gebhart/patrepeval huggingface dataset:
Microparticle-enhanced nephelometric immunoassay (Nephelia) for immunoglobulins G, A, and M (1991)

Covalent binding of gamma chains of IgG, whole IgA, and mu chains of IgM on polyfunctional hydrophilic microspheres (MS) yields MS-Ig conjugates, usable as reagents in new microparticle-enhanced nephelometric immunoassays (Nephelia). The principle of the assays is inhibition by free analyte (IgG, IgA, and IgM) of agglutination of the MS-Ig conjugate with specific antiserum, the light scattered by the aggregates being measured with a nephelometer. The immunoglobulin assays developed are easy to perform (single-step assays, no washing or phase separation) and sensitive (high dilution of biological samples to exclude interferences and pretreatment). Analytical recovery results (95.4-101.2%) and correlations with generally used commercial assays (r = 0.86-0.98) indicate that the assays are accurate for large concentration ranges of immunoglobulins. Precision study gives CVs = 2.8-9.6%. Nephelia appears to be useful for quantifying a large variety of biological molecules.
Determining the Relationship Between Clofazimine Gastrointestinal Levels and anti‐ Cryptosporidium Efficacy in Mice (2022)

Introduction Cryptosporidiosis, the disease caused by parasitic infections with Cryptosporidium spp. can cause long‐term adverse impacts and even death in malnourished children and immunocompromised patients. The only FDA‐approved drug for treating cryptosporidiosis, nitazoxanide, has limited efficacy in the populations that are impacted most by the disease. A large‐scale phenotypic screening campaign identified clofazimine as active in both in vitro and in vivo preclinical models of Cryptosporidium infection. However, clofazimine was not effective in controlling Cryptosporidium infection in a subsequent Phase 2a clinical trial in HIV‐positive adults with cryptosporidiosis. Our recent pharmacokinetic/pharmacodynamic (PK/PD) modeling work demonstrated that plasma clofazimine levels observed in the Phase 2a clinical trial fell well below projected efficacious plasma concentrations estimated with preclinical in vivo data. Therefore, suboptimal clofazimine exposure in the Phase 2a trial likely contributed to the observed lack of efficacy. Nevertheless, plasma clofazimine levels may not represent local concentrations at the gastrointestinal (GI) tract, the site of action for treatment of Cryptosporidium infection. Thus, the objective of our current study is to build a physiologically based pharmacokinetic (PBPK) model of clofazimine in mice to simulate clofazimine GI pharmacokinetics (PK), estimate efficacious clofazimine concentrations at the tissue level, and explore important factors that can impact clofazimine exposure at the site of infection. Methods C57BL/6 mice were administered a single oral dose of clofazimine at dose levels ranging 0.03‐300 mg/kg. Blood samples were collected up to 240 hours post‐dosing and GI samples were collected at 240 hours post‐dosing. In tandem, an efficacy study treated C. parvum ‐infected IFN‐γ‐/‐ mice with equivalent clofazimine dosing and oocysts in fecal samples were quantified over time. GastroPlus (Simulations Plus) was used for modeling and simulation. Results The final PBPK model captured clofazimine plasma PK in mice well across most doses (within a 2‐fold margin). The simulated clofazimine GI concentrations increased with increasing dose in a non‐proportional manner, similar to what was observed with the plasma PK. As expected for a drug with poor solubility, the non‐linearity was attributed to diminished drug dissolution at higher dose levels. The simulated clofazimine tissue concentrations were used to construct PK/PD models to predict efficacious tissue concentrations. Conclusion A clofazimine PBPK model was generated in mice to simulate clofazimine levels in plasma and the GI tract. By incorporating clofazimine efficacy data from a mouse model of Cryptosporidium infection, we identified a relationship between tissue drug concentrations and reduction in infection burden. Establishing a PK/PD relationship informed by GI drug levels will assist future drug development efforts for cryptosporidiosis.
Phase-conjugate optical coherence tomography (2006)

Quantum optical coherence tomography (Q-OCT) offers a factor-of-2 improvement in axial resolution and the advantage of even-order dispersion cancellation when it is compared to conventional OCT (C-OCT). These features have been ascribed to the nonclassical nature of the biphoton state employed in the former, as opposed to the classical state used in the latter. Phase-conjugate OCT (PC-OCT) shows that nonclassical light is not necessary to reap Q-OCT's advantages. PC-OCT uses classical-state signal and reference beams, which have a phase-sensitive cross correlation, together with phase conjugation to achieve the axial resolution and even-order dispersion cancellation of Q-OCT with a signal-to-noise ratio that can be comparable to that of C-OCT.
Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes (1998)

A new set of united-atom Lennard-Jones interaction parameters for n-alkanes is proposed from fitting to critical temperatures and saturated liquid densities. Configurational-bias Monte Carlo simulations in the Gibbs ensemble were carried out to determine the vapor−liquid coexistence curves for methane to dodecane using three united-atom force fields:  OPLS [Jorgensen, et al. J. Am. Chem. Soc. 1984, 106, 813], SKS [Siepmann, et al. Nature 1993, 365, 330], and TraPPE. Standard specific densities and the high-pressure equation-of-state for the transferable potentials for phase equilibria (TraPPE) model were studied by simulations in the isobaric−isothermal and canonical ensembles, respectively. It is found that one set of methyl and methylene parameters is sufficient to accurately describe the fluid phases of all n-alkanes with two or more carbon atoms. Whereas other n-alkane force fields employ methyl groups that are either equal or larger in size than the methylene groups, it is demonstrated here that usin...
Universal Paralinguistic Speech Representations Using self-Supervised Conformers (2022)

Many speech applications require understanding aspects beyond the words being spoken, such as recognizing emotion, detecting whether the speaker is wearing a mask, or distinguishing real from synthetic speech. In this work, we introduce a new state-of-the-art paralinguistic representation derived from large-scale, fully self-supervised training of a 600M+ parameter Conformer-based architecture. We benchmark on a diverse set of speech tasks and demonstrate that simple linear classifiers trained on top of our time-averaged representation outperform nearly all previous results, in some cases by large margins. Our analyses of context-window size demonstrate that, surprisingly, 2 second context-windows achieve 96% the performance of the Conformers that use the full long-term context on 7 out of 9 tasks. Furthermore, while the best per-task representations are extracted internally in the network, stable performance across several layers allows a single universal representation to reach near optimal performance on all tasks.
A novel lysosome-targeted fluorogenic probe based on 5-triazole-quinoline for the rapid detection of hydrogen sulfide in living cells (2018)

A fluorogenic probe based on the novel fluorophore 5-triazole-quinoline was developed for the detection of hydrogen sulfide, an endogenous signaling molecule associated with the development of various diseases. The lysosome-targeted probe Lyso-HS was synthesized via C-H direct azidation from 8-aminoquinoline; it was able to detect H<sub>2</sub>S in 1 min and exhibited excellent turn-on ability with 95-fold fluorescence enhancement based on a new fluorochrome. The high quenching efficiency was further verified using time-dependent density functional theory (TDDFT). The probe also exhibited high selectivity and a low detection limit (as low as 214.5 nM), which has practical applications for disease detection and monitoring.
Doped luminescent materials and particle discrimination using same (2023)

Doped luminescent materials are provided for converting excited triplet states to radiative hybrid states. The doped materials may be used to conduct pulse shape discrimination (PSD) using luminescence generated by harvested excited triplet states. The doped materials may also be used to detect particles using spectral shape discrimination (SSD).
Preliminary study into query translation for patent retrieval (2010)

Patent retrieval is a branch of Information Retrieval (IR) aiming to support patent professionals in retrieving patents that satisfy their information needs. Often, patent granting bodies require patents to be partially translated into one or more major foreign languages, so that language boundaries do not hinder their accessibility. This multilinguality of patent collections offers opportunities for improving patent retrieval. In this work we exploit these opportunities by applying query translation to patent retrieval. We expand monolingual patent queries with their translations, using both a domain-specific patent dictionary that we extract from the patent collection, and a general domain-free dictionary. Experimental evaluation on a standard CLEF-IP dataset shows that using either translation dictionary fetches similar results: query translation can help patent retrieval, but not always, and without great improvement compared to standard statistical monolingual query expansion (Rocchio). The improvement is greater when the source language is English, as opposed to French or German, a finding partly due to the effect of the complex French and German morphology upon translation accuracy, but also partly due to the prevalence of English in the collection. A thorough per-query analysis reveals that cases where standard query expansion fails (e.g. zero recall) can benefit from query translation.
Tunable bandgap opening in the proposed structure of silicon-doped graphene (2011)

A specific structure of doped graphene with substituted silicon impurity is introduced and ab initio density-functional approach is applied for the energy band structure calculation of the proposed structure. Using the band structure calculation for different silicon sites in the host graphene, the effect of silicon concentration and unit cell geometry on the bandgap of the proposed structure is also investigated. Chemically, silicon-doped graphene results in an energy gap as large as 2 eV according to density-functional theory calculations. As the authors will show, in contrast to previous bandgap engineering methods, such structure has significant advantages including wide gap tuning capability and its negligible dependency on lattice geometry.
Profiling Carbohydrate Metabolism in Liver and Hepatocellular Carcinoma with [ 13 C]‐Glycerate Probes (2021)

The interplay between glycolysis and gluconeogenesis is central to carbohydrate metabolism. Here, we describe novel methods to assess carbohydrate metabolism using [<sup>13</sup>C]-probes derived from glycerate, a molecule whose metabolic fate in mammals remains underexplored. Isotope-based studies were conducted via NMR and mass spectrometry analyses of freeze-clamped liver tissue extracts after [2,3-<sup>13</sup>C<sub>2</sub>]glycerate infusion. The <i>ex vivo</i> investigations were correlated with <i>in vivo</i> measurements using hyperpolarized [1-<sup>13</sup>C]glycerate. Application of [<sup>13</sup>C]glycerate to N-nitrosodiethylamine (DEN)-treated rats provided further assessments of intermediary carbohydrate metabolism in hepatocellular carcinoma. This method afforded direct analyses of control versus DEN tissues, and altered ratios of <sup>13</sup>C metabolic products as well as unique glycolysis intermediates were observed in the DEN liver/tumor. Isotopomer studies showed increased glycerate uptake and altered carbohydrate metabolism in the DEN rats.
Determinants of Lung Function, COPD, and Asthma (2011)

n engl j med 364;1 nejm.org january 6, 2011 86 replacement therapy in patients with severe hereditary angioedema refractory to danazol prophylaxis. Transfusion 2009;49: 1987-95. 2. Bowen T, Cicardi M, Farkas H, Bork K, et al. 2010 International consensus algorithm for the diagnosis, therapy and management of hereditary angioedema. Allergy Asthma Clin Immunol 2010;6:24. 3. Longhurst HJ, Farkas H, Craig T, et al. HAE international home therapy consensus document. Allergy Asthma Clin Immunol 2010;6:22.
Nutrition and the developing brain: nutrient priorities and measurement (2007)

Nutrients and growth factors regulate brain development during fetal and early postnatal life. The rapidly developing brain is more vulnerable to nutrient insufficiency yet also demonstrates its greatest degree of plasticity. Certain nutrients have greater effects on brain development than do others. These include protein, energy, certain fats, iron, zinc, copper, iodine, selenium, vitamin A, choline, and folate. The effect of any nutrient deficiency or overabundance on brain development will be governed by the principle of timing, dose, and duration. The ability to detect the specific effects of nutrient deficiencies is dependent on knowing which area of the brain is preferentially affected and on having neurologic assessments that tap into the functions of those specific areas. As examples, protein-energy malnutrition causes both global deficits, which are testable by general developmental testing, and area-specific effects on the hippocampus and the cortex. Iron deficiency alters myelination, monoamine neurotransmitter synthesis, and hippocampal energy metabolism in the neonatal period. Assessments of these effects could include tests for speed of processing (myelination), changes in motor and affect (monoamines), and recognition memory (hippocampus). Zinc deficiency alters autonomic nervous system regulation and hippocampal and cerebellar development. Long-chain polyunsaturated fatty acids are important for synaptogenesis, membrane function, and, potentially, myelination. Overall, circuit-specific behavioral and neuroimaging tests are being developed for use in progressively younger infants to more accurately assess the effect of nutrient deficits both while the subject is deficient and after recovery from the deficiency.
Response to “Comments on ‘Evaluation of a Microfocused Ultrasound System for Improving Skin Laxity and Tightening in the Lower Face’” (2015)

We thank Dr Friedmann for his thoughtful comments.1 Striving for objective measurements to guide clinical efficacy is clearly important, particularly in this field.2 Our study has tried to address this issue by utilizing a number of measurements, both qualitative and quantitative.3 We recognize that validated subjective and objective measurements remain the gold standard in clinical research.

Three-dimensional (3D) imaging was used for all our subjects (Vectra M3, Canfield Imaging, Fairfield, NJ). We captured the 3D images using Mirror software's alignment method, which utilizes two pairs of vertical lines and one pair of horizontal lines to align the position of the subject's head. This …
NMR Imaging of Intracranial Hemorrhage (1984)

Twenty-one intracranial hemorrhagic lesions were imaged at 0.15 and 0.6 T using inversion recovery (IR), spin echo (SE), and multiple SE (Carr-Purcell-Meiboom-Gill, CPMG) pulse sequences. Two subarachnoid hemorrhages (SAH), nine acute intraparenchymal hemorrhages (IPH), ten chronic IPH, and one subdural hematoma were studied. Acute SAH could not be identified on the T1-weighted, IR images but was clearly seen on a T2-weighted, CPMG image. Acute (7 days or less) intraparenchymal hematoma showed signal intensity on IR and CPMG images similar to white matter. The T1 and T2 times of acute intraparenchymal hematoma were also similar to white matter. Some small acute hematomas could not be distinguished from white matter on IR and CPMG images. Acute hemorrhagic tissue showed image intensities and relaxation times similar to gray matter. All acute hemorrhages were identified on CT. Chronic IPH lesions (14 days or more) showed high signal intensity, greater than white matter, on IR, SE, and CPMG images. The T1 of the chronic lesions was similar to the acute lesions but T2 was significantly longer (p less than 0.05). Available evidence suggests that the nonspecificity of acute IPH signal and relaxation times may not be restricted to our pulse sequences or magnetic field strengths.
Characterization of Two Soybean Repetitive Proline-Rich Proteins and a Cognate cDNA from Germinated Axes (1989)

Ketaki Datta, Albert Schmidt, Abraham Marcus, Characterization of Two Soybean Repetitive Proline-Rich Proteins and a Cognate cDNA from Germinated Axes, The Plant Cell, Vol. 1, No. 9 (Sep., 1989), pp. 945-952
A WIRELESS EMBEDDED DEVICE FOR PERSONALIZED ULTRAVIOLET MONITORING (2009)

The skin care product market is growing due to the threat of ultraviolet (UV) radiation caused by the destruction of the ozone layer, increasing demand for tanning, and the tendency to wear less clothing. Accordingly, there is a potential demand for a personalized UV monitoring device, which can play a fundamental role in skin cancer prevention by providing measurements of UV radiation intensities and corresponding recommendations. This paper highlights the development and initial validation of a wireless and portable embedded device for personalized UV monitoring which is based on a novel software architecture, a high-end UV sensor, and conventional PDA (or a cell phone). In terms of short-term applications, by calculating the UV index, it informs the users about their maximum recommended sun exposure time by taking their skin type and sun protection factor (SPF) of the applied sunscreen into consideration. As for long-term applications, given that the damage caused by UV light is accumulated over days, it displays the amount of UV received over a certain course of time, from a single day to a month.
Changes in Turkey Semen Lipids During Liquid In Vitro Storage1 (2000)

The changes in lipid composition of spermatozoa and seminal plasma and changes in motility, viability, and morphological integrity of spermatozoa were measured in turkey semen diluted in Beltsville poultry semen extender and stored for 48 h (4 degrees C). The total phospholipid content of spermatozoa decreased during storage, while no quantitative decrease was observed in seminal plasma. More precisely, significant decreases in phosphatidylcholine, and to a lesser extent in sphingomyeline, phosphatidylserine, and phosphatidylinositol were observed in spermatozoa. The fatty acid profile of turkey spermatozoa partly reflected diet composition and had a high level of n-9 polyunsaturated fatty acids. Neither fatty acid profile nor free cholesterol were affected by storage. The lipid composition of seminal plasma was quite different from that observed in spermatozoa and was similar to the high density lipoprotein composition of chicken seminal plasma. In vitro storage did not significantly affect lipid classes and only small changes were observed in phospholipid classes of seminal plasma. The motility, viability, and morphological integrity of spermatozoa decreased during storage. These changes in phospholipid content may be explained by membrane phospholipid lysis followed by endogenous metabolism or by a complex combination of lysis, metabolism, and peroxidation. They are likely to affect semen quality and the success of in vitro storage severely.
Platelet glycoprotein IIb/IIIa inhibition in acute coronary syndromes. Gradient of benefit related to the revascularization strategy (2002)

This analysis, including the entire large-scale trial experience of intravenous glycoprotein IIb/IIIa inhibitors in patients with acute coronary syndromes primarily medically managed, demonstrates an overall significant, albeit moderate, reduction in 30-day death or myocardial infarction associated with therapy. Although not based on a prospectively defined hypothesis, the findings suggest a gradient of benefit conferred by these agents depending on the revascularization strategy used.
Human cell engraftment after busulfan or irradiation conditioning of NOD/SCID mice. (2006)

Human hematopoietic stem cell (HSC) xenotransplantation in NOD/SCID mice requires recipient conditioning, classically achieved by sublethal irradiation. Pretreatment with immunosuppressive and alkylating agents has been reported, but has not been rigorously tested against standard irradiation protocols. Here, we report that treatment of mice with a single dose (35 mg/kg) of Busilvex, an injectable form of busulfan, enables equivalent engraftment compared to 3.5 Gy irradiation. Mice treated with two doses of 25 mg/kg to reduce busulfan toxicity showed increased chimerism. Busulfan conditioning and irradiation resulted in comparable sensitivity of HSC detection as evaluated by limiting dilution analysis.
Endoscopic treatment of bronchopleural fistulas using N-butyl-2-cyanoacrylate. (1994)

Bronchopleural fistulas represent a serious complication of pulmonary surgery. Surgical treatment of bronchopleural fistulas has a high morbidity and mortality rate. Endoscopic sealing procedures are less invasive and more effective. We describe two patients successfully treated for fistulas stemming from pulmonary surgery. Biological (Tissucol) and synthetic glues (N-butyl-2-cyanoacrylate: Histoacryl) have been used. The technique must be chosen according to the fistulas' characteristics: Tissucol for small and medium-size fistulas, Histoacryl for large ones.
The carboxyl terminus of bradykinin and amino terminus of the light chain of kininogens comprise an endothelial cell binding domain. (1994)

Bradykinin (BK), a potent vasoactive nonapeptide formed by proteolytic cleavage of kininogen, mediates its activity by binding to specific cell surface receptors. Delivery of BK to these receptors is limited by cell-bound and plasma kininases that degrade BK to inactive fragments. Binding of its parent compound, kininogen, to specific endothelial cell receptors may provide an environment in which the degradation of BK by kininases is restricted. The determinants that mediate kininogen binding to endothelial cells have not been fully elucidated. The present studies suggest that part of BK and the amino-terminal amino acids of kininogens' common light chain constitute part of this recognition sequence. Human umbilical vein endothelial cells (HUVEC) in culture at 37 degrees C express 2-3-fold more binding sites for biotinylated high molecular weight kininogen (biotin-HK) containing BK than for biotin-HK from which BK has been liberated by plasma kallikrein. Binding of BK-free biotin-HK was not restored by preincubating HUVEC with BK, arguing against the possibility that BK released from biotin-HK stimulated expression of additional HK receptors. The extent of biotin-HK binding to HUVEC at 37 degrees C directly correlated with the amount of BK retained within the protein. Four lines of evidence suggest that part of BK and the amino terminus of the light chain of kininogens are part of the sequence recognized by the endothelial cell kininogen receptor. First, monoclonal antibodies to the carboxyl terminus of BK (MBK3) and the common light chains of the kininogens (HKL6, HKL8) inhibited biotin-HK binding to HUVEC. Second, a synthetic, dimeric bradykinin receptor antagonist blocked biotin-HK (IC50 = 9 microM) binding to HUVEC as did two synthetic tissue kallikrein inhibitors modeled after the carboxyl-terminal sequence of BK. Third, synthetic peptides containing the carboxyl-terminal portion of BK and the amino terminus of kininogens' common light chain, MKRPPGFSPFRSSRIG and GFSPFRSSRIG, blocked binding of biotin-HK (IC50 = 2-3 mM), whereas an overlapping peptide, SPFRSSRIGEIKEETT, at 5 mM and a scrambled peptide, FSGPKRSPIMGRPSFR, did not. Fourth, biotinylated GMKRPPGFSPFRSSRIG specifically bound to HUVEC, and its binding was blocked by HK. Since the presence of the nonapeptide BK in HK contributes to maximal binding of HK to HUVEC, there is a novel type of BK receptor in which part of the nonapeptide is recognized within the context of its parent molecule.(ABSTRACT TRUNCATED AT 400 WORDS)