gebhart/patrepeval huggingface dataset:
Lipid management in rheumatoid arthritis: a position paper of the Working Group on Cardiovascular Pharmacotherapy of the European Society of Cardiology (2019)

Rheumatoid arthritis (RA) is associated with increased cardiovascular morbidity, partly due to alterations in lipoprotein quantity, quality and cell cholesterol trafficking. Although cardiovascular disease significantly contributes to mortality excess in RA, cardiovascular prevention has been largely insufficient. Because of limited evidence, optimal strategies for lipid management (LM) in RA have not been determined yet, and recommendations are largely based on expert opinions. In this position paper, we describe abnormalities in lipid metabolism and introduce a new algorithm for estimation of cardiovascular risk (CVR) and LM in RA. The algorithm stratifies patients according to RA-related factors impacting CVR (such as RA activity and severity and medication). We propose strategies for monitoring of lipid parameters and treatment of dyslipidaemia in RA (including lifestyle, statins and other lipid-modifying therapies, and disease modifying antirheumatic drugs). These opinion-based recommendations are meant to facilitate LM in RA until more evidence is available.
Utilizing Y Chromosome FISH to Determine the Origin of Post-Transplant Lymphoproliferative Disease in Solid Organ Transplant Recipients (2018)

Abstract Background: Post-Transplant Lymphoproliferative Disease (PTLD) is a heterogeneous disease that arises as a complication after solid organ transplants (SOT) and unusually after bone marrow transplants (BMT). PTLD is generally of recipient origin in SOT patients and donor origin in BMT patients. Knowing the cellular origin of PTLD may provide insight into tumorigenesis and potentially guide treatment options. Design/Methods: We identified gender mismatched SOT patients from our institutional databases who had PTLD tumor tissue for FISH analysis to determine the tumor origin (donor vs. recipient). From these samples, lesional and normal (when present) tissue was delineated by a hematopathologist (TG), and subsequent XY FISH studies were performed according to standard protocols for detection of the Y chromosome. Results: Thirty-one gender mismatched PTLD patients were examined (20 were pediatric patients &lt;18 yrs old). Transplants were: 8 isolated liver (L), 7 kidney (K), 3 small bowel (SB), 6 L/SB, 4 L/SB/pancreas (P), 2 K/L and one L/K/P. Of the 31 patients: 25 were 100% recipient origin; 5/31 demonstrated mixed chimerism; and 1 was 100 % donor origin. Of the 6 patients with chimerism (3 children), the percentage of donor cells ranged between 23% and 100%. Three of 31 had PTLD in the allograft, with 2 of 3 demonstrating mixed chimerism. One was a 2 y.o. F 3 months after a SB transplant and the other a 10 m.o. M 12 months after a L/SB/P transplant. Of the 28 with tumor tissue at other sites, 3 had mixed chimerism: a 60 y.o. M 9 months after a K/L transplant; a 7 m.o. M 8 months after a L/SB transplant; and a 64 y.o. F 3 months after a L transplant. The single patient with 100 % donor chimerism was a 27 year old female 5 months after a L/SB transplant. The 6 chimeric patients developed PTLD on average earlier than the 25 patients of recipient origin (6.9 months vs. 18.1 months). Of the 20 pediatric patient, 12 had transplants including small bowel and 3/12 demonstrated mixed chimerism. Mortality rate was similar between pediatric and adult populations (40% and 45% respectively). Conclusion: As expected, the majority of patients in our series had tumors of recipient origin. However, 3/20 pediatric patients (15%) and 3/11 (27%) adult patients were chimeric in 23% to 100% of their tumor cells. Chimerism was more common in patients who received transplants that included L (4/5) and SB (3/5). Disclosures Ford: Novartis: Consultancy, Honoraria.
Dityrosine, 3,4-Dihydroxyphenylalanine (DOPA), and Radical Formation from Tyrosine Residues on Milk Proteins with Globular and Flexible Structures as a Result of Riboflavin-Mediated Photo-oxidation (2011)

Riboflavin-mediated photo-oxidative damage to protein Tyr residues has been examined to determine whether protein structure influences competing protein oxidation pathways in single proteins and protein mixtures. EPR studies resulted in the detection of Tyr-derived o-semiquione radicals, with this species suggested to arise from oxidation of 3,4-dihydroxyphenylalanine (DOPA). The yield of this radical was lower in samples containing β-casein than in samples containing only globular proteins. Consistent with this observation, the yield of DOPA detected on β-casein was lower than that on two globular proteins, BSA and β-lactoglobulin. In contrast, samples with β-casein gave higher yields of dityrosine than samples containing BSA and β-lactoglobulin. These results indicate that the flexible structure of β-casein favors radical-radical termination of tyrosyl radicals to give dityrosine, whereas the less flexible structure of globular proteins decreases the propensity for tyrosyl radicals to dimerize, with this resulting in higher yields of DOPA and its secondary radical.
Probabilistic Time-Frequency Source-Filter Decomposition Of Non-Stationary Signals (2013)

Publication in the conference proceedings of EUSIPCO, Marrakech, Morocco, 2013
Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases (2007)

We present a library of Gaussian basis sets that has been specifically optimized to perform accurate molecular calculations based on density functional theory. It targets a wide range of chemical environments, including the gas phase, interfaces, and the condensed phase. These generally contracted basis sets, which include diffuse primitives, are obtained minimizing a linear combination of the total energy and the condition number of the overlap matrix for a set of molecules with respect to the exponents and contraction coefficients of the full basis. Typically, for a given accuracy in the total energy, significantly fewer basis functions are needed in this scheme than in the usual split valence scheme, leading to a speedup for systems where the computational cost is dominated by diagonalization. More importantly, binding energies of hydrogen bonded complexes are of similar quality as the ones obtained with augmented basis sets, i.e., have a small (down to 0.2 kcal/mol) basis set superposition error, and the monomers have dipoles within 0.1 D of the basis set limit. However, contrary to typical augmented basis sets, there are no near linear dependencies in the basis, so that the overlap matrix is always well conditioned, also, in the condensed phase. The basis can therefore be used in first principles molecular dynamics simulations and is well suited for linear scaling calculations.
The Human Nephron Filter: Toward a Continuously Functioning, Implantable Artificial Nephron System (2005)

The HNF system, by eliminating dialysate and utilizing a novel membrane system created through applied nanotechnology may represent a breakthrough in renal replacement therapy based on the functioning of native kidneys. The enhanced solute removal and wearable design should substantially improve patient outcomes and quality of life.
Critical design of the Ka-band on-board switching transponder for communication, oceanographic, and meteorological satellite (COMS) (2006)

This paper discusses the detail design of Ka-band on-board switching transponder that ETRI has applied the development of a new communication payload system for communication, oceanographic, and meteorological satellite (COMS). The satellite communication (SATCOM) system which to be designed to acquire the communication mission of COMS consists of communication payload, satellite ground control system, and experimental test Earth Station. This paper focuses on the technology development being performed for the space segment of SATCOM system at the ETRI, principally related to the COMS project. For critical design of Ka-band transponder subsystem, the trade-off design has been performed with emphasis on the improving performances and optimizing the payload system. In this paper, introduction of SATCOM system and major RF performances analysis will be mainly presented.
Pigs transgenic for human thrombomodulin have elevated production of activated protein C (2009)

For the first time, healthy hTM-transgenic pigs could be successfully generated by somatic cell nuclear transfer. hTM can be expressed in porcine organs without perturbation of the porcine coagulation system. hTM-transgenic porcine fibroblasts showed elevated aPC production in an in vitro hTM coactivity assay. These findings warrant further work on the control of the xenogenic activation of coagulation by transgenic approaches.
Expression of TGF-beta receptors type I and II in human glomerulonephritis. (1998)

Our data show that TGF-beta expression is a good indicator of the severity of proliferative glomerular lesions in most, if not all cases and that RI-RII expression occurs at levels detectable with indirect immunofluorescence in limited number of glomerulonephritides, mostly associated with systemic diseases. A complex interaction between TGF-beta and its ligand may represent a critical factor conditioning the tissue response to immunological injury.
Selective extraction of lithium from a spent lithium iron phosphate battery by mechanochemical solid-phase oxidation (2021)

Lithium was selectively and environmentally friendly extracted from spent LiFePO<sub>4</sub>batteries<italic>via</italic>mechanochemical solid-phase oxidation process.
Kainic acid-induced excitotoxicity is associated with a complex c-Fos and c-Jun response which does not preclude either cell death or survival. (1997)

c-fos and c-jun mRNA induction and c-Fos and c-Jun protein expression were examined in the brains of adult rats subjected to systemic kainic acid (KA) injection at convulsant doses. Induction of c-fos and c-jun mRNA, as seen with in situ hybridization, occurred in the piriform and entorhinal cortices, neocortex, amygdala, hippocampus, dentate gyrus, and discrete thalamic nuclei. This was followed by c-Fos protein expression, as revealed with immunohistochemistry, in the same regions. However, the distribution of c-Jun protein expression differed depending on the antibody used. The distribution of cells immunostained with the antibody c-Jun (AB-1) was similar to that of c-jun mRNA, but the distribution of cells immunostained with the antibody c-Jun/AP1 (N) was restricted to a few neurons in the pyramidal cell layer of CA1 and CA3, layer II of the piriform and entorhinal cortices, basal amygdala, and discrete thalamic nuclei. Although the regional distribution of c-Fos- and c-Jun-immunoreactive cells in the hippocampus, layer II of the entorhinal and piriform cortices, basal amygdala, and discrete thalamic nuclei matched the distribution of cells committed to dying, c-Fos- and c-Jun-immunoreactive cells in the neocortex and dentate gyrus survived. Therefore, the present data show that c-fos and c-jun are not predictors of either cell death or survival, but rather, markers of cells sensitive to KA excitotoxicity. Western blots to c-Fos showed a double band at p62 in samples containing the hippocampus and entorhinal and piriform cortices (hip samples) and in samples containing the neocortex (cortex samples). The upper band was abolished following preincubation of the samples with alkaline phosphatase, thus suggesting c-Fos phosphorylation. Western blots to c-Jun (AB-1) showed a single band at about p39 in hip and cortex. However, Western blots to c-Jun/AP1 (N) identified two bands. One band at about p39 was seen in control rats and the cortex of KA-treated rats. Another band at p26 was observed only in hip samples of KA-treated rats. In addition, decreased c-Jun N-terminal kinase 1 (JNK-1) expression, as revealed on Western blots, was coincidental with the appearance of the p26 c-Jun-immunoreactive band in KA-treated rats. These results show that c-Fos and different Jun-related antigens are expressed following KA excitotoxicity, and that posttranslational modifications involving phosphorylation of c-Fos and Jun(s) may occur following KA injection. These results also stress the necessity of examining the composition of Fos and Jun-related antigens and the metabolic state of Fos and Jun(s) in different experimental models of nervous system injury.
A Viscoelastic Model to Evidence Reduced Upper-Limb-Swing Capabilities during Gait for Parkinson’s Disease-Affected Subjects (2023)

Parkinson’s disease (PD) is a chronic neurodegenerative disorder with high worldwide prevalence that manifests with muscle rigidity, tremor, postural instability, and slowness of movement. These motor symptoms are mainly evaluated by clinicians via direct observations of patients and, as such, can potentially be influenced by personal biases and inter- and intra-rater differences. In order to provide more objective assessments, researchers have been developing technology-based systems aimed at objective measurements of motor symptoms, among which are the reduced and/or trembling swings of the lower limbs during gait tests, resulting in data that are potentially prone to more objective evaluations. Within this frame, although the swings of the upper limbs during walking are likewise important, no efforts have been made to reveal their support significance. To fill this lack, this work concerns a technology-based assessment of the forearm-swing capabilities of PD patients with respect to their healthy counterparts. This was obtained by adopting a viscoelastic model validated via measurements during gait tests tackled as an inverse dynamic problem aimed at determining the torque forces acting on the forearms. The obtained results evidence differences in the forearm movements during gait tests of healthy subjects and PD patients with different pathology levels, and, in particular, we evidenced how the worsening of the disease can cause the worsening of the mechanical support offered by the forearm’s swing to the walking process.
T‐cell‐mediated and antigen‐dependent differentiation of human monocyte into different dendritic cell subsets: a feedback control of Th1/Th2 responses (2008)

It is well established that human monocytes differentiate into dendritic cells (DCs) when cultured with certain cytokine cocktails, such as granulocyte-macrophage colony-stimulating factor and interleukin-4. Conversely, it is not completely established which cell population synthesizes the cytokines required for monocyte differentiation and how their secretion is regulated. We show that on specific activation T cells induce the differentiation into DCs of antigen-presenting and bystander monocytes. Monocytes exposed to cytokines released by Th1 and Th0 lymphocytes differentiate into DCs with a reduced antigen uptake and antigen presentation capacity. Moreover, these DCs show a limited capacity to induce Th1 polarization of naive T cells but are capable of priming interleukin-10-secreting T cells. Conversely, DCs derived from monocytes sensing cytokines released by Th2 lymphocytes are antigen-presenting-cell (APC) endowed with a marked Th1 polarization capacity. Monocytes are corecruited with lymphocytes in chronic inflammation sites; thus our results suggest that functionally different DCs can be generated in environments characterized by the prevalent release of Th1-, Th0-, or Th2-associated cytokines. Because the APC capacities of these DCs have opposite functional consequences, a contribution in the regulation of the ongoing immune response by monocyte-derived inflammatory DCs is envisaged.
Kinetic Analysis of Lauric Acid Hydroxylation by Human Cytochrome P450 4A11 (2014)

Cytochrome P450 (P450) 4A11 is the only functionally active subfamily 4A P450 in humans. P450 4A11 catalyzes mainly ω-hydroxylation of fatty acids in liver and kidney; this process is not a major degradative pathway, but at least one product, 20-hydroxyeicosatetraenoic acid, has important signaling properties. We studied catalysis by P450 4A11 and the issue of rate-limiting steps using lauric acid ω-hydroxylation, a prototypic substrate for this enzyme. Some individual reaction steps were studied using pre-steady-state kinetic approaches. Substrate and product binding and release were much faster than overall rates of catalysis. Reduction of ferric P450 4A11 (to ferrous) was rapid and not rate-limiting. Deuterium kinetic isotope effect (KIE) experiments yielded low but reproducible values (1.2-2) for 12-hydroxylation with 12-(2)H-substituted lauric acid. However, considerable "metabolic switching" to 11-hydroxylation was observed with [12-(2)H3]lauric acid. Analysis of switching results [Jones, J. P., et al. (1986) J. Am. Chem. Soc. 108, 7074-7078] and the use of tritium KIE analysis with [12-(3)H]lauric acid [Northrop, D. B. (1987) Methods Enzymol. 87, 607-625] both indicated a high intrinsic KIE (>10). Cytochrome b5 (b5) stimulated steady-state lauric acid ω-hydroxylation ∼2-fold; the apoprotein was ineffective, indicating that electron transfer is involved in the b5 enhancement. The rate of b5 reoxidation was increased in the presence of ferrous P450 mixed with O2. Collectively, the results indicate that both the transfer of an electron to the ferrous·O2 complex and C-H bond-breaking limit the rate of P450 4A11 ω-oxidation.
Wettability Control by Laser Texturing Process Generating Localized Gold Nanoparticles on Polymeric Thin Films (2012)

In this work a new approach is introduced for surface properties control by laser texturing process. By UV laser irradiation, we are able to control the surface wettability of a chitosan polymeric film in which is introduced a chloroauric acid salt by immersion. Specifically the UV irradiation is responsible for the creation of gold nanoparticles at the irradiated surface of the polymeric film. This photolytic process allows us to localize and design accurately surface patterns and moreover to tune metallic particle size in the range of nanoscale. After the characterization of our gold textured surfaces by atomic force and scanning electron microscopies, we demonstrate the link between wettability surface properties and gold nanoparticles size. The experimental results indicate the influence of the laser intensity, the irradiation time and the polymer film thickness (by increasing the gold concentration) on the gold nanoparticle density and size.
Neonatal and maternal outcomes following midtrimester preterm premature rupture of the membranes: a retrospective cohort study (2016)

This study provides useful and contemporary data on midtrimester PPROM. Whilst fetal and neonatal mortality is high, long-term survival is not impossible. The increased risk of maternal morbidity necessitates close surveillance.
Dysautonomia in hypermobile Ehlers–Danlos syndrome and hypermobility spectrum disorders is associated with exercise intolerance and cardiac atrophy (2021)

Dysautonomia is a recognized manifestation in patients with joint hypermobility (JH) disorders. Symptoms can be highly debilitating and commonly include physical deconditioning and poor aerobic fitness. In this study, the prevalence of dysautonomia, range of associated symptoms, patient-reported physical activity levels, and echocardiographic features were assessed retrospectively in a cohort of 144 patients (94% female) with hypermobile Ehlers-Danlos syndrome (hEDS) or hypermobility spectrum disorder (HSD). Echocardiographic parameters of left ventricular size and function were compared between patients with and without dysautonomia as well as to reported values from healthy controls. Dysautonomia was identified in 65% of female and 44% of male subjects and was associated with a high burden of symptomatology, most commonly exercise intolerance (78%). Exercise capacity was limited by dysautonomia, often postural symptoms, in half of all patients. We observed a reduction in physical activity following the onset or significant flare of hEDS/HSD, most strikingly noting the proportion of dysautonomic patients with sedentary lifestyle, which increased from 44% to 85%. JH-related dysautonomia was associated with smaller cardiac chamber sizes, consistent with the previous reports in positional orthostatic tachycardia syndrome. Dysautonomia is prevalent in patients with hEDS/HSD, and exercise intolerance is a key feature and leads to drastic decline in physical activity. Unfavorable cardiac geometry may underlie dysautonomia symptoms and may be due to cardiac atrophy in the setting of aerobic deconditioning.
Purification, Crystallization and Properties of NADP+-Specific Glutamate Dehydrogenase fromLactobacillus fermentum (1985)

The distribution of amino acid dehydrogenases in lactic acid bacteria was investigated. Several lactic acid bacteria were found to have NADP+-specific glutamate dehydrogenase, but NAD+-specific glutamate dehydrogenase activity was not detected in the bacteria tested. No alanine, leucine or lysine dehydrogenase activity was detected either, though serine and proline dehydrogenases occur in some of the bacteria. NADP+-specific glutamate dehydrogenase was purified to homogeneity and crystallized from Lactobacillus fermentum IFO 3071. The enzyme had a molecular weight of about 300,000 and consisted of six subunits identical in molecular weight (50,000). The enzyme is highly specific for l-glutamate and a-ketoglutarate, and the activity of the reductive amination is much higher than that of the oxidative deamination. The pH optima for the deamination and the amination were about 9.0 and 8.0, respectively. The apparent Km values were determined to be 79 mm for l-glutamate, 44µm for NADP+, 5.6 mm for α-ketoglutarate, 6.76 mm for NH3, and 77.5 µm for NADPH.
Mutations in the PIG-A gene causing paroxysmal nocturnal hemoglobinuria are mainly of the frameshift type (1995)

Paroxysmal nocturnal hemoglobinuria is an acquired hemolytic anemia associated with somatic mutations in the X-linked gene PIG-A, which encodes a protein involved in the biosynthesis of glycosyl phosphatidylinositol anchors. To further elucidate the molecular basis of paroxysmal nocturnal hemoglobinuria, we have worked out a systematic and relatively rapid methodology to scan for mutations in the entire coding region of the PIG-A gene. By this methodology, we have identified 15 different somatic mutations in 12 patients. The mutations were spread throughout the entire PIG-A-coding region. Of the mutations, 10 caused frameshifts, 6 caused small deletions, 3 caused small insertions, and 1 caused deletion-insertion. Five single base pair substitutions caused three missense mutations, one nonsense mutation, and one defect in the donor splice site of intron 4. In each of 3 patients, two independent mutations were identified. The predominance of frameshift mutations may reflect selection for somatic mutations giving rise to clones with a completely nonfunctional PIG-A protein.
Hysteresis control of epithelial-mesenchymal transition dynamics conveys a distinct program with enhanced metastatic ability (2018)

Epithelial-mesenchymal transition (EMT) have been extensively characterized in development and cancer, and its dynamics have been modeled as a non-linear process. However, less is known about how such dynamics may affect its biological impact. Here, we use mathematical modeling and experimental analysis of the TGF-β-induced EMT to reveal a non-linear hysteretic response of E-cadherin repression tightly controlled by the strength of the miR-200s/ZEBs negative feedback loop. Hysteretic EMT conveys memory state, ensures rapid and robust cellular response and enables EMT to persist long after withdrawal of stimuli. Importantly, while both hysteretic and non-hysteretic EMT confer similar morphological changes and invasive potential of cancer cells, only hysteretic EMT enhances lung metastatic colonization efficiency. Cells that undergo hysteretic EMT differentially express subsets of stem cell and extracellular matrix related genes with significant clinical prognosis value. These findings illustrate distinct biological impact of EMT depending on the dynamics of the transition.