gebhart/patrepeval huggingface dataset:
Wild ducks are the reservoir for only a limited number of influenza A subtypes (1993)

Analysis of cloacal samples collected from 12,321 wild ducks in Alberta, Canada, from 1976 to 1990 showed influenza A infections to be seasonal, with prevalences increasing as the population became increasingly more dense. Viruses with 3 haemagglutinin (H3, H4, and H6) and 3 neuraminidase subtypes (N2, N6, and N8) were found consistently to infect both adult and juvenile ducks each year, indicating that wild ducks may be a reservoir for these viruses. In contrast, viruses with 7 haemagglutinin (H2, H5, H7, H8, H9, H11, and H12) and 3 neuraminidase subtypes (N1, N3, and N4) were not found for prolonged periods during the study; when they were found, they primarily infected juveniles at moderate levels. Whilst wild ducks appear to perpetuate some influenza A viruses, they apparently do not act as a reservoir for all such viruses.
Implementation of scalable blocking locks using an adaptive thread scheduler (2002)

Blocking locks are commonly used in parallel programs to improve application performance and system throughput. However, most implementations of such locks suffer from two major problems-latency and scalability. We propose an implementation of blocking locks using scheduler adaptation which exploits the interaction between thread schedulers and locks. By experimentation using well-known multiprocessor applications on a KSR2 multiprocessor, we demonstrate how such an implementation considerably reduces the latency, and improves the scalability of blocking locks.
Computational simulations of local vascular heparin deposition and distribution (1996)

Local vascular drug delivery systems provide elevated concentrations in target arterial tissues while minimizing systemic side effects; however, definition of their precise pharmacokinetics remains elusive. The standard labeled tracer assays used in experimental vascular pharmacokinetic studies of these systems are limited because they quantify the arterial average drug concentration as opposed to transmural concentration profiles, require many animal experiments to elucidate the time-varying deposition, and track label rather than intact biologically active drug. In this study, computational simulations of drug deposition and distribution in vascular tissues after release from these systems have provided two important insights. First, simulations of arteries that were uniformly loaded with heparin predicted that most of the drug is cleared in &lt; 1 h, illustrating the need for sustained modes of delivery. Second, some of the limitations of labeled tracers can be over come by combining experimental data with simulations that provided high spatial resolution. This enabled us to describe the kinetics of the deposited drug and distinguish soluble from reversibly bound and internalized drug within cells. The latter can help differentiate biologically viable drug from its committed inactive form or metabolites. These points have been illustrated through simulations of a novel endovascular hydrogel heparin-delivery system that has been applied to the porcine coronary artery. The basic models used in these simulations are generalized, and with the appropriate boundary conditions, binding and distribution constants can be used to study the physical interactions between any compound and tissue.
Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects (2017)

We describe the clinical and whole genome sequencing (WGS) study of a non-consanguineous Italian family in which two siblings, a boy and a girl, manifesting a severe epileptic encephalopathy (EE) with skeletal abnormalities, carried novel SLC35A3 compound heterozygous mutations. Both siblings exhibited infantile spasms, associated with focal, and tonic vibratory seizures from early infancy. EEG recordings showed a suppression-burst (SB) pattern and multifocal paroxysmal activity in both. In addition both had quadriplegia, acquired microcephaly, and severe intellectual disability. General examination showed distal arthrogryposis predominant in the hands in both siblings and severe left dorso-lumbar convex scoliosis in one. WGS of the siblings-parents quartet identified novel compound heterozygous mutations in SLC35A3 in both children. SLC35A3 encodes the major Golgi uridine diphosphate N-acetylglucosamine transporter. With this study, we add SLC35A3 to the gene list of epilepsies. Neurological symptoms and skeletal abnormalities might result from impaired glycosylation of proteins involved in normal development and function of the central nervous system and skeletal apparatus.
Provably good global buffering by generalized multiterminal multicommodity flow approximation (2002)

To implement high-performance global interconnect without impacting the placement and performance of existing blocks, the use of buffer blocks is becoming increasingly popular in structured-custom and block-based application specified integrated circuit methodologies. We address the problem of how to perform the buffering of global multiterminal nets given an existing buffer block plan. We give provably good and heuristic algorithms for this problem. The method routes connections using available buffer blocks, such that required upper and lower bounds on buffer intervals are satisfied. In addition, the algorithms allow more than one buffer to be inserted into any given connection and observe upper bounds and parity constraints on the number of buffers per connection. Most importantly, and unlike previous works on the problem, we take into account: 1) multiterminal nets; 2) multiple routing layers; 3) simultaneous buffered routing and compaction; and 4) buffer libraries. Our method outperforms existing algorithms for the problem, based on two-pin decompositions of the nets, and has been validated on top-level layouts extracted from a recent high-end microprocessor design.
Location-Based Large-Scale Landmark Image Recognition Scheme for Mobile Devices (2012)

In this paper, we propose a location-based large-scale landmark image recognition scheme for mobile devices such as smart phones. To achieve this goal, we collected landmark images all around the world, which were available on the web. For each landmark, we detected interest points and constructed their feature descriptors using SURF. Next, we performed a statistical analysis on the local features to select representative points among them. Intuitively, the representative points of an object are the interest points that best characterize the object. Similar representative points are merged for filtering and fast matching purposes. These points are indexed using an R-tree based on GPS information. Our scheme is based on client-server architecture. When the user takes a picture of a landmark using a mobile device, the client module on the mobile device extracts the local features from the image and sends them to the server, along with location and other sensor data. For the query, the server searches its index using the location data first to find nearby landmarks and then compares their local features. Matched landmark images are sent back to the client. We implemented a prototype system and performed various experiments. Through experiments, we showed that our scheme achieves reasonable performance.
Structural Biology and the Design of Effective Vaccines for HIV-1 and Other Viruses (2010)

Structural biology provides a wealth of information about the three-dimensional organization and chemical makeup of proteins. An understanding of atomic-level structure offers enormous potential to design rationally proteins that stimulate specific immune responses. Yet current vaccine development efforts makes little use of structural information. At the Vaccine Research Center, a major goal is to apply structural techniques to vaccine design for challenging pathogens, that include human immunodeficiency virus type 1 (HIV-1) and other enveloped viruses such as influenza, Ebola, and respiratory syncytial viruses. Our three-part strategy involves 1.) the definition of the functional viral spike at the atomic level 2.) achieving a structural understanding of how neutralizing antibodies recognize the spike, and 3.) rational development of proteins that can elicit a specific antibody response. Overall, our strategy aims to incorporate information about viral spike-antibody interactions, to assimilate immunogenic feedback, and to leverage recent advances in immunofocusing and computational biology.
Simulation of the Manufacturing Process of Braided Composite Tubes for Realistic Microstructure Representation (2015)

In order to create representative numerical models of textile composite structures and their underlying microstructure, the braiding process of a composite tube made from a triaxial braided textile fabric is simulated. The tows are treated as a collection of representative fibers. The kinematics of the braiding process are modeled completely and the typical cross sectional shape of the tows emerge automatically. Then a procedure is outlined on how to convert the results of the braiding simulation to a solid mesh model that can be used for further structural investigations. The plausibility of the resulting model of the microstructure of a composite tube is shown through an example of a simple tension test.
Improved programming performance of EEPROM/flashcell using post-poly-Si gate N 2 O annealing (1999)

The effect of post poly-Si N2O annealing on the programming performance and reliability of split-gate source-side-injection EEPROM/flash memory cells has been investigated. It is found that by employing post-poly-Si gate N2O-annealing, the programming efficiency and the immunity to program disturbances can be significantly improved.
Abnormal interleukin 10Ralpha expression contributes to the maintenance of elevated cyclooxygenase-2 in non-small cell lung cancer cells. (2003)

Non-small cell lung cancer (NSCLC) cells are known to constitutively overexpress cyclooxygenase (COX)-2. Tumor COX-2-dependent production of PGE(2) triggers the synthesis of lymphocyte and macrophage interleukin (IL)-10 that, in turn, is known to potently suppress COX-2 in normal cells. Thus, we investigated the capacity of IL-10 to down-regulate COX-2 expression in NSCLC cells. Western blotting and ELISA analyses revealed that IL-10 did not affect COX-2 expression and subsequent PGE(2) production in NSCLC cells. Although normal human bronchial epithelial cells expressed both intracellular and membrane IL-10Ralpha, NSCLC cells only expressed intracellular but not cell surface membrane IL-10Ralpha. Unresponsiveness of COX-2 to IL-10 is due to the deficiency of IL-10Ralpha on the surface of NSCLC cells. Our findings highlight a novel mechanism contributing to maintenance of elevated COX-2 and PGE(2) in the lung tumor environment.
Jointly Optimal Rate Control and Relay Selection for Cooperative Wireless Video Streaming (2013)

Physical-layer cooperation allows leveraging the spatial diversity of wireless channels without requiring multiple antennas on a single device. However, most research in this field focuses on optimizing physical-layer metrics, with little consideration for network-wide and application-specific performance measures. This paper studies cross-layer design techniques for video streaming over cooperative networks. The problem of joint rate control, relay selection, and power allocation is formulated as a mixed-integer nonlinear problem, with the objective of maximizing the sum peak signal-to-noise ratio (PSNR) of a set of concurrent video sessions. A global optimization algorithm based on the branch and bound framework and on convex relaxation of nonconvex constraints is then proposed to solve the problem. The proposed algorithm can provide a theoretical upper bound on the achievable video quality and is shown to provably converge to the optimal solution. In addition, it is shown that cooperative relaying allows nodes to save energy without leading to a perceivable decrease in video quality. Based on this observation, an uncoordinated, distributed, and localized low-complexity algorithm is designed, for which we derive conditions for convergence to a Nash equlibrium (NE) of relay selection. The distributed algorithm is also shown to achieve performance comparable in practice to the optimal solution.
Molecular design of artificial hydrolytic nucleases and ribonucleases. (1993)

Artificial nucleases and ribonucleases, which selectively hydrolyze the specific phosphodiester linkages in DNAs and RNAs, are prepared by the attachment of organic and inorganic catalysts to DNA oligomers as sequence-recognizing moieties. A hybrid of ethylenediamine and a 19-mer DNA selectively hydrolyzes tRNA(Phe) at the 3'-side of C63. Site-selective hydrolysis of DNAs has been accomplished by the lanthanide complexes bound to DNA oligomers. No concurrent oxidative cleavage of the ribose or the deoxyribose takes place.
Multidisciplinary Experiences For Undergraduate Engineering Students (2020)

While there he was involved in a variety of real-time image processing projects including a high-compression video transmission system for remote driving and several laser-based ranging systems. Fred began
ChemInform Abstract: Synthesis, Structure, and Magnetic Properties of a New Ternary Zintl Phase: Sr21Mn4Sb18. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Stacking interactions by two Phe side chains stabilize and orient assemblies of even the minimal amphiphilic β-sheet motif (2015)

Correction for 'Stacking interactions by two Phe side chains stabilize and orient assemblies of even the minimal amphiphilic β-sheet motif' by Shlomo Zarzhitsky et al., Chem. Commun., 2015, 51, 3154-3157.
Concrete-polymer composites: current status and future research needs (1981)

When plastics are combined with mixtures of inorganic materials, high-strength, durable, fast-setting composites are produced. These materials are used in structural engineering and other applications, and as a result of the successes obtained to date, considerable research and development work is in progress throughout the world. One family of polymer-based composites receiving considerable attention is the concrete-polymer materials. Work in this area is directed toward developing new high-strength durable materials by combining cement and concrete technology with that of polymer chemistry. In addition to the significant property enhancement, many combinations of siliceous materials with polymers require lower energy inputs per unit of performance than either component alone.
Anticyclic Citrullinated Peptide Antibodies in Patients with Rheumatic Diseases other than Rheumatoid Arthritis: Clinical or Pathogenic Significance? (2015)

To the Editor: We read with interest about the study by Payet, et al investigating prevalence and discriminatory value of anticyclic citrullinated peptide (anti-CCP) antibodies in patients with rheumatic diseases other than rheumatoid arthritis (RA)1. Although several studies have been published aiming to identify the prevalence of anti-CCP in patients with different rheumatic conditions2,3,4, Payet’s study was performed in a very large patient cohort and represents, therefore, a relevant information source on this topic. The overall prevalence of anti-CCP in the 723 non-RA patients was rather high compared to other studies5,6,7, with a very high proportion of patients with connective tissue disease (CTD) with anti-CCP (17.5%). This allowed the conclusion that, although anti-CCP are rather specific for RA, they are consistently expressed in patients with other rheumatic diseases. However, it should be noted that, unlike previously published studies analyzing anti-CCP prevalence in non-RA disorders, the design of Payet’s investigation considered the analysis of … Address correspondence to Prof. R. Gerli, Rheumatology Unit, Department of Medicine, University of Perugia, Via Enrico dal Pozzo snc, I-06122, Perugia, Italy. E-mail: roberto.gerli{at}unipg.it
Multispectral observations of marine environments (1972)

It is demonstrated that the multispectral scanner, using multiple channels in registry and recorded on magnetic tape, can be used in variety of applications in the marine environment.
Analysis of primary aromatic amines using precolumn derivatization by HPLC fluorescence detection and online MS identification (2008)

2-(2-phenyl-1H-phenanthro-[9,10-d]imidazole-1-yl)-acetic acid (PPIA) and 2-(9-acridone)-acetic acid (AAA), two novel precolumn fluorescent derivatization reagents, have been developed and compared for analysis of primary aromatic amines by high performance liquid chromatographic fluorescence detection coupled with online mass spectrometric identification. PPIA and AAA react rapidly and smoothly with the aromatic amines on the basis of a condensation reaction using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) as dehydrating catalyst to form stable derivatives with emission wavelengths at 380 and 440 nm, respectively. Taking six primary aromatic amines (aniline, 2-methylaniline, 2-methoxyaniline, 4-methylaniline, 4-chloroaniline, and 4-bromoaniline) as testing compounds, derivatization conditions such as coupling reagent, basic catalyst, reaction temperature and time, reaction solvent, and fluorescent labeling reagent concentration have also been investigated. With the better PPIA method, chromatographic separation of derivatized aromatic amines exhibited a good baseline resolution on an RP column. At the same time, by online mass spectrometric identification with atmospheric pressure chemical ionization (APCI) source in positive ion mode, the PPIA-labeled derivatives were characterized by easy-to-interpret mass spectra due to the prominent protonated molecular ion m/z [M + H](+) and specific fragment ions (MS/MS) m/z 335 and 295. The linear range is 24.41 fmol-200.0 pmol with correlation coefficients in the range of 0.9996-0.9999, and detection limits of PPIA-labeled aromatic amines are 0.12-0.21 nmol/L (S/N = 3). Method repeatability, precision, and recovery were evaluated and the results were excellent for the efficient HPLC analysis. The most important argument, however, was the high sensitivity and ease-of-handling of the PPIA method. Preliminary experiments with wastewater samples collected from the waterspout of a paper mill and its nearby soil where pollution with aromatic amines may be expected show that the method is highly validated with little interference in the chromatogram.
2.4 GHz BiCMOS front-end receiver design driven by gain, linearity and noise trade-offs (2004)

This paper evaluates the design trade-offs for a high frequency RF front-end. The main three factors - gain, linearity, noise - influence is analyzed, in order to get an optimum performance for the receiver. The analysis is focused on the weight of the main blocks (the low noise amplifier - LNA and the mixer) parameters oil the RF frontend operation. These main parameters are the down conversion gain, input referred third order interception point (iIP3) and noise figure (NF). The high performance RF process IBM's BiCMOS-6HP Si-Ge 0.25 /spl mu/m was used to design the circuit.
How Well do Feature Visualizations Support Causal Understanding of CNN\n Activations? (2021)

A precise understanding of why units in an artificial network respond to\ncertain stimuli would constitute a big step towards explainable artificial\nintelligence. One widely used approach towards this goal is to visualize unit\nresponses via activation maximization. These synthetic feature visualizations\nare purported to provide humans with precise information about the image\nfeatures that cause a unit to be activated - an advantage over other\nalternatives like strongly activating natural dataset samples. If humans indeed\ngain causal insight from visualizations, this should enable them to predict the\neffect of an intervention, such as how occluding a certain patch of the image\n(say, a dog's head) changes a unit's activation. Here, we test this hypothesis\nby asking humans to decide which of two square occlusions causes a larger\nchange to a unit's activation. Both a large-scale crowdsourced experiment and\nmeasurements with experts show that on average the extremely activating feature\nvisualizations by Olah et al. (2017) indeed help humans on this task ($68 \\pm\n4$% accuracy; baseline performance without any visualizations is $60 \\pm 3$%).\nHowever, they do not provide any substantial advantage over other\nvisualizations (such as e.g. dataset samples), which yield similar performance\n($66\\pm3$% to $67 \\pm3$% accuracy). Taken together, we propose an objective\npsychophysical task to quantify the benefit of unit-level interpretability\nmethods for humans, and find no evidence that a widely-used feature\nvisualization method provides humans with better "causal understanding" of unit\nactivations than simple alternative visualizations.\n
SARS-CoV-2 protein encoded by ORF8 contains a histone mimic that disrupts chromatin regulation (2021)

Abstract SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this novel virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for a cell’s ability to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of two critical histone 3 sites containing an ARKS motif. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) while Orf8 lacking this histone mimic motif does not. Orf8 binds to numerous histone-associated proteins and to DNA, and is itself acetylated within the histone mimic site. Importantly, SARS-CoV-2 infection of multiple susceptible cell types causes the same global changes of histone post-translational modifications that are disrupted by Orf8 expression; these include induced pluripotent stem cell-derived alveolar type 2 cells (iAT2) and cardiomyocytes (iCM) and postmortem patient lung tissue. These findings demonstrate a novel function for the poorly understood SARS-CoV-2 ORF8 encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Notably, this work provides a potential mechanism for emerging findings from human patients indicating that ORF8 deletion results in less severe illness and describes a potentially druggable pathway that may contribute to the virulence of SARS-CoV-2.
Special Features of Electro-Membrane Recovery of Acids and Alkalis from the Water-Soluble Wastes of Nuclear Power Plants (2022)

The results of studying of the nitric acid and NaOH + KOH alkalis’ mixture recovery from concentrated solutions in filter-press-type electrodialyzers with anion-exchange, cation-exchange, and bipolar membranes are presented. The necessity of the technological solutions preliminary purification from calcium and boron compounds was established, in order to obtain crystalline boric acid (H3BO3) and gypsum (CaSO4·2H2O). The possibility of obtaining, from purified concentrated salt solutions, acids and alkalis with a concentration of ~300–600 g/L suitable for reuse is shown. This can be provided only by the electrodialysis with anion- and cation-exchange membranes, while electrodialysis with bipolar membranes is complicated by noticeable contamination of both acidic and alkaline solutions with salts.