gebhart/patrepeval huggingface dataset:
Comprehensive analysis of HIV reservoirs in elite controllers (2023)

To the Editor: HIV remains an uncurable disease in infected individuals receiving antiretroviral therapy (ART).Despite unparalleled research efforts to find a cure, there is a growing sentiment in the field that complete viral eradication is unlikely with existing therapies.Therefore, an approach involving immune-mediated virologic control without ART represents a realistic goal, even if the HIV reservoir persists (1).In this regard, the ability of some individuals to control HIV replication (i.e., elite controllers [ECs]) illustrates the feasibility of achieving ART-free virologic remission.Prior studies have established that ECs carry low HIV DNA burdens and exhibit robust HIV-specific immune responses (2).However, there are few studies directly comparing the composition and frequencies of HIV reservoirs in ECs with those in chronically infected individuals receiving ART (CAs).We conducted the present study to address this issue.We studied 9 ECs and 22 CAs (Supplemental Table 1 and Supplemental Methods; supplemental material available online with this article; https://doi.org/10.1172/JCI165446DS1).Blood products were obtained in accordance with a protocol approved by the Institutional Review Board of the National Institute of Allergy and Infectious Diseases of the NIH.All participants provided written informed consent.We first compared the composition and size of HIV reservoirs in the EC and CA groups.The levels of total HIV DNA (P < 0.0001), cell-associated HIV RNA (P < 0.0001), intact proviral DNA (IPD) (P = 0.0026), and defective HIV DNA (P < 0.0001) in CD4 + T cells were significantly lower in the EC group compared with those in the CA group (Figure 1, A and B) (2).To assess the replication competency of infected cells, we measured the levels of inducible virion-associated HIV RNA (ivRNA) and replication-competent virus in CD4 + T cells.In contrast to the above data, there was no significant difference in the levels of ivRNA (P = 0.4187) and replication-competent HIV (P = 0.9303) between the two groups (Figure 1C).Three ECs had exceptionally low infectious HIV burdens in their CD4 + T cells.EC-6 and EC-7 had no detectable infectious virus (<1 copy in 245 × 10 6 CD4 + T cells), despite repeated testing.The ratio of intact-to-defective HIV DNA was similar in the EC and CA groups (P = 0.7471; Figure 1D); however, the ratio of IPD to replication-competent virus was significantly lower in the EC group compared with that in the CA group (P = 0.0052; Figure 1D).The frequencies of IFN-γ + and CD107a + IFN-γ + TNF-α + MIP-1β + HIV Gag-specific CD8 + T cells were significantly higher in the EC group compared with those in the CA group (P = 0.0315 and P = 0.0001, respectively; Figure 1E), suggesting that ECs may express sufficient viral antigens.IPD burdens were relatively high in EC-4 and EC-6 (75 and 105 copies/10 6 cells, respectively).Therefore, we conducted longitudinal measurements of ivRNA and IPD (EC-4) and near full-length sequencing of HIV DNA from a sorted CD4 + T subset (EC-6).
AMMONIA TOXICITY IN CULTURED LARVAE OF THE AMERICAN LOBSTER (Homarus americanus)<sup>1</sup> (1977)

ABSTRACT Ammonia is the chief nitrogenous excretory product of lobsters and is known to be toxic to these crustaceans at relatively low concentrations. The primary purpose of this study was to determine tolerance limits of larval Homarus americanus to ammonia in order to optimize design of the seawater circulation and waste treatment components of a lobster mariculture system. This is often a critical problem in culture systems in which a major part of the seawater is recycled. The incipient median lethal concentration (LC 50 ) and tentatively safe ammonia concentration were determined for fourth stage larvae of H. americanus to be 1.4 and 0.14 mg/liter un‐ionized ammonia‐nitrogen (NH 3 ‐N), respectively. The effects of pH, temperature, and salinity on ammonia toxicity also were evaluated. Increasing pH from 7.4 to 8.4 increases toxicity markedly. Increasing temperature from 21°C, near the optimum for growth, to 25°C increases toxicity only slightly. Changes in salinity from 31 to 36 ppt produce no appreciable effect. These increase in pH or temperature shift the NH 3 /NH+ 4 equilibrium unfavorably toward the more toxic NH 3 negligible effect on the equilibrium. A simplified steady‐state equation was developed for predicting the optimum biomass loading for a lobster culture system, based on the ammonia toxicity determined for fourth stage larval lobsters. This equation relates the ammonia tolerance limit, ammonia excretion rate, ambient ammonia concentration of the water source, water flow rate, degree of water reuse, and efficiency of ammonia removal. The time lag required for the culture system to attain steady‐state conditions also is considered.
Iridium-catalyzed Asymmetric Hydrogenation of Pyridinium Salts for Constructing Multiple Stereogenic Centers on Piperidines (2013)

Abstract A salt formation strategy for asymmetric hydrogenation of pyridines is described. Poly-substituted pyridinium salts were successfully hydrogenated using chiral iridium dinuclear complexes to afford substituted piperidines with multiple stereogenic centers after a simple basic workup.
Immature dendritic cell-derived exosomes rescue septic animals via milk fat globule epidermal growth factor VIII (2009)

Miksa, M., R. Wu, W. Dong, H. Komura, D. Amin, Y. Ji, Z. Wang, H. Wang, T. S. Ravikumar, K. J. Tracey, and P. Wang. 2009. Immature dendritic cell-derived exosomes rescue septic animals via milk fat globule epidermal growth factor VIII. [ J. Immunol. 183: 5983–5990][1] . The title of this article
Isentropic (2023)

This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.
Accurate viscosity measurements of flowing aqueous glucose solutions with suspended scatterers using a dynamic light scattering approach with optical coherence tomography (2017)

The viscosity of turbid colloidal glucose solutions has been accurately determined from spectral domain optical coherence tomography (OCT) M-mode measurements and our recently developed OCT dynamic light scattering model. Results for various glucose concentrations, flow speeds, and flow angles are reported. The relative "combined standard uncertainty" uc(η) on the viscosity measurements was ±1% for the no-flow case and ±5% for the flow cases, a significant improvement in measurement robustness over previously published reports. The available literature data for the viscosity of pure water and our measurements differ by 1% (stagnant case) and 1.5% (flow cases), demonstrating good accuracy; similar agreement is seen across the measured glucose concentration range when compared to interpolated literature values. The developed technique may contribute toward eventual noninvasive glucose measurements in medicine.
OPTIMISATION OF THE STRUCTURE AND ACTIVITY OF FUEL CONVERSION CATALYSTS. NATIONAL ENERGY RESEARCH, DEVELOPMENT AND DEMONSTRATION PROGRAM END OF GRANT REPORT (1989)

Coal derived heavy oils contain significant quantities of heteroatoms, which must be removed during upgrading to produce transport fuels. The heteroatoms are chemically combined with components of the oil and are best removed by hydrotreating, usually over a catalyst. Optimisation of the preparation of such catalysts has been carried out previously (NERDDP Project 958: March 1988). The present studies are focused on the optimisation of the structure of supports to control surface area, porosity and strength.
Membrane Environment Exerts an Important Influence on Rac-Mediated Activation of Phospholipase Cγ2 (2011)

We performed analyses of the molecular mechanisms involved in the regulation of phospholipase Cγ2 (PLCγ2). We identified several regions in the PLCγ-specific array, γSA, that contribute to autoinhibition in the basal state by occlusion of the catalytic domain. While the activation of PLCγ2 by Rac2 requires stable translocation to the membrane, the removal of the domains required for membrane translocation in the context of an enzyme with impaired autoinhibition generated constitutive, highly active PLC in cells. We further tested the possibility that the interaction of PLCγ2 with its activator protein Rac2 was sufficient for activation through the release of autoinhibition. However, we found that Rac2 binding in the absence of lipid surfaces was not able to activate PLCγ2. Together with other observations, these data suggest that an important consequence of Rac2 binding and translocation to the membrane is that membrane proximity, on its own or together with Rac2, has a role in the release of autoinhibition, resulting in interfacial activation.
Spatio-temporal interaction model for crowd video analysis (2017)

We present an unsupervised approach to analyze crowd at various levels of granularity $-$ individual, group and collective. We also propose a motion model to represent the collective motion of the crowd. The model captures the spatio-temporal interaction pattern of the crowd from the trajectory data captured over a time period. Furthermore, we also propose an effective group detection algorithm that utilizes the eigenvectors of the interaction matrix of the model. We also show that the eigenvalues of the interaction matrix characterize various group activities such as being stationary, walking, splitting and approaching. The algorithm is also extended trivially to recognize individual activity. Finally, we discover the overall crowd behavior by classifying a crowd video in one of the eight categories. Since the crowd behavior is determined by its constituent groups, we demonstrate the usefulness of group level features during classification. Extensive experimentation on various datasets demonstrates a superlative performance of our algorithms over the state-of-the-art methods.
Supplementary Figure 2 from Effect of Niclosamide on Basal-like Breast Cancers (2023)

&lt;p&gt;PDF file - 209KB, Supplementary Figure S2. Niclosamide effect on Wnt/beta-catenin signaling. Activity of TCF/LEF plasmid reporter in the TOPflash assay was evaluated on adherent 2LMP, SUM159, HCC143 and HCC1187 cells. Cell lines were treated with 1 microM niclosamide for 24 hours (SUM159, HCC1143 and HCC1187) or with 0.25 microM niclosamide (2LMP). Each cell line was also treated with Wnt3A ligand (5 ng/mL) alone and in combination with niclosamide. The experiment was performed in triplicate. The bars represent means plus-minus SE. Treatment was compared to control or Wnt3A. Niclosamide vs. control (*P &lt; 0.05), niclosamide vs. control (**P &lt; 0.01), niclosamide vs. Wnt3A (#P &lt; 0.05), niclosamide + Wnt3A vs. Wnt3A (##P &lt; 0.01).&lt;/p&gt;
Crystal Structures of C<sub>94</sub>(CF<sub>3</sub>)<sub>20</sub> and C<sub>96</sub>(C<sub>2</sub>F<sub>5</sub>)<sub>12</sub> Reveal the Cage Connectivities in C<sub>94</sub> (61) and C<sub>96</sub> (145) Fullerenes (2009)

Perfluoroalkylation of a mixture of higher fullerenes has yielded the first direct proof of the cage connectivities in C94 (isomer 61) and C96 (isomer 145). The addition patterns of the RF groups on these fullerene cages, the largest to be structurally investigated to date, were determined by X-ray structure analyses of C94(CF3)20 (see structure; gray C, green F) and C96(C2F5)12.
Functions for the analysis of exploration and exploitation (2013)

Real parameter optimization is one of the most common applications of evolutionary computation. In this study we define a protocol to understand the exploratory and exploitative behaviors of evolutionary algorithms and evaluate two representations on four test functions. The first representation, storing the real parameters in an array, is a standard representation. The second representation, called the walking triangle representation is introduced in this study. This representation is a generative one which models a set of real parameters as the center of mass of a simplex. The generative rules modify the simplex through reflection, scaling, and deformation. It is shown that this representation behaves in a substantially different manner from the standard one and has very different capabilities. On two of the four test problems, one variation of the walking triangle yields an improvement of hundreds orders of magnitude in fitness. This paper suggests that representations themselves are just as important to consider when optimizing evolutionary algorithms for a balance of exploration and exploitation, and further that our system of open-ended test functions can be used to monitor this balance and adjust these considerations accordingly.
Viral inhibitors of NKG2D ligands: Friends or foes of immune surveillance? (2008)

NKG2D is a potent activating receptor on NK cells and a co-stimulatory receptor on CD8+ T cells. Through its ability to recognize a panel of ligands inducible by stress or infection, it plays an important role in the control of viral infections. The viruses have evolved robust mechanisms to counteract NKG2D-dependent immune response. The functions of these viral inhibitors are well characterized during the early days post-infection but less so during the chronic viral infection.
Engineering Methods for Europan Relevant Biosignature Development (2004)

&lt;div class="htmlview paragraph"&gt;One of the primary driving forces for space exploration in the foreseeable future is astrobiology, and specifically the search for a plausible sign of life beyond Earth. Because of the size of the potential saltwater ocean involved, Europa is potentially the most interesting, and possibly the only, currently viable (for life) environment in the solar system. It also presents the possibility of remote sensing evaluation for presence or absence of biotic and/or pre-biotic organic material. The material of interest is the non-ice (referring to water ice) surface material near features that have the potential of being in recent communication with the postulated ocean below. An analysis of this material using a full range of inorganic, pre-biotic organic, and metabolically relevant biologic materials as spectrum calibrating target materials, examined under Europan surface conditions, is a daunting proposition. A comprehensive attempt is still pending.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This study involves the collection and growth of psychrophilic (low temperature), halophilic (high salt), anaerobic cultures in high sulfate environments. These cultures are intended as reflected spectrum target materials, based on relevant biomass, for comparison to Europan non-ice surface materials. The selection, collection, development (growth) and examination of this biotic material (biomass) requires the use of stringent, and in some cases extreme, environmental controls. It also requires the extrapolation of standard environmental engineering sampling and laboratory analysis procedures for use in comparison with, and interpretation of, data from a profoundly extreme and unfamiliar environment. The function of this study is to demonstrate the use of environmental engineering techniques and processes (test methodology) necessary to develope a reasonable biosignature related to the Europan target environment.&lt;/div&gt;
Complex High Internal-Phase Emulsions that can Form Interfacial Films with Tuneable Morphologies (2021)

High internal phase emulsions (HIPEs) are considered as an important functional material and have been the focus of intense development effort, but it has not been possible to alter their fundamental attributes at either the microcosmic or macroscopic level, which severely limits their practical applications in various areas. In this work, we report a general strategy for creating complex HIPEs and we additionally show a route to forming HIPE films at liquid interfaces. Double HIPEs and Janus HIPEs are both realized for the first time. They feature complex microscopic patterns with a short-range anisotropy, and exhibit non-Newtonian pseudoplastic flow behavior. By taking advantage of their response to a high-pH subphase, interfacial films can be successfully obtained, which are tunable in thickness and morphologies under compression.
Repositioning study of flubendazole for treating lung cancer and meningoencephalitis using an oral lipid nanosystem (2023)

YUKUYAMA, M.N.Repositioning study of flubendazole for treating lung cancer
Substrates for Rapid Delivery of Electrons and Holes to Buried Active Sites in Proteins (1999)

New reduced and oxidized states of cytochrome P450cam have been generated by electron transfer to and from the heme group of the buried active site. This is achieved with the photosensitizer [Ru(bpy)3]2+ (bpy=2,2′-bipyridine), which is linked through a hydrocarbon chain to a species with high affinity for the heme cavity (see picture). The direction of photoinduced charge transfer is controlled with a suitable quencher; the new oxidation states are formed in about 0.1 ms and persist for approximately 100 ms.
High-Throughput Immunogenetics Reveals a Lack of Physiological T Cell Clusters in Patients With Autoimmune Cytopenias (2019)

Autoimmune cytopenias (AIC) such as immune thrombocytopenia or autoimmune hemolytic anemia are claimed to be essentially driven by a dysregulated immune system. Using next-generation immunosequencing we profiled 59 T and B cell repertoires (<i>TRB</i> and <i>IGH</i>) of 25 newly diagnosed patients with primary or secondary (lymphoma-associated) AIC to test the hypothesis if these patients present a disease-specific immunological signature that could reveal pathophysiological clues and eventually be exploited as blood-based biomarker. Global <i>TRB</i> and <i>IGH</i> repertoire metrics as well as <i>VJ</i> gene usage distribution showed uniform characteristics for all lymphoma patients (high clonality and preferential usage of specific <i>TRBV</i>- and <i>TRBJ</i> genes), but no AIC-specific signature. Since T cell immune reactions toward antigens are unique and polyclonal, we clustered TCRβ clones <i>in-silico</i> based on target recognition using the GLIPH (grouping of lymphocyte interactions by paratope hotspots) algorithm. This analysis revealed a considerable lack of physiological T cell clusters in patients with primary AIC. Interestingly, this signature did not discriminate between the different subentities of AIC and was also found in an independent cohort of 23 patients with active autoimmune hepatitis. Taken together, our data suggests that the identified T cell cluster signature could represent a blood biomarker of autoimmune conditions in general and should be functionally validated in future studies.
An Improved Physics-based LTSpice Compact Electro-Thermal Model for a SiC Power MOSFET with Experimental Validation (2018)

A compact electro-thermal SiC Power MOSFET model implemented in LTSpice is presented in this paper. A 1200 V, 90A CREE SiC power MOSFET (C2M0025120D) has been used in this work to illustrate the parameter extraction and experimental model validation. The dynamic validation has been shown using a double-pulse test circuit. The convergence has been tested with the 4-switch topology of an inverter and a comparison between MAST, Verilog-A and CREE's empirical model of the same device has also been presented.
A TRNSYS Simulation Case Study on Utilization of Heat Pump (2012)

This paper presents a TRNSYS simulation case study on the integration of a heat pump into a hot water and cold water storage systems for the purpose of providing heating and cooling to a residential home or office building in a tropical climate. The motivation is to utilize waste heat rejected by the heat pump.The heat pump is integrated with two water storage tanks. One is the cold water tank where heat is extracted by the heat pump and the other is the hot water which stores the heat rejected by the heat pump. The cold water tank provides cooling water for air conditioning to the building. The hot water tank is used for daily usage like bathing and washing. The sizing of the two storage tanks and the balancing of the heat transfer between the two tanks are important design factors to maintain suitable temperatures in the storage tanks. The paper discusses the performance of the integrated system under different operational modes and the effects of each storage tank size on the performance. Key words : Heat pump; Heating; Cooling; TRNSYS; Simulation; Air conditioning
Multi-view 3D analysis with applications for augmented reality and enhanced video visualization (2002)

The article presents methods for 3D scene geometry recovery/refinement and pose estimation from motion imagery in two representative scenarios. First, we present a method for pose estimation and scene geometry recovery from extended sequences without prior knowledge of the scheme. Second, we discuss how to recover camera poses when a rough scene model is provided. We show how to extend and refine the scene model using the recovered poses. Finally, we present applications of the above techniques for 3D imagery manipulation such as enhanced visualization for video and 3D insertion of synthetic objects in the imagery.
IMCT-07THERAPEUTIC OUTCOMES OF INTRATHECAL INTERLEUKIN-2 IN METASTATIC MELANOMA PATIENTS WITH LEPTOMENINGEAL DISEASE (LMD) (2015)

BACKGROUND: Melanoma patients with LMD have a median survival of 1.8 months; there is significant medical need for innovative therapeutic strategies. METHODS: Stage IV melanoma patients were diagnosed with LMD by positive CSF cytology and/or leptomeningeal enhancement on post-contrast MRI. Patients received treatment with 1-5 doses/week of intrathecal IL-2 (IT IL2) for 4 weeks, followed by weekly injections for 4 weeks, then every other week depending on tolerance and response. The patients were ultimately given maintenance dosing of a single injection every 1-3 months under FDA approved compassionate-use investigational new drug application. Log-rank tests and Cox proportional hazards regression were used to assess statistical significance. RESULTS: The median age among 42 pts (32 male, 10 female) was 46.7 years (range 18.8-71.0). Symptoms due to increased intracranial pressure developed initially in all pts, and were controlled with supportive medications and/or CSF removal. The median overall survival (OS) was 9.1 months (range 0.7 - 86.2); 16% of pts had OS > 24 mos. Pts with LMD only without extracranial disease (ECD) (n = 4) had a median OS of 38.4 months. Pts with LMD with controlled ECD (n = 19, median OS 11.0 months) survived longer than pts with progressive ECD (n = 11, 6.5 mos; p = 0.30). Previous or concurrent brain metastases had no impact on OS. Shorter OS was associated with the presence of neurological symptoms at baseline (HR 2.1, p = 0.03). OS was not significantly associated with age, gender, LDH, or BRAF mutation status. CONCLUSIONS: The results support that IT IL2 can potentially improve the OS in a subset of pts, particularly those with no or controlled ECD, negative cytology, and no neurological symptoms. Furthermore, these results provide a strong rationale to evaluate IT immunotherapy in prospective clinical trials.