gebhart/patrepeval huggingface dataset:
The appearance of a second genotype of Japanese encephalitis virus in the Australasian region. (2001)

In mid-January 2000, the reappearance of Japanese encephalitis (JE) virus activity in the Australasian region was first demonstrated by the isolation of JE virus from 3 sentinel pigs on Badu Island in the Torres Strait. Further evidence of JE virus activity was revealed through the isolation of JE virus from Culex gelidus mosquitoes collected on Badu Island and the detection of specific JE virus neutralizing antibodies in 3 pigs from Saint Pauls community on Moa Island. Nucleotide sequencing and phylogenetic analyses of the premembrane and envelope genes were performed which showed that both the pig and mosquito JE virus isolates (TS00 and TS4152, respectively) clustered in genotype I, along with northern Thai, Cambodian, and Korean isolates. All previous Australasian JE virus isolates belong to genotype II, along with Malaysian and Indonesian isolates. Therefore, for the first time, the appearance and transmission of a second genotype of JE virus in the Australasian region has been demonstrated.
Morphologies in solvent-annealed thin films of symmetric diblock copolymer (2006)

We have systematically studied the thin film morphologies of symmetric poly(styrene)-block-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer after annealing to solvents with varying selectivity. Upon neutral solvent vapor annealing, terraced morphology is observed without any lateral structures on the surfaces. When using PS-selective solvent annealing, the film exhibits macroscopically flat with a disordered micellar structure. While PMMA-selective solvent annealing leads to the dewetting of the film with fractal-like holes, with highly ordered nanoscale depressions in the region of undewetted films. In addition, when decreasing the swelling degree of the film in the case of PMMA-selective solvent annealing, hills and valleys are observed with the coexistence of highly ordered nanoscale spheres and stripes on the surface, in contrast to the case of higher swelling degree. The differences are explained qualitatively on the basis of polymer-solvent interaction parameters of the different components.
Influence of Piperine on Transcutaneous Permeation of Repaglinide in Rats and on Tight Junction Proteins in HaCaT Cells: Unveiling the Mechanisms for Enhanced Permeation (2009)

The purpose of this study was to evaluate the influence of piperine on permeation of repaglinide (RGE) across rat epidermis. In addition, the role of chitosan (CTN) and its combination with piperine was investigated for exploring the possibility of further enhancing the permeation of RGE. The permeation of RGE across excised rat epidermis was, respectively, ~4-fold, ~5-fold and ~6- fold higher when piperine (0.008% w/v), CTN (1% w/v), or piperine – CTN mixture was used as donor vehicle as compared to propylene glycol: ethanol (PG: EtOH) (7:3) mixture. The merger of T2 and T3 (lipid-specific) and obliteration of T4 (protein-specific) endothermic transitions in the thermograms of excised rat epidermis suggested overwhelming influence of these treatments on skin lipids and proteins. Further, the observed increase in intercellular space, disordering of lipid structure and corneocyte detachment indicated considerable effect on the ultrastructure of rat epidermis. The enhancement in permeation of RGE across rat epidermis excised after various treatments for different periods was correlated with the transepidermal water loss of similarly treated viable rat skin. The treatment of HaCaT cell line with piperine influenced the TJ plaque protein zonula occludens (ZO-1) as evidenced by reduced immunofluorescence of anti-TJP1 (ZO-1) antibody in confocal laser scanning microscopic studies. Treatment of HaCaT cells with CTN decreased the intensity of fluorescence on the cell walls only marginally. However, remarkable decrease in the immunofluorescence of anti-TJP1 (ZO-1) antibody was observed after treatment of HaCaT cells with mixture of piperine and CTN. The systemic delivery of RGE in rats was enhanced by 8-fold and 9.5-fold from transdermal formulations containing, respectively, piperine (0.008 % w/v) or piperine (0.008 % w/v)–CTN (1% w/v) mixture as enhancer. Overall, the observations suggested overwhelming influence of piperine and CTN on ZO-1 protein to be responsible for enhancing the percutaneous permeation of RGE.
Architectural Support for Network Applications on Simultaneous MultiThreading Processors (2007)

As network applications become increasingly sophisticated and Internet traffic is getting heavier, future network processors must continue processing computation-intensive network applications at line rates. Most programmable network processors on the market today, such as the Intel IXP2800, target low performance (from 100 Mbps to 10 Gbps). However, low cost edge routers find it hard to cope with the forthcoming sophistication of network applications to be processed at those speeds. Hence, new architectures should be designed for the programmable network processors of the future. The goal of this paper is to evaluate the applicability and efficiency of simultaneous multi-threaded (SMT) as a network processor. Indeed, the SMT model inherently allows the multiple parallel threads which must be dealt with in network processor applications. In this paper, we investigate the architectural implications of network applications on the SMT architecture. We demonstrate that, when executed as independent threads, applications chosen from different network layers show an improved IPC and cache behavior when compared with the situation where the program executed comes from a single network application. Finally, a new architectural solution to cope with packet dependency is proposed and evaluated.
Application of an MEG eigenspace beamformer to reconstructing spatio‐temporal activities of neural sources (2002)

We have applied the eigenspace-based beamformer to reconstruct spatio-temporal activities of neural sources from MEG data. The weight vector of the eigenspace-based beamformer is obtained by projecting the weight vector of the minimum-variance beamformer onto the signal subspace of a measurement covariance matrix. This projection removes the residual noise-subspace component that considerably degrades the signal-to-noise ratio (SNR) of the beamformer output when errors in estimating the sensor lead field exist. Therefore, the eigenspace-based beamformer produces a SNR considerably higher than that of the minimum-variance beamformer in practical situations. The effectiveness of the eigenspace-based beamformer was validated in our numerical experiments and experiments using auditory responses. We further extended the eigenspace-based beamformer so that it incorporates the information regarding the noise covariance matrix. Such a prewhitened eigenspace beamformer was experimentally demonstrated to be useful when large background activity exists.
Bayesian Unsupervised Learning of Higher Order Structure (1996)

Multilayer architectures such as those used in Bayesian belief networks and Helmholtz machines provide a powerful framework for representing and learning higher order statistical relations among inputs. Because exact probability calculations with these models are often intractable, there is much interest in finding approximate algorithms. We present an algorithm that efficiently discovers higher order structure using EM and Gibbs sampling. The model can be interpreted as a stochastic recurrent network in which ambiguity in lower-level states is resolved through feedback from higher levels. We demonstrate the performance of the algorithm on benchmark problems.
The Role of Three Domains in the Biological Activity of Human Interferon-α (1989)

Earlier studies showed that minor differences in primary structure among the interferon-alpha (IFN-alpha) protein family are reflected in their potency in selected biological assays. These studies have been extended and results from assays of antiviral, growth inhibitory and 2',5'-oligoadenylate (2-5A) synthetase activities indicate that the various novel hybrid and analog species are differentially biologically active. Overall these observations suggest a correlation between predicted secondary structure characteristics, receptor binding affinity, and 2-5A synthetase, antiviral and growth inhibitory activities. Studies with a consensus IFN-alpha analog particularly implicated the region around residues 78 and 79 as influencing antiviral activity. Neutralization experiments with a monoclonal antibody directed against a conserved region from residues 113 to 149 indicated that although this region of the IFN-alpha molecule may be important for antiviral activity, altering residues at sites removed from this region may reduce the effectiveness of the neutralizing antibody. Receptor binding experiments suggested that no single site at either the amino or carboxyl terminus of IFN-alpha alone determines receptor affinity or biological activity: apparently three distinct domains along IFN-alpha are involved (10-35, 78-107, 123-166). Overall, the data indicate that the three sites contribute toward the active configuration of human IFN-alpha.
Cloning of Human Ubiquitin-conjugating Enzymes UbcH6 and UbcH7 (E2-F1) and Characterization of Their Interaction with E6-AP and RSP5 (1996)

E6-AP, a 100-kDa cellular protein, was originally identified through its interaction with the E6 protein of the oncogenic human papillomavirus types 16 and 18. The complex of E6-AP and E6 specifically interacts with p53 and mediates ubiquitination of p53 in concert with the E1 ubiquitin-activating enzyme and the E2 ubiquitin-conjugating enzyme UbcH5. Recent results suggest that E6-AP is representative of a family of putative ubiquitin-protein ligases. Members of this family are characterized by a conserved C-terminal region, termed hect domain. In this paper, we describe the isolation of two human E2s, designated as UbcH6 and UbcH7, that in addition to UbcH5 can interact with E6-AP. UbcH6 is a novel member of an evolutionally conserved subfamily of E2s that includes UbcH5 and Saccharomyces cerevisiae UBC4. Although UbcH7 does not appear to be a member of this subfamily, UbcH7 efficiently substitutes for UbcH5 in E6-AP-dependent ubiquitination. Surprisingly, UbcH6 was only weakly active in this particular assay. In addition, UbcH5 but not UbcH6 or UbcH7 efficiently interacts with the heet protein RSP5. These results indicate that E6-AP can interact with at least two species of E2 and that different hect proteins may interact with different E2s.
Resource utilization and costs of age-related macular degeneration. (2006)

Data were analyzed from the 1999-2001 Medicare Beneficiary Encrypted Files for patients with age-related macular degeneration (AMD), an ophthalmic condition characterized by central vision loss. Classifying AMD subtype by International Classification of Diseases, Ninth Revision, Clinical Modifications (ICD-9-CM) (Centers for Disease Control and Prevention, 2003) code, resource utilization rates increased with disease progression. Individuals with more severe disease (wet only or wet and dry AMD) had greater costs than did those with less severe disease (drusen only or dry only). Costs among patients with wet disease increased yearly at rates exceeding inflation, possibly due in part to increased rates of treatment with photodynamic therapy among these individuals and the aging of the population.
MRI Plaque Imaging Detects Carotid Plaques with a High Risk for Future Cerebrovascular Events in Asymptomatic Patients (2013)

MRI plaque imaging has the potential to identify patients with asymptomatic carotid stenosis who are particularly at risk of developing future cerebral ischemia. MRI could improve selection criteria for invasive therapy in the future.
Tobramycin and daptomycin disposition when co-administered to healthy volunteers (1994)

Journal Article Tobramycin and daptomycin disposition when co-administered to healthy volunteers Get access James R. Woodworth, James R. Woodworth Lilly Laboratory for Clinical Research, Eli Lilly and Company, Wishard Memorial Hospital1001 W. 10th Street, Indianapolis, Indiana 46202, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Eldon H. Nyhart, Eldon H. Nyhart Lilly Laboratory for Clinical Research, Eli Lilly and Company, Wishard Memorial Hospital1001 W. 10th Street, Indianapolis, Indiana 46202, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar James D. Wolny, James D. Wolny Lilly Laboratory for Clinical Research, Eli Lilly and Company, Wishard Memorial Hospital1001 W. 10th Street, Indianapolis, Indiana 46202, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Gordon L. Brier, Gordon L. Brier Lilly Laboratory for Clinical Research, Eli Lilly and Company, Wishard Memorial Hospital1001 W. 10th Street, Indianapolis, Indiana 46202, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Henry R. Black Henry R. Black Lilly Laboratory for Clinical Research, Eli Lilly and Company, Wishard Memorial Hospital1001 W. 10th Street, Indianapolis, Indiana 46202, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 33, Issue 3, March 1994, Pages 655–659, https://doi.org/10.1093/jac/33.3.655 Published: 01 March 1994 Article history Received: 01 April 1993 Accepted: 29 October 1993 Published: 01 March 1994
Radiographic changes in the feet of patients with early rheumatoid arthritis. GRISAR (Gruppo Reumatologi Italiani Studio Artrite Reumatoide) (1997)

Foot radiographs facilitate the identification of patients with early erosive RA. Foot involvement is indicative of more aggressive disease. Assessment of foot radiographs allows the most adequate therapeutic strategy to be adopted.
The Stability of Holomyoglobin Is Determined by Heme Affinity (1996)

The properties of wild-type, V68T, and H97D sperm whale myoglobins were compared to determine the relative importance of heme affinity and globin stability on the resistance of the holoprotein to denaturation. The V68T mutation decreases apoglobin stability by placing a polar side chain in the interior heme pocket. However, this substitution increases hemin affinity by formation of a strong hydrogen bond between coordinated water and the Thr68(E11) side chain. The H97D substitution disrupts favorable contacts with Ser92(F7) and the heme-7-propionate and causes a large increase in the rate of hemin dissociation. The Asp replacement has little affect on apoglobin stability because His97(FG3) is a surface residue. The aquomet, cyanomet, deoxyferrous, and apoglobin forms of each mutant and wild-type myoglobin were unfolded by titration with guanidinium chloride. Even though holomyoglobin denaturation involves the dissociation of heme and should be dependent on protein concentration, nonspecific heme binding to unfolded states makes the overall process appear to be a simple, unimolecular unfolding transition. The equilibrium constants for the denaturation of the holomyoglobin mutants correlate almost exclusively with heme affinity and not with the stability of the globin portion of the molecule. The strong correlation with heme affinity explains quantitatively why the stability of myoglobin is enhanced approximately 60-fold by reduction of iron to the ferrous deoxy state and by another approximately 100-fold with CO coordination. Parameters measured for GdmCl-, urea-, acid-, and heat-induced denaturation of holomyoglobins and hemoglobins reflect heme affinity and not the folding properties of the corresponding apoproteins. This conclusion suggests that (1) many previous studies of the denaturation of intact heme proteins need to be reevaluated in terms of heme affinity and (2) measurements with apoproteins are required for unambiguous determinations of the stability of globin structures.
Ocular Drug Delivery Nanowafer with Enhanced Therapeutic Efficacy (2015)

Presently, eye injuries are treated by topical eye drop therapy. Because of the ocular surface barriers, topical eye drops must be applied several times in a day, causing side effects such as glaucoma, cataract, and poor patient compliance. This article presents the development of a nanowafer drug delivery system in which the polymer and the drug work synergistically to elicit an enhanced therapeutic efficacy with negligible adverse immune responses. The nanowafer is a small transparent circular disc that contains arrays of drug-loaded nanoreservoirs. The slow drug release from the nanowafer increases the drug residence time on the ocular surface and its subsequent absorption into the surrounding ocular tissue. At the end of the stipulated period of drug release, the nanowafer will dissolve and fade away. The in vivo efficacy of the axitinib-loaded nanowafer was demonstrated in treating corneal neovascularization (CNV) in a murine ocular burn model. The laser scanning confocal imaging and RT-PCR study revealed that once a day administered axitinib nanowafer was therapeutically twice as effective, compared to axitinib delivered twice a day by topical eye drop therapy. The axitinib nanowafer is nontoxic and did not affect the wound healing and epithelial recovery of the ocular burn induced corneas. These results confirmed that drug release from the axitinib nanowafer is more effective in inhibiting CNV compared to the topical eye drop treatment even at a lower dosing frequency.
Fusion of time-of-flight depth and stereo for high accuracy depth maps (2008)

Time-of-flight range sensors have error characteristics which are complementary to passive stereo. They provide real time depth estimates in conditions where passive stereo does not work well, such as on white walls. In contrast, these sensors are noisy and often perform poorly on the textured scenes for which stereo excels. We introduce a method for combining the results from both methods that performs better than either alone. A depth probability distribution function from each method is calculated and then merged. In addition, stereo methods have long used global methods such as belief propagation and graph cuts to improve results, and we apply these methods to this sensor. Since time-of-flight devices have primarily been used as individual sensors, they are typically poorly calibrated. We introduce a method that substantially improves upon the manufacturerpsilas calibration. We show that these techniques lead to improved accuracy and robustness.
A Blocker-Tolerant, Noise-Cancelling Receiver Suitable for Wideband Wireless Applications (2012)

A new wideband receiver architecture is proposed that employs two separate passive-mixer-based downconversion paths, which enables noise cancelling, but avoids voltage gain at blocker frequencies. This approach significantly relaxes the trade-off between noise, out-of-band linearity and wideband operation. The resulting prototype in 40 nm is functional from 80 MHz to 2.7 GHz and achieves a 2 dB noise figure, which only degrades to 4.1 dB in the presence of a 0 dBm blocker.
Nucleosides and Nucleotides. Part 7. Four dithymidine monophosphates with different anomeric configurations, their synthesis and behaviour towards phosphodiesterases (1974)

Abstract The four isomeric dithymidine monophosphates βT d ‐βT d ( 1 ), αT d ‐βT d (2), βT d ‐αT d ( 3 ) and αT d ‐αT d ( 4 ), differing only by the anomeric configurations of the nucleoside units, were prepared from the suitably protected nucleosides and nucleotides. The four dinucleoside monophosphates were tested as substrates of snake venom phosphodiesterase and spleen phosphodiesterase. Both enzymes accept all four compounds as substrates, however, the rate of the hydrolysis is considerably smaller if the enzymic attack takes place at the α‐nucleoside moiety of the dinucleoside monophosphate.
Nystatin Perforated Patch Recording and Its Applications to Analyses of Intracellular Mechanisms. (1994)

We have reviewed the basic aspects of history, physicochemical properties, advantages, disadvantages, and applications of nystatin- and amphotericin B-perforated patch recording. Recently, we have developed a novel perforated patch technique using gramicidin [49, 132, 133]. Since gramicidin pores are permeable to Na+ and K+ but not to Cl-, it is possible to maintain the physiological concentration of intracellular Cl- and thereby to measure it in real-time from small neurons. Further improvement of the perforated patch techniques would be possible by limiting redistribution of specific intracellular ions. In light of their broad applicability, the perforated patch techniques will prove indispensable for electrophysiologists working on the functions and modulations of receptors, ion channels and transport phenomena. Research with the perforated patch should continue to provide important information relevant to the physiological and pathological conditions of cells.
A Nutrition Support Service Web Application to Manage Patients Receiving Parenteral Nutrition (2009)

Parenteral nutrition (PN) is a complex therapy that requires expertise and experience to avoid errors in prescribing and management. Because of care coordination issues, one medical center has developed and implemented a Web-based application to manage PN patients. PN orders have already been programmed into the physician order entry system, but the nutrition support service (NSS) consult and daily PN management have been performed using paper forms. The Web system is developed for ease of use by clinicians and accessibility at any computer within the medical center. The database consists of 12 tables interrelated by the patient medical record number, admission number, or location. The NSS consult is the main table used to navigate to the other tables. Update of the laboratory and PN formula table must be done through the consult table. The system is compliant with the Health Insurance Portability and Accountability Act guidelines, and has been developed so that the forms that are required to be placed in the patient's permanent record can be printed. Demographic information and laboratory data are automatically populated via a link to the medical center's medication management system. At present, there are 1393 patients in the database and 21,000 pages are viewed each month during daily PN management by clinicians. Data can be easily retrieved for management reports. Data elements can be exported directly from the database to worksheets. This function has been used for projects designed to improve the efficiency of this PN system.
CTLA-4 and PD-L1 Checkpoint Blockade Enhances Oncolytic Measles Virus Therapy (2014)

We hypothesized that the combination of oncolytic virotherapy with immune checkpoint modulators would reduce tumor burden by direct cell lysis and stimulate antitumor immunity. In this study, we have generated attenuated Measles virus (MV) vectors encoding antibodies against CTLA-4 and PD-L1 (MV-aCTLA-4 and MV-aPD-L1). We characterized the vectors in terms of growth kinetics, antibody expression, and cytotoxicity in vitro. Immunotherapeutic effects were assessed in a newly established, fully immunocompetent murine model of malignant melanoma, B16-CD20. Analyses of tumor-infiltrating lymphocytes and restimulation experiments indicated a favorable immune profile after MV-mediated checkpoint modulation. Therapeutic benefits in terms of delayed tumor progression and prolonged median overall survival were observed for animals treated with vectors encoding anti-CTLA-4 and anti-PD-L1, respectively. Combining systemic administration of antibodies with MV treatment also improved therapeutic outcome. In vivo oncolytic efficacy against human tumors was studied in melanoma xenografts. MV-aCTLA-4 and MV-aPD-L1 were equally efficient as parental MV in this model, with high rates of complete tumor remission (> 80%). Furthermore, we could demonstrate lysis of tumor cells and transgene expression in primary tissue from melanoma patients. The current results suggest rapid translation of combining immune checkpoint modulation with oncolytic viruses into clinical application.