gebhart/patrepeval huggingface dataset:
Ion-Solid Interactions (1996)

Modern technology depends on materials with precisely controlled properties. Ion beams are a favoured method to achieve controlled modification of surface and near-surface regions. In every integrated circuit production line, for example, there are ion implantation systems. In addition to integrated circuit technology, ion beams are used to modify the mechanical, tribological and chemical properties of metal, intermetallic and ceramic materials without altering their bulk properties. Ion–solid interactions are the foundation that underlies the broad application of ion beams to the modification of materials. This text is designed to cover the fundamentals and applications of ion–solid interactions and is aimed at graduate students and researchers interested in electronic devices, surface engineering, reactor and nuclear engineering and material science issues associated with metastable phase synthesis.
Footprint characteristics revised for field-scale soil moisture monitoring with cosmic-ray neutrons (2024)

Cosmic-ray neutron probes are widely used to monitor environmental water content near the surface. The method averages over tens of hectares and is unrivaled in serving representative data for agriculture and hydrological models at the hectometer scale. Recent experiments, however, indicate that the sensor response to environmental heterogeneity is not fully understood. Knowledge of the support volume is a prerequisite for the proper interpretation and validation of hydrogeophysical data. In a previous study, several physical simplifications have been introduced into a neutron transport model in order to derive the characteristics of the cosmic-ray probe's footprint. We utilize a refined source and energy spectrum for cosmic-ray neutrons and simulate their response to a variety of environmental conditions. Results indicate that the method is particularly sensitive to soil moisture in the first tens of meters around the probe, whereas the radial weights are changing dynamically with ambient water. The footprint radius ranges from 130 to 240 m depending on air humidity, soil moisture, and vegetation. The moisture-dependent penetration depth of 15 to 83 cm decreases exponentially with distance to the sensor. However, the footprint circle remains almost isotropic in complex terrain with nearby rivers, roads or hill slopes. Our findings suggest that a dynamically weighted average of point measurements is essential for accurate calibration and validation. The new insights will have important impact on signal interpretation, sensor installation, data interpolation from mobile surveys, and the choice of appropriate resolutions for data assimilation into hydrological models.
Multi-view depth video coding using depth view synthesis (2008)

Depth information indicates the distance of an object in the three dimensional (3D) scene from the camera view-point, typically represented by eight bits. Since the depth map is useful in various multimedia applications, such as three dimensional television (3DTV) and free-viewpoint television (FTV), we need to acquire a single or multi-view depth maps and process them effectively. In this paper, we propose a new coding scheme for multi-view depth video data using depth view synthesis. We first apply a 3D warping method to synthesize a virtual depth image for the current view using the multi-view depth information. We also propose a hole filling method to compensate for the holes generated during the depth map synthesis process. Finally, we utilize the synthesized depth map for the current view as an additional reference frame in encoding the current depth map. Experimental results show that the proposed algorithm achieves approximately 0.69 dB of PSNR gain on average, compared to JMVM 1.0.
The immunoglobulin heavy chain variable region (Igh‐V) locus in the mouse. I. One hundred Igh‐V genes comprise seven families of homologous genes (1984)

Seven families of Igh-V genes have been defined by Southern blot analysis of genomic DNA from eighteen inbred strains of mice. Each of twenty-four cloned Vh genes hybridized to one of seven nonoverlapping sets of Eco RI restriction fragments. These families contain from 2 to approximately 40 hybridizing fragments. From these data we estimate that the mouse Igh-V locus consists of one hundred Vh genes. Genes within a Vh family share greater than 80% sequence homology while the sequence homology between families is generally less than 70%. There is extensive restriction fragment length polymorphism among the strains analyzed allowing the assignment of complete (Igh-V + Igh-C) Igh haplotypes for eighteen inbred mouse strains.
Comparison between Theoretical Calculation and Experimental Results of Excitation Functions for Production of Relevant Biomedical Radionuclides (2005)

The radionuclide production for biomedical applications has been brought up in the years, as a special nuclear application, at INFN LASA Laboratory, particularly in co‐operation with the JRC‐Ispra of EC. Mainly scientific aspects concerning radiation detection and the relevant instruments, the measurements of excitation functions of the involved nuclear reactions, the requested radiochemistry studies and further applications have been investigated. On the side of the nuclear data evaluations, based on nuclear model calculations and critically selected experimental data, the appropriate competence has been developed at ENEA Division for Advanced Physics Technologies. A series of high specific activity accelerator‐produced radionuclides in no‐carrier‐added (NCA) form, for uses in metabolic radiotherapy and for PET radiodiagnostics, are investigated. In this work, last revised measurements and model calculations are reviewed for excitation functions of natZn(d,X)64Cu, 66Ga reactions, referring to irradiation experiments at K=38 variable energy Cyclotron of JRC‐Ispra. Concerning the reaction data for producing 186gRe and 211At/211gPo (including significant emission spectra) and 210At, most recent and critically selected experimental results are considered and discussed in comparison with model calculations paying special care to pre‐equilibrium effects estimate and to the appropriate overall parameterization. Model calculations are presented for 226Ra(p,2n)225Ac reaction, according to the working program of the ongoing IAEA CRP on the matter.
An exploratory dose-escalating study investigating the safety, tolerability, pharmacokinetics and pharmacodynamics of intravenous atacicept in patients with systemic lupus erythematosus (2009)

Atacicept, a recombinant fusion protein containing the extracellular, ligand-binding portion of the transmembrane activator and calcium modulator and cyclophilin-ligand interactor receptor, and the Fc portion of human immunoglobulin (Ig) G, is designed to block the activity of B-lymphocyte stimulator and a proliferation-inducing ligand, and may have utility as a treatment for B-cell-mediated diseases, such as systemic lupus erythematosus (SLE). This Phase Ib study investigated the safety, tolerability, pharmacokinetics (PK) and pharmacodynamics of intravenous (i.v.) atacicept in patients with mild-to-moderate SLE. Patients (n = 24) were randomised (5:1) to receive atacicept (single dose: 3, 9 or 18 mg/kg; or multiple dose: 2 x 9 mg/kg) or matching placebo. Patients were followed for 6 weeks after dosing (9 weeks in the 2 x 9 mg/kg cohort). Local tolerability of atacicept was comparable with that of placebo, with only mild injection-site reactions reported with atacicept. Atacicept i.v. was generally well tolerated, both systemically and locally, in patients with mild-to-moderate SLE. Atacicept displayed non-linear PK, which was predictable across doses and between single and repeat doses. The biological activity of atacicept was demonstrated by its marked effect in reducing B-cells and Ig levels in patients with SLE. This supports the utility of this therapeutic approach in the treatment of autoimmune diseases, such as SLE.
Modular Organization of Genes Required for Complex Polyketide Biosynthesis (1991)

In Saccharopolyspora erythraea, the genes that govern synthesis of the polyketide portion of the macrolide antibiotic erythromycin are organized in six repeated units that encode fatty acid synthase (FAS)-like activities. Each repeated unit is designated a module, and two modules are contained in a single open reading frame. A model for the synthesis of this complex polyketide is proposed, where each module encodes a functional synthase unit and each synthase unit participates specifically in one of the six FAS-like elongation steps required for formation of the polyketide. In addition, genetic organization and biochemical order of events appear to be colinear. Evidence for the model is provided by construction of a selected mutant and by isolation of a polyketide of predicted structure.
Correlation between Bacillus subtilis scoC Phenotype and Gene Expression Determined Using Microarrays for Transcriptome Analysis (2001)

The availability of the complete sequence of the Bacillus subtilis chromosome (F. Kunst et al., Nature 390:249-256, 1997) makes possible the construction of genome-wide DNA arrays and the study of this organism on a global scale. Because we have a long-standing interest in the effects of scoC on late-stage developmental phenomena as they relate to aprE expression, we studied the genome-wide effects of a scoC null mutant with the goal of furthering the understanding of the role of scoC in growth and developmental processes. In the present work we compared the expression patterns of isogenic B. subtilis strains, one of which carries a null mutation in the scoC locus (scoC4). The results obtained indicate that scoC regulates, either directly or indirectly, the expression of at least 560 genes in the B. subtilis genome. ScoC appeared to repress as well as activate gene expression. Changes in expression were observed in genes encoding transport and binding proteins, those involved in amino acid, carbohydrate, and nucleotide and/or nucleoside metabolism, and those associated with motility, sporulation, and adaptation to atypical conditions. Changes in gene expression were also observed for transcriptional regulators, along with sigma factors, regulatory phosphatases and kinases, and members of sensor regulator systems. In this report, we discuss some of the phenotypes associated with the scoC mutant in light of the transcriptome changes observed.
Heparin and low-molecular-weight heparin (2008)

Heparin is one of the oldest biological medicines, and has an established place in the prevention and treatment of venous thrombosis. Low-molecular-weight heparins (LMWH) have been developed by several manufacturers and have advantages in terms of pharmacokinetics and convenience of administration. They have been shown to be at least as effective and safe as unfractionated heparin and have replaced the latter in many indications. In this article the chemistry, mechanisms of action, measurement of anticoagulant activities, and clinical status of heparin and LMWH are reviewed.
A Framework for Filtering News and Managing Distributed Data. (1997)

: With the development and diffusion of the Internet worldwide connection, a large amount of information is available to the users. Methods of information filtering and fetching are then required. This paper presents two approaches. The first concerns the information filtering system ProFile based on an adaptation of the generalized probabilistic model of information retrieval. ProFile filters the netnews and uses a scale of 11 predefined values of relevance. ProFile allows the user to update on--line the profile and to check the discrepancy between the assessment and the prediction of relevance of the system. The second concerns ABIS, an intelligent agent for supporting users in filtering data from distributed and heterogeneous archives and repositories. ABIS minimizes user&amp;apos;s effort in selecting the huge amount of available documents. The filtering engine memorizes both user preferences and past situations. ABIS compares documents with the past situations and finds the similarity scor...
Development of HIV vectors for anti-HIV gene therapy. (1996)

Current gene therapy protocols for HIV infection use transfection or murine retrovirus mediated transfer of antiviral genes into CD4+ T cells or CD34+ progenitor cells ex vivo, followed by infusion of the gene altered cells into autologous or syngeneic/allogeneic recipients. While these studies are essential for safety and feasibility testing, several limitations remain: long-term reconstitution of the immune system is not effected for lack of access to the macrophage reservoir or the pluripotent stem cell population, which is usually quiescent, and ex vivo manipulation of the target cells will be too expensive and impractical for global application. In these regards, the lentivirus-specific biologic properties of the HIVs, which underlie their pathogenetic mechanisms, are also advantageous as vectors for gene therapy. The ability of HIV to specifically target CD4+ cells, as well as non-cycling cells, makes it a promising candidate for in vivo gene transfer vector on one hand, and for transduction of non-cycling stem cells on the other. Here we report the use of replication-defective vectors and stable vector packaging cell lines derived from both HIV-1 and HIV-2. Both HIV envelopes and vesicular stomatitis virus glycoprotein G were effective in mediating high-titer gene transfer, and an HIV-2 vector could be cross-packaged by HIV-1. Both HIV-1 and HIV-2 vectors were able to transduce primary human macrophages, a property not shared by murine retroviruses. Vesicular stomatitis virus glycoprotein G-pseudotyped HIV vectors have the potential to mediate gene transfer into non-cycling hematopoietic stem cells. If so, HIV or other lentivirus-based vectors will have applications beyond HIV infection.
[Double-blind trial of the effectiveness of antibodies to interferon-gamma and tumor necrosis factor-alpha in rheumatoid arthritis (preliminary results)]. (2001)

Administration of antibodies to INF-a proved ineffective and well tolerated method in the treatment of severe RA resistant for a number of standard basic drugs. Anti-IFN-a holds great promise when used in combination with classic antirheumatoid drugs, primarily with methotrexate.
Cell Migration and Invasion Assays as Tools for Drug Discovery (2011)

Cell migration and invasion are processes that offer rich targets for intervention in key physiologic and pathologic phenomena such as wound healing and cancer metastasis. With the advent of high-throughput and high content imaging systems, there has been a movement towards the use of physiologically relevant cell-based assays earlier in the testing paradigm. This allows more effective identification of lead compounds and recognition of undesirable effects sooner in the drug discovery screening process. This article will review the effective use of several principle formats for studying cell motility: scratch assays, transmembrane assays, microfluidic devices and cell exclusion zone assays.
Biomechanical properties of the human umbilical cord (2001)

The umbilical cord is a complex and fascinating structure that connects the fetus to the placenta and encases the umbilical vessels. The response of its tissues to mechanical loading due to fetal movements and uterine contractions is not well understood. The aim of this study is the evaluation of the mechanical properties of the main components of the human umbilical cord. Fresh umbilical cord specimens were collected from neonates born at term of the gestation and submitted to compliance tests. Furthermore, uniaxial tensile and stress-relaxation tests were performed on samples of umbilical vein and Wharton's jelly. Both materials exhibited nonlinear stress-strain response with increasing strain, increasing the elastic modulus (E(high) about 10-20 times E(low)) and significant viscoelastic behavior. In addition, anisotropy of the vein was observed. Although the circumferential properties of the vein (mean E(high) about 2.4 MPa) were similar to those after birth, the longitudinal stiffness of both materials was higher (mean E(high) over 10 MPa) and comparable to that of the ligaments. These findings suggest a mechanism of protection acting against excessive elongations of the cord, which could cause undue restriction of the umbilical vessel area and interference with the fetal blood circulation.
Television watching and incident diabetes: Findings from the European Prospective Investigation into Cancer and Nutrition–Potsdam Study* (2009)

In the present study, the amount of time spent watching television was an independent predictor of incident diabetes only in models that adjusted for sociodemographic characteristics, lifestyle behaviors, and systolic blood pressure. The attenuation of the association after adjusting for anthropometric measures may represent an explanatory mechanism for our findings.
Electrochemical etching of porous silicon sacrificial layers for micromachining applications (1997)

Using porous silicon (PS) as a thick sacrificial layer, free-standing structures at a large distance from the bulk can be obtained. The very high specific surface of PS makes its removal using dilute alkaline solutions possible. In this work different technological conditions, such as adding ethanol or ultrasonic stirring, are studied in order to optimize the removal of PS using a one-step process with 0.1% KOH solution. Finally, cathodic polarization of the sample during the removal process is proposed as a method to enhance and improve the etching of PS whilst avoiding possible oxide formation. This electrochemical etching of a PS sacrificial layer allows good quality free-standing polysilicon structures featuring a smooth substrate to be obtained.
Extent of Antigenic Diversity in the V3 Region of the Surface Glycoprotein, gp120, of Human Immunodeficiency Virus Type 1 Group M and Consequences for Serotyping (1998)

Human immunodeficiency virus type 1 (HIV-1) may be studied by molecular or immunological approaches. Most analyses have been performed by genetic comparison of isolates and have led to the definition of clades or subtypes within the major (M) group of HIV-1. Five subtypes (A to E) were initially identified by comparison of genomic sequences. Four new subtypes (F to I) were identified more recently. Amino acid differences in the immunogenic V3 loop between isolates have also been studied, leading to a phenetic classification of at least 14 clusters (1 to 14) of sequences (B. T. M. Korber, K. McInnes, R. F. Smith, and G. Myers, J. Virol. 68:6730-6744, 1994). In this study, we compared the antigenicity of the V3 consensus sequences defined by phylogenetic analysis to the antigenicity of those defined by phenetic analysis. We used a recently developed subtype-specific enzyme immunoassay (SSEIA) that uses the principle of blocking with an excess of peptide in the liquid phase. Two SSEIAs were performed, the first with five V3 sequences defined by phylogenetic analysis and the second with 14 V3 sequences defined by phenetic analysis. A total of 168 HIV-1 sera taken from seropositive individuals from seven different countries or regions were studied. Experimental and statistical data, including correlation matrix and cluster analyses, demonstrated associations between the genetic subtypes and phenetically associated groups. Most of these were predicted by Korber et al. (J. Virol. 68:6730-6744, 1994) by theoretical analysis. We also found that V3 sequences can be grouped into between three and five antigenically unrelated categories. Residues that may be responsible for major antigenic differences were identified at the apex of the V3 loop, within the octapeptide xIGPGxxx, where x represents the critical positions. Our study provides evidence that there is a limited number of V3 serotypes which could be easily monitored by serological assays to study the diversity and dynamics of HIV-1 strains.
The Role of Lipopolysaccharide and Shiga-like Toxin in a Mouse Model of Escherichia coli O157:H7 Infection (1997)

The role of lipopolysaccharide (LPS) and Shiga-like toxin (SLT) in the pathogenesis of hemolytic uremic syndrome (HUS) was studied in a mouse model. Mice inoculated intragastrically with Escherichia coli O157:H7 developed gastrointestinal, neurologic, and systemic symptoms, necrotic foci in the colon, glomerular and tubular histopathology, and fragmented erythrocytes. LPS-responder (C3H/HeN) mice developed a combination of neurologic and systemic symptoms, whereas LPS-nonresponder (C3H/HeJ) mice had a biphasic course of disease, first developing systemic symptoms and later severe neurologic symptoms. Mice inoculated with SLT-II-positive strains developed severe neurotoxic symptoms and a higher frequency of systemic symptoms and glomerular pathology compared with SLT-II-negative strains. Anti-SLT-II antibodies protected against these symptoms and pathology. These results demonstrate that this model could be used to study aspects of human HUS and that both LPS and SLT are important for disease development.
Pseudomonas aeruginosainduces MUC5AC productionviaepidermal growth factor receptor (2002)

Hypersecretory disease associated with Pseudomonas aeruginosa (PA) infections is characterised by increased goblet cells and increased mucin production. Recently, an epidermal growth factor receptor (EGFR) signalling cascade was shown to be a common pathway through which many stimuli induce mucin MUC5AC expression in airways by differentiation to a goblet cell phenotype. This study looked at whether PA products induce EGFR expression and activation and thus result in mucin MUC5AC production. Human airway epithelial (NCI-H292) cells were stimulated with PA culture supernatant (Sup). MUC5AC protein production, MUC5AC and EGFR messenger ribonucleic acid (mRNA) expression, and phosphorylated EGFR and phosphorylated p44/42 mitogen-activated protein kinase (MAPK) were all examined using enzyme-linked immunosorbent assay, by in situ hybridisation and by immunoblotting. PA Sup induced MUC5AC mRNA and subsequent protein expression, EGFR and p44/42 MAPK phosphorylation and EGFR mRNA expression. Induction of MUC5AC mRNA and protein expression and EGFR and p44/42 MAPK phosphorylation were inhibited completely by pretreatment with a selective EGFR tyrosine kinase inhibitor. Pretreatment with a selective inhibitor of MAPK kinase prevented MUC5AC production and p44/42 MAPK phosphorylation but not EGFR phosphorylation. The authors conclude that PA products induce mucin MUC5AC production in human airway epithelial cells via the expression and activation of epidermal growth factor receptor.
Contribution of conformational stability of hen lysozyme to induction of type 2 T‐helper immune responses (2001)

It is important to identify characteristics that confer on proteins the potential to induce allergenic sensitization and allergenic disease. Protein allergens carry T-cell epitopes that are capable of inducing a type 2 T helper (Th2) cell response. There is limited information regarding factors that govern the allergenicity of proteins. We previously reported that a decrease in the conformational stability of hen-egg lysozyme (HEL) enhanced its capacity to activate HEL-specific T cells owing to the increased susceptibility to intracellular antigen processing. To determine whether the conformational stability of HEL makes for a critical contribution to allergenic sensitization in vivo, we immunized BALB/c mice with HEL derivatives of different conformational stability, but which retained a similar three-dimensional structure. The magnitude of in vivo T-cell responses, evaluated by ex vivo proliferative responses of lymph node T cells from mice primed with various HEL derivatives, was inversely correlated with conformational stability, as was interferon-gamma (IFN-gamma) and interleukin-4 (IL-4) production by splenic T cells in response to HEL. Immunization of the least stable derivative led to a potent IL-4 response and to immunoglobulin E (IgE) antibody production. We propose that the intrinsic allergenicity of proteins can be determined by the degree of conformational stability.