gebhart/patrepeval huggingface dataset:
SARS-CoV-2 variants resist antibody neutralization and broaden host ACE2 usage (2021)

Abstract New SARS-CoV-2 variants continue to emerge from the current global pandemic, some of which can replicate faster and with greater transmissibility and pathogenicity. In particular, UK501Y.V1 identified in UK, SA501Y.V2 in South Africa, and BR501Y.V3 in Brazil are raising serious concerns as they spread quickly and contain spike protein mutations that may facilitate escape from current antibody therapies and vaccine protection. Here, we constructed a panel of 28 SARS-CoV-2 pseudoviruses bearing single or combined mutations found in the spike protein of these three variants, as well as additional nine mutations that within or close by the major antigenic sites in the spike protein identified in the GISAID database. These pseudoviruses were tested against a panel of monoclonal antibodies (mAbs), including some approved for emergency use to treat SARS-CoV-2 infection, and convalescent patient plasma collected early in the pandemic. SA501Y.V2 pseudovirus was the most resistant, in magnitude and breadth, against mAbs and convalescent plasma, followed by BR501Y.V3, and then UK501Y.V1. This resistance hierarchy corresponds with Y144del and 242-244del mutations in the N-terminal domain as well as K417N/T, E484K and N501Y mutations in the receptor binding domain (RBD). Crystal structural analysis of RBD carrying triple K417N-E484K-N501Y mutations found in SA501Y.V2 bound with mAb P2C-1F11 revealed a molecular basis for antibody neutralization and escape. SA501Y.V2 and BR501Y.V3 also acquired substantial ability to use mouse and mink ACE2 for entry. Taken together, our results clearly demonstrate major antigenic shifts and potentially broadening the host range of SA501Y.V2 and BR501Y.V3, which pose serious challenges to our current antibody therapies and vaccine protection.
The Effects of Fuels on Diesel Oxidation Catalyst Performance and the Physical, Chemical, and Biological Character of Diesel Particulate Emissions (1981)

<div class="htmlview paragraph">The effect of fuel changes on diesel oxidation catalyst performance was studied by comparing the physical, chemical and biological character of the particulate emissions using three different fuels. Baseline (uncatalyzed) emissions were also compared for these same fuels. The fuels used for this study were: a typical No. 2 fuel, a No. 1 fuel, and a shale oil-derived diesel fuel. Comparisons of NO<sub>X</sub>, NO, NO<sub>2</sub>, HC and particulate mass emissions using each fuel were made using selected modes from the EPA 13 mode cycle. Changes in the chemical and biological character of the soluble organic fraction (SOF) were also studied. Fuel properties, most notably fuel sulfur content, were found to affect the performance of the oxidation catalyst used. Fuel sulfur content should be kept as low as possible if catalytic converters are used on diesel powered equipment.</div>
tPA-S481A Prevents Neurotoxicity of Endogenous tPA in Traumatic Brain Injury (2012)

Traumatic brain injury (TBI) is associated with loss of autoregulation due to impaired responsiveness to cerebrovascular dilator stimuli, which leads to cerebral hypoperfusion and neuronal impairment or death. Upregulation of tissue plasminogen activator (tPA) post-TBI exacerbates loss of cerebral autoregulation and NMDA-receptor-mediated impairment of cerebral hemodynamics, and enhances excitotoxic neuronal death. However, the relationship between NMDA-receptor activation, loss of autoregulation, and neurological dysfunction is unclear. Here, we evaluated the potential therapeutic efficacy of a catalytically inactive tPA variant, tPA S481A, that acts by competing with wild-type tPA for binding, cleavage, and activation of NMDA receptors. Lateral fluid percussion brain injury was produced in anesthetized piglets. Pial artery reactivity was measured via a closed cranial window, and cerebrospinal fluid (CSF) extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) was quantified by enzyme-linked immunosorbent assay (ELISA). tPA-S481A prevented impairment of cerebral autoregulation and reduced histopathologic changes after TBI by inhibiting upregulation of the ERK isoform of MAPK. Treatment with this tPA variant provides a novel approach for limiting neuronal toxicity caused by untoward NMDA-receptor activation mediated by increased tPA and glutamate following TBI.
Turing equivalence of neural networks with second order connection weights (2002)

In principle, a potentially infinitely large neural network (either in number of neurons or in the precision of a single neural activity) could possess an equivalent computational power to a Turing machine. The authors show such an equivalence of Turing machines to several explicitly constructed neural networks. It is proven that for any given Turing machine there exists a recurrent neural network with local, second-order, and uniformly connected weights (i.e., the weights connecting the second-order product of local 'input neurons' with their corresponding 'output neurons') which can simulate it. The numerical implementation and learning of such a neural Turing machine are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Differential Effects of Depleting versus Programming Tumor-Associated Macrophages on Engineered T Cells in Pancreatic Ductal Adenocarcinoma (2019)

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy resistant to therapies, including immune-checkpoint blockade. We investigated two distinct strategies to modulate tumor-associated macrophages (TAM) to enhance cellular therapy targeting mesothelin in an autochthonous PDA mouse model. Administration of an antibody to colony-stimulating factor (anti-Csf1R) depleted Ly6C<sup>low</sup> protumorigenic TAMs and significantly enhanced endogenous T-cell intratumoral accumulation. Despite increasing the number of endogenous T cells at the tumor site, as previously reported, TAM depletion had only minimal impact on intratumoral accumulation and persistence of T cells engineered to express a murine mesothelin-specific T-cell receptor (TCR). TAM depletion interfered with the antitumor activity of the infused T cells in PDA, evidenced by reduced tumor cell apoptosis. In contrast, TAM programming with agonistic anti-CD40 increased both Ly6C<sup>high</sup> TAMs and the intratumoral accumulation and longevity of TCR-engineered T cells. Anti-CD40 significantly increased the frequency and number of proliferating and granzyme B<sup>+</sup> engineered T cells, and increased tumor cell apoptosis. However, anti-CD40 failed to rescue intratumoral engineered T-cell IFNγ production. Thus, although functional modulation, rather than TAM depletion, enhanced the longevity of engineered T cells and increased tumor cell apoptosis, ultimately, anti-CD40 modulation was insufficient to rescue key effector defects in tumor-reactive T cells. This study highlights critical distinctions between how endogenous T cells that evolve <i>in vivo</i>, and engineered T cells with previously acquired effector activity, respond to modifications of the tumor microenvironment.
Randomized phase 2 study of otlertuzumab and bendamustine <i>versus</i> bendamustine in patients with relapsed chronic lymphocytic leukaemia (2016)

Otlertuzumab (TRU-016) is a humanized anti-CD37 protein therapeutic that triggers direct caspase-independent apoptosis of malignant B cells and induces antibody-dependent cell-mediated cytotoxicity. Patients with relapsed chronic lymphocytic leukaemia (CLL) received either otlertuzumab (20 mg/kg) weekly by IV infusion for two 28-day cycles then every 14 days for four 28-day cycles and IV bendamustine (70 mg/m<sup>2</sup> ) on Days 1 and 2 of each cycle for up to six 28-day cycles or bendamustine alone. Thirty-two patients were treated with otlertuzumab and bendamustine and 33 with bendamustine alone. Overall response rate according to the International Workshop on Chronic Lymphocytic Leukaemia criteria was 69% in the otlertuzumab and bendamustine arm and 39% in the bendamustine alone arm (P = 0·025). Median progression-free survival (PFS) was 15·9 months in the otlertuzumab and bendamustine arm and 10·2 months in the bendamustine alone arm (P = 0·0192). There was a higher incidence of pyrexia (34% vs. 12%) and neutropenia (59% vs. 39%) with the combination but this did not result in a higher incidence of severe (grade 3/4) infections (13% vs. 27%). This combination significantly increased the response rate and prolonged the PFS over single agent bendamustine in patients with relapsed or refractory CLL.
The Effect of Physician Behavior on the Collection of Data (1984)

Determining the patient's major reasons for seeking care is of critical importance in a successful medical encounter. To study the physician's role in soliciting and developing the patient's concerns at the outset of a clinical encounter, 74 office visits were recorded. In only 17 (23%) of the visits was the patient provided the opportunity to complete his or her opening statement of concerns. In 51 (69%) of the visits the physician interrupted the patient's statement and directed questions toward a specific concern; in only 1 of these 51 visits was the patient afforded the opportunity to complete the opening statement. In six (8%) return visits, no solicitation whatever was made. Physicians play an active role in regulating the quantity of information elicited at the beginning of the clinical encounter, and use closed-ended questioning to control the discourse. The consequence of this controlled style is the premature interruption of patients, resulting in the potential loss of relevant information.
A Survey of Traction Control and Antilock Braking Systems of Full Electric Vehicles With Individually Controlled Electric Motors (2014)

Wheel slip control for ground vehicles with individually controlled electric motors can be realized with strategies that can significantly differ from the conventional antilock braking system (ABS) and traction control (TC) system. This paper provides a review of state-of-the-art technology and recent developments in TC and ABSs using the actuation of electric motors. Particular attention is paid to the realization of slip estimators, the formalization of torque demand, and the control methods applied for the implementation of TC and ABSs. The performed analysis allowed for the differentiation of several most elaborated methods for slip and torque control and defining still imperfectly investigated problems to be covered by the further development of TC and ABSs for full electric vehicles.
DAP: Dynamic Address Assignment Protocol in Mobile Ad-hoc Networks (2007)

In general IP networks, addresses can be assigned to hosts manually by a network administrator or automatically by a DHCP server. Mobile ad-hoc network (MANET), which is a self-configuring network, is the union of mobile hosts that form an arbitrary topology. Most research related to the MANET assumes that host's IP address is configured, prior to the node joining the MANET. However, it is impossible that a network administrator or DHCP server configures host IP addresses in MANETs because there is no infra-structure. For this reason, a dynamic address management protocol is essential in MANETs. Thus, this paper proposes a novel self-configuring address management protocol, referred to as DAP (distributed address pool), in which IP addresses can be dynamically allocated to a newly-joined host in MANETs with no network infra-structure. In DAP, every host in a MANET has a unique IP address pool (a set of unused addresses that will be used for new joined hosts in MANETs) and address assignments are performed locally in the host. The advantage of this method is that it does not generate any broadcasting messages and, in turn, address allocation time can be significantly reduced. From our simulations, DAP showed a superior performance to a random address allocation scheme (RADA) in terms of both address allocation time and message exchange overhead.
Solution Growth of <i>p</i>-Type 4H-SiC Bulk Crystals with Low Resistivity (2014)

P-type 4H-SiC bulk crystals have been grown at a high growth rate of 1.0 mm/h by solution growth using Si-Cr-Al based melt. The crystals grown from solution with an Al content of 10at% show low resistivity of 35 mcm, which is two orders of magnitude lower than commercialwafers (Resistivity: 2500 mcm). The low-resistivity crystals have flat surface and few solvent inclusions. These results indicate that solution growth is a suitable method for fabricating low-resistivity p-type substrates with low cost.
The virtual data grid: a new model and architecture for data-intensive collaboration (2003)

It is increasingly common to encounter communities engaged in the collaborative analysis and transformation of large quantities of data over extended periods of time. I argue that these communities require a scalable system for managing, tracing, exploring and communicating the derivation and analysis of diverse data objects. Such a system could bring significant productivity increases facilitating discovery, understanding, assessment, and sharing of both data and transformation resources for computation, storage, and collaboration. I define a model and architecture for a virtual data grid capable of addressing these requirements. I define a broadly applicable model of a "typed dataset" as the unit of derivation tracking, and simple constructs for describing how datasets are derived from transformations and from other datasets. I also define mechanisms for integrating with, and adapting to, existing data management systems and transformation and analysis tools, as well as grid mechanisms for distributed resource management and computation planning. Finally, I report on successful application results obtained with a prototype implementation called Chimera, involving challenging analysis of high-energy physics and astronomy data.
Immunization with a Mixture of HIV Env DNA and VLP Vaccines Augments Induction of CD8 T Cell Responses (2010)

The immune response induced by immunization with HIV Env DNA and virus-like particle (VLP) vaccines was investigated. Immunization with the HIV Env DNA vaccine induced a strong CD8 T cell response but relatively weak antibody response against the HIV Env whereas immunization with VLPs induced higher levels of antibody responses but little CD8 T cell response. Interestingly, immunization with a mixture the HIV Env DNA and VLP vaccines induced enhanced CD8 T cell and antibody responses. Further, it was observed that the mixing of DNA and VLP vaccines during immunization is necessary for augmenting induction of CD8 T cell responses and such augmentation of CD8 T cell responses was also observed by mixing the HIV Env DNA vaccine with control VLPs. These results show that immunization with a mixture of DNA and VLP vaccines combines advantages of both vaccine platforms for eliciting high levels of both antibody and CD8 T cell responses.
High resolution microscopic mapping of DNA using multicolor fluorescent hybridization (1995)

We describe a procedure for microscopically mapping the relative positions of DNA probes along extended strands of DNA. The procedure referred to as direct visual hybridization (DIRVISH) DNA mapping involves the simultaneous hybridization of multiple probes and the fluorescent colors, red green and blue to produce images that convey high-resolution mapping information. The images appear as long strings of fluorescent signals positioned as they are in the genome. A visual multi-color map is generated within 2 days. Cosmid probes span a distance of 10 microms or more and have been observed to contain patterns within the strings of signals. We have developed computer imaging programs to scan through the strings of signals and plot the intensities. Scans through multiple signal strings for one cosmid probe revealed consistent patterns. We have interpreted the patterns as the result of suppression of repetitive DNA sequence hybridization. These patterns may prove useful as fingerprints for regions of DNA.
Rational Design and Synthesis of an Orally Active Indolopyridone as a Novel Conformationally Constrained Cannabinoid Ligand Possessing Antiinflammatory Properties (2003)

A series of unique indazoles and pyridoindolones have been rationally designed and synthesized as novel classes of cannabinoid ligands based on a proposed bioactive amide conformation. This has led to the discovery of the novel indolopyridone 3a as a conformationally constrained cannabinoid ligand that displays high affinity for the CB2 receptor (K(i)(CB2) = 1.0 nM) and possesses antiinflammatory properties when administered orally in an in vivo murine inflammation model.
An improved weighted signal averaging method for high-resolution ECG signals (2002)

Proposes a new technique to estimate the coefficients for the weighted averaging of high-resolution ECG (HRECG) records. The purpose was to minimize the number of beats to average in records contaminated with non-stationary noise. The following averaging methods were studied: (1) linear averaging of all beats (LA), (2) linear averaging rejecting very noisy beats (RA), and (3) weighted averaging (WA). For WA, two techniques for noise variance estimation in each beat were analysed: (a) a noise estimation in a 60-ms window on the ST segment (WA-W), and (b) a new algorithm that estimates the noise variance from the difference signal obtained by subtracting the averaged beat from the individual beat (WA-D). All methods were tested in simulated HRECG records contaminated with several types of noise. We conclude that WA methods minimize the number of averaged beats compared with the LA and RA methods in situations of non-stationary noise. However, the proposed WA-D method shows a higher effectiveness than the WA-W method due to a better estimation of the noise variance in individual beats.
Integrating State-of-the-Art CNNs for Multi-Sensor 3D Vehicle Detection in Real Autonomous Driving Environments (2019)

This paper presents two new approaches to detect surrounding vehicles in 3D urban driving scenes and their corresponding Bird's Eye View (BEV). The proposals integrate two state-of-the-art Convolutional Neural Networks (CNNs), such as YOLOv3 and Mask-RCNN, in a framework presented by the authors in [1] for 3D vehicles detection fusing semantic image segmentation and LIDAR point cloud. Our proposals take advantage of multimodal fusion, geometrical constrains, and pre-trained modules inside our framework. The methods have been tested using the KITTI object detection benchmark and comparison is presented. Experiments show new approaches improve results with respect to the baseline and are on par with other competitive state-of-the-art proposals, being the only ones that do not apply an end-to-end learning process. In this way, they remove the need to train on a specific dataset and show a good capability of generalization to any domain, a key point for self-driving systems. Finally, we have tested our best proposal in KITTI in our driving environment, without any adaptation, obtaining results suitable for our autonomous driving application.
Hand-portable Capillary Liquid Chromatography Instrumentation (2015)

This dissertation focuses on the development of hand-portable capillary liquid chromatography (LC) instrumentation. In this work, battery-operable nano-flow pumping systems (isocratic and gradient) were developed and integrated with portable UV-absorption detectors for capillary LC. The systems were reduced in size to acceptable weights and power usage for field operation. A major advantage of the pumps is that they do not employ a splitter, since they were specifically designed for capillary column use, thereby greatly reducing solvent consumption and waste generation. UV-absorption detectors were specifically designed and optimized for on-column detection to minimize extra-column band broadening. Initially, an isocratic nano-flow pumping system with a stop-flow injector was integrated with an on-column UV-absorption detector (254 nm). The pumping system gave excellent flow rate accuracy (<99.94%) and low percent injection carry-over (RSD 0.31%) suitable for quantitative analysis. Using sodium anthraquinone-2-sulfonate, the detector gave an LOD (S/N = 3) of 0.13 µM, which was 12 times lower than a commercial UV-absorption detector. Reversed-phase separations of a homologous series of alkyl benzenes was demonstrated. Further miniaturization of UV-absorption detection was accomplished using a 260 nm deep UV LED. The detector was small in size and weighed only 85 g (without electronics). No optical reference was included due to the low drift in the signal. Two ball lenses, one of which was integrated with the LED, were used to increase light throughput through the capillary column. Stray light was minimized by the use of a band-pass filter and an adjustable slit. Signals down to the ppb level (nM) were easily detected with a short-term noise level of 4.4 µAU, confirming a low limit of detection and low noise. The detection limit for adenosine-5'-monophosphate was 230 times lower than any previously reported values. Isocratic separations of phenolic compounds were performed using a poly(ethylene glycol) diacrylate monolithic capillary column. Finally, a novel nano-flow gradient generator integrated with a stop-flow injector was developed. Gradient performance was found to be excellent for gradient step accuracy (RSD < 1.2%, n = 4) and linear gradient reproducibility (RSD < 1.42%, n = 4). Separations of five phenols were demonstrated using the nano-flow gradient system. Efforts to develop a 405 nm laser diode-based UV-absorption detector for hemoglobin analysis were described.
Lightning strike protection of aircraft structural joints (2014)

Lightning protection of aircraft has been a topic considered by the aerospace industry for many years. Protection principles are well defined for traditional metallic aircraft; however, the move to using novel materials for structural components has produced new challenges for the aerospace industry. Surface damage to CFRP wing skin is commonly addressed by the introduction of a highly conductive surface layer. An additional concern is the potential for sparking within the fuel tank as a result of a lightning strike to a fastened CFRP joint. The paper describes the sparking joint problem and the corresponding certification requirements. It reviews current understanding of the sparking phenomenology and suggests the future direction for the development of lightning strike protection.
Resistive-Polymer Versus Forced-Air Warming: Comparable Efficacy in Orthopedic Patients (2010)

RP warming performed as efficiently as FA warming in patients undergoing orthopedic surgery.
Evaluation of a novel choanoid fluidized bed bioreactor for future bioartificial livers (2014)

The CFBB can function as a bioartificial liver based on a bioreactor. The efficacy of this novel bioreactor is promising for the study of liver failure.
Magnetic resonance imaging of musculoskeletal trauma. (1986)

Magnetic resonance imaging has unique capabilities for evaluating musculoskeletal trauma. It can clearly delineate tears and hemorrhage in muscles, ligaments, and tendons and can provide clinically useful information in patients with joint injuries. Other developing applications include evaluation of compartment syndromes, injuries of peripheral nerves and blood vessels, and chronic sequelae of trauma. If a correct technical approach is employed, MRI has a clinical role that is complementary to other imaging modalities.