gebhart/patrepeval huggingface dataset:
Hemagglutinin destabilization in H3N2 vaccine reference viruses skews antigenicity and prevents airborne transmission in ferrets (2023)

During influenza virus entry, the hemagglutinin (HA) protein binds receptors and causes membrane fusion after endosomal acid activation. To improve vaccine efficiency and pandemic risk assessment for currently-dominant H3N2 influenza viruses, we investigated HA stability of 6 vaccine reference viruses and 42 circulating viruses. Recent vaccine reference viruses had destabilized HA proteins due to egg-adaptive mutation HA1-L194P. Virus growth in cell culture was independent of HA stability. In ferrets, the vaccine reference viruses and circulating viruses required a relatively stable HA (activation and inactivation pH < 5.5) for airborne transmissibility. The recent vaccine reference viruses with destabilized HA proteins had reduced infectivity, had no airborne transmissibility unless reversion to HA1-P194L occurred, and had skewed antigenicity away from the studied viruses and circulating H3N2 viruses. Other vaccine reference viruses with stabilized HAs retained infectivity, transmissibility, and antigenicity. Therefore, HA stabilization should be prioritized over destabilization in vaccine reference virus selection to reduce mismatches between vaccine and circulating viruses.
ACM-W Athena Lecture -- Large-Scale Behavioral Data (2015)

Over the last decade, the rise of web services has made it possible to gather traces of human behavior in situ at a scale and fidelity previously unimaginable. Large-scale behavioral data enables researchers and practitioners to detect adverse drug reactions and interactions, to understand how information diffuses through social networks, how people browse and search for information, how individual learning strategies are related to educational outcome, etc. Using examples from search, I will highlight how observational logs provide a rich new lens onto the diversity of searchers, tasks, and interactivity that characterize information systems today, and how experimental logs have revolutionized the way in which web-based systems are designed and evaluated. Although logs provide a great deal of information about what people are doing, they provide little insight about why they are doing so or whether they are satisfied. Complementary methods from observations, laboratory studies and panels are necessary to provide a more complete understanding of and support for search which is increasingly a core fabric of people's everyday lives. The CHI community should lead the way in shaping best practices and policy in behavioral log studies.
Chemo‐ and Periselectivity in the Addition of [OsO2(CH2)2] to Ethylene: A Theoretical Study (2005)

Quantum chemical calculations by using density functional theory at the B3LYP level have been carried out to elucidate the reaction course for the addition of ethylene to [OsO2(CH2)2] (1). The calculations predict that the kinetically most favorable reaction proceeds with an activation barrier of 8.1 kcal mol(-1) via [3+2] addition across the O=Os=CH2 moiety. This reaction is -42.4 kcal mol(-1) exothermic. Alternatively, the [3+2] addition to the H2C=Os=CH2 fragment of 1 leads to the most stable addition product 4 (-72.7 kcal mol(-1)), yet this process has a higher activation barrier (13.0 kcal mol(-1)). The [3+2] addition to the O=Os=O fragment yielding 2 is kinetically (27.5 kcal mol(-1)) and thermodynamically (-7.0 kcal mol(-1)) the least favorable [3+2] reaction. The formal [2+2] addition to the Os=O and Os=CH2 double bonds proceeds by initial rearrangement of 1 to the metallaoxirane 1 a. The rearrangement 1-->1 a and the following [2+2] additions have significantly higher activation barriers (>30 kcal mol(-1)) than the [3+2] reactions. Another isomer of 1 is the dioxoosmacyclopropane 1 b, which is 56.2 kcal mol(-1) lower in energy than 1. The activation barrier for the 1-->1 b isomerization is 15.7 kcal mol(-1). The calculations predict that there are no energetically favorable addition reactions of ethylene with 1 b. The isomeric form 1 c containing a peroxo group is too high in energy to be relevant for the reaction course. The accuracy of the B3LYP results is corroborated by high level post-HF CCSD(T) calculations for a subset of species.
Active Histoplasma Meningitis of 22 Years' Duration (1975)

HISTOPLASMA meningitis without infection of other organs is an exceedingly rare disease. We have had the opportunity to follow-up a case of<i>Histoplasma</i>meningitis, previously reported 11 years ago,<sup>1</sup>that has now been active for 22 years without major sequelae, a degree of chronicity unique for meningeal infection due to any cause. This case suggests that histoplasmosis that is confined clinically to the meninges may follow a much more chronic course than<i>Histoplasma</i>meningitis with other organ involvement. <h3>Report of a Case</h3> A 58-year-old man was first hospitalized in 1952 for severe headaches. Lumbar puncture and analysis of cerebrospinal fluid (CSF) disclosed an elevated protein level, lymphocytosis, and hypoglycorrhachia. Cultures on this and on subsequent admissions were negative until 1959, when culture of 30 ml of CSF, removed during pneumoencephalography, was positive for<i>Histoplasma capsulatum</i>. Physical examination, roentgenograms, and cultures from multiple sites, including sputum, blood, urine, and bone
Circuit design advances to enable ubiquitous sensing environments (2010)

This paper describes critical circuit building blocks for emerging sensing applications, particularly those where volume, and therefore power consumption constraints are orders of magnitude below current state of the art. Developments in ultra-low power microprocessors and memories are described, along with sub-nW timekeeping circuits, pW voltage references, and efficient DC-DC voltage conversion circuits at sub-μA current loads. Taken together, these circuit design advances point to a vision of true mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> low-cost sensing nodes with hybrid power sources, i.e., scavenged and micro-battery, providing long lifetime and reliable operation.
Evaluation of Hydrogel Tissue Sealant in Porcine Laparoscopic Partial-Nephrectomy Model (2005)

CoSeal is not as effective as fibrin glue in adhering to the cut renal surface and sealing the collecting system during laparoscopic partial nephrectomy.
Recursive identification of Hammerstein models (2014)

The nonlinear Hammerstein model, which consists of a static nonlinear block followed by a linear dynamic block, is considered. A recursive prediction error algorithm is derived. The linear block is modelled as a single-input single-output transfer function, and the nonlinearity as a linear combination of basis functions. The case when the nonlinear block is modelled as a piecewise linear function is studied in detail. A direct computation of the gradient allows the number of estimated parameters to be minimized, a fact that is crucial when small data sets are used. Numerical examples validate the algorithm, and shows that the scheme successfully identifies a biomedical model from 200 measurements.
Graph-based multiple panorama extraction from unordered image sets (2007)

This paper presents a multi-image registration method, which aims at recognizing and extracting multiple panoramas from an unordered set of images without user input. A method for panorama recognition introduced by Lowe and Brown is based on extraction of a full set of scale invariant image features and fast matching in feature space, followed by post-processing procedures. We propose a different approach, where the full set of descriptors is not required, and a small number of them are used to register a pair of images. We propose feature point indexing based on corner strength value. By matching descriptor pairs with similar corner strengths we update clusters in rotation-scale accumulators, and a probabilistic approach determines when these clusters are further processed with RANSAC to find inliers of image homography. If the number of inliers and global similarity between images are sufficient, a fast geometry-guided point matching is performed to improve the accuracy of registration. A global registration graph, whose node weights are proportional to the image similarity in the area of overlap, is updated with each new registration. This allows the prediction of undiscovered image registrations by finding the shortest paths and corresponding transformation chains. We demonstrate our approach using typical image collections containing multiple panoramic sequences.
Theoretical Considerations on Molecular Transport in Dialysis and Sorbent Therapy for Uremia (1976)

The technology of uremic blood purification has grown rapidly over the past decade and has provided the clinician with a wide range of therapeutic options. These options involve mass transfer processes which may be primarily due to diffusion or convection, or a combination of both mechanisms. However, regardless of the mechanism of molecular transport, evaluation of the clinical utility of these therapies requires studies which provide sufficient data to solve the appropriate rate equations and to close mass balances. Data from the recent hemodialysis, peritoneal dialysis and sorbent literature are analyzed to show the magnitude of variability in both patient and therapy-related mass balance paramters for urea nitrogen (U) and middle molecules (MM) and to provide unambiguous comparisons for some of these therapies. A theoretical model is developed to describe sorbent-mediated gut elimination of solute as a first-order clearance limited by sorbent saturation. The model is used to analyze data in the literature on AL (OH)3 facilitated gut clearance of phosphate and indicates a gut P clearance of approximately 20 ml/min with maximum removal of approximately 800 mg P/24 hrs. Similar analysis of oxystarch indicated a gut U clearance of 2.5 ml/min and maximum removal of 1.5 gm/24 hrs.
Polymer-tetrodotoxin conjugates to induce prolonged duration local anesthesia with minimal toxicity (2019)

There is clinical and scientific interest in developing local anesthetics with prolonged durations of effect from single injections. The need for such is highlighted by the current opioid epidemic. Site 1 sodium channel blockers such as tetrodotoxin (TTX) are extremely potent, and can provide very long nerve blocks but the duration is limited by the associated systemic toxicity. Here we report a system where slow release of TTX conjugated to a biocompatible and biodegradable polymer, poly(triol dicarboxylic acid)-co-poly(ethylene glycol) (TDP), is achieved by hydrolysis of ester linkages. Nerve block by the released TTX is enhanced by administration in a carrier with chemical permeation enhancer (CPE) properties. TTX release can be adjusted by tuning the hydrophilicity of the TDP polymer backbone. In vivo, 1.0-80.0 µg of TTX released from these polymers produced a range of durations of nerve block, from several hours to 3 days, with minimal systemic or local toxicity.
Deep Annotation of Therapeutic Working Alliance in Psychotherapy (2022)

The therapeutic working alliance is an important predictor of the outcome of the psychotherapy treatment. In practice, the working alliance is estimated from a set of scoring questionnaires in an inventory that both the patient and the therapists fill out. In this work, we propose an analytical framework of directly inferring the therapeutic working alliance from the natural language within the psychotherapy sessions in a turn-level resolution with deep embeddings such as the Doc2Vec and SentenceBERT models. The transcript of each psychotherapy session can be transcribed and generated in real-time from the session speech recordings, and these embedded dialogues are compared with the distributed representations of the statements in the working alliance inventory. We demonstrate, in a real-world dataset with over 950 sessions of psychotherapy treatments in anxiety, depression, schizophrenia and suicidal patients, the effectiveness of this method in mapping out trajectories of patient-therapist alignment and the interpretability that can offer insights in clinical psychiatry. We believe such a framework can be provide timely feedback to the therapist regarding the quality of the conversation in interview sessions.
Exploring material chemistry for direct ink writing of reactively formed conductors (2020)

Rational design of a reactive material for 3D printing robust electrical conductors which can be integrated into parts or systems.
Delay tolerant disaster communication with the One Laptop per Child XO laptop. (2013)

In this paper, we describe the design, implementation, and evaluation of a mesh network based messaging application for the One Laptop Per Child XO laptop. We outline the creation of an easy-to-use OLPC Activity that exchanges Ushahidi-style messages with nearby OLPC users through the Internet or a mesh network. Our contributions are to implement an epidemic messaging scheme on mesh networks of OLPC XO laptops, to extend the Ushahidi web application to efficiently exchange messages with nodes in mesh networks, and to allow the Ushahidi server to distribute cures, notifications of message delivery, for each received message. Testing and analysis revealed substantial overhead is introduced by the OLPC’s use of Telepathy Salut for activity sharing.
Pertussis Immunization for Adolescents: What Are We Waiting for? (2001)

Immunization against pertussis (whooping cough) has been part of the routine childhood immunization program for over 50 years. Until 1997, a whole cell pertussis vaccine was used, most often combined with diphtheria and tetanus toxoids; in some jurisdictions it was combined with inactivated poliovirus vaccine and later with Haemophilus influenzae type b (Hib)‐conjugate vaccine. Vaccine doses were given at two, four, six and 18 months of age, and again at four to six years of age. Use of the whole cell vaccine in children seven years of age and older was not recommended because "the incidence and severity of the disease greatly decrease with age, and because adverse reactions are (may be) more common in older children and adults…" (1‐3). Over a one‐year period in 1997/98, all provinces in Canada began using an acellular pertussis vaccine, again combined with diphtheria and tetanus toxoids, inactivated poliovirus vaccine and Hib‐conjugate vaccine. In 1999, an acellular pertussis vaccine that was combined with tetanus and diphtheria toxoids (TdaP) (Adacel, Aventis Pasteur, Canada) was licensed for use in individuals 12 to 54 years of age in Canada. In Germany, a similar adolescent and adult TdaP was licensed in 2000 (Boostrix, SmithKline Beecham, Belgium). With the availability of a TdaP product in Canada, should routine universal immunization against pertussis be provided for all adolescents and adults? Some of the key issues to be considered when answering this question are addressed in the questions and answers that follow. The focus of the present paper is on the adolescent population; however, similar issues about adult immunization need to be addressed by internal medicine and family practice practitioners.
Molecular structure of a protein-tyrosine/threonine kinase activating p42 mitogen-activated protein (MAP) kinase: MAP kinase kinase. (1993)

MAP kinases p42mapk and p44mapk participate in a protein kinase cascade(s) important for signaling in many cell types and contexts. Both MAP kinases are activated in vitro by MAP kinase kinase, a protein-tyrosine and threonine kinase. A MAP kinase kinase cDNA was isolated from a rat kidney library by using peptide sequence data we obtained from MAP kinase kinase isolated from rabbit skeletal muscle. The deduced sequence, containing 393 amino acids (predicted mass, 43.5 kDa), is most similar to byr1 (Bypass of ras1), a yeast protein kinase functioning in the mating pathway induced by pheromones in Schizosaccharomyces pombe. An unusually large insert is present in MAP kinase kinase between domains IX and X and may contribute to protein-protein interactions with MAP kinase. Major (2.7 kilobases) and minor (1.7 kilobases) transcripts are widely expressed in rat tissues and appear to be derived from a single gene.
Penicillin-Binding Proteins in the Soluble Fraction of Caulobacter crescentus (1982)

Four penicillin-binding proteins (PBPs) were observed in the soluble fraction of Caulobacter crescentus CB13, and designated PBP S1 (mol. wt 60000), PBP S2 (55000), PBP S3 (45000) and PBP S4 (40000). Caulobacter crescentus CB15, an independent isolate, possessed similar soluble PBPs, but not PBP S2. These soluble PBPs could be observed even when a cell suspension was directly reacted with [14C]penicillin G. Two of the soluble PBPs, S1 and S2, released half their bound [14C]penicillin G during a 10 min incubation, indicating that these PBPs have penicillinase-like activity. PBP S2 was very thermolabile and lost its penicillin-binding activity after incubation at 40 °C for 10 min. Mecillinam did not show selective binding to any of the Caulobacter soluble PBPs or to PBPs in the cell envelope.
Quantifying in vivo hemodynamic response to exercise in patients with intermittent claudication and abdominal aortic aneurysms using cine phase‐contrast MRI (2010)

Abdominal aortic hemodynamic changes due to lower extremity exercise can be quantified in patients with AAA and claudication using PC-MRI. The redistribution of blood flow during exercise was significant and different between the two disease states.
Mapping concurrent applications on network-on-chip platforms (2006)

Networks-on-chip have been proposed as the interconnect solution for building large systems-on-chip. Such platforms will be made of hardware cores, running concurrently to achieve high compute power and keep power consumption low. These platforms have many things in common with distributed systems. In this article we analyze the issues related to mapping concurrent applications on a networks-on-chip based platform. We show that the quality of the decisions made at different stages of mapping has a high impact on the overall system performance. The critical stages of application mapping for networks-on-chip platforms include partitioning the application into processing cores, mapping the communication between the cores, and resolving platform-dependent problems such as race conditions and multipoint-to-point communications. We investigate these problems using an MPEG4 video decoder application and we evaluate the performance of the mapped system in a simulation environment, using a SystemC networks-on-chip simulator.
Range-Separated Hybrid Functionals for Mixed-Dimensional Heterojunctions: Application to Phthalocyanines/MoS2 (2021)

We analyze the electronic structure and level alignment of transition-metal phthalocyanine (MPc) molecules adsorbed on two-dimensional MoS$_2$ employing density functional theory (DFT) calculations. We develop a procedure for multi-objective optimal tuning of parameters of range-separated hybrid functionals in these mixed-dimensional systems. Using this procedure, which leads to the asymptotically-correct exchange-correlation potential between molecule and two-dimensional material, we obtain electronic structures consistent with experimental photoemission results for both energy level alignment and electronic bandgaps, representing a significant advance compared to standard DFT methods. We elucidate the MoS$_2$ valence resonance with the transition-metal phthalocyanine non-frontier 3$d$ orbitals and its dependence on the transition metal atomic number. Based on our calculations, we derive parameter-free, model self-energy corrections that quantitatively accounts for the effects of the heterogeneous dielectric environment on the electronic structure of these mixed-dimensional heterojunctions.
Microelectromechanical System Pressure Sensor for Projectile Applications (2004)

A miniaturized high pressure sensor for cannon-launched munitions was fabricated, based on microelectromechanical system (MEMS) technology. It uses a 0.5 microns thin film of lead zirconate titanate (PZT) material for producing an electrical charge that is directly proportional to the pressure. The sensor was mounted on a customized stainless steel housing, placed into a high pressure vessel, and tested to a maximum pressure of 40,000 psi. The shape and configuration of the platinum (Pt)/PZT/Pt layered structure has been redesigned to reduce the complexity of wire interconnections and to increase the charge output of the device.
Regulation of the Immune Response to Tumor Antigen (1978)

Abstract The nature and function of suppressor factor(s) elaborated by suppressor T cells in response to certain chemically induced tumors have been further defined. Thus, suppressor factor(s) specific for the S1509a methylcholanthrene-induced fibrosarcoma have been shown to bear determinants encoded by the I-J subregion of the murine MHC since suppressive activity is removed by passage of the factor through an immunoadsorbent composed of anti-I-Jk coupled to Sepharose. No loss of activity was observed after passage of factor through control columns composed of normal mouse globulin. Furthermore, activity could be recovered from the relevant immunoadsorbent by elution with high salt. The administration of crude suppressor factor(s) to normal animals for 4 days resulted in the development of a population of suppressor cells that act in a manner analogous to the suppressor cell population used for production of factor. These factor-induced suppressor cells are T cells and exhibit an antigen specificity similar to that displayed by the tumor-induced suppressor cells. Thus, tumor-specific suppressor factor(s) bear I-J determinants and are capable of inducing the appearance of suppressor T cells in the nontumor-bearing host, which may then act in a specific manner to limit host responsiveness to tumor antigen.
Uplink resource partitioning in relay enhanced LTE-Advanced networks (2009)

This paper investigates the uplink performance of LTE-Advanced cellular networks upon relay node deployment. The uplink interference upon deploying relays is analyzed, and a resource partitioning scheme based on user grouping is proposed to mitigate the interference and improve system performance. Simulation results for the proposed resource partitioning scheme reveal that the throughput experienced by the user equipment upon relay deployment is clearly better than the throughput in conventional macro cellular deployments. Also, an improvement in the user equipment's battery life is foreseen.
Some substituted polysaccharides as low temperature middle distillate additives (1984)

Abstract Substituted polysaccharides with different molecular weights (mol. wt 12 000–15 500) were synthesised by reacting aliphatic acid chlorides with different carbon numbers (C 12 ‐C 18 ) with dextrin. The resulting polymers were purified and tested as pour point depressants and flow improvers for middle distillates (gas oils). Comparative evaluation of these polysaccharides with some commercial additives showed their good activity, especially as flow improvers.