gebhart/patrepeval huggingface dataset:
Thymidine kinase-negative herpes simplex virus mutants establish latency in mouse trigeminal ganglia but do not reactivate. (1989)

Herpes simplex virus infection of mammalian hosts involves lytic replication at a primary site, such as the cornea, translocation by axonal transport to sensory ganglia and replication, and latent infection at a secondary site, ganglionic neurons. The virus-encoded thymidine kinase, which is a target for antiviral drugs such as acyclovir, is not essential for lytic replication yet evidently is required at the secondary site for replication and some phase of latent infection. To determine the specific stage in viral pathogenesis at which this enzyme is required, we constructed virus deletion mutants that were acyclovir resistant and exhibited no detectable thymidine kinase activity. After corneal inoculation of mice, the mutants replicated to high titers in the eye but were severely impaired for acute replication in trigeminal ganglia and failed to reactivate from ganglia upon cocultivation with permissive cells. Nevertheless, latency-associated transcripts were expressed in neuronal nuclei of ganglia from mutant-infected mice and superinfection of the ganglia with a second virus rescued the latent mutant virus. Thus, contrary to a widely accepted hypothesis, the thymidine kinase-negative mutants established latent infections, implying that neither thymidine kinase activity nor ganglionic replication is necessary for establishment of latency. Rather, thymidine kinase appears to be necessary for reactivation from latency. These results suggest that acyclovir-resistant viruses could establish latent infections in clinical settings and have implications for the use of genetically engineered herpesviruses to deliver foreign genes to neurons.
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging (2018)

A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus (MRL/lpr) murine spleens. CODEX iteratively visualizes antibody binding events using DNA barcodes, fluorescent dNTP analogs, and an in situ polymerization-based indexing procedure. An algorithmic pipeline for single-cell antigen quantification in tightly packed tissues was developed and used to overlay well-known morphological features with de novo characterization of lymphoid tissue architecture at a single-cell and cellular neighborhood levels. We observed an unexpected, profound impact of the cellular neighborhood on the expression of protein receptors on immune cells. By comparing normal murine spleen to spleens from animals with systemic autoimmune disease (MRL/lpr), extensive and previously uncharacterized splenic cell-interaction dynamics in the healthy versus diseased state was observed. The fidelity of multiplexed spatial cytometry demonstrated here allows for quantitative systemic characterization of tissue architecture in normal and clinically aberrant samples.
Powered Lower Limb Orthoses: Applications in Motor Adaptation and Rehabilitation (2005)

Task-specific practice can be beneficial for motor rehabilitation after neurological injury. Unfortunately, high labor demands have limited its clinical acceptance, especially for gait rehabilitation. A number of research teams around the world are testing large robotic devices for assisting treadmill stepping as a means for reducing therapist labor. We propose that powered lower limb orthoses may also have a role in assisting gait rehabilitation. Powered orthoses could assist task specific practice of gait with the long-term goal of improving patients' inherent locomotor capabilities. We present data showing that: (1) pneumatically powered lower limb orthoses can provide substantial mechanical assistance to human walking, (2) powered orthoses can lead to motor adaptation of gait in healthy subjects, and (3) powered lower limb orthoses may have positive benefits during gait rehabilitation.
Appliance Commitment for Household Load Scheduling (2011)

This paper presents a novel appliance commitment algorithm that schedules thermostatically controlled household loads based on price and consumption forecasts considering users' comfort settings to meet an optimization objective such as minimum payment or maximum comfort. The formulation of an appliance commitment problem is described using an electrical water heater load as an example. The thermal dynamics of heating and coasting of the water heater load is modeled by physical models; random hot water consumption is modeled with statistical methods. The models are used to predict the appliance operation over the scheduling time horizon. User comfort is transformed to a set of linear constraints. Then, a novel linear-sequential-optimization-enhanced, multiloop algorithm is used to solve the appliance commitment problem. The simulation results demonstrate that the algorithm is fast, robust, and flexible. The algorithm can be used in home/building energy-management systems to help household owners or building managers to automatically create optimal load operation schedules based on different cost and comfort settings and compare cost/benefits among schedules.
Forced engagement of a RNA/protein complex by a chemical inducer of dimerization to modulate gene expression (2002)

A general strategy is described for forcing the engagement of an RNA/protein complex by using small-molecule ligands. A bivalent molecule was created by linking a protein-binding ligand to an RNA-binding ligand. On presentation of the chemical inducer of dimerization to the RNA by the protein, cooperative binding ensued, resulting in higher-affinity complexes. When the chemical inducer of dimerization was used to target the protein to an mRNA template, the resulting RNA/protein complex was sufficiently stable to inhibit mRNA translation. This approach provides a logic to modulate gene expression by using small-molecule ligands to recruit protein surfaces to mRNAs.
Hierarchy of α Fetoprotein (AFP)-Specific T Cell Responses in Subjects with AFP-Positive Hepatocellular Cancer (2006)

We identified a series of immunodominant and subdominant epitopes from alpha fetoprotein (AFP), restricted by HLA-A*0201, which are recognized by the human T cell repertoire. The four immunodominant epitopes have been tested for immunogenicity in vivo, in HLA-A*0201+AFP+ advanced stage hepatocellular cancer (HCC) patients, and have activated and expanded AFP-specific IFN-gamma-producing T cells in these patients, despite high serum levels of this self Ag. Here, we have examined the frequency, function, and avidity of the T cells specific for subdominant epitopes from AFP. We find that T cells specific for several of these epitopes are of similar or higher avidity than those specific for immunodominant epitopes. We then tested the peripheral blood of subjects ex vivo with different levels of serum AFP for the hierarchy of response to epitopes from this Ag and find that HCC patients have detectable frequencies of circulating IFN-gamma-producing AFP-specific CD8+ T cells to both immunodominant and subdominant epitopes. We find the immunodominant and subdominant peptide-specific T cells to be differentially expanded with different modes of Ag presentation. Whereas spontaneous and AFP protein-stimulated responses show evidence for immunodominance, AdVhAFP-transduced dendritic cell-stimulated responses were broader and not skewed. Importantly, these data identify subdominant epitopes from AFP that can activate high-avidity T cells, and that can be detected and expanded in HCC subjects. These subdominant epitope-specific T cells can also recognize tumor cells and may be important therapeutically.
Microwave Assisted Magnetic Recording (2007)

In this paper, we present a novel mechanism for recording at a head held significantly below the medium coercivity in a perpendicular recording geometry. By applying a localized ac field at adequate frequency to the perpendicular recording medium, saturation recording can be achieved with recording field amplitudes significantly below the medium coercivity, or the medium perpendicular anisotropy field. A scheme utilizing spin torque to generate a localized ac field at high frequency (tens of gigahertz) with kilo-oersted field amplitude in the medium is proposed along with a systematic modeling analysis. Recording simulations at high linear densities are presented.
Epithelial sodium channel (ENaC) subunit mRNA and protein expression in rats with puromycin aminonucleoside-induced nephrotic syndrome (2003)

In experimental nephrotic syndrome, urinary sodium excretion is decreased during the early phase of the disease. The molecular mechanism(s) leading to salt retention has not been completely elucidated. The rate-limiting constituent of collecting duct sodium transport is the epithelial sodium channel (ENaC). We examined the abundance of ENaC subunit mRNAs and proteins in puromycin aminonucleoside (PAN)-induced nephrotic syndrome. The time courses of urinary sodium excretion, plasma aldosterone concentration and proteinuria were studied in male Sprague–Dawley rats treated with a single dose of either PAN or vehicle. The relative amounts of αENaC, βENaC and γENaC mRNAs were determined in kidneys from these rats by real-time quantitative TaqMan PCR, and the amounts of proteins by Western blot. The kinetics of urinary sodium excretion and the appearance of proteinuria were comparable with those reported previously. Sodium retention occurred on days 2, 3 and 6 after PAN injection. A significant up-regulation of αENaC and βENaC mRNA abundance on days 1 and 2 preceded sodium retention on days 2 and 3. Conversely, down-regulation of αENaC, βENaC and γENaC mRNA expression on day 3 occurred in the presence of high aldosterone concentrations, and was followed by a return of sodium excretion to control values. The amounts of αENaC, βENaC and γENaC proteins were not increased during PAN-induced sodium retention. In conclusion, ENaC mRNA expression, especially αENaC, is increased in the very early phase of the experimental model of PAN-induced nephrotic syndrome in rats, but appears to escape from the regulation by aldosterone after day 3.
Optimal routing in circuit switched communication networks (1989)

Consideration is given to the optimal circuit routing problem in an existing circuit-switched network. The objective is to find circuit routing which accommodates a given circuit demand while maximizing the residual capacity of the network. In addition, the cost of accommodating the circuit demand should not exceed a given amount. Practical considerations require that a solution be robust to the variations in circuit demand and cost. The objective function for the optimal circuit routing problem is not a smooth one. In order to overcome the difficulties of nonsmooth optimization, the objective function is approximated by smooth concave functions. The optimization algorithm for the circuit routing problem is obtained as a limiting case of the sequence of optimal routing strategies for the corresponding smooth convex optimization problems, and the proof of its convergence to the optimal solution is given. An approach to calculating the optimal multicommodity flow is presented. The optimization algorithm efficiently handles networks with a large number of commodities, satisfies the robustness requirements, and can be used to solve circuit routing problems for large networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heparin as an anticancer therapeutic (2008)

The investigation of anticoagulants as anticancer agents is now an innovative and rapidly growing field. Greater understanding of the interaction between coagulation and cancer will lead to improved patient care.
Exceptionally Potent Cross-Reactive Neutralization of Nipah and Hendra Viruses by a Human Monoclonal Antibody (2008)

We have previously identified neutralizing human monoclonal antibodies against Nipah virus (NiV) and Hendra virus (HeV) by panning a large nonimmune antibody library against a soluble form of the HeV attachment-envelope glycoprotein G (sG HeV). One of these antibodies, m102, which exhibited the highest level of cross-reactive neutralization of both NiV and HeV G, was affinity maturated by light-chain shuffling combined with random mutagenesis of its heavy-chain variable domain and panning against sGHeV. One of the selected antibody Fab clones, m102.4, had affinity of binding to sGHeV that was equal to or higher than that of the other Fabs; it was converted to IgG1 and tested against infectious NiV and HeV. It exhibited exceptionally potent and cross-reactive inhibitory activity with 50% inhibitory concentrations below 0.04 and 0.6 microg/mL, respectively. The virus-neutralizing activity correlated with the binding affinity of the antibody to sG HeV and sG NiV. m102.4 bound a soluble form of NiV G (sG NiV) better than it bound sG HeV, and it neutralized NiV better than HeV, despite being originally selected against sG HeV. These results suggest that m102.4 has potential as a therapeutic agent for the treatment of diseases caused by henipaviruses. It could be also used for prophylaxis and diagnosis, and as a research reagent.
Tissue engineering of cartilage in space (1997)

Tissue engineering of cartilage, i.e., the in vitro cultivation of cartilage cells on synthetic polymer scaffolds, was studied on the Mir Space Station and on Earth. Specifically, three-dimensional cell-polymer constructs consisting of bovine articular chondrocytes and polyglycolic acid scaffolds were grown in rotating bioreactors, first for 3 months on Earth and then for an additional 4 months on either Mir (10(-4)-10(-6) g) or Earth (1 g). This mission provided a unique opportunity to study the feasibility of long-term cell culture flight experiments and to assess the effects of spaceflight on the growth and function of a model musculoskeletal tissue. Both environments yielded cartilaginous constructs, each weighing between 0.3 and 0.4 g and consisting of viable, differentiated cells that synthesized proteoglycan and type II collagen. Compared with the Earth group, Mir-grown constructs were more spherical, smaller, and mechanically inferior. The same bioreactor system can be used for a variety of controlled microgravity studies of cartilage and other tissues. These results may have implications for human spaceflight, e.g., a Mars mission, and clinical medicine, e.g., improved understanding of the effects of pseudo-weightlessness in prolonged immobilization, hydrotherapy, and intrauterine development.
The ALIVE system: full-body interaction with autonomous agents (2002)

The cumbersome nature of wired interfaces and the limited nature of the interaction with graphical objects has so far limited the range of application of virtual environments. We discuss the design and implementation of a novel system, called ALIVE, which allows wireless full-body interaction between a human participant and a rich graphical world inhabited by autonomous agents. Based on results obtained with real users, the paper argues that this kind of system can provide more complex and very different experiences than traditional virtual reality systems. The ALIVE system significantly broadens the range of potential applications of virtual reality systems; in particular the paper discusses novel applications in the area of training and teaching, entertainment and last but not least, digital assistants or interface agents.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Co-infection with SARS-CoV-2 and Influenza A Virus in Patient with Pneumonia, China (2020)

We report co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus in a patient with pneumonia in China. The case highlights possible co-detection of known respiratory viruses. We noted low sensitivity of upper respiratory specimens for SARS-CoV-2, which could further complicate recognition of the full extent of disease.
A Bayesian statistical theory of the phase problem. I. A multichannel maximum-entropy formalism for constructing generalized joint probability distributions of structure factors (1988)

In this first of three papers on a full Bayesian theory of crystal structure determination, it is shown that all currently used sources of phase information can be represented and combined through a universal expression for the joint probability distribution of structure factors. Particular attention is given to situations arising in macromolecular crystallography, where the proper treatment of non-uniform distributions of atoms is absolutely essential. A procedure is presented, in stages of gradually increasing complexity, for constructing the joint probability distribution of an arbitrary collection of structure factors. These structure factors may be gathered from one or several crystal forms of an unknown molecule, each comprising one or several isomorphous structures related by substitution operations, possibly containing solvent regions and known fragments, and/or obeying a set of non-crystallographic symmetries. This universal joint probability distribution can be effectively approximated by the saddlepoint method, using maximum-entropy distributions of atoms [Bricogne (1984). Acta Cryst. A40, 410-445] and a generalization of structure-factor algebra. Atomic scattering factors may assume arbitrary complex values, so that this formalism applies to neutron as well as to X-ray diffraction methods. This unified procedure will later be extended by the construction of conditional distributions allowing phase extension, and of likelihood functions capable of detecting and characterizing all potential sources of phase information considered so far, thus completing the formulation of a full Bayesian inference scheme for crystal structure determination.
To Study on the Relationship of Casting Uniformization to the data Disposing of Customers' Voice (2009)

在顾客声音教据一致化处理过程中,原始客户需求信息容易丢失是企业营销决策难题.文中尝试用图形化形式描述顾客声音数据一致化转化过程,给出了一种面向群决策的三类不同顾客声音(效用值型的顾客声音、次序值型的顾客声音、语言短语型的顾客声音)的一致化映射方法.该方法是一种考虑企业知识背景等相关要素的非强制性数据转换方法,能最大限度地保证数据在转换的过程中不丢失,对支持企业营销决策具有重要理论意义及实用价值.
Nonlinear optical chromophores containing dithienothiophene as a new type of electron relay (1999)

Nonlinear optical (NLO) donor-acceptor (D-A) chromophores containing a fused terthiophene, namely dithienothiophene (DTT) as electron relay, and various strength acceptors were synthesized to evaluate the relay's role in the solvatochromism as well as in the molecular nonlinearity, µβ(0). Their solvatochromic behavior, which is dependent on acceptor strength, is correlated to their µβ(0). The static quadratic hyperpolarizability, β(0), of DTT-containing chromophores was determined by EFISH measurements. From the comparison of µβ(0) values of D-A chromophores based on oligothiophenes, it was assessed that DTT as relay is significantly more efficient compared to bithiophene (the same number of conjugated double bonds) and terthiophene. An additional merit of DTT is that chromophores containing DTT have a noticeably high thermal stability.
Influence of sleep on tensor palatini EMG and upper airway resistance in normal men (1991)

We propose that a sleep-induced decrement in the activity of the tensor palatini (TP) muscle could induce airway narrowing in the area posterior to the soft palate and therefore lead to an increase in upper airway resistance in normal subjects. We investigated the TP to determine the influence of sleep on TP muscle activity and the relationship between changing TP activity and upper airway resistance over the entire night and during short sleep-awake transitions. Seven normal male subjects were studied on a single night with wire electrodes placed in both TP muscles. Sleep stage, inspiratory airflow, transpalatal pressure, and TP moving time average electromyogram (EMG) were continuously recorded. In addition, in two of the seven subjects the activity (EMG) of both the TP and the genioglossus muscle simultaneously was recorded throughout the night. Upper airway resistance increased progressively from wakefulness through the various non-rapid-eye-movement sleep stages, as has been previously described. The TP EMG did not commonly demonstrate phasic activity during wakefulness or sleep. However, the tonic EMG decreased progressively and significantly (P less than 0.05) from wakefulness through the non-rapid-eye-movement sleep stages [awake, 4.6 +/- 0.3 (SE) arbitrary units; stage 1, 2.6 +/- 0.3; stage 2, 1.7 +/- 0.5; stage 3/4, 1.5 +/- 0.8]. The mean correlation coefficient between TP EMG and upper airway resistance across all sleep states was (-0.46). This mean correlation improved over discrete sleep-awake transitions (-0.76). No sleep-induced decrement in the genioglossus activity was observed in the two subjects studied.(ABSTRACT TRUNCATED AT 250 WORDS)
Online learning of robust object detectors during unstable tracking (2009)

This work investigates the problem of robust, longterm visual tracking of unknown objects in unconstrained environments. It therefore must cope with frame-cuts, fast camera movements and partial/total object occlusions/dissapearances. We propose a new approach, called Tracking-Modeling-Detection (TMD) that closely integrates adaptive tracking with online learning of the object-specific detector. Starting from a single click in the first frame, TMD tracks the selected object by an adaptive tracker. The trajectory is observed by two processes (growing and pruning event) that robustly model the appearance and build an object detector on the fly. Both events make errors, the stability of the system is achieved by their cancellation. The learnt detector enables re-initialization of the tracker whenever previously observed appearance reoccurs. We show the real-time learning and classification is achievable with random forests. The performance and the long-term stability of TMD is demonstrated and evaluated on a set of challenging video sequences with various objects such as cars, people and animals.
Ca2+-dependent Activation of the 33-kDa Protein Kinase Transmits Thrombin Receptor Signals in Human Platelets (1996)

Thrombin stimulation induces a dramatic increase in the activity of the 33-kDa serine/threonine kinase (PK33) in human platelets (10). The Arg-Gly-Asp (RGD) peptide, an inhibitor of the thrombin-mediated aggregation of platelets, did not affect the PK33 activation induced by thrombin suggesting that the activation of this kinase occurs independently from platelet aggregation. To identify a potential role of Ca2+ and calmodulin in the regulation of PK33, the effect of several Ca2+/calmodulin inhibitors on the thrombin-induced activation of PK33 was assessed using denaturation/renaturation method. Pretreatment of platelets with EGTA decreased the maximum PK33 activity induced by thrombin. The chelation of both the extra- and the intracellular Ca2+ by EGTA and by acetoxymethyl ester of 5,5'-dimethyl-bis-(0-aminophenoxy) ethane-N,N,N',N'-tetraacetic acid (BAPTA-AM) decreased further the PK33 activation by thrombin. Preincubation of platelets with the anticalmodulin agent, N-(4-aminobutyl)-5-chloro-2-naphthalenesulfonamide (W13), inhibited markedly the activation of PK33 by thrombin, whereas the inactive structural analog N-(4-aminobutyl)-2-naphthalenesulfonamide (W12) and the myosin light chain kinase inhibitor 1-(5-chloronaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine (ML9) showed very weak inhibitory effects. Treatment of resting platelets with the calcium ionophore, A23187, activated PK33 in a dose-dependent manner; phorbol 12-myristate 13-acetate enhanced this effect. However, the two foregoing agents did not induce similar degree of PK33 activities as thrombin. These results indicate that the activation of PK33 is independent of the formation of the GPIIb/IIIa-fibrinogen complex and that it might be regulated by a Ca(2+)-dependent pathway.