gebhart/patrepeval huggingface dataset:
Dispersal capacities of anadromous Allis shad population inferred from a coupled genetic and otolith approach (2015)

Understanding dispersal capacities for migratory species is crucial for their management. By coupling otolith microchemistry and microsatellite genetic analyses, we provided information on snapshot and long-term dispersal capacity of Allis shad (Alosa alosa), an anadromous clupeid in decline throughout its distribution range. The allocation of natal origin was obtained from water chemistry and signatures in otoliths of juveniles and spawners within a Bayesian model. The majority of adults were assigned to a source river with high degrees of confidence; only 4% were undetermined. Otolith natal origins were used to define a population baseline by grouping individuals from the same natal river and not from the same sampling location as usually done. While A. alosa exhibited a high level of natal site fidelity, this species showed weak genetic structure, which supported the evidence of a substantial flow of strayers between river basins in the vicinity or at longer distances. However, long distance straying was probable but not frequent. In a context of global change, straying would be a key mechanism to drive dispersal and allow resilience of Allis shad populations.
Identification of biomarkers to measure HIV-specific mucosal and systemic CD8+ T-cell immunity using single cell Fluidigm 48.48 Dynamic arrays (2015)

Thirty genes composed of cytokines, chemokines, granzymes, perforin and integrins were evaluated in gut and splenic K(d)Gag197-205-specific single CD8(+) T cells using Fluidigm 48.48 Dynamic arrays, with the aim of identifying biomarkers to predict effective mucosal and systemic vaccine efficacy. The mRNA expression profiles were analyzed in three ways: (i) the "number" of K(d)Gag197-205-specific CD8(+) T cells expressing the biomarker, (ii) "level" of mRNA expression using principal component analysis (PCA) and (iii) poly-functionality in relation to RANTES expression. In total, 21 genes were found to be differentially expressed between the vaccine groups and the immune compartments tested. Overall, the PCA indicated that IL-13Rα2 or IL-4R antagonist adjuvanted vaccines that previously induced high-avidity mucosal/systemic CD8(+) T cells with better protective efficacy, the "level" of mRNA expression, specifically RANTES, MIP-1β, and integrin α4 in gut K(d)Gag197-205-specific single CD8(+) T cells, were significantly elevated compared to unadjuvanted vaccine. Furthermore, significantly elevated granzymes/perforin levels were detected in IL-13(-/-) mice given the unadjuvanted vaccine, indicating that the degree of IL-13 inhibition (total, transient or no inhibition) can considerably alter the level of T-cell activity/poly-functionality. When splenic- and gut-K(d)Gag197-205-specific CD8(+) T cells were compared, PC1 vs. PC2 scores revealed that not only RANTES, MIP-1β, and integrin α4 mRNA, but also perforin, granzymes A/B, and integrins β1 and β2 mRNA were elevated in spleen. Collectively, data suggest that RANTES, MIP-1β, perforin, and integrins α4, β1 and β7 mRNA in single HIV-specific CD8(+) T cells could be used as a measure of effective mucosal and systemic vaccine efficacy.
Utility of Three-Protein Panels in the Separation of Aggressive Prostate Cancer from Non-Aggressive Tumors (2021)

Abstract Background Prostate cancer (PCa) is a heterogeneous group of tumors, including non-aggressive (NAG) and aggressive (AG) subtypes, with variable clinical outcomes. We assessed the diagnostic utility of selected protein markers to identify AG tumors. Methods The TMA was constructed, including NAG and AG. 12 protein markers were evaluated using the TMA by IHC stains. The makers were also evaluated for their potential utility as single or panels for distinguishing AG from NAG tumors. Results The higher expressions of four protein markers, including prostate specific membrane antigen (PSMA), phospho-EGFR, androgen receptor (AR), and P16, were identified in AG tumors of Gleason score 4 and 5. In contrast, Galectin-3, DPP4 and MAN1B1 revealed stronger staining patterns in NAG tumors. Sensitivity and specificity of individual marker varied widely. In tow-marker panels, especially in the panel of DPP4 and PSMA, the specificity was 38.46% at 95% sensitivity. To further improve the detection ability, we combined DPP4 and PSMA with either Galectin-3 or phospho-EGFR into three-marker panels. The specificity achieved &gt;46% at 95% sensitivity and AUC was &gt;0.85. Conclusions Our panels can be used to improve the separation of AG from NAG tumor and to add in the optimization of the treatment strategy for patients.
Probiotics in Primary Prevention of Atopic Dermatitis (2009)

The incidence of allergic diseases has been increasing in industrialized countries during recent years. Although several environmental factors are thought be involved, lack of moderate level of microbial challenges during the infantile period is known to skew the immune status toward the development of allergic diseases. Various strains of probiotics such as Bifidobacterium, Lactobacillus, and Lactococcus have been assessed for their ability to suppress the occurrence of atopic dermatitis (AD) in animal models and human studies. Although the effect of probiotics on allergic responses is different depending on the strains, doses, and experimental protocols, animal studies generally have shown immunomodulatory activities of probiotics including suppression of specific or nonspecific IgE production, reduction of infiltrated eosinophils and degranulated mast cells, potentiation of regulatory T cell cytokines such as IL-10 and TGF-beta relative to IL-4 and IL-5, and potentiation of Th1/Th2 activity along with reduced symptoms of AD. Several well-designed double-blind placebo-controlled human studies showed that some probiotic strains administered during perinatal period prevented the occurrence of AD but could not consistently show a reduction in specific or nonspecific IgE or a change in specific immunomodulatory cytokines. Taken together, published results suggest that the administration of selected strains of probiotics during the perinatal period may be helpful in the prevention of AD.
Thermochemistry of Sulfur-Based Vulcanization and of Devulcanized and Recycled Natural Rubber Compounds (2022)

The vulcanization of rubber compounds is an exothermal process. A carbon black-filled and natural rubber-based (NR) formulation was mixed with different levels of sulfur (0.5, 1.0, 2.0, 4.0 and 6.0 phr) and studied with Differential Scanning Calorimetry (DSC) for the determination of the vulcanization enthalpy. It was found that the vulcanization enthalpy is dependent from the amount of sulfur present in the compound and the vulcanization heat released was -18.4 kJ/mol S if referred to the entire rubber compound formulation or -46.0 kJ/mol S if the heat released is referred only to the NR present in the compound. The activation energy for the vulcanization of the rubber compounds was also determined by a DSC study at 49 kJ/mol and found quite independent from the sulfur content of the compounds under study. A simplified thermochemical model is proposed to explain the main reactions occurring during the vulcanization. The model correctly predicts that the vulcanization is an exothermal process although it gives an overestimation of the vulcanization enthalpy which is larger for the EV vulcanization package and smaller for the conventional vulcanization system. If the devulcanization is conducted mechanochemically in order to break selectively the sulfur-based crosslinks, then the natural rubber compounds recovered from used tires can be re-vulcanized again and the exothermicity of such process can be measured satisfactorily with DSC analysis. This paper not only proposes a simplified mechanism of vulcanization and devulcanization but also proposes an analytical method to check the devulcanization status of the recycled rubber compound in order to distinguish truly devulcanized rubber from reclaimed rubber.
Lentiviral Gene Therapy for Artemis-Deficient SCID (2022)

Infusion of lentiviral gene-corrected autologous CD34+ cells, preceded by pharmacologically targeted low-exposure busulfan, in infants with newly diagnosed ART-SCID resulted in genetically corrected and functional T and B cells. (Funded by the California Institute for Regenerative Medicine and the National Institute of Allergy and Infectious Diseases; ClinicalTrials.gov number, NCT03538899.).
Computationally efficient multidimensional analysis of complex flow cytometry data using second order polynomial histograms (2015)

Many methods have been described for automated clustering analysis of complex flow cytometry data, but so far the goal to efficiently estimate multivariate densities and their modes for a moderate number of dimensions and potentially millions of data points has not been attained. We have devised a novel approach to describing modes using second order polynomial histogram estimators (SOPHE). The method divides the data into multivariate bins and determines the shape of the data in each bin based on second order polynomials, which is an efficient computation. These calculations yield local maxima and allow joining of adjacent bins to identify clusters. The use of second order polynomials also optimally uses wide bins, such that in most cases each parameter (dimension) need only be divided into 4-8 bins, again reducing computational load. We have validated this method using defined mixtures of up to 17 fluorescent beads in 16 dimensions, correctly identifying all populations in data files of 100,000 beads in <10 s, on a standard laptop. The method also correctly clustered granulocytes, lymphocytes, including standard T, B, and NK cell subsets, and monocytes in 9-color stained peripheral blood, within seconds. SOPHE successfully clustered up to 36 subsets of memory CD4 T cells using differentiation and trafficking markers, in 14-color flow analysis, and up to 65 subpopulations of PBMC in 33-dimensional CyTOF data, showing its usefulness in discovery research. SOPHE has the potential to greatly increase efficiency of analysing complex mixtures of cells in higher dimensions.
Compact High Gain Dual-Band Dual-Polarized Base Station Antenna (2018)

This paper presents a compact ± 45° dual-band dual-polarized base station antenna. The lower band element is composed of two layer of patches. The upper layer patch provides a boresight radiation null in its higher band-edge for reducing the mutual coupling with higher band element. The higher band element is made up of 4 dipole antennas around the patch antenna. The balun feeding line of the dipole antenna is designed with a band-stop response in its lower band-edge by an open stub. In this way, compactness and high isolation can be obtained by the proposed dual-band filtering antenna unit. The proposed dual-band antenna is designed to fit the specification of DCS and WCDMA bands (1710-1880 MHz & 1920-2170 MHz for SWR $\lt 1.5$). The overall width of the antenna is only 140 mm. The antenna gains are over 8.6 dBi; and the 3-dB beamwidths of the horizontal radiation patterns are 60°-69°. The cross-polarizations are all lower than -20 dB, and the front –to-back ratios are more than 25 dB. Without extra filtering circuit, an isolation between the two bands is 15 dB, and the isolations between the two polarizations can reach 30dB.
Gender Influences Radicular Pain Perception in Patients with Lumbar Disc Herniation (2015)

Our results clearly indicate that sex differences in pain perception not only exist in healthy subjects, but also in patients with lumbar disc herniation. Therefore, it is essential to provide different treatment modalities to women and men.
Comparison of the bligh and dyer and folch methods for total lipid determination in a broad range of marine tissue (2001)

For many studies, it is important to measure the total lipid content of biological samples accurately. The Bligh and Dyer method of extraction was developed as a rapid but effective method for determining total lipid content in fish muscle. However, it is also widely used in studies measuring total lipid content of whole fish and other tissues. Although some investigators may have used modified Bligh and Dyer procedures, rarely have modifications been specified nor has their effectiveness been quantitatively evaluated. Thus, we compared this method with that of the classic Folch extraction in determining total lipid content of fish samples ranging from 0.5 to 26.6% lipid. We performed both methods as originally specified, i.e., using the chloroform/methanol/water ratios of 1:2:0.8 and 2:2:1.8 (before and after dilution, respectively) for Bligh and Dyer and of 8:4:3 for Folch, and with the initial solvent/sample ratios of (3+1):1 (Bligh and Dyer) and 20:1 (Folch). We also compared these with several other solvent/sample ratios. In samples containing <2% lipid, the results of the two methods did not differ. However, for samples containing >2% lipid, the Bligh and Dyer method produced significantly lower estimates of lipid content, and this underestimation increased significantly with increasing lipid content of the sample. In the highest lipid samples, lipid content was underestimated by up to 50% using the Bligh and Dyer method. However, we found a highly significant linear relationship between the two methods, which will permit the correction of reported lipid levels in samples previously analyzed using an unmodified Bligh and Dyer extraction. In the future, modifications to procedures and solvent/sample ratios should be described.
[Fundamental and clinical studies of imipenem/cilastatin sodium in the field of obstetrics and gynecology]. (1986)

Seven patients with gynecologic infections were treated with the new carbapenem class of antibiotic, imipenem/cilastatin sodium (MK-0787/MK-0791) at a dose level of 500 mg/500 mg or 250 mg/250 mg administered intravenously every 12 hours for 5 days. The results obtained were as follows. Clinical effects of MK-0787/MK-0791 were analyzed in 7 patients, including 1 case with pelvic peritonitis, 2 cases with endometritis, adnexitis and pelvic peritonitis, abdominal abscess, vaginal cuff infection and parametritis, and pyometra. Excellent clinical response was seen in 3 cases and good response in 4 cases. No side effect nor abnormal finding in clinical laboratory values was seen in all patients.
Effect of Cu/Ta duplex metal coating on interface characterization in SiC fibre-reinforced Ti-15 wt% V-3 wt% Cr-3 wt% Al-3 wt% Sn matrix composite (2000)

Abstract The interfacial reaction behaviour, alloying element diffusion behaviour and interface shear mechanical properties in Cu/Ta-duplex-metal-coated SiC(SCS-6)-fibre-reinforced Ti—15-3 matrix composite (SiC/Cu/Ta/(Ti—15-3)) have been studied. The results are compared with the original SiC(SCS-6)-fibre-reinforced Ti—15-3 matrix composite (SiC/(Ti—15-3)), and the effect of the Cu/Ta duplex metal coating on the interface characterizations has been discussed. The interface reaction occurs between the coating layer and the matrix, and the thickness of the reaction layer in the SiC/Cu/Ta/(Ti—15-3) increases slightly more than that of the SiC/(Ti—15-3). Electron probe microanalysis shows that the Cu and Ta diffuse into both the SCS coating and the matrix and that a large amount of Cu and Ta exists in the interface reaction region. The Cu/Ta coating acts as a diffusion barrier layer on Ti; however, the coating has no significant effect on the diffusion behaviours of C and Si. Fibre push-out test results indicate that the Cu Ta coating layer reduced significantly the interfacial shear debond stress and frictional stress. The interfacial shear mechanical properties of the composite have significantly degenerated after thermal exposure. This degeneration is attributed to a microstructure change of the matrix, which is associated with thermal exposure and the diffusion of alloying elements during fabrication and/or following heat treatment and/or thermal exposure processes.
The Outcomes of Two Knee Scoring Questionnaires in a Normal Population (1998)

The Noyes and Lysholm knee scoring questionnaires, commonly used for follow-up assessment after knee surgery, were developed based on knees with preexisting pathologic changes and have not been standardized to normal knees. We administered both questionnaires to normal subjects. Any subject reporting a history of injury or surgery to either knee, or preexisting knee pathologic changes, was excluded. From a total of 492 knees evaluated, 418 knees (253 male, 165 female) qualified for statistical analysis. The average age of the group was 17.6 years (range, 13 to 25). For male subjects, the total Noyes and Lysholm scores averaged 99.10 (range, 68 to 100) and 99.10 (range, 77 to 100), respectively. For female subjects, the average Noyes and Lysholm scores were 97.82 (range, 72 to 100) and 97.16 (range, 75 to 100), respectively. The 95% confidence interval computed for each of these groups did not contain the maximal value of 100. The female athletes reported significantly lower total scores than the male athletes on both questionnaires. For the Lysholm questionnaire, the male athletes scored significantly lower than the maximum in all categories except support and stair climbing, and the female athletes scored significantly lower than the maximum in all categories except limp and thigh atrophy. The range of scores found in this highly selected, "normal" population exemplifies the need for more accurate instruments in the evaluation of knee surgical outcomes.
GPU-Accelerated FDTD Modeling of Radio-Frequency Field-Tissue Interactions in (2011)

The analysis of high-field RF field-tissue interac- tions requires high-performance finite-difference time-domain (FDTD) computing. Conventional CPU-based FDTD calculations offer limited computing performance in a PC environment. This study presents a graphics processing unit (GPU)-based parallel- computing framework, producing substantially boosted comput- ing efficiency (with a two-order speedup factor) at a PC-level cost. Specific details of implementing the FDTD method on a GPU archi- tecture have been presented and the new computational strategy has been successfully applied to the design of a novel 8-element transceive RF coil system at 9.4 T. Facilitated by the powerful GPU-FDTD computing, the new RF coil array offers optimized fields (averaging 25% improvement in sensitivity, and 20% reduc- tion in loop coupling compared with conventional array structures of the same size) for small animal imaging with a robust RF config- uration. The GPU-enabled acceleration paves the way for FDTD to be applied for both detailed forward modeling and inverse design of MRI coils, which were previously impractical. Index Terms—Finite-difference time-domain (FDTD), graph- ics processing unit (GPU), high-field, MRI, parallel computing, RF coil.
Stereochemical Aspects of Lotaustralin Biosynthesis (1974)

Abstract The methyl linamarin that occurs naturally in linen flax (Linum usitatissimum L.) seedlings was shown to have the R configuration, i.e. it is identical with (R)-lotaustralin, (R)-2-hydroxy-2-methylbutyronitrile-β-d-glucopyranoside. However, when a mixture of the two enantiomers (R,S)-2-hydroxy-2-methylbutyronitrile, was administered to excised flax shoots, both (R)-lotaustralin and its epimer (S)-epilotaustralin ((S)-2-hydroxy-2-methylbutyronitrile-β-d-glucopyranoside) were formed. Similarly, both (R)-lotaustralin and (S)-epi-lotaustralin were formed when (R,S)-2-hydroxy-2-methylbutyronitrile served as substrate for the UDP-glucose:ketone cyanohydrin-β-d-glucosyltransferase of flax. These results demonstrate that the glucosyltransferase does not distinguish either in vitro or in vivo between the two enantiomeric forms of this glucose acceptor. Since, however, only (R)-lotaustralin occurs in the intact plant, the glucosyltransferase must be presented with only the R enantiomer as a substrate. This form is produced from l-isoleucine ([3S]-ls-isoleucine) due to retention of the S configuration at carbon atom 3. When (3R)-ls-isoleucine (threo-ls-isoleucine) was administered to flax shoots, (S)-epi-lotaustralin was formed due to retention of configuration at carbon atom 3 of the amino acid.
Patient Support Program Increased Medication Adherence with Lower Total Health Care Costs Despite Increased Drug Spending (2019)

Design, study conduct, and financial support for this study were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the manuscript; all authors contributed to the development of the publication and maintained control over the final content. Brixner reports consulting fees from AbbVie, AstraZeneca, Becton Dickinson, Millcreek Outcomes Group, Sanofi, and UCB Pharma. Rubin reports consulting fees from AbbVie, Abgenomics, Allergan, Forward Pharma, Genentech/Roche, Janssen Pharmaceuticals, Merck & Co., Napo Pharmaceuticals, Pfizer, Shire, Takeda, and Target Pharmaceuticals and research support from AbbVie, Genentech/Roche, Janssen Pharmaceuticals, Prometheus Laboratories, Shire, and Takeda. Mease reports grant/research support from AbbVie, Amgen, BMS, Celgene, Genentech, Janssen, Lilly, Merck, Novartis, Pfizer, SUN Pharma, and UCB; consulting fees from AbbVie, Amgen, BMS, Celgene, Genentech, Janssen, Lilly, Merck, Novartis, Pfizer, SUN Pharma, and UCB; and served on the speakers bureaus for AbbVie, Amgen, BMS, Celgene, Genentech, Janssen, Lilly, Merck, Novartis, Pfizer, Roche, and UCB. Mittal and Ganguli are employees and stockholders of AbbVie. Liu has no financial conflict of interest. Davis is an employee of Medicus Economics, which reports payment from AbbVie to participate in this research. Fendrick reports personal fees from Merck, AstraZeneca, Trizetto, Amgen, Lilly, AbbVie, Johnson & Johnson, and Sanofi; grants from the National Pharmaceutical Council, PhRMA, the Gary and Mary West Health Foundation, the states of New York and Michigan, the Laura and John Arnold Foundation, the Robert Wood Johnson Foundation, and the Agency for Healthcare Research and Quality; and has equity in Zansors, Sempre Health, Wellth, and V-BID Health. Data from this study were presented in part at the Academy of Managed Care & Specialty Pharmacy Annual Meeting; April 25, 2018; Boston, MA.
Coherent Transfer of Light Polarization to Electron Spins in a Semiconductor (2008)

We demonstrate that the superposition of light polarization states is coherently transferred to electron spins in a semiconductor quantum well. By using time-resolved Kerr rotation, we observe the initial phase of Larmor precession of electron spins whose coherence is transferred from light. To break the electron-hole spin entanglement, we utilized the big discrepancy between the transverse g factors of electrons and light-holes. The result encourages us to make a quantum media converter between flying photon qubits and stationary electron-spin qubits in semiconductors.