gebhart/patrepeval huggingface dataset:
Abstract 5128: Polyethnic-1000: Advancing cancer genomics by studying ethnically diverse, underserved patient populations in New York (2019)

Abstract Background and aims Recent advances in DNA sequencing technologies have revolutionized approaches to the prevention, risk assessment, early detection, diagnosis, and treatment of cancers. However, many ethnic groups, especially non-European populations, have been significantly under-represented in cancer research, including clinical trials, and have not received equal benefits in clinical practice. As a result, our current knowledge about tumor biology, cancer risk, and response to treatment has primarily been derived from patients of European descent. These inequities limit our understanding of the many types of cancer and may exacerbate health disparities in the United States. This multi-institutional study, named Polyethnic-1000, aims to address both the scientific and social issues by creating a dynamic research platform within the ethnically diverse greater New York City area. Methods and results Polyethnic-1000 is a collaborative effort organized by the New York Genome Center (NYGC), involving staff and patients at academic centers and partnering hospitals in the New York City region. The genomics and informatics capabilities of the NYGC will be used to determine how inherited and somatically acquired genetic variations affect the behavior of cancers occurring in ethnically diverse populations. In a first, retrospective stage we are establishing the necessary infrastructure and workflow from sample acquisition to whole-exome and RNA sequencing, data analysis and data sharing within the consortium. Then we will start a prospective study enabling the formation of cohorts of interest for particular cancer types and particular ethnicities, with uniform consent allowing germline and somatic sequencing with broad data sharing of the somatic variants identified. Conclusion By establishing a collaborative network, Polyethnic-1000 will deepen our understanding of the contributions that ethnicities make to the incidence and biology of cancers, potentially improving outcomes for patients who currently lack access to the most recent advances in medical science. Citation Format: Fieke E. Froeling, Nicolas Robine, Benjamin Hubert, Michael Zody, Dayna Oschwald, Harold E. Varmus, Charles L. Sawyers, David A. Tuveson, On behalf of the NYGC P1000 Consortium. Polyethnic-1000: Advancing cancer genomics by studying ethnically diverse, underserved patient populations in New York [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5128.
Consensus-based distributed expectation-maximization algorithm for density estimation and classification using wireless sensor networks (2008)

The present paper develops a decentralized expectation-maximization (EM) algorithm to estimate the parameters of a mixture density model for use in distributed learning tasks performed with data collected at spatially deployed wireless sensors. The E-step in the novel iterative scheme relies on local information available to individual sensors, while during the M-step sensors exchange information only with their one- hop neighbors to reach consensus and eventually percolate the global information needed to estimate the wanted parameters across the wireless sensor network (WSN). Analysis and simulations demonstrate that the resultant consensus-based distributed EM (CB-DEM) algorithm matches well the resource- limited characteristics of WSNs and compares favorably with existing alternatives because it has wider applicability and remains resilient to inter-sensor communication noise.
Novel P2X7 Antagonist Ameliorates the Early Phase of ALS Disease and Decreases Inflammation and Autophagy in SOD1-G93A Mouse Model (2021)

Amyotrophic lateral sclerosis (ALS) is a disease with a resilient neuroinflammatory component caused by activated microglia and infiltrated immune cells. How to successfully balance neuroprotective versus neurotoxic actions through the use of anti-inflammatory agents is still under debate. There has been a boost of awareness regarding the role of extracellular ATP and purinergic receptors in modulating the physiological and pathological mechanisms in the nervous system. Particularly in ALS, it is known that the purinergic ionotropic P2X7 receptor plays a dual role in disease progression by acting at different cellular and molecular levels. In this context, we previously demonstrated that the P2X7 receptor antagonist, brilliant blue G, reduces neuroinflammation and ameliorates some of the pathological features of ALS in the SOD1-G93A mouse model. Here, we test the novel, noncommercially available, and centrally permeant Axxam proprietary P2X7 antagonist, AXX71, in SOD1-G93A mice, by assessing some behavioral and molecular parameters, among which are disease progression, survival, gliosis, and motor neuron wealth. We demonstrate that AXX71 affects the early symptomatic phase of the disease by reducing microglia-related proinflammatory markers and autophagy without affecting the anti-inflammatory markers or motor neuron survival. Our results suggest that P2X7 modulation can be further investigated as a therapeutic strategy in preclinical studies, and exploited in ALS clinical trials.
A role for semaphorin 3A signaling in the degeneration of hippocampal neurons during Alzheimer's disease (2004)

Among the earliest invariant neuropathological changes in Alzheimer's disease (AD) is the degeneration of vulnerable hippocampal CA1 and subicular pyramidal neurons. Semaphorin 3A (Sema3A) is a secreted protein that functions in signaling growth cone collapse, chemorepulsion and neuronal apoptosis during early development of the central nervous system. In this report we show that accumulation of an internalized form of Sema3A is associated with degeneration of neurons in vulnerable fields of the hippocampus during AD. Accumulation of Sema3A overlaps the appearance of phosphorylated MAP1B and tau in many neurons, suggesting that Sema3A signaling at some level may be coupled to these previously identified cytoskeletal markers of neurodegeneration. Consistent with this, we isolated and partially characterized a multiprotein complex from the hippocampus of patients with AD that contains phosphorylated MAP1B, collapsin-response mediator protein 2 (CRMP-2), Plexins A1 and A2, and a processed form of Sema3A. A model is presented in which aberrant release of Sema3A from expressing neurons in the subiculum during AD results in the internalization and transport of Sema3A from this field to CA1. Within the context of the myriad of potential insults that contribute to Alzheimer's and other neurodegenerative diseases, the bioactivity of Sema3A may contribute either directly to neurodegeneration by inducing neuronal collapse, or indirectly by abrogating the recovery capabilities of adult neurons faced with these insults.
Errata-Low Earth Orbit Simulation and Materials Characterization (1993)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
<title>Imaging-eclipsing-Z-scan method for measurement of the nonlinear refractive index of materials</title> (1999)

We present a new variation of the Z-scan technique, which provides a sensitive method for measurement of the nonlinear refractive index of materials. The method is based on imaging of a top hat beam onto a blocking disk; therefore, it is very sensitive. In addition to greater sensitivity the method offers the advantage that it does not require a Gaussian beam, therefore it can be used with low energy lasers with any beam profile.
Activation of DOR Attenuates Anoxic K+ Derangement via Inhibition of Na+ Entry in Mouse Cortex (2008)

We have recently found that in the mouse cortex, activation of delta-opioid receptor (DOR) attenuates the disruption of K(+) homeostasis induced by hypoxia or oxygen-glucose deprivation. This novel observation suggests that DOR may protect neurons from hypoxic/ischemic insults via the regulation of K(+) homeostasis because the disruption of K(+) homeostasis plays a critical role in neuronal injury under hypoxic/ischemic stress. The present study was performed to explore the ionic mechanism underlying the DOR-induced neuroprotection. Because anoxia causes Na(+) influx and thus stimulates K(+) leakage, we investigated whether DOR protects the cortex from anoxic K(+) derangement by targeting the Na(+)-based K(+) leakage. By using K(+)-sensitive microelectrodes in mouse cortical slices, we showed that 1) lowering Na(+) concentration and substituting with impermeable N-methyl-D-glucamine caused a concentration-dependent attenuation of anoxic K(+) derangement; 2) lowering Na(+) concentration by substituting with permeable Li(+) tended to potentiate the anoxic K(+) derangement; and 3) the DOR-induced protection against the anoxic K(+) responses was largely abolished by low-Na(+) perfusion irrespective of the substituted cation. We conclude that external Na(+) concentration greatly influences anoxic K(+) derangement and that DOR activation likely attenuates anoxic K(+) derangement induced by the Na(+)-activated mechanisms in the cortex.
Quantifying the uncertainty imposed by inaccurate modeling of active distribution grids (2022)

Replacing conventional generation with inverter-interfaced units has turned distribution networks (DNs) from consumers to active and responding intelligent DNs. These modern DNs contain several devices that can support the transmission network (TN) and system stability. Typically, deterministic and aggregated models for inverter-interfaced generation and conventional loads are used to include entire DNs in bulk system stability studies, and contributions from smart loads are neglected. This approach introduces errors to the dynamic modeling that can lead to instabilities. In this paper, we first present a full detailed model of a modern DN, enhancing existing thermal load and distributed generation models to include frequency and voltage support and protection functions required in low-inertia systems. Then, we incorporate the uncertainty that stems from the parameterization of such units using a Monte-Carlo method. Finally, we assess the impact of neglecting specific protection and support functions against frequency disturbances. The results show the crucial importance of accurately modeling protection and support functions to analyze the impact of modern DNs on bulk system stability. In addition, the findings highlight the increased relevance of considering uncertainty in stability studies of weak and low-inertia power systems.
Full Stokes polarization imaging camera (2011)

Objective and background: We present a new version of Bossa Nova Technologies' passive polarization imaging camera. The previous version was performing live measurement of the Linear Stokes parameters (S<sub>0</sub>, S<sub>1</sub>, S<sub>2</sub>), and its derivatives. This new version presented in this paper performs live measurement of Full Stokes parameters, i.e. including the fourth parameter S<sub>3</sub> related to the amount of circular polarization. Dedicated software was developed to provide live images of any Stokes related parameters such as the Degree Of Linear Polarization (DOLP), the Degree Of Circular Polarization (DOCP), the Angle Of Polarization (AOP). Results: We first we give a brief description of the camera and its technology. It is a Division Of Time Polarimeter using a custom ferroelectric liquid crystal cell. A description of the method used to calculate Data Reduction Matrix (DRM)<sup>5,9</sup> linking intensity measurements and the Stokes parameters is given. The calibration was developed in order to maximize the condition number of the DRM. It also allows very efficient post processing of the images acquired. Complete evaluation of the precision of standard polarization parameters is described. We further present the standard features of the dedicated software that was developed to operate the camera. It provides live images of the Stokes vector components and the usual associated parameters. Finally some tests already conducted are presented. It includes indoor laboratory and outdoor measurements. This new camera will be a useful tool for many applications such as biomedical, remote sensing, metrology, material studies, and others.
Apparatus for obtaining silicon from fluosilicic acid (2023)

Apparatus for producing low cost, high purity solar grade Si wherein a reduction reaction, preferably the reduction of SiF.sub.4, by an alkali metal (Na preferred) is carried out by jetting a spray of reactants into a reaction chamber at a rate and temperature which causes the reaction to take place far enough away from the entry region to avoid plugging of reactants at the entry region and wherein separation in the melt is carried out continuously from the reaction and the Si can be cast directly from the melt. The melt separation is provided by openings in the reaction chamber wall between about 2 and 3.5 millimeters in width. The Si is retained within the reaction chamber due to its surface tension.
Postquantum Cryptography, Part 2 (2018)

This is part 2 of IEEE Security & Privacy magazine’s special issue on Postquantum Cryptography. As explained in the introduction to part 1, public-key cryptography is indispensable for the security of open computer networks, particularly the Internet. Because of public-key cryptography’s relevance and quantum computers’ increasingly realistic threat to this technology, it’s necessary to come up with practical and secure postquantum cryptography—that is, public-key cryptography that can be expected to resist quantum computer attacks.
Lommel Expansions in Electromagnetics (2009)

Lommel expansions and the important role they play in electromagnetic theory are reviewed in this chapter. These expansions are shown to be useful in developing an exact integration procedure for evaluating electromagnetic field quantities associated with current-carrying wire antennas such as cylindrical dipoles and circular loops. Several exact series representations are introduced in this chapter which are valid not only in the far-field of the source, but also in its near-field region. These series expansions are general and can be shown to contain all of the well-known classical approximations as special limiting cases. Some applications of these recently found exact series expansions are discussed, including their use in the development of efficient yet accurate algorithms for computational modeling of moderately thick cylindrical wire antennas.
Engineering a novel c‐di‐GMP‐binding protein for biofilm dispersal (2010)

Bacteria prefer to grow attached to themselves or an interface, and it is important for an array of applications to make biofilms disperse. Here we report simultaneously the discovery and protein engineering of BdcA (formerly YjgI) for biofilm dispersal using the universal signal 3,5-cyclic diguanylic acid (c-di-GMP). The bdcA deletion reduced biofilm dispersal, and production of BdcA increased biofilm dispersal to wild-type level. Since BdcA increases motility and extracellular DNA production while decreasing exopolysaccharide, cell length and aggregation, we reasoned that BdcA decreases the concentration of c-di-GMP, the intracellular messenger that controls cell motility through flagellar rotation and biofilm formation through synthesis of curli and cellulose. Consistently, c-di-GMP levels increase upon deleting bdcA, and purified BdcA binds c-di-GMP but does not act as a phosphodiesterase. Additionally, BdcR (formerly YjgJ) is a negative regulator of bdcA. To increase biofilm dispersal, we used protein engineering to evolve BdcA for greater c-di-GMP binding and found that the single amino acid change E50Q causes nearly complete removal of biofilms via dispersal without affecting initial biofilm formation.
Sessile serrated adenomas and classical adenomas: An epigenetic perspective on premalignant neoplastic lesions of the gastrointestinal tract (2010)

The diagnosis of sessile serrated adenomas (SSAs) is challenging, and there is a great deal of interobserver variability amongst pathologists in differentiating SSAs from hyperplastic polyps (HPPs). The aim of this study was (i) to assess the utility of epigenetic changes such as DNA methylation in differentiating SSAs from HPPs and (ii) to identify common methylation based molecular markers potentially useful for early detection of premalignant neoplastic lesions of gastrointestinal tract. A total of 97 primary patient adenoma samples were obtained from The Johns Hopkins Hospital pathology archive with IRB approval and HIPAA compliance. We analyzed the promoter associated CpG island methylation status of 17 genes using nested multiplex methylation specific PCR (MSP). Methylation of CDX2, hMLH1 and TLR2 was detected in SSAs and SSAs with dysplasia but not in HPPs. A subset of genes including EVL, GATAs (4 and 5), HIN-1, SFRPs (1, 2, 4 and 5), SOX17 and SYNE1 were methylated frequently in all premalignant gastrointestinal adenomas including tubular adenomas, villous adenomas, SSAs and SSAs with dysplasia but infrequently in non-premalignant polyps such as HPPs. Methylation of CDX2, hMLH1 and TLR2 may be of diagnostic utility in differentiating, histologically challenging cases of SSAs from HPPs. Genes such as EVL, GATAs, HIN-1, SFRPs, SOX17 and SYNE1, which are frequently methylated in all types of tested premalignant adenomas, may be useful as biomarkers in stool-based strategies for early detection of these adenomas and CRCs in future.
Large-scale Radiomic Profiling of Recurrent Glioblastoma Identifies an Imaging Predictor for Stratifying Anti-Angiogenic Treatment Response (2016)

Our radiomic-based superpc signature emerges as a putative imaging biomarker for the identification of patients who may derive the most benefit from antiangiogenic therapy, advances the knowledge in the noninvasive characterization of brain tumors, and stresses the role of radiomics as a novel tool for improving decision support in cancer treatment at low cost. Clin Cancer Res; 22(23); 5765-71. ©2016 AACR.
Shear Rolling of Magnesium Sheet for Automotive, Defense, and Energy Applications (2013)

Magnesium is the lightest structural metal known: at approximately 1/5 the density of steel, 1/2 the density of titanium and 2/3 the density of aluminum. Hence magnesium alloys represent potential weight savings across the entire transportation industry. The major hurdle to the deployment of magnesium products by the transportation industry is the price barrier that exists due to the current high cost of producing magnesium alloy sheet on a volume basis. Proven technology (e.g., twin roll sheet casting and hot reversing coil mill technology) exists which could lower the cost of magnesium alloy sheet by as much as 50%, but needs to be demonstrated and implemented in high volume production to achieve benefits. In addition, the predominant basal texture (alignment of basal planes parallel to the sheet surface) that exists in magnesium alloy sheet results in poor low temperature formability resulting in added fabrication costs. Cost reduction achieved through energy efficiency, coupled with even greater energy savings by deployment of this “lightest of metals”, will help the United States achieve its goal to eliminate dependence on foreign fossil fuel. Oak Ridge National Laboratory (ORNL), Magnesium Elektron North America (MENA), and FATA Hunter collaborated on this project to develop shear rolling technology of magnesium sheet to enable improvement of the formability of magnesium sheet while addressing cost and lower energy consumption.
Single Cell Transcriptomics and Flow Cytometry Reveal Disease-associated Fibroblast Subsets in Rheumatoid Arthritis (2017)

Abstract Fibroblasts mediate normal tissue matrix remodeling, but they can cause fibrosis or tissue destruction following chronic inflammation. In rheumatoid arthritis (RA), synovial fibroblasts expand, degrade cartilage, and drive joint inflammation. Little is known about fibroblast heterogeneity or if aberrations in fibroblast subsets relate to disease pathology. Here, we used an integrative strategy, including bulk transcriptomics on targeted subpopulations and unbiased single-cell transcriptomics, to analyze fibroblasts from synovial tissues. We identify 7 phenotypic fibroblast subsets with distinct surface protein phenotypes, and these collapsed into 3 subsets based on transcriptomics data. One subset expressing PDPN, THY1, but lacking CD34 was 3-fold expanded in RA relative to osteoarthritis (P=0.007); most of these cells expressed CDH11. The subsets were found to differ in expression of cytokines and matrix metalloproteinases, localization in synovial microanatomy, and in response to TNF. Our approach provides a template to identify pathogenic stromal cellular subsets in complex diseases.
Incremental Trace-Buffer Insertion for FPGA Debug (2013)

As integrated circuits encapsulate more functionality and complexity, verifying that these devices operate correctly under all scenarios is an increasingly difficult task. Rather than using traditional verification techniques such as software simulation, more and more designers are taking advantage of the significantly higher clock speeds that can be achieved by using field-programmable gate-array (FPGA)-based prototypes. A key challenge to these prototypes is the lack of on-chip observability during debugging; one popular solution is to insert trace-buffers into the design to record a limited set of internal signals, but modifying this trace configuration often requires the entire circuit to be recompiled. In this paper, we propose that the original circuit mapping is fully preserved and incremental techniques are used to eliminate the need for a full recompilation, thereby accelerating the debugging process. By exploiting two opportunities available during trace-insertion: the ability to connect from any point of a signal to any trace-pin, and the internal symmetry of the FPGA architecture, we find that incremental trace-insertion can be 98 times faster than a full recompilation, return a routing solution with a shorter wirelength, and have a negligible effect on the critical-path delay of the original circuit when reclaiming 75% of the leftover memory capacity for tracing.
Supplementary Figure 1 Legend from Immunoediting Sculpts Tumor Epitopes during Immunotherapy (2023)

Supplementary Figure 1 Legend from Immunoediting Sculpts Tumor Epitopes during Immunotherapy
Inhibition of phenylalanine hydroxylase, a pterin-requiring monooxygenase, by oudenone and its derivatives. (1982)

Phenylalanine hydroxylase was shown to be inhibited by oudenone and its derivatives in vitro. At a concentration of 2.3 x 10(-3) M, oudenone inhibited phenylalanine hydroxylase by 50%, and some of the oudenone derivatives showed more potent inhibition. The kinetic data have shown that the inhibition by oudenone is competitive with a tetrahydropterin cofactor (6,7-dimethyltetrahydropterin, DMPH4) and noncompetitive with phenylalanine and oxygen. Among 12 oudenone derivatives, there was no parallel structure-activity relationship between the inhibitory effect for phenylalanine hydroxylase and that for tyrosine hydroxylase. A derivative of oudenone, [compound No. 142; 2-(3,4-dihydroxyphenyl)-1-oxopropyl)cyclohexan-1,3-dione] showed the most potent inhibition among the oudenone derivatives. It inhibited phenylalanine hydroxylase by 50% at a concentration of 1.8 x 10(-5) M. This inhibition was a mixed type with either a tetrahydropterin cofactor, DMPH4, or with the substrate phenylalanine, which was different from the inhibition by oudenone. However, the same noncompetitive inhibition was shown toward oxygen.