gebhart/patrepeval huggingface dataset:
Revolution: In communication; in education (2014)

Radical change is being demanded of engineering education today–the result of the electronic-information revolution. Other information revolutions have occurred in the past; and each has led to radical changes in education. We look at some of these, giving particular attention to the little-recognized fast press revolution of the early 19th century. Perhaps these examples will help us to better see, and cope with, present change.
Ultrasound Modulates the Splenic Neuroimmune Axis in Attenuating AKI (2015)

We showed previously that prior exposure to a modified ultrasound regimen prevents kidney ischemia-reperfusion injury (IRI) likely via the splenic cholinergic anti-inflammatory pathway (CAP) and α7 nicotinic acetylcholine receptors (α7nAChR). However, it is unclear how ultrasound stimulates the splenic CAP. Further investigating the role of the spleen in ischemic injury, we found that prior splenectomy (-7d) or chemical sympathectomy of the spleen with 6-hydroxydopamine (6OHDA; -14d) exacerbated injury after subthreshold (24-minute ischemia) IRI. 6-OHDA-induced splenic denervation also prevented ultrasound-induced protection of kidneys from moderate (26-minute ischemia) IRI. Ultrasound-induced protection required hematopoietic but not parenchymal α7nAChRs, as shown by experiments in bone marrow chimeras generated with wild-type and α7nAChR(-/-) mice. Ultrasound protection was associated with reduced expression of circulating and kidney-derived cytokines. However, splenocytes isolated from mice 24 hours after ultrasound treatment released more IL-6 ex vivo in response to LPS than splenocytes from sham mice. Adoptive transfer of splenocytes from ultrasound-treated (but not sham) mice to naïve mice was sufficient to protect kidneys of recipient mice from IRI. Ultrasound treatment 24 hours before cecal ligation puncture-induced sepsis was effective in reducing plasma creatinine in this model of AKI. Thus, splenocytes of ultrasound-treated mice are capable of modulating IRI in vivo, supporting our ongoing hypothesis that a modified ultrasound regimen has therapeutic potential for AKI and other inflammatory conditions.
Nucleation-Dependent Polymerization Is an Essential Component of Amyloid-Mediated Neuronal Cell Death (2005)

Accumulating evidence suggests that amyloid protein aggregation is pathogenic in many diseases, including Alzheimer's disease. However, the mechanisms by which protein aggregation mediates cellular dysfunction and overt cell death are unknown. Recent reports have focused on the potential role of amyloid oligomers or protofibrils as a neurotoxic form of amyloid-beta (Abeta) and related amyloid aggregates. Here we describe studies indicating that overt neuronal cell death mediated by Abeta(1-40) is critically dependent on ongoing Abeta(1-40) polymerization and is not mediated by a single stable species of neurotoxic aggregate. The extent and rate of neuronal cell death can be controlled by conditions that alter the rate of Abeta polymerization. The results presented here indicate that protofibrils and oligomeric forms of Abeta most likely generate neuronal cell death through a nucleation-dependent process rather than acting as direct neurotoxic ligands. These findings bring into question the use of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide formazan assay (MTT assay) as a reporter of Abeta-mediated neuronal cell death and suggest that diffusible Abeta protofibrils and oligomers more likely mediate subtle alterations of synaptic function and long-term potentiation rather than overt neuronal cell death. These results have been extended to Abeta(1-42), the non-Abeta component of Alzheimer's disease amyloid plaques, and human amylin, suggesting that nucleation-dependent polymerization is a common mechanism of amyloid-mediated neuronal cell death. Our findings indicate that ongoing amyloid fibrillogenesis may be an essential mechanistic process underlying the pathogenesis associated with protein aggregation in amyloid disorders.
Ecological memory of prior nutrient exposure in the human gut microbiome (2021)

Abstract Many ecosystems retain an ecological memory of past conditions that affects responses to future stimuli. However, it remains unknown what mechanisms and dynamics may govern such a memory in microbial communities. Here, in both a human dietary intervention cohort and an artificial gut, we show that the human gut microbiome encodes a memory of past carbohydrate exposures. Changes in the relative abundance of primary degraders were sufficient to enhance metabolism, and these changes were mediated by transcriptional changes within hours of initial exposure. We further found that ecological memory of one carbohydrate species impacted metabolism of others. These findings demonstrate that the human gut microbiome’s metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. One Sentence Summary Recent nutrient exposures are encoded into the structure and activity of human gut microbial communities, which enables more efficient future metabolic responses.
Potential adjuvantic properties of innate immune stimuli (2009)

Toll-like receptors (TLRs) are a family of conserved pattern recognition receptors (PRRs) that recognize pathogen associated molecular patterns and serve as primary sensors of the innate immune system. Ten members of the TLR family have so far been identified in the human genome. The ligands for these receptors are structurally highly conserved microbial molecules such as lipopolysaccharides (LPS) (recognized by TLR4), lipopeptides (TLR2 in combination with TLR1 or TLR6), flagellin (TLR5), single stranded RNA (TLR7 and TLR8), double-stranded RNA (TLR3), CpG motif-containing DNA (TLR9) and profilin present on uropathogenic bacteria (TLR 11). Complementing the TLRs are the nucleotide-binding domain (NOD), leucine rich repeat containing family (or Nod-like Receptors, NLRs), which detect muramylpeptides released from bacterial peptidoglycan (PGN) in the intracytoplasmic compartment, as well as the retinoic-acid-inducible protein 1 (RIG-I-like receptors; RLRs) which sense single-stranded RNA of viral origin. The activation of PRRs by their cognate ligands leads to production of inflammatory cytokines, upregulation of MHC molecules and co-stimulatory signals in antigen-presenting cells as well as activating natural killer cells, in addition to priming and amplifying antigen-specific T-, and B-cell effector functions. Thus, these stimuli serve to link innate and adaptive immunity and can therefore be exploited as powerful adjuvants in eliciting both primary and anamnestic immune responses. This review summarizes what is currently known about the immunopotentiatory and adjuvantic activities of innate immune stimuli.
The predictability of acoustic receptions on gliders in the Arctic (2017)

Acoustic transmissions from shallow sources in the Arctic Ocean can propagate several hundred kilometers due to the presence of an Arctic acoustic duct. Receptions of these long-range transmissions are complex patterns of arrivals which are strongly dependent upon upper ocean sound-speed structure. In addition to measuring sound-speed parameters, gliders equipped with acoustic recorders can measure these arrivals and can complement moored receptions, providing data at many ranges with respect to the moored sources. There is a higher degree of uncertainty in glider position compared with moored receivers, but localization can be improved in post-processing with enhanced acoustic predictability. Two acoustic Seagliders were deployed for a short pilot study in late Summer 2016 in the vicinity of an array of acoustic tomography sources with frequencies on the order of 250 Hz in the Arctic Ocean in anticipation of a longer deployment in Summer 2017. Source receptions recorded on the gliders are compared with acoustic predictions based on sound-speed profiles generated from environmental data collected on the gliders themselves to begin to understand the predictability of transmissions received on gliders in an Arctic environment. Acoustic predictions are analyzed for receptions both within the acoustic duct and at depths exceeding the acoustic duct.
Nongenomic Actions of 1,25-Dihydroxyvitamin D3in Rat Osteosarcoma Cells: Structure-Function Studies Using Ligand Analogs* (1991)

Osteoblast-like osteosarcoma cells (ROS 17/2.8) display a rapid transmembrane influx of extracellular calcium after stimulation by 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3] that is mediated largely by the opening of voltage-gated calcium channels. These cells also constitutively express high numbers (greater than 18,000/cell) of nuclear receptors for this seco-steroid hormone that are involved in the modulation of genomic activity in the osteoblast and in the up-regulation of transcript ion of osteoblast-specific genes such as osteocalcin. The objective of this study was to determine the structural hierarchy of vitamin D3 analogs with regard to their efficacy as molecular transducers of the genomic and nongenomic pathways that are activated upon treatment of osteoblasts with 1,25-(OH)2D3. To test the structural features of the agonist required for initiation of these distinct pathways, a series of ligand analogs and naturally occurring metabolites of 1,25-(OH)2D3 were used that contain A-ring, D-ring, and side-chain modifications. The abilities of these analogs/metabolites to 1) bind to nuclear receptors and 2) stimulate transmembrane calcium influx were measured. Several analogs (25-hydroxy-16-ene-23-yne-D3 and 25-hydroxy-23-yne D3) were found to stimulate Ca2+ channel opening, but bind only poorly to the 1,25-(OH)2D3 nuclear receptor. Conversely, other analogs (1,24-dihydroxy-22-ene-24-cyclopropyl D3 and 1,25-dihydroxy-16-ene-23-yne,26,27 F6-D3) were found to bind very well to the nuclear receptor, but displayed little or no activity in opening Ca2+ channels. Pertussis toxin, which interferes with coupling of certain ligand-gated receptors to ion channels, failed to block the activation of calcium channels by 1,25-(OH)2D3 or active agonist analogs. Our results indicate that there are likely to be distinct nuclear and plasma membrane-associated forms of the 1,25-(OH)2D3 receptor that are involved in genomic and nongenomic activation of osteoblast activity, respectively. The membrane-associated receptors do not appear to be coupled to pertussis toxin-sensitive G-proteins.
Surgical and interventional palliative treatment of upper gastrointestinal malignancies (2000)

Malignancies of the upper gastrointestinal tract, including the oesophagus, stomach, liver, bile ducts and pancreas, are highly virulent diseases. While curative therapies relieve symptoms caused by these cancers, most of these treatments prove unsuccessful in the control of tumour due to occult residual disease. This review covers only planned palliative procedures for these conditions where patient factors (e.g. performance status or patient wishes) or tumour factors (e.g. locally advanced or known metastatic disease) prevent potentially curative intervention. For most patients, palliation of luminal obstruction, pain or other symptoms is the most worthwhile treatment that can be offered with present therapies.
Posterior Cervical Spine Fixation (1993)

Neurological Surgery, University of Florida, College of Medicine, P.O. Box 100265, Gainesville, FL 32610
A Flow-Based Approach to Vehicle Detection and Background Mosaicking in Airborne Video (2005)

In this work, we address the detection of vehicles in a video stream obtained from a moving airborne platform. We propose a Bayesian framework for estimating dense optical flow over time that explicitly estimates a persistent model of background appearance. The approach assumes that the scene can be described by background and occlusion layers, estimated within an expectation-maximization framework. The mathematical formulation of the paper is an extension of the work in (H. Yalcin et al., 2005) where motion and appearance models for foreground and background layers are estimated simultaneously in a Bayesian framework.
Conformational Effects on the Electron‐Transfer Efficiency in Peptide Foldamers Based on α,α‐Disubstituted Glycyl Residues (2008)

Peptide foldamers based on alpha,alpha-disubstituted glycyl residues were synthesized and chemically characterized to investigate the effects of the electric field generated by a 3(10)-helix on the rate of intramolecular photoinduced electron-transfer reactions. To this end, two new octapeptides having identical sequences were suitably side-chain functionalized with the same electron-transfer donor-acceptor pair, but inverting the position of the pair along the main chain. The electron-transfer rate constants, measured by time-resolved spectroscopy techniques (nanosecond transient absorption and time-resolved fluorescence), indicated that, in the case of the 3(10)-helix, the electrostatic effect is significant, but smaller than that obtained for alpha-helical peptides. This finding can be likely ascribed to the distortion of the H-bond network with respect to the helical axis taking place in the former secondary structure. Overall, these results could have implications on electron-transfer phenomena in model and biomembranes facilitated by peptaibiotics.
Bone morphogenetic proteins in total hip arthroplasty, osteonecrosis and trauma surgery (2008)

This review provides an overview of the use of bone morphogenetic proteins to enhance bone healing and bone graft incorporation in difficult defects created from failed total hip arthroplasties, osteonecrosis of the femoral head and trauma. Multiple publications have demonstrated that bone morphogenetic proteins are osteoinductive in preclinical trials (i.e., animal models); however, there is controversy and limited understanding of the use of this technology in orthopedic surgical practice. The question remains as to whether they are useful in difficult fractures, nonunions and large defects created from failed total hip arthroplasty or femoral head osteonecrosis. There might be a small risk for infection by the process of introducing foreign materials in a clinical situation, but this has not yet been realized to date. In addition, these materials offer an advantage in large defects where there is not enough transplantable material available from the host. We believe that the use of these materials will become more widespread with newer carriers, minimally invasive applications and diminished commercial costs.
One-Pot Synthesis of 2,5-Disubstituted Pyrimidines from Nitriles (2013)

A practical, one-step process for the synthesis of 2,5-disubstituted pyrimidines is presented. The protocol proved to be general for the synthesis of a variety of pyrimidine-containing compounds bearing an assortment of functional groups.
Abstract 5340: Impact of binding epitope and antigen size on the cytotoxic activity of MCSP-specific BiTE antibodies for treatment of melanoma (2010)

Abstract Melanoma chondroitin sulphate proteoglycan (MCSP; also called CSPG4, HMW-MAA, MSK16, MCSPG, MEL-CSPG, NG2, or gp240) is a surface antigen frequently expressed on human melanoma cells, which is involved in cell adhesion, invasion and spreading, angiogenesis, complement inhibition, and signalling. MCSP has therefore been frequently selected as target antigen for development of antibody- and vaccine-based therapeutic approaches. We have here used a large panel of monoclonal antibodies against human MCSP for generation of single-chain MCSP/CD3-bispecific antibodies of the BiTE (for bispecific T cell engager) class. BiTE antibodies can transiently connect the T cell receptor subunit CD3 on T cells with a surface antigen on target cells leading to a highly efficient redirected lysis of target cells. This involves cytolytic synapse formation and delivery of perforin and granzymes. BiTE-engaged T cells are capable of serial target cell lysis, and are not affected by immune escape mechanisms interfering with peptide antigen processing and presentation, or clonal T cell differentiation. Despite similar binding affinity to MCSP, respective BiTE antibodies greatly differed in their potency of redirected lysis of CHO target cells stably transfected with full-length human MCSP, MCSP deletion mutants or fusion proteins. BiTE antibodies binding to the membrane proximal domain D3 of MCSP were more potent than those binding to more distal domains. This epitope distance effect was corroborated with EpCAM/CD3-bispecific BiTE antibody MT110 by using MCSP/EpCAM fusion proteins as surface target antigens. Generally, CHO cells expressing small surface antigens were better lysed than those with large antigens, indicating that antigen size is also an important factor for BiTE potency. This is in line with the observation that target cell lysis by membrane proximally-binding BiTE antibodies improved upon omission of more distal MCSP domains. The present study for the first time relates the size of surface antigens and positioning of binding domains to BiTE potency of target cell lysis via redirected cytotoxic T cells. In case of the MCSP antigen, this provides the basis for selection of a maximally potent BiTE antibody candidate for development of a novel melanoma therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5340.
Fig. S6 from Small-Molecule–Mediated Stabilization of PP2A Modulates the Homologous Recombination Pathway and Potentiates DNA Damage-Induced Cell Death (2023)

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FPN Sources in Bolometric Infrared Detectors (2009)

Low manufacturing cost and ease of use favor spreading of 2-D bolometric infrared detector arrays over various application domains such as predictive maintenance, medical imaging, automotive industry, and security. The infrared detector's main figure of merit has long been the noise equivalent temperature difference (NETD), which sets the minimum temperature difference distinguishable from background noise at sensor output. However, while nowadays uncooled detectors have achieved sufficient NETD, fixed pattern noise (FPN) is indeed becoming a crucial figure of merit especially when the focal plane array (FPA) is not regulated by a thermoelectric cooler (TEC). In this paper, we study the various sources of dispersion of infrared bolometric detectors and their respective impact on FPN in the resulting image. We propose an analytical model to identify main sources of nonuniformity, and the confrontation of results with actual measurements leads to the ability of a highly accurate on-chip thermal drift compensation.
Identification of the E1A-Regulated Transcription Factor p120E4F as an Interacting Partner of the RASSF1A Candidate Tumor Suppressor Gene (2004)

Epigenetic inactivation of the candidate tumor suppressor gene RASSF1A is a frequent and critical event in the pathogenesis of many human cancers. The RASSF1A protein contains a Ras association domain, suggesting a role in Ras-like signaling pathways, and has also been implicated in cell cycle progression. However, the preliminary data suggests that the RASSF1A gene product is likely to have multiple functions. To identify novel RASSF1A functions, we have sought to identify interacting proteins by yeast two-hybrid analysis in a human brain cDNA library. We identified the E1A-regulated transcription factor p120(E4F) as a RASSF1A interacting partner in yeast and mammalian cells, and demonstrated that RASSF1A protein and p120(E4F) form a complex in vivo. The interaction between RASSF1A and p120(E4F) was confirmed by both in vitro and in vivo pull downs and coimmunoprecipitation assays. In addition, specific inactivation of RASSF1A by short interfering RNA disrupts binding of RASSF1A to p120(E4F) in coimmunoprecipitation assays. In addition, we demonstrated enhanced G(1) cell cycle arrest and S phase inhibition by propidium iodide staining of p120(E4F) in the presence of RASSF1A. As p120(E4F) has been reported previously to interact with p14ARF, retinoblastoma, and p53, these findings provide an important link between the function of RASSF1A and other major human tumor suppressor genes.
Prospective feasibility trial of radiotherapy target definition for head and neck cancer using 3-dimensional PET and CT imaging. (2004)

Inclusion of (18)F-FDG PET data resulted in modified target volumes in radiotherapy planning for HNC. PET and CT data acquired on separate, dedicated scanners may be coregistered for therapy planning; however, dual-acquisition PET/CT systems may be considered to reduce the need for reregistrations. It is possible to use IMRT to target dose to metabolically active sites based on coregistered PET/CT data.
Gene therapy for late infantile neuronal ceroid lipofuscinosis: neurosurgical considerations (2010)

The neurosurgical considerations and results of this study are presented to offer guidance and a basis for the design of future gene therapy or other clinical trials in children that utilize direct therapeutic delivery.
Real-time Concealed Weapon Detection on 3D Radar Images for Walk-through Screening System (2023)

This paper presents a framework for real-time concealed weapon detection (CWD) on 3D radar images for walk-through screening systems. The walk-through screening system aims to ensure security in crowded areas by performing CWD on walking persons, hence it requires an accurate and real-time detection approach. To ensure accuracy, a weapon needs to be detected irrespective of its 3D orientation, thus we use the 3D radar images as detection input. For achieving real-time, we reformulate classic U-Net based segmentation networks to perform 3D detection tasks. Our 3D segmentation network predicts peak-shaped probability map, instead of voxel-wise masks, to enable position inference by elementary peak detection operation on the predicted map. In the peak-shaped probability map, the peak marks the weapon’s position. So, weapon detection task translates to peak detection on the probability map. A Gaussian function is used to model weapons in the probability map. We experimentally validate our approach on realistic 3D radar images obtained from a walk-through weapon screening system prototype. Extensive ablation studies verify the effectiveness of our proposed approach over existing conventional approaches. The experimental results demonstrate that our proposed approach can perform accurate and real-time CWD, thus making it suitable for practical applications of walk-through screening.
Advanced High-Power-Density Interior Permanent Magnet Motor for Traction Applications (2014)

Electric drive systems, which include electric machines and power electronics, are a key enabling technology for advanced vehicle propulsion systems that reduce the petroleum dependence of the ground transportation sector. To have significant effect, electric drive technologies must be economical in terms of cost, weight, and size while meeting performance and reliability expectations. This paper will provide details of the design, analysis, and testing of an advanced interior permanent magnet (PM) machine that was developed to meet the FreedomCAR 2020 specifications. The 12-slot/10-pole machine has segmented stator structure equipped with fractional-slot nonoverlapping concentrated windings. The rotor has a novel spoke structure/assembly. Several prototypes with different thermal management schemes have been built and tested. This paper will cover the test results for all these prototypes and highlight the tradeoffs between the various schemes. Due to the high machine frequency (~1.2 kHz at the top speed), detailed analysis of various loss components and ways to reduce them will be presented. In addition, due to the high coolant inlet temperature and the fact that the machine is designed to continuously operate at 180 °C, detailed PM demagnetization analysis will be presented. The key novelty in this paper is the advanced rotor structure and the thermal management schemes.