gebhart/patrepeval huggingface dataset:
Pressure-enhanced crystallization kinetics of amorphous Si and Ge: Implications for point-defect mechanisms (1991)

The effects of hydrostatic pressure on the solid-phase epitaxial growth (SPEG) rate v of intrinsic Ge(100) and undoped and doped Si(100) into their respective self-implanted amorphous phases are reported. Samples were annealed in a high-temperature, high-pressure diamond anvil cell. Cryogenically loaded fluid Ar, used as the pressure transmission medium, ensured a clean and hydrostatic environment. v was determined by in situ time-resolved visible (for Si) or infrared (for Ge) interferometry. v increased exponentially with pressure, characterized by a negative activation volume of −0.46Ω in Ge, where Ω is the atomic volume, and −0.28Ω in Si. The activation volume in Si is independent of both dopant concentration and dopant type. Structural relaxation of the amorphous phases has no significant effect on v. These and other results are inconsistent with all bulk point-defect mechanisms, but consistent with all interface point-defect mechanisms, proposed to date. A kinetic analysis of the Spaepen–Turnbull interfacial dangling bond mechanism is presented, assuming thermal generation of dangling bonds at ledges along the interface, independent migration of the dangling bonds along the ledges to reconstruct the network from the amorphous to the crystalline structure, and unimolecular annihilation kinetics at dangling bond ‘‘traps.’’ The model yields v = 2 sin(θ)vsnr exp[(ΔSf + ΔSm)/k] exp− [(ΔHf + ΔHm)/kT], where ΔSf and ΔHf are the standard entropy and enthalpy of formation of a pair of dangling bonds, ΔSm and ΔHm are the entropy and enthalpy of motion of a dangling bond at the interface, vs is the speed of sound, θ is the misorientation from {111}, and nr is the net number of hops made by a dangling bond before it is annihilated. It accounts semiquantitatively for the measured prefactor, orientation dependence, activation energy, and activation volume of v, and the pressure of a ‘‘free-energy catastrophe’’ beyond which the exponential pressure enhancement of SPEG cannot continue uninterrupted due to a vanishing barrier to dangling bond migration. The enhancement of v by doping can be accounted for by an increased number of charged dangling bonds, with no change in the number of neutrals, at the interface. Quantitative models for the doping dependence of v are critically reviewed. At low concentrations the data can be accounted for by either the fractional ionization or the generalized Fermi-level-shifting models; methods to further test these models are enumerated. Ion irradiation may affect v by altering the populatio
Common variable immunodeficiency (CVID): exploring the multiple dimensions of a heterogeneous disease (2012)

Common variable immunodeficiency (CVID) represents a large heterogeneous group of antibody deficiency syndromes associated with a plethora of clinical features and as yet largely undefined molecular causes. We are now seeing this heterogeneous group being increasingly defined into single-gene and polygenic disorders after stratification into homogeneous patient subgroups based on improved clinical and immunological criteria, including molecular, functional, immunohistological, and longitudinal and outcome information. In this perspective, we highlight recent developments in CVID, addressing mainly its genetic and immunological dimensions.
Early transcriptional changes linked to naturally occurring Huntington's disease mutations in neural derivatives of human embryonic stem cells (2012)

Huntington's disease (HD) is characterized by a late clinical onset despite ubiquitous expression of the mutant gene at all developmental stages. How mutant huntingtin impacts on signalling pathways in the pre-symptomatic period has remained essentially unexplored in humans due to a lack of appropriate models. Using multiple human embryonic stem cell lines derived from blastocysts diagnosed as carrying the mutant huntingtin gene by pre-implantation genetic diagnosis, we explored early developmental changes in gene expression using differential transcriptomics, combined with gain and loss of function strategies. We demonstrated a down-regulation of the HTT gene itself in HD neural cells and identified three genes, the expression of which differs significantly in HD cells when compared with wild-type controls, namely CHCHD2, TRIM4 and PKIB. Similar dysregulation had been observed previously for CHCDH2 and TRIM4 in blood cells from patients. CHCHD2 is involved in mitochondrial function and PKIB in protein kinase A-dependent pathway regulation, which suggests that these functions may be precociously impacted in HD.
Dissection of IncP conjugative plasmid transfer: definition of the transfer region Tra2 by mobilization of the Tra1 region in trans (1992)

We constructed a transfer system consisting of two compatible multicopy plasmids carrying the transfer regions Tra1 and Tra2 of the broad-host-range IncP plasmid RP4. In this system, the plasmid containing the Tra1 region with the origin of transfer (oriT) was transferred, whereas additional functions essential for the conjugative process were provided from the Tra2 plasmid in trans. The Tra2 region, as determined for matings between Escherichia coli cells, maps between coordinates 18.03 and 29.26 kb of the RP4 standard map. The section of Tra2 required for mobilization of the plasmid RSF1010 (IncQ) and the propagation of bacteriophages Pf3 and PRD1 appears to be the same as that needed for RP4 transfer. Tra2 regions of RP4 (IncP alpha) and R751 (IncP beta) are interchangeable, facilitating mobilization of the plasmid carrying the RP4 Tra1 region. The transfer frequencies of both systems are similar. Transcription of Tra2 proceeds clockwise relative to the standard map of RP4 and is probably initiated at a promoter region located upstream of trbB (kilB). From this promoter region the trfA operon and the Tra2 operon are likely to be transcribed divergently. A second potential promoter has been located immediately upstream of trbB (kilB). Plasmids encoding the functional Tra2 region can only be maintained stably in host cells in the presence of the RP4 regulation region carrying the korA-korB operon or part of it. This indicates the involvement of RP4 key regulatory functions that apparently are active not only in the control of replication but also in conjugation.
Birth of offspring following transplantation of cryopreserved immature testicular pieces and in-vitro microinsemination (2002)

This approach of 'testicular tissue banking' is a promising technique for the preservation of fertility in prepubertal male oncology patients. Xenogeneic transplantation into immunodeficient mice may provide a system for studying spermatogenic failure in infertile men.
Phylogenetic Analyses Identify 10 Classes of the Protein Disulfide Isomerase Family in Plants, Including Single-Domain Protein Disulfide Isomerase-Related Proteins (2005)

Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I-V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5'-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell.
The multi-streamed solid-state drive (2014)

This paper makes a case for the multi-streamed solid-state drive (SSD). It offers an intuitive storage interface for the host system to inform the SSD about the expected lifetime of data being written. We show through experimentation with a real multi-streamed SSD prototype that the worst-case update throughput of a Cassandra NoSQL DB system can be improved by nearly 56%. We discuss powerful use cases of the proposed SSD interface.
Non-Thermal Atmospheric-Pressure Plasma Possible Application in Wound Healing (2014)

Non-thermal atmospheric-pressure plasma, also named cold plasma, is defined as a partly ionized gas. Therefore, it cannot be equated with plasma from blood; it is not biological in nature. Non-thermal atmospheric-pressure plasma is a new innovative approach in medicine not only for the treatment of wounds, but with a wide-range of other applications, as e.g. topical treatment of other skin diseases with microbial involvement or treatment of cancer diseases. This review emphasizes plasma effects on wound healing. Non-thermal atmospheric-pressure plasma can support wound healing by its antiseptic effects, by stimulation of proliferation and migration of wound relating skin cells, by activation or inhibition of integrin receptors on the cell surface or by its pro-angiogenic effect. We summarize the effects of plasma on eukaryotic cells, especially on keratinocytes in terms of viability, proliferation, DNA, adhesion molecules and angiogenesis together with the role of reactive oxygen species and other components of plasma. The outcome of first clinical trials regarding wound healing is pointed out.
Deletion analysis of the Clostridium perfringens enterotoxin (1997)

To further our knowledge of the structure-function relationship and mechanism of action of the Clostridium perfringens enterotoxin (CPE), a series of recombinant CPE (rCPE) species containing N- and C-terminal CPE deletion fragments was constructed by recombinant DNA approaches. Each rCPE species was characterized for its ability to complete the first four early steps in the action of CPE, putatively ordered as specific binding, a postbinding physical change to bound CPE, large-complex formation, and induction of alterations in small-molecule membrane permeability. These studies demonstrated that (i) at least 44 amino acids can be removed from the N terminus of CPE without loss of cytotoxicity, (ii) removal of the first 53 amino acids from the N terminus of CPE produces a fragment that appears to be noncytotoxic because it cannot undergo the post-binding physical change step in CPE action, (iii) removal of as few as five amino acids from the C terminus of CPE produces a noncytotoxic fragment lacking receptor binding activity, and (iv) a fragment lacking the first 44 N-terminal amino acids of native CPE formed twice as much large complex and was twice as cytotoxic as native CPE. From these structure-function results, it appears that the minimum-size cytotoxic CPE fragment comprises approximately residues 45 to 319 of native CPE. Results from these deletion fragment studies have also contributed to our understanding of CPE action by (i) independently supporting previous suggestions that binding, the postbinding physical change step, and large-complex formation represent important steps in CPE cytotoxicity and (ii) providing independent evidence confirming the putative sequential order of these early events in CPE action.
Historique de l’aménagement du lit de la Saône (2002)

Il est indispensable, dans une approche globale de la rivière, de prendre en compte les travaux du XIXe siècle ainsi que les modifications qu’ils ont pu occasionner. De plus, ce sont les projets et réalisations de ces aménagements qui ont nécessité la rédaction des plans et documents étudiés aux chapitres suivants.Au tout début du XIXe siècle, la Grande Saône n’avait bénéficié que de quelques améliorations, comme le creusement du canal d’Épervans (fig. 6), alors que d’autres cours d’eau avai...
Genetic algorithms in search, optimization, and machine learning (1989)

From the Publisher:
This book brings together - in an informal and tutorial fashion - the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields. 

Major concepts are illustrated with running examples, and major algorithms are illustrated by Pascal computer programs. No prior knowledge of GAs or genetics is assumed, and only a minimum of computer programming and mathematics background is required.
Human leukocytic pyrogen test for detection of pyrogenic material in growth hormone produced by recombinant Escherichia coli (1984)

Human growth hormone is biosynthetically produced in recombinant strains of Escherichia coli as methionyl human growth hormone (met-hGH). When purified from the bacterial culture, met-hGH is biologically active in established assays for growth hormone. Therefore, a phase I trial of met-hGH was carried out in healthy human adults; during the first trial, however, signs, symptoms, and clinical laboratory tests characteristic of an acute-phase response to pyrogenic agents was observed. Prior testing of the met-hGH preparation used in the phase I trial did not reveal evidence of toxicity, and the U.S. Pharmacopeial Convention rabbit pyrogen test, as well as the Limulus amoebocyte lysate (LAL) test, had not detected significant levels of exogenous pyrogens or endotoxin. In addition, standard inhibition studies with added endotoxin showed no inhibition by the LAL test. When this preparation of met-hGH was incubated with human blood mononuclear cells, leukocytic pyrogen (LP) was released into the supernatant medium, suggesting that the preparation contained pyrogenic material. Various lots of met-hGH based on different purification and formulating methods were tested by the human LP assay for contaminating pyrogens. The results of these tests aided in the identification of procedures for met-hGH preparations which did not induce LP in vitro. Thus, subsequent lots of met-hGH which had passed the LP test were used in repeat clinical studies, and no inflammatory or pyrogenic reactions were observed. When the LP test was used, experiments revealed that the original lot of met-hGH was contaminated with endotoxin which had not been detected in the LAL or rabbit pyrogen tests. Lyophilization in glycine-phosphate buffer had resulted in a 10- to 20-fold reduction of endotoxin reactivity in the LAL test and the U.S. Pharmacopeial Convention rabbit pyrogen test. These data provide a probable explanation for the negative result from the LAL and rabbit pyrogen test in the initial lot of met-hGH which induced acute-phase reactions. In addition, these studies demonstrate that the release of LP from human cells is a reliable indicator of the presence of materials that are pyrogenic for humans.
Erythropoietin reduces storage lesions and decreases apoptosis indices in blood bank red blood cells (2015)

Under standard blood bank conditions, an important proportion of red blood cells satisfy the criteria of apoptosis. Recombinant human erythropoietin beta seems to improve storage lesion parameters and mitigate apoptosis.
Expression of human adenosine deaminase in mice reconstituted with retrovirus-transduced hematopoietic stem cells. (1990)

Recombinant retroviruses encoding human adenosine deaminase (ADA; adenosine aminohydrolase, EC 3.5.4.4) have been used to infect murine hematopoietic stem cells. In bone marrow transplant recipients reconstituted with the genetically modified cells, human ADA was detected in peripheral blood mononuclear cells of the recipients for at least 6 months after transplantation. In animals analyzed in detail 4 months after transplantation, human ADA and proviral sequences were detected in all hematopoietic lineages; in several cases, human ADA activity exceeded the endogenous activity. These studies demonstrate the feasibility of introducing a functional human ADA gene into hematopoietic stem cells and obtaining expression in multiple hematopoietic lineages long after transplantation. This approach should be helpful in designing effective gene therapies for severe combined immunodeficiency syndromes in humans.
Construction of Targeting Vector and Expression of Green Fluorescent Protein in the Silkworm, Antheraea pernyi (2003)

The transcription initiation site of Anrheraea pernyi was identified, and a gene targeting vector was constructed. The green fluorescent protein (GFP) gene was inserted into this vector under the control of a fibroin promoter. This recombinant vector was used to target the GFP gene to the fibroin region of the silkworm genome. The DNA was injected into the testes during the pupae, and was also transferred into the egg via the sperm during fertilization. The analysis showed that the GFP gene was integrated into the fibroin gene on the genome by homologous recombination, and was expressed in the silk gland.
Control of T‐cell activation by CD4+ CD25+ suppressor T cells (2001)

Depletion of the minor ( approximately 10%) subpopulation of CD4+ T cells that co-expresses CD25 (interleukin (IL)-2 receptor alpha-chain) by thymectomy of neonates on the third day of life or by treatment of adult CD4+ T cells with anti-CD25 and complement results in the development of organ-specific autoimmunity. Autoimmune disease can be prevented by reconstitution of the animals with CD4+ CD25+ cells. CD4+ CD25+-mediated protection of autoimmune gastritis does not require the suppressor cytokines IL-4, IL-10, or transforming growth factor (TGF)-beta. Mice that express a transgenic T-cell receptor (TCR) derived from a thymectomized newborn that recognizes the gastric parietal cell antigen H/K ATPase all develop severe autoimmune gastritis very early in life. CD4+ CD25+ T cells are also powerful suppressors of the activation of both CD4+ and CD8+ T cells in vitro. Suppression is mediated by a cell contact-dependent, cytokine-independent T-T interaction. Activation of CD4+ CD25+ via their TCR generates suppressor effector cells that are capable of non-specifically suppressing the activation of any CD4+ or CD8+ T cell. Activation of suppressor effector function is independent of co-stimulation mediated by CD28/CTLA-4 interactions with CD80/CD86. We propose that CD4+ CD25+ T cells recognize organ-specific antigens, are recruited to sites of autoimmune damage where they are activated by their target antigen, and then physically interact with autoreactive CD4+ or CD8+ effector cells to suppress the development of autoimmune disease.
Remote detection of virtual machine monitors with fuzzy benchmarking (2008)

We study the remote detection of virtual machine monitors (VMMs) across the Internet, and devise fuzzy benchmarking as an approach that can successfully detect the presence or absence of a VMM on a remote system. Fuzzy benchmarking works by making timing measurements of the execution time of particular code sequences executing on the remote system. The fuzziness comes from heuristics which we employ to learn characteristics of the remote system's hardware and VMM configuration. Our techniques are successful despite uncertainty about the remote machine's hardware configuration.
Quantum Confinement in Size-Selected, Surface-Oxidized Silicon Nanocrystals (1993)

The dynamics and spectroscopy of silicon nanocrystals that emit at visible wavelengths were analyzed. Size-selective precipitation and size-exclusion chromatography cleanly separate the silicon nanocrystals from larger crystallites and aggregates and provide direct evidence for quantum confinement in luminescence. Measured quantum yields are as high as 50 percent at low temperature, principally as a result of efficient oxide passivation. Despite a 0.9—electron-volt shift of the band gap to higher energy, the nanocrystals behave fundamentally as indirect gap materials with low oscillator strength.
Survey of Human Chromosome 21 Gene Expression Effects on Early Development in Danio rerio (2018)

Trisomy for human chromosome 21 (Hsa21) results in Down syndrome (DS), one of the most genetically complex conditions compatible with human survival. Assessment of the physiological consequences of dosage-driven overexpression of individual Hsa21 genes during early embryogenesis and the resulting contributions to DS pathology in mammals are not tractable in a systematic way. A recent study looked at loss-of-function of a subset of <i>Caenorhabditis elegans</i> orthologs of Hsa21 genes and identified ten candidates with behavioral phenotypes, but the equivalent over-expression experiment has not been done. We turned to zebrafish as a developmental model and, using a number of surrogate phenotypes, we screened Hsa21 genes for effects on early embyrogenesis. We prepared a library of 164 cDNAs of conserved protein coding genes, injected mRNA into early embryos and evaluated up to 5 days post-fertilization (dpf). Twenty-four genes produced a gross morphological phenotype, 11 of which could be reproduced reliably. Seven of these gave a phenotype consistent with down regulation of the sonic hedgehog (Shh) pathway; two showed defects indicative of defective neural crest migration; one resulted consistently in pericardial edema; and one was embryonic lethal. Combinatorial injections of multiple Hsa21 genes revealed both additive and compensatory effects, supporting the notion that complex genetic relationships underlie end phenotypes of trisomy that produce DS. Together, our data suggest that this system is useful in the genetic dissection of dosage-sensitive gene effects on early development and can inform the contribution of both individual loci and their combinatorial effects to phenotypes relevant to the etiopathology of DS.
INFLUENZA VIRUS TRANSCRIPTION (1979)

Journal Article INFLUENZA VIRUS TRANSCRIPTION Get access A J HAY, PhD, A J HAY, PhD National Institute for Medical ResearchLondon Search for other works by this author on: Oxford Academic PubMed Google Scholar J J SKEHEL, PhD J J SKEHEL, PhD National Institute for Medical ResearchLondon Search for other works by this author on: Oxford Academic PubMed Google Scholar British Medical Bulletin, Volume 35, Issue 1, January 1979, Pages 47–50, https://doi.org/10.1093/oxfordjournals.bmb.a071541 Published: 01 January 1979