gebhart/patrepeval huggingface dataset:
Integrative Analysis of Human Macrophage Inflammatory Response Related to Mycobacterium tuberculosis Virulence (2021)

<i>Mycobacterium tuberculosis</i> (Mtb), the etiological agent of tuberculosis, kills 1.5 to 1.7 million people every year. Macrophages are Mtb's main host cells and their inflammatory response is an essential component of the host defense against Mtb. However, Mtb is able to circumvent the macrophages' defenses by triggering an inappropriate inflammatory response. The ability of Mtb to hinder phagolysosome maturation and acidification, and to escape the phagosome into the cytosol, is closely linked to its virulence. The modulation of the host inflammatory response relies on Mtb virulence factors, but remains poorly studied. Understanding macrophage interactions with Mtb is crucial to develop strategies to control tuberculosis. The present study aims to determine the inflammatory response transcriptome and miRNome of human macrophages infected with the virulent H37Rv Mtb strain, to identify macrophage genetic networks specifically modulated by Mtb virulence. Using human macrophages infected with two different live strains of mycobacteria (live or heat-inactivated Mtb H37Rv and <i>M. marinum</i>), we quantified and analyzed 184 inflammatory mRNAs and 765 micro(mi)RNAs. Transcripts and miRNAs differently modulated by H37Rv in comparison with the two other conditions were analyzed using in silico approaches. We identified 30 host inflammatory response genes and 37 miRNAs specific for H37Rv virulence, and highlight evidence suggesting that Mtb intracellular-linked virulence depends on the inhibition of IL-1β-dependent pro-inflammatory response, the repression of apoptosis and the delay of the recruitment and activation of adaptive immune cells. Our findings provide new potential targets for the development of macrophage-based therapeutic strategies against TB.
X-ray contact microscopy system for spectromicroscopy of biological specimens (1998)

An X-ray contact microscopy system has been developed for the study of molecular and elemental distributions in biological specimens based on X-ray absorption characteristics. The system consists of a chamber for measuring XANES (X-ray absorption near-edge structure) of biomolecules, and a contact microscopy system for dried specimens with an electronic zooming tube. With this system the elemental distribution of carbon, nitrogen, oxygen, Ca and Fe in an HeLa cell has been studied, and the DNA-related image using a peak from the XANES profile of the DNA at the K-absorption edge of phosphorus has been obtained.
Origin of the Stereoselectivity in (Ethoxycarbonyl)‐, Cyano‐, and Phenyl‐Substituted (Arylsulfinyl)methyl Radicals (1998)

Abstract An explanation for the very high diastereoselectivity observed for the reactions of carbonyl‐substituted (arylsulfinyl)methyl radicals is presented, based on experimental results and semiempirical calculations. The influence of dipole‐dipole interactions, allylic 1,3‐strain ( A 1,3 strain), allylic 1,2‐strain ( A 1,2 strain), and coulombic interactions is discussed based on stereoselectivities observed with (alkoxycarbonyl)‐, cyano‐, and aryl‐substituted (arylsulfinyl)methyl radicals. In the second part, the effect of solvents and Lewis acids on the stereoselectivity of reactions of (arylsulfinyl)‐ and (alkylsulfinyl)benzyl radicals has been examined.
Phonon-boundary scattering in thin silicon layers (1997)

Temperature fields in microdevices made from silicon-on-insulator (SOI) wafers are strongly influenced by the lateral thermal conductivity of the silicon overlayer, which is diminished by phonon scattering on the layer boundaries. This study measures the thermal conductivity of single-crystal silicon layers in SOI substrates at temperatures between 20 and 320 K using Joule heating and electrical-resistance thermometry in microfabricated structures. Data for layers of thickness between 0.4 and 1.6 μm demonstrate the large reduction resulting from phonon-boundary scattering, particularly at low temperatures, and are consistent with predictions based on the phonon Boltzmann transport equation.
Synthesis of polyfluoroalkylamines by the Gabriel method. (1985)

2, 2, 2-Trifluoroethylamine [3a] and a, a, co-trihydroperfluoro alkylamines [3a-d] were synthesized by the Gabriel method and their physical properties were measured (Table 1). N-(polyfluoro alkyl)phthalimides [2] were produced by the reaction of potassium phthalimide with polyfluoroalkyl o-nitrobenzenesulfonates [1]. The hydrolysis of the condensation products, formed in the reaction of [2] with hydrazine hydrate in ethanol at 60°C for 2 h, gave [3] in 65-74% yields. The boiling points of [3b-d] were about 30°C higher than those of the corresponding α, α-dihydroperfluoroalkyl amines. The basicities of [3] were very weak (pKσ=7.9-9.1) compared to those of the corresponding alkylamines (pKσ=3.34-3.47).
The Viral E4 Protein Is Required for the Completion of the Cottontail Rabbit Papillomavirus Productive Cycle In Vivo (2004)

Expression of the papillomavirus E4 protein correlates with the onset of viral DNA amplification. Using a mutant cottontail rabbit papillomavirus (CRPV) genome incapable of expressing the viral E4 protein, we have shown that E4 is required for the productive stage of the CRPV life cycle in New Zealand White and cottontail rabbits. In these lesions, E4 was not required for papilloma development, but the onset of viral DNA amplification and L1 expression were abolished. Viral genome amplification was partially restored when mutant genomes able to express longer forms of E4 were used. These findings suggest that efficient amplification of the CRPV genome is dependent on the expression of a full-length CRPV E4 protein.
Real‐world comparative effectiveness of adalimumab, etanercept and methotrexate: a Swedish register analysis (2019)

Adalimumab is superior to MTX in clinical practice whereas the relative effectiveness between ETN and MTX is less clear. This study also highlights the importance of appropriate confounding control in effectiveness analysis.
Diagnostic differentiel du syndrome "piro-like" chez les équidés (2007)

peer reviewed
Estradiol, Testosterone, and Androstenedione in Ovine Follicular Fluid During Growth and Atresia of Ovarian Follicles (1981)

Measurement of estradiol-17β, testosterone, and androstenedione in follicular fluid obtained from groups of antral follicles of known diameter and stage of morphological atresia indicates two phases of steroidogenesis during nonatretic growth. In pools of fluid obtained from follicles of 1 to 3 mm diameter, a transient fourfold increase in testosterone concentrations from 99 to 420 nM was observed soon after antrum formation, whereas concentrations of androstenedione and estradiol-17β ranged from 4 to 16 and 10 to 47 nM, respectively. In the pooled fluid of nonatretic follicles of greater than 3 mm diameter, concentrations of estradiol-17β exceeded that of either testosterone or androstenedione, and increased from 9 to 341 nM as follicular diameter increased. Testosterone concentrations progressively decreased from 247 to 56 nM, and the concentration of androstenedione decreased from 22 to 7 nM as follicular diameter increased beyond 3 mm. Concentrations of all three steroids in pools of fluid from early atretic follicles were not significantly different from those of nonatretic follicles, but in the later stages of atresia concentrations of testosterone remained elevated and those of estradiol stayed low at all stages of growth. Data obtained from individual follicles confirmed the initial finding that a reduction in the ratio of estrogen to total follicular androgen in pools of follicular fluid was associated with atresia of all sizes of follicles. We propose that the changes in patterns of steroidogenesis which accompany atresia reflect some of the earliest changes in the functional capacity of follicles undergoing atresia, but are not necessarily the primary cause of atresia.
Development of a database for prompt gamma-ray neutron activation analysis: Summary report of the third research coordination meeting (2003)

The main discussions and conclusions from the Third Co-ordination Meeting on the Development of a Database for Prompt Gamma-ray Neutron Activation Analysis are summarized in this report. All results were reviewed in detail, and the final version of the TECDOC and the corresponding software were agreed upon and approved for preparation. Actions were formulated with the aim of completing the final version of the TECDOC and associated software by May 2003.
Characterization Methods (2018)

The industrial use of diamond stems directly from its unique properties. Characterization is the key link for understanding how these properties are related to the microstructure of diamond and to its growth conditions. Fourier transform (FTIR) spectroscopy is an attractive technique for analyzing impurities in diamond since it is non-destructive and measurement times are relatively short. Both transmission and reflection, FTIR spectroscopies are performed using an incident beam of IR irradiation which interacts with the sample, being absorbed, transmitted, reflected, or since these techniques require a directed beam and specific geometries, they are typically performed ex-situ. Raman spectroscopy is one of the most common methods of diamond film characterization because of the ability to distinguish between different forms of carbon. Raman spectroscopy is used to investigate quantized molecular resonances by observing transitions between vibrational energy levels caused by inelastic scattering of high energy visible photons.
EMG-Torque Estimation at Future Times (2013)

This paper investigates the ability of surface electromyogram (EMG) to estimate joint torque at future times, up to 1 s. EMG was recorded from the biceps and triceps muscles of 54 subjects during constant-posture, force-varying contractions and related to the torque produced about the elbow. EMG to joint torque was predicted up to 80 ms into the future without any changes in the minimum least square error of 5.48% of maximum voluntary contraction for the best estimation model investigated: whitened, multiple-channel EMG used with a nonlinear model. Error progressively increased for prediction times above 80 ms.
Molecular epidemiology and transmission of hepatitis B virus in close family contacts of HBV‐related chronic liver disease patients (2003)

There is limited data on the patterns of HBV mutation in family contacts of chronic liver disease (CLD) patients in India. DNA sequence analysis is an important tool to study this viral epidemiology. Transmission and prevalence of mutations in the S and pre-C gene region in HBV infected close family contacts of HBV-related CLD patients were studied. Twelve HBsAg(+) index patients and their 20 HBV DNA contacts were studied in detail. The S ORF and the pre-C region were sequenced using direct PCR products. S-gene sequencing included 32 specimens (12 index cases and all 20 contacts). Pre-C gene sequencing included 26 specimens (12 index cases and all the 14 HBsAg(+) contacts irrespective of their HBeAg status). More than 98% sequence homology was found between the index patients and their contacts. The in-depth study of 12 families revealed that the transmission pattern was primarily horizontal in 6 (50%) and vertical in 2 (17%) families (P < 0.05). The remaining four families had evidence of both horizontal and vertical transmission. Mutations in the S-gene were found in 80% of HBsAg(+) and 17% HBsAg(-) subjects (P < 0.05). A total of 22-point mutations at different nucleotide positions were found. In these, 16 (72%) were mutation of the "a" determinant region and 14 (64%) resulted in missense mutations. The commonest S-gene mutations were T118V and A128V, present in 44 and 38% specimens, respectively. T143M and G145R mutations in the second loop of the "a" determinant were found in 9% of the specimens. Novel mutations, C137stp and C138stp were found in only one HBsAg(-) subject. Mutations in the pre-C gene were common (91%) in patients with HBeAg(-) phenotype. G1896A mutation was found in 7 of 11 (64%) specimens changing amino acid tryptophane (W) to stop codon. Other mutations were at codons 25 and 29. The results of the study, demonstrate (1) clustering of Pre-C and S-gene mutations in the families, (2) horizontal mode of transmission and a common source infection appears to be frequent as evidenced by sequence homology and detailed history, (3) T118V and A128V were the commonest mutations in the S-gene region, while (4) M2 (G1896A) was the commonest pre-C gene mutation, and (5) long-term follow-up evaluation of these mutations suggested.
Simulating 2+1d $\mathbb{Z}_3$ lattice gauge theory with iPEPS (2020)

We simulate a zero-temperature pure $\mathbb{Z}_3$ Lattice Gauge Theory in 2+1 dimensions by using an iPEPS (Infinite Projected Entangled-Pair State) ansatz for the ground state. Our results are therefore directly valid in the thermodynamic limit. They clearly show two distinct phases separated by a phase transition. We introduce an update strategy that enables plaquette terms and Gauss-law constraints to be applied as sequences of two-body operators. This allows the use of the most up-to-date iPEPS algorithms. From the calculation of spatial Wilson loops we are able to prove the existence of a confined phase. We show that with relatively low computational cost it is possible to reproduce crucial features of gauge theories. We expect that the strategy allows the extension of iPEPS studies to more general LGTs.
Exceptional response and multisystem autoimmune-like toxicities associated with the same T cell clone in a patient with uveal melanoma treated with immune checkpoint inhibitors (2019)

Balancing the potential for durable remissions with autoimmune-like toxicities is a key clinical challenge in the use of immune checkpoint inhibitors (ICI). Certain toxicities are associated with an increased response rate; however, the molecular underpinnings of this association are poorly understood. Here, we report a patient with wide spread uveal melanoma who had an exceptional response to treatment with ipilimumab and nivolumab, but suffered severe immune-related sequelae, including central serous retinopathy with retinal detachment, tinnitus, and vitiligo resembling Vogt-Koyanagi-Harada disease, and refractory enteritis. TCR-sequencing of the primary tumor, a hepatic metastasis, duodenal biopsy and peripheral blood mononuclear cells, identified the identical T cell clone in all four tissues. This case provides preliminary evidence for cross-reactivity as a mechanism for the association between effect and toxicity of ICIs.
Influence of Dietary Genistein and Polyunsaturated Fatty Acids on Lipid Peroxidation, and Fatty Acid Composition of Meat in Quail Exposed to Heat Stress (2021)

Abstract This experiment was conducted to investigate the effects of polyunsaturated fatty acids (PUFA) and genistein on performance and meat fatty acid profiles in quail exposed to heat stress. A total of 360 Japanese quail were divided into 12 groups in a 2x2x3 factorial design; each group comprised 30 quail with five replicates and were kept either at 22 ± 2°C for 24h/d (Thermoneutral,TN) and 34 ± 2°C for 8 h/d (08:00 to 17:00 h) followed by 22°C for 16 h (Heat Stress,HS) conditions. The diet contained either two levels of PUFA at 15 or 45% of total fat or three levels of genistein at 0, 400, or 800 mg/kg. Bodyweight gain, feed intake, and feed efficiency were lower ( p ≥ 0.01 ) for quail reared under heat stress and fed low PUFA. Increasing dietary genistein in a linear manner improved the productive performance ( p &lt; 0.001 ). Heat stress caused increases in serum and thigh meat malondialdehyde (MDA) concentrations and decreases in genistein, vitamin E and A concentrations in serum and thigh meat ( p &lt; 0.001 ). High PUFA (PUFA45) in diet of quail caused greater 18:2, 18:3 ALA, EPA, DHA, n-6, and n-3 PUFA as well as total PUFA and total USFA percentages ( p &lt; 0.001 ) in thigh muscle, some of which decreased with heat stress ( p ≥ 0.006 ) with no regards to genistein supplementation. This study revealed that genistein with greater doses along with greater PUFA inclusion to the diet of quail reared under heat stress is recommended for alleviating adverse effects of heat stress and for yielding healthier meat for human consumption.
Lattice Ciphertext-Policy Attribute-Based encryption from ring-LWE (2015)

The recent promising results on the hardness of lattice problems have inspired the construction of several Attribute-based Encryption (ABE) schemes from the quantum resistant perspective. However, these schemes are insufficient enough for supporting real-world applications due to inherent quadratic overhead problem in the use of Learning With Error (LWE). To solve this problem, this paper proposed a Ciphertext-Policy Attribute-Based Encryption (CP-ABE) scheme from a more lightweight ideal lattice classes- Ring-Learning with Errors (Ring-LWE), that further called as CP-ABE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R-LWE</inf> scheme. Compared to existing R-LWE based ABE scheme, the proposed CP-ABE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R-LWE</inf> is capable to handle a monotone access structure and enjoys collusion resistance properties. We exploited Linear Secret Scheme (LSSS) to express a monotone access structure. For resist to collusion attack, we applied the private key randomization technique to blind the user's private key. The proposed scheme CP-ABE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R-LWE</inf> is further proven to be secure under the Decision Ring-LWE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d,q,χ</inf> problem in the selective set model.
ChemInform Abstract: SYNTHESIS OF 5‐DIALKYLAMINO‐1,2,3‐TRIAZOLES AND 2‐AMINO‐1‐AZIRINES FROM TERTIARY AMIDES (1980)

Abstract Aus den Amiden (I) erhält man mit HCl und Phosgen die Chlorenamine (II), die zu den Aziden (III) umgesetzt werden können.
SARS-CoV-2: a storm is raging (2020)

The pandemic coronavirus infectious disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is rapidly spreading across the globe. In this issue of the JCI, Chen and colleagues compared the clinical and immunological characteristics between moderate and severe COVID-19. The authors found that respiratory distress on admission is associated with unfavorable outcomes. Increased cytokine levels (IL-6, IL-10, and TNF-α), lymphopenia (in CD4+ and CD8+ T cells), and decreased IFN-γ expression in CD4+ T cells are associated with severe COVID-19. Overall, this study characterized the cytokine storm in severe COVID-19 and provides insights into immune therapeutics and vaccine design.
Mapping of the Novel Protein Kinase Catalytic Domain of Dictyostelium Myosin II Heavy Chain Kinase A (1997)

Myosin heavy chain kinase A (MHCK A) in Dictyostelium was identified as a biochemical activity that phosphorylates threonine residues in the myosin II tail domain and regulates myosin filament assembly. The catalytic domain of MHCK A has now been mapped through the functional characterization of a series of MHCK A truncation mutants expressed in Escherichia coli. A recombinant protein comprising the central nonrepetitive domain of MHCK A (residues 552-841) was isolated in a soluble form and shown to phosphorylate Dictyostelium myosin II, myelin basic protein, and a synthetic peptide substrate. The functionally mapped catalytic domain of MHCK A shows no detectable sequence similarity to known classes of eukaryotic protein kinases but shares substantial sequence similarity with a transcribed Caenorhabditis elegans gene and with the mammalian elongation factor-2 kinase (calcium/calmodulin-dependent protein kinase III). We suggest that MHCK A represents the prototype for a novel, widely occurring protein kinase family.
Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk (2016)

The bacterial groups that are less abundant in early infancy, and that increase in relative abundance after weaning, likely are responsible for the expulsion of C. difficile.
Development of a practical photochemical energy storage system. Quarterly report, July 1, 1977--September 30, 1977 (1977)

During this quarter the portion of this project concerned with catalysis has concentrated on the development of increased understanding of the cobalt(II) porphyrin catalyst. Of potential importance is the observation that the activity of partially deactivated catalysts can be partially restored by treatment with titanium(III) solutions thereby suggesting that a major cause of the losses of activity of catalysts upon repeated recycling arises from oxidation of cobalt(II) to cobalt(III). The previously discovered molybdenum catalyst ((CF/sub 3/)/sub 2/C/sub 2/S/sub 2/)/sub 3/Mo and the closely related nickel catalyst ((CF/sub 3/)/sub 2/C/sub 2/S/sub 2/)/sub 2/Ni were also studied in detail.
Expression of adiponectin in choroidal tissue and inhibition of laser induced choroidal neovascularization by adiponectin (2007)

The aim of this study was to investigate the role of adiponectin (APN) in a mouse model of laser induced choroidal neovascularization (CNV). We have shown by immunohistochemistry that the expression of APN, adiponectin receptor 1, adiponectin receptor 2 and T cadherin gradually increased from day 1 to day 7 post-laser in laser treated mice compared to controls. Recombinant APN (rAPN) was injected intraperitoneally (i.p., 25 microg/mouse) or intravitreally (2 microg/eye) in lasered mice. Another set of lasered mice received APN peptide via i.p. (75 microg/mouse) or intravitreal (30 microg/eye) route. Control mice received a similar treatment with PBS, control protein or control peptide after laser treatment. We found that in the i.p. and intravitreal injection of rAPN resulted in 78% and 68% inhibition respectively in the size of CNV complex compared to control mice. Similar results were observed when APN peptide was injected intravitreally or i.p. Treatment with rAPN or the peptide resulted in decreased levels of vascular endothelial growth factor. Thus, APN inhibited choroidal angiogenesis and may have therapeutic implications in the treatment of wet age related macular degeneration.
Pharmacokinetics, Safety, and Tolerability of Metformin in Healthy Elderly Subjects (2015)

Age-related physiological changes are known to alter the pharmacokinetics (PK) and pharmacodynamics (PD) of drugs. Metformin is commonly used as first-line medication for management of diabetes in elderly patients. However, the PK and PD of metformin have not been sufficiently studied in elderly subjects. Here, 12 elderly subjects, aged 65 to 85 years, and 20 younger healthy volunteers were orally administered 750 mg of metformin 2 hours after dinner, followed by administration of a second dose (500 mg) 12 hours later. An oral glucose tolerance test (OGTT) was performed 2 hours after the second dose, with 75 g of glucose administered. Blood samples were collected at specific time points after the second metformin dose for the assessment of PK and the glucose-lowering effect of metformin. Elderly subjects exhibited 1.7 and 2.0 times higher average Cmax and AUC∞ than the younger subjects, respectively (P = .007 and .001, respectively), and t1/2 was comparable between the elderly and younger subjects. However, relative glucose level changes from baseline after metformin administration tended to be lower in elderly subjects. Systemic exposure to metformin was elevated by 50% or more in elderly subjects, whereas the glucose-lowering effect was similar compared to younger subjects after 2 doses of metformin.