gebhart/patrepeval huggingface dataset:
Abstract 512: Leukemia-specific immunity in healthy individuals and patients post-transplant targets phosphorylated tumor antigens (2012)

Abstract The major antigenic targets of endogenous tumor immunity remain unknown although many minor targets have been identified. At a proteomic level, cancer is considered a disease of deregulated cell signal pathway activation; therefore we investigated whether endogenous anti-tumor immunity targeted phosphorylated protein antigens generated through the transformation process. In previous work we identified phosphorylated peptides differentially expressed on primary leukemia samples: 58 for acute myeloid leukemia (AML) samples and 31 for chronic lymphocytic leukemia (CLL). Many of the identified phosphopeptides were derived from established leukemogenic oncoproteins such as MLL, RUNX1, c-Myc, EP300, CXCR4, SKI, GRK, CD19, CD20, NCOA1, and TLK1 among others and differentially expressed between malignant and healthy counterpart tissue (splenic B cells, bone marrow). Using ELISpot and HLA-phosphopeptide multimers, we screened 10 healthy donors, 17 patients in complete remission with underlying AML and 14 patients with CLL. Healthy donors (HD) exhibited a highly heterogeneous reactivity against this panel of phosphoantigens but all responded to at least 10/57 phosphoantigens tested. Further investigation revealed this immunity resided within the central memory CD8 T cell compartment at the same magnitude of responses as those against influenza and adenovirus. By contrast only 2/12 AML and 5/14 CLL patients demonstrated anti-phosphopeptide immunity compared to 10/10 HDs (≥2&amp;lt; 0.01 for both). In contrast immunity against viral and mitogenic stimuli was similar between patients and HDs. Following allogeneic stem cell transplantation the majority (10/12) AML patients reconstituted anti-phosphopeptide immunity. In some cases dramatic expansions, of similar magnitude to cytomegalovirus responses, were observed approaching 1% of CD8 T cells for a single phosphopeptide epitope. In CLL, none of whom were transplanted, we found that over the study period of 12 months that among the patients with anti-phosphopeptide immunity only 1 of 5 patients required treatment compared to 4 of 9 patients requiring treatment where no anti phosphopeptide responses were seen (≥2=NS). Importantly, ex vivo expanded phosphopeptide specific T cells isolated from both healthy individuals and patients post-transplant were able to kill both HLA-matched primary leukemia samples and AML cell lines in a phosphopeptide-specific manner. These data suggest a prominent role for tumor-associated phosphopeptide antigens in the prevention and control of haematolymphoid disease in man. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 512. doi:1538-7445.AM2012-512
Pathologic Lesions in Chimpanzees (Pan trogylodytes schweinfurthii) from Gombe National Park, Tanzania, 2004–2010 (2011)

During a population decline or disease outbreak, the true risk of specific diseases to a wild population is often difficult to determine because of a lack of baseline disease information. To better understand the risk of disease in an endangered and scientifically important population of chimpanzees (Pan trogylodytes schweinfurthii), a health monitoring program was initiated in Gombe National Park, Tanzania. As part of this health monitoring program, comprehensive necropsies with histopathology were conducted on chimpanzees (n = 11; 5 male, 6 female), ranging in age from fetal to 44 yr, that were found dead between August 2004 and January 2010. In contrast to previous reports, respiratory disease was not noted as a cause of morbidity or mortality. Trauma was the most common cause of death in these 11 chimpanzees. All of the chimpanzees greater than 1 yr of age had intestinal and mesenteric parasitic granulomas associated with true strongyles consistent with Oesophagostomum spp. The relative numbers of granulomas increased with age and, in some cases, may have been a cause of weight loss and diarrhea. Simian immunodeficiency virus (SIV)cpz infection was documented in four deceased apes, all of whom exhibited varying amounts of lymphoid depletion including two females with marked CD4+ T cell loss consistent with endstage SIVmac or human immunodeficiency virus infections. Myocardial megalokaryosis was common in chimpanzees greater than 1 mo of age; yet myocardial interstitial fibrosis, a common lesion in captive chimpanzees, was uncommon and only noted in two aged chimpanzees. These findings provide important information on causes of morbidity and mortality in wild chimpanzees, information that can be used to interpret findings during population declines and lead to better management of this population in the context of disease risk.
Video-Based Lane Detection Using a Fast Vanishing Point Estimation Method (2012)

Lane detection algorithms constitute a basis for intelligent vehicle systems such as lane tracking and involuntary lane departure detection. In this paper, we propose a simple and video-based lane detection algorithm that uses a fast vanishing point estimation method. The first step of the algorithm is to extract and validate the line segments from the image with a recently proposed line detection algorithm. In the next step, an angle based elimination of line segments is done according to the perspective characteristics of lane markings. This basic operation removes many line segments that belong to irrelevant details on the scene and greatly reduces the number of features to be processed afterwards. Remaining line segments are extrapolated and superimposed to detect the image location where majority of the linear edge features converge. The location found by this efficient operation is assumed to be the vanishing point. Subsequently, an orientation-based removal is done by eliminating the line segments whose extensions do not intersect the vanishing point. The final step is clustering the remaining line segments such that each cluster represents a lane marking or a boundary of the road (i.e. sidewalks, barriers or shoulders). The properties of the line segments that constitute the clusters are fused to represent each cluster with a single line. The nearest two clusters to the vehicle are chosen as the lines that bound the lane that is being driven on. The proposed algorithm works in an average of 12 milliseconds for each frame with 640×480 resolution on a 2.20 GHz Intel CPU. This performance metric shows that the algorithm can be deployed on minimal hardware and still provide real-time performance.
Fin-shape optimization of an impingement-parallel plate heat sink (2010)

As the power dissipated by advanced microelectronic devices continues to increase, the demand for reliability also increases. This increases the requirements on the thermal performance of every part of the system, including the heat sink. One of the objectives of this study is to examine the effect of shape of the heat sink fins on the thermal performance of the system. The pressure gradient from the fan to the base of the heat sink, near the center, tends to be high. This significantly reduces the airflow at that location and, hence, decreases transport in that region. Parallel plate heat sinks have been investigated by removing fin material near the center along the length and height of the fins. The junction-to-ambient temperature difference and pressure drop are adopted as thermal performance characteristics. Five design variables related to the fin shape were considered and the most significant influential geometric parameters for minimizing the objective functions identified using the analysis of variance (ANOVA) approach. Different fin shapes have been studied with the objective of searching for a new optimal heat sink design by optimizing the variables that improve the thermal performance without increasing pressure drop across the heat sink.
“Magic Radius” Phenomenon in Thin-ridge SOI Ring Resonators: Theory and Preliminary Observations (2010)

The lateral leakage loss mechanism of the TM-like mode in thin-ridge SOI ring resonators is significantly impacted by the ring radius and waveguide width. This behavior is analyzed using rigorous modeling techniques and verified experimentally.
Validation of A Computer‐Assisted Dynamic Simulation For Treatment of Femoroacetabular Impingement (FAI) (2014)

An incomplete resection with residual deformity is a common cause for failure after arthroscopic hip preservation surgery for femoroacetabular impingement (FAI). The purpose of this study was (i) to compare the morphology of a virtual osteoplasty as templated by CT-based, 3D dynamic simulation modeling to the morphology after actual operative treatment of symptomatic FAI by a high volume surgeon, and (ii) to compare the morphology of a virtual osteoplasty to the actual operative treatment executed by less experienced surgeons in patients presenting for revision FAI surgery.
High-Efficiency Grating Couplers Near 1310 nm Fabricated by 248-nm DUV Lithography (2014)

We demonstrate a highly efficient grating coupler with center wavelength near 1310 nm fabricated on a silicon-on-insulator (SoI) wafer by 248-nm deep ultraviolet lithography. One of the lowest reported losses of 2 dB is achieved using feature sizes of 200 nm and without other process enhancements, such as polysilicon. The higher efficiency is obtained through improved mode-matching based on a novel genetic algorithm, which utilizes two different etch depths. The 3-dB bandwidth is 50 nm, and the back-reflection to the waveguide is better than 20 dB. The result shows low-loss coupling between waveguides and single-mode fibers for 1310~nm applications suitable for mass production on the commonly used 220-nm SoI platform.
Continuous Renal Replacement Therapy for Congestive Heart Failure: The Wearable Continuous Ultrafiltration System (2006)

Ultrafiltration is effective in the treatment of fluid and sodium overload in congestive heart failure. There is no available device to provide this therapy to ambulatory patients. We built and tested in vivo a wearable belt that can provide continuous ultrafiltration, 168 hours a week. Nine pigs underwent ureteral ligation and subsequently were allowed fluids ad lib, producing fluid overload. Next day, ultrafiltration was performed for 8 hours. The device consists of a hollow-fiber filter, a 9 V battery-operated pulsatile blood pump, a micro pump for heparin infusion, and another micro pump to control ultrafiltration rate. Blood flow was 65 ml/min and the weight of the device is less than 2.5 lb. Fluid removal rate ranged from 0 to 700 ml/h and averaged 106 ml/h. Salt removed was 7.6 g. No complications were observed. The potential impact on the quality of life of these patients by reducing the shortness of breath, leg swelling, and returning their ability to enjoy salt in their food might be significant, and a reduction in morbidity could be expected. The economic impact in reducing hospital admissions and length of stay, intensive care unit utilization, and drug consumption could be significant. Further studies are needed to compare this innovative approach with traditional drug-based therapy.
Identification of GLPG/ABBV-2737, a Novel Class of Corrector, Which Exerts Functional Synergy With Other CFTR Modulators (2019)

The deletion of phenylalanine at position 508 (F508del) in cystic fibrosis transmembrane conductance regulator (CFTR) causes a severe defect in folding and trafficking of the chloride channel resulting in its absence at the plasma membrane of epithelial cells leading to cystic fibrosis. Progress in the understanding of the disease increased over the past decades and led to the awareness that combinations of mechanistically different CFTR modulators are required to obtain meaningful clinical benefit. Today, there remains an unmet need for identification and development of more effective CFTR modulator combinations to improve existing therapies for patients carrying the F508del mutation. Here, we describe the identification of a novel F508del corrector using functional assays. We provide experimental evidence that the clinical candidate GLPG/ABBV-2737 represents a novel class of corrector exerting activity both on its own and in combination with VX809 or GLPG/ABBV-2222.
Lithium‐Ion Batteries: Layered Heterostructure Ionogel Electrolytes for High‐Performance Solid‐State Lithium‐Ion Batteries (Adv. Mater. 13/2021) (2021)

Ionogel electrolytes with a layered heterostructure are developed by Mark C. Hersam and co-workers in article number 2007864, using hexagonal boron nitride nanoplatelets and two imidazolium ionic liquids with different electrochemical stability windows. Compared with ionogels using the individual ionic liquids, the layered heterostructure ionogels provide broadened electrochemical stability windows while maintaining desirable ionic conductivity, suggesting a promising electrolyte strategy for high operating voltages and rate performance in solid-state lithium-ion batteries.
X-ray nanotomography using near-field ptychography (2015)

Propagation-based imaging or inline holography in combination with computed tomography (holotomography) is a versatile tool to access a sample's three-dimensional (3D) micro or nano structure. However, the phase retrieval step needed prior to tomographic reconstruction can be challenging especially for strongly absorbing and refracting samples. Near-field ptychography is a recently developed phase imaging method that has been proven to overcome this hurdle in projection data. In this work we extend near-field ptychography to three dimensions and we show that, in combination with tomography, it can access the nano structure of a solid oxide fuel cell (SOFC). The quality of the resulting tomographic data and the structural properties of the anode extracted from this volume were compared to previous results obtained with holotomography. This work highlights the potential of 3D near-field ptychography for reliable and detailed investigations of samples at the nanometer scale, with important applications in materials and life sciences among others.
Synchronizing Gait with Cardiac Cycle Phase Alters Heart Rate Response during Running (2017)

Synchronizing foot strikes when running to the diastolic portion of the cardiac cycle results in a significantly reduced HR and minute ventilation compared with stepping during systole. This cardiac and ventilatory response to diastolic stepping may be beneficial to distance running performance.
Cytotoxic T lymphocytes show HLA-C-restricted recognition of EBV-bearing cells and allorecognition of HLA class I molecules presenting self-peptides (1992)

Human CTL have been isolated that show self-restricted recognition of autologous lymphoblastoid cell lines and allorecognition. The lymphoblastoid cell line ligand most likely used a peptide that is expressed in EBV-bearing cells when the virus enters the lytic cycle. This peptide is presented to CD8+ CTL by HLA-Cw7 molecules. The allogeneic ligand recognized on non-EBV-infected cells is composed of a class I glycoprotein and a naturally selected self-peptide. In previous studies we demonstrated that this ligand is determined by two MHC-linked genes: one gene encodes the allogeneic class I molecule whereas the other controls the self-peptide. Despite the use of different peptides and different class I molecules, seemingly equivalent structures are formed that enable these two ligands to function as antigenic mimics of each other. CTL with the same patterns of dual specificity could be isolated from four unrelated donors, indicating that HLA-Cw7 is frequently involved in self-restricted recognition of EBV-harboring cells. Such CTL could help not only to contain lytic virus during a primary infection but also may be maintained life-long to eliminate cells in which reactivated virus appears.
CONHECIMENTO DOS HOMENS SOBRE O CÂNCER DE PRÓSTATA: A VIRILIDADE E O ESTIGMA DA DOENÇA (2021)

Este estudo teve como objetivo analisar o conhecimento dos homens usuários de serviços de saúde sobre prevenção do câncer de próstata. Estudo qualitativo, realizado com 25 homens, com idade acima dos 40 anos, em quatro Centros de Saúde e um serviço ambulatorial especializado em urologia. Os dados foram coletados por meio de uma entrevista semiestruturada e analisados conforme a técnica de análise de conteúdo, modalidade temática, emergindo duas categorias: o estigma do câncer e o conhecimento dos sintomas; a virilidade e o preconceito com o exame preventivo. Os resultados demonstraram que os entrevistados carregam em seu imaginário a visão estigmatizada do câncer de alta morbimortalidade, dor e sofrimento e que esta visão, traduzida pelo medo de adoecer, é a motivação para prevenir-se através da busca dos serviços de saúde. No que concerne às manifestações clínicas da doença, observou-se que a maioria dos entrevistados possui conhecimento daquelas mais comuns à fase inicial e desconhecem as manifestações da fase avançada. Por já conhecerem o exame do toque retal, muitos o recomendam, porém reconhecem que o preconceito associado à virilidade e ao machismo constitui-se como uma barreira à prevenção. Conclui-se que é fundamental a realização de atividades educativas que divulguem a importância do diagnóstico precoce do câncer de próstata, especialmente relacionado à desmistificação do exame de toque retal, objetivando a redução da morbimortalidade da doença.
Low-cost volumetric imaging with large footprint 11x11-element matrix array probe on a 128 channel ultrasound research scanner (2019)

Volumetric imaging in real time can only be realized using matrix array transducers and electronic beam steering requiring cost intensive ultrasound devices. Furthermore, matrix array transducers typically come with a small footprint that limits the total amount of energy that can be applied to the tissue caused by fulfilling the λ/2 element pitch criteria for best beam steering possibilities. This results in a reduction of maximum penetration of the sound wave caused by its attenuation and therefore reduces the possible imaging depth. By choosing a larger element pitch of 2.8125 mm (3.6x lambda) in both dimensions in our approach, we increase the maximum amount of energy to be generated while reducing beam steering capabilities. While generating enough acoustic energy to image deeper tissue, this design significantly limits the beam steering possibilities still allowing for plane wave compounding.
Micro-Simulation of Truck Platooning with Cooperative Adaptive Cruise Control: Model Development and a Case Study (2018)

Cooperative adaptive cruise control (CACC) systems have the potential to improve traffic flow and fuel efficiency, but these effects are challenging to estimate. This paper reports the development of a micro-simulation model to represent these impacts for heavy trucks using CACC when they share a freeway with manually driven passenger cars. The simulation incorporates automated truck-following models that have been derived from experimental data recorded on heavy trucks driven under CACC, adaptive cruise control (ACC), and conventional cruise control (CC). The simulation includes other behavioral models for lane changing, lane change cooperation and lane use restrictions for trucks to better capture real-world traffic dynamics. The paper explains the calibration of the simulation method for a 15-mile urban freeway corridor with heavy truck traffic and significant congestion. Simulation results for different market penetration rates show that truck CACC improved traffic operations for trucks in terms of vehicle miles traveled, average speed, and flow rate. In addition, truck CACC did not adversely affect passenger car operations and in some locations it even produced considerable improvements in the general traffic conditions.
48th Silicon Symposium Proceedings (2017)

Silylene Transfer Reactions for Synthesis of Strained Alkenes, Keith Woerpel; Methylsilicones Pushed in Several Directions, Thomas McCarthy; N-Heterocyclic Silylenes, Matthias Dreiss; Surface Modification of Silicon Nanostructures; Michael Sailor; Silicon-Hybrid Materials, Joseph Mabry; Silicon Nanocrystal Assemblies; Brian Korgel; New Materials Properties Through a Silicone Blend Strategy, Francois Ganachaud; New Methods for Tethered Carbonyl Silylations, Gregory O'Neil; Advances in Preparation of Organosilanes Using Palladium Catalysis, Donald Watson; Synthesis and Applications of Silicone Copolymers, Ramesh Kumar; Towards Controlled Synthesis and Characterization of Complex Silicone Architectures; Use of Nanocatalysis in the Direct Synthesis of Methylchlorosilanes and Alkoxysilanes; Kendrick Lewis; Material Behavior of Self-Aligned Silicon Carbide Nanowire Arrays; Spyros Gallis; Cyclohexasilane, A Source of Quantum Dots, Nanowires, Philip Boudjouk; Mechanism of Oligomerization of N-Heterocyclic Silylenes, Andrey Rogachev; The Addition of Isocyanides to Disilenes, Kim Baines; Oscilations in the mSR Spectra of Muionated Organosilyl Free Radicals, Kerim Samedov; Electrophilic Substitution on Phenylsilsesquioxanes, Richard Laine; Synthesis and Reaction of Janus Prisms, Masafumi Unno; Investigation of Hydrogen-Bonding Ability of 1,3-Disiloxanediols and Polyhedral Oligomeric Silsesquioxanes with Applications for Catalysis, Kayla Diemoz; Evolution of the Photoluminescence Properties of Colloidal Silicon Nanoparticles over Time and with Environmental Changes, Andrea Goforth; Novel Synthesis of Spirocyclic Silicones and Subsequent Branching, Jennifer Morgan; Study of Polydimethy
Asymmetric Hydrogenation of Protected Allylic Amines (2010)

A general method for the enantioselective hydrogenation of protected allylic amine derivatives is described. This procedure relies on the generation of a cationic ruthenium complex with the axially chiral ligand (-)-TMBTP. The utility is highlighted by the highly enantioselective hydrogenation of a diene substrate that can then be elaborated to prepare Telcagepant, a compound currently in Phase III clinical trials. The scope of the hydrogenation reaction was studied, and a variety of substituted allylic amine derivatives could be hydrogenated with enantiomeric ratios of 92:8 or higher.
Cross neutralization of emerging SARS-CoV-2 variants of concern by antibodies targeting distinct epitopes on spike (2021)

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have arisen that exhibit increased viral transmissibility and partial evasion of immunity induced by natural infection and vaccination. To address the specific antibody targets that were affected by recent viral variants, we generated 43 monoclonal antibodies (mAbs) from 10 convalescent donors that bound three distinct domains of the SARS-CoV-2 spike. Viral variants harboring mutations at K417, E484 and N501 could escape most of the highly potent antibodies against the receptor binding domain (RBD). Despite this, we identified 12 neutralizing mAbs against three distinct regions of the spike protein that neutralize SARS-CoV-2 and the variants of concern, including B.1.1.7 (alpha), P.1 (gamma) and B.1.617.2 (delta). Notably, antibodies targeting distinct epitopes could neutralize discrete variants, suggesting different variants may have evolved to disrupt the binding of particular neutralizing antibody classes. These results underscore that humans exposed to wildtype (WT) SARS-CoV-2 do possess neutralizing antibodies against current variants and that it is critical to induce antibodies targeting multiple distinct epitopes of the spike that can neutralize emerging variants of concern.
Immobilization of π-Assembled Metallo-Supramolecular Arrays in Thin Films: From Crystal-Engineered Structures to Processable Materials (2001)

Layer-by-layer deposition of π-assembled arrays of discrete metallo units with aryl tails and polystyrenesulfonate gives structurally well-defined thin films. The formation of these films, which is controlled by π-π interactions, metal-ion coordination, and electrostatic interactions, bridges the gap between supramolecular crystal engineering and design of layered materials.