mislocalize RhoB and prevent RhoB from inhibiting anchorage-dependent and anchorage-independent tumor growth and colony formation as well as prevent it from inducing apoptosis. The cysteine 192 RhoB mutant is farnesylated and geranylgeranylated as efficiently as wild type RhoB. A RhoA-(1-180)/RhoB-(181-196) chimera inhibited tumor cell proliferation and induced apoptosis as efficiently as RhoB. These results demonstrate that the presence of neither cysteine 193 nor cysteine 192 alone is sufficient and that both palmitoylated cysteine 192 and prenylated cysteine 193, but not palmitoylated cysteine 189, are required for RhoB tumor-suppressive and proapoptotic activities.
Search for Large Extra Dimensions in theMonojet+ETChannel with the DØ Detector (2003)

We present a search for large extra dimensions (ED) in pp collisions at a center-of-mass energy of 1.8 TeV using data collected by the DØ detector at the Fermilab Tevatron in 1994-1996. Data corresponding to 78.8+/-3.9 pb(-1) are examined for events with large missing transverse energy, one high-p(T) jet, and no isolated muons. There is no excess observed beyond expectation from the standard model, and we place lower limits on the fundamental Planck scale of 1.0 and 0.6 TeV for 2 and 7 ED, respectively.
Defect-Engineered β-MnO2−δ Precursors Control the Structure–Property Relationships in High-Voltage Spinel LiMn1.5Ni0.5O4−δ (2021)

This study examines the role of defects in structure-property relationships in spinel LiMn<sub>1.5</sub>Ni<sub>0.5</sub>O<sub>4</sub> (LMNO) cathode materials, especially in terms of Mn<sup>3+</sup> content, degree of disorder, and impurity phase, without the use of the traditional high-temperature annealing (≥700 °C used for making disordered LMNO). Two different phases of LMNO (i.e., highly <i>P</i>4<sub>3</sub>32-ordered and highly <i>Fd</i>3̅<i>m</i>-disordered) have been prepared from two different β-MnO<sub>2-δ</sub> precursors obtained from an argon-rich atmosphere (β-MnO<sub>2-δ</sub> (Ar)) and a hydrogen-rich atmosphere [β-MnO<sub>2-δ</sub> (H<sub>2</sub>)]. The LMNO samples and their corresponding β-MnO<sub>2-δ</sub> precursors are thoroughly characterized using different techniques including high-resolution transmission electron microscopy, field-emission scanning electron microscopy, Raman spectroscopy, powder neutron diffraction, X-ray photoelectron spectroscopy, synchrotron X-ray diffraction, X-ray absorption near-edge spectroscopy, and electrochemistry. LMNO from β-MnO<sub>2-δ</sub> (H<sub>2</sub>) exhibits higher defects (oxygen vacancy content) than the one from the β-MnO<sub>2-δ</sub> (Ar). For the first time, defective β-MnO<sub>2-δ</sub> has been adopted as precursors for LMNO cathode materials with controlled oxygen vacancy, disordered phase, Mn<sup>3+</sup> content, and impurity contents without the need for conventional methods of doping with metal ions, high synthetic temperature, use of organic compounds, postannealing, microwave, or modification of the temperature-cooling profiles. The results show that the oxygen vacancy changes concurrently with the degree of disorder and Mn<sup>3+</sup> content, and the best electrochemical performance is only obtained at 850 °C for LMNO-(Ar). The findings in this work present unique opportunities that allow the use of β-MnO<sub>2-δ</sub> as viable precursors for manipulating the structure-property relationships in LMNO spinel materials for potential development of high-performance high-voltage lithium-ion batteries.
Dye‐Anchored Mesoporous Antimony‐Doped Tin Oxide Electrochemiluminescence Cell (2009)

A ruthenium-based dye chemically tethered to a novel high surface area, conductive, transparent, and well-ordered mesoporous antimony-doped tin oxide film is shown for the first time to function as the working electrode in a high-efficiency electrochemiluminescence cell, suggesting thereby opportunities for its use in a range of optoelectronic device applications. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Interleukin 2 Therapy for Disseminated Cancer-Reply (1987)

<h3>In Reply.—</h3> Our article demonstrated that IL-2 administered in high doses was capable of mediating the regression of cancer in some patients with metastatic melanoma. Subsequent to this report, we have demonstrated that objective responses can be obtained in patients with renal cell cancer and have confirmed the efficacy of IL-2 therapy in additional patients with melanoma. Complete responses have been observed with both IL-2 therapy alone as well as with LAK cells. These are new treatments, but the first patient to show a complete response to therapy with IL-2 and LAK cells is alive without evidence of cancer two years after her original treatment. Dr Moertel's editorial, which focused on the media response to our earlier report of therapy with LAK cells and IL-2,<sup>1</sup>published in December 1985, reflects a misunderstanding of a major point of our report. These reports describe our experience with new approaches to immunotherapy
Electron-transfer processes: metal salt catalysed oxidation of olefins by peroxydisulphate (1983)

The reaction of simple olefins (oct-1-ene, oct-2-ene, cyclohexene, cycloheptene) with peroxydisulphate has been investigated under several conditions: (i) in aqueous medium and catalysis by AgI, FeII, and CuII; (ii) in acetic medium and catalysis by CuII, FeIII; (iii) in the presence of traps of nucleophilic alkyl radicals (protonated heteroaromatic bases and 1,4-benzoquinone either in water or in acetic acid). The catalyst and the radical trap govern the selectivity and allow a variety of new synthetic achievements. Evidence for a unified initial mechanism of electron transfer with formation of a radical cation from the olefin is reported to explain all the results. In water the radical cation gives a β-hydroxyalkyl radical, which, depending on the nature of the catalyst and the trap, can give the corresponding saturated alcohol by hydrogen abstraction, the products of CuII oxidation, or β-hydroxyalkylation of the heteroaromatic compound or 1,4-benzoquinone. In acetic acid the radical cation gives a β-acetoxyalkyl radical, which is oxidized to the corresponding allylic acetate by copper(II) acetate or trapped by the heteroaromatic base.
Geosemantic Snapping for Sketch‐Based Modeling (2013)

Abstract Modeling 3D objects from sketches is a process that requires several challenging problems including segmentation, recognition and reconstruction. Some of these tasks are harder for humans and some are harder for the machine. At the core of the problem lies the need for semantic understanding of the shape's geometry from the sketch. In this paper we propose a method to model 3D objects from sketches by utilizing humans specifically for semantic tasks that are very simple for humans and extremely difficult for the machine, while utilizing the machine for tasks that are harder for humans. The user assists recognition and segmentation by choosing and placing specific geometric primitives on the relevant parts of the sketch. The machine first snaps the primitive to the sketch by fitting its projection to the sketch lines, and then improves the model globally by inferring geosemantic constraints that link the different parts. The fitting occurs in real‐time, allowing the user to be only as precise as needed to have a good starting configuration for this non‐convex optimization problem. We evaluate the accessibility of our approach with a user study.
High-performance sensorless injection force control based on nonlinear friction phenomenon (2010)

Currently, most plastic products are manufactured using injection molding machines. The quality of plastic products depends largely on the injection force. In a typical force control system of an injection molding machine, force information from the machine environment is obtained by a force sensor. However, force sensors have a few disadvantages in terms of signal noise, sensor cost, narrow bandwidth, etc. We have proposed the use of a reaction force observer based on the two-inertia resonant model. However, this method has some estimated error because of the influence of nonlinear characteristics of the holding process and the screw back-pressure process. The estimation accuracy of the reaction force observer depends on parameter variations and the non-linear friction phenomenon. This paper proposes a new injection force estimation method based on a proposed high-order reaction force observer, which is not influenced by the nonlinear friction phenomenon significantly. This paper evaluates the effectiveness and the sensorless feedback control of the proposed method through experiments.
Preparation and screening of crystalline inorganic materials (2023)

Methods and apparatus for the preparation and use of a substrate having an array of diverse materials in predefined regions thereon. A substrate having an array of diverse materials thereon is generally prepared by delivering components of materials to predefined regions on a substrate, and simultaneously reacting the components to form at least two materials. Materials which can be prepared using the methods and apparatus of the present invention include, for example, covalent network solids, ionic solids and molecular solids. More particularly, materials which can be prepared using the methods and apparatus of the present invention include, for example, inorganic materials, intermetallic materials, metal alloys, ceramic materials, organic materials, organometallic materials, non-biological organic polymers, composite materials (e.g., inorganic composites, organic composites, or combinations thereof), etc. Once prepared, these materials can be screened for useful properties including, for example, electrical, thermal, mechanical, morphological, optical, magnetic, chemical, or other properties. Thus, the present invention provides methods for the parallel synthesis and analysis of novel materials having useful properties.
Abstract PR07: Mechanisms of stromal reprogramming mediated by heat shock factor 1 (2016)

Abstract For tumors to form, progress and metastasize, they must recruit and reprogram normal cells in their microenvironment into a pro-tumorigenic stroma. Yet little is known about the pathways leading to stromal reprogramming. We hypothesized that such reprogramming would not be mediated by classic oncogenes, since the stroma is relatively genetically stable. Instead we propose that cancer cells hijack normal cytoprotective stress responses, and subvert them to enable stromal reprogramming. We found that Heat-shock factor 1 (HSF1), master regulator of the heat-shock response, plays a crucial role in this process. Across a broad range of human cancers, HSF1 is activated in cancer-associated fibroblasts (CAFs). In early stage breast and lung cancer, high stromal HSF1 activation is strongly associated with poor patient outcome. In fibroblasts co-cultured with cancer cells, HSF1 drives a transcriptional program that supports cancer phenotypes. This program is profoundly different from the transcriptional program it drives in cancer cells or in heat-shocked cells. Here we characterize mechanisms leading to activation of this unique stromal program and describe the contribution of cancer cells to this process. We then explore the stromal HSF1 program in patients. We apply computational and experimental approaches to define independent cancer and stromal HSF1 signatures and highlight the prognostic value of these signatures in human breast cancer. Billions of years of evolution through changing environments led organisms to develop an arsenal of cytoprotective pathways to promote their survival under stressful conditions. Our work provides insights into the ways by which tumors co-opt these normal biological networks to support their survival in the stressful tumor microenvironment. This abstract is also presented as Poster B40. Citation Format: Ruth Scherz-Shouval, Marc L. Mendillo, Giorgio Gaglia, Irit Ben-Aharon, Andrew H. Beck, Luke Whitesell, Susan Lindquist. Mechanisms of stromal reprogramming mediated by heat shock factor 1. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr PR07.
Germicidal Ultraviolet Light Does Not Damage or Impede Performance of N95 Masks Upon Multiple Uses (2020)

The COVID-19 pandemic is increasing the need for personal protective equipment (PPE) worldwide, including the demand for facial masks used by healthcare workers. Disinfecting and reusing these masks may offer benefits in the short term to meet urgent demand. Germicidal ultraviolet light provides a nonchemical, easily deployable technology capable of achieving inactivation of H1N1 virus on masks. Working with N95-rated masks and nonrated surgical masks, we demonstrated that neither 254 nor 265 nm UV-C irradiation at 1 and 10 J/cm<sup>2</sup> had adverse effects on the masks' ability to remove aerosolized virus-sized particles. Additional testing showed no change in polymer structure, morphology, or surface hydrophobicity for multiple layers in the masks and no change in pressure drop or tensile strength of the mask materials. Results were similar when applying 254 nm low-pressure UV lamps and 265 nm light-emitting diodes. On the basis of the input from healthcare workers and our findings, a treatment system and operational manual were prepared to enable treatment and reuse of N95 facial masks. Knowledge gained during this study can inform techno-economic analyses for treating and reusing masks or lifecycle assessments of options to reduce the enormous waste production of single-use PPE used in the healthcare system, especially during pandemics.
Superabsorbent Polymers: High Capacity Functionalized Protein Superabsorbents from an Agricultural Co‐Product: A Cradle‐to‐Cradle Approach (Adv. Sustainable Syst. 9/2020) (2020)

The development of environmentally-friendly materials for the growing superabsorbent polymer industry is essential. In article number 2000110, Antonio Jose Capezza, Mikael Stefan Hedenqvist, and co-workers use a readily available protein co-stream functionalized with green and harmless reagents as a sustainable alternative for the fabrication of liquid-absorbent materials. The potential applications are many, and include single-use disposable products such as diapers.
Enzyme Immobilization in Biomimetically-Derived Oxide Matrices for Bio-Fuel Cell Applications (2008)

Abstract not Available.
Understanding sanction under variable observability in a secure, collaborative environment (2015)

Norms are a promising basis for governance in secure, collaborative environments---systems in which multiple principals interact. Yet, many aspects of norm-governance remain poorly understood, inhibiting adoption in real-life collaborative systems. This work focuses on the combined effects of sanction and the observability of the sanctioner in a secure, collaborative environment. We present CARLOS, a multiagent simulation of graduate students performing research within a university lab setting, to explore these phenomena. The simulation consists of agents maintaining "compliance" to enforced security norms while remaining "motivated" as researchers. We hypothesize that (1) delayed observability of the environment would lead to greater motivation of agents to complete research tasks than immediate observability and (2) sanctioning a group for a violation would lead to greater compliance to security norms than sanctioning an individual. We find that only the latter hypothesis is supported. Group sanction is an interesting topic for future research regarding a means for norm-governance which yields significant compliance with enforced security policy at a lower cost. Our ultimate contribution is to apply social simulation as a way to explore environmental properties and policies to evaluate key transitions in outcome, as a basis for guiding further and more demanding empirical research.
Infrared Study of Single Cells in Aqueous Media (2013)

Using FT-IR micro-spectroscopy, we are able to discriminate between pluripotent stem cells and their differentiating derivatives based each cells spectral fingerprint. With a new algorithm created using MATLAB, we are now able to accurately remove out the buffer contribution (water/PBS contribution) from IR spectra recorded from fixed and live cells in an aqueous environment. With accurate pure cell absorption spectra being produced from cells in an aqueous environment, spectral analysis of live single cells is now possible, opening the door for live stem cell screening using infrared microspectroscopy, in an environment close to the in vivo conditions of the cells.
Parasiticidal, antifungal and antibacterial activities of Onosma griffithii Vatke (2009)

Onosma griffithii was screened for possible pharmacological activities. The crude methanolic extract (MeOH) and its fractions demonstrated parasiticidal activity (IC 50 (ig/ml ± S.D) = 31.03 ± 0.23) against Leishmania major. Based on the IC 50 values, the potency of the standard drug (Pentamidine) and test fractions were of the order as: Pentamidine > crude extract > n-hexane fraction > ethyl acetate (ETOAc) fraction > chloroform fraction (CHCl3) fraction > n-butanol (BUOH) fraction > aqueous fraction. Similarly moderate antifungal activity was displayed by the crude methanolic extract against Aspergillus flavus and Fusarium solani. Against the Staphylococcus aureus, the aqueous fraction demonstrated moderate antibacterial activity.