gebhart/patrepeval huggingface dataset:
Applications of Four-Colour Fluorescent Primer Extension Technology for SNP Analysis and Discovery (2010)

Studies on genetic variation can reveal effects on traits and disease, both in humans and in model organisms. Good technology for the analysis of DNA sequence variations is critical. Currently the development towards assays for large-scale and parallel DNA sequencing and genotyping is progressing rapidly. Single base primer extension (SBE) is a robust reaction principle based on four-colour fluorescent terminating nucleotides to interrogate all four DNA nucleotides in a single reaction. In this thesis, SBE methods were applied to the analysis and discovery of single nucleotide polymorphism (SNP) in the model organism Drosophila melanogaster and in humans. The tag-array minisequencing system in a microarray format is convenient for intermediate sized genotyping projects. The system is scalable and flexible to adapt to specialized and novel applications. In Study I of the thesis a tool was established to automate quality control of clustered genotype data. By calculating “Silhouette scores”, the SNP genotype assignment can be evaluated by a single numeric measure. Silhouette scores were then applied in Study I to compare the performance of four DNA polymerases and in Study III to evaluate freeze-dried reagents in the tag-array minisequencing system. The characteristics of the tag-array minisequencing system makes it suitable for inexpensive genome-wide gene mapping in the fruit fly. In Study II a high-resolution SNP map, and 293 genotyping assays, were established across the X, 2nd and 3rd chromosomes to distinguish commonly used Drosophila strains. A database of the SNP markers and a program for automatic allele calling and identification of map positions of mutants was also developed. The utility of the system was demonstrated by rapid mapping of 14 genes that disrupt embryonic muscle patterning. In Study III the tag-array minisequencing system was adapted to a lab-on-a-chip format for diagnostic testing for mutations in the TP53 gene. Freeze-drying was evaluated for storing reagents, including thermo-sensitive enzymes, on the microchip to reduce the complexity of the integrated test. Correct genotyping results were obtained using freeze-dried reagents in each reaction step of the genotyping protocol, both in test tubes and in single polymer test chambers. The results showed the potential of the approach to be implemented in fully integrated systems. The four-colour chemistry of SBE has been developed further to allow massively parallel sequencing (MPS) of short DNA fragments as in the Genome Analyzer system (Solexa/Illumina). In Study IV MPS was used to compare Nimblegen arrays and the SureSelect solution-based system for targeted enrichment of 56 continuous human candidate-gene regions totalling 3.1 Mb in size. Both methods detected known SNPs and discovered novel SNPs in the target regions, demonstrating the feasibility for complexity reduction of sequencing libraries by hybridization methods.
Ethylene and Defoliation of Ornamental Lime Plants in Transit1 (1975)

Abstract Ethylene concentration greater than 1 ppm added to ornamental lime plants ( Citrus latifolia Tan. cv. Persian), held in air-tight containers caused serious defoliation of intact plants. No C 2 H 4 was detectable in cartons of lime plants shipped from Florida to Ohio although defoliation occurred.
Basic Principles of Osmotic Computing: Secure and Dependable MicroElements (MELs) Orchestration Leveraging Blockchain Facilities (2018)

In recent years, the rapid development of Cloud, Edge and Internet of Things (IoT) technologies has accelerated the advancement trends forcing applications and information systems (IS) to evolve. In this new ecosystem, ISs are federated and usually highly distributed becoming complex and very dynamic that have to extend not only through the Cloud/Edge and IoT layers but also the federated organizational boundaries. In this context, Osmotic Computing (OC) is a new paradigm driven by the significant increase in capacity/capability of resources in highly distributed and federated environments, that solves problems related to the deployment, networking and security of microservices called MicroElements (MEL) that are composed and interconnected over Cloud/Edge and IoT infrastructures with specified levels of QoS and security constraints. In this federated collaborative system, each organization needs to have proper administration and security policies to maintain data security while allowing selective sharing of resources. Classical models of access control are not effective in protecting resources while allowing users to access to the resources within their privileges. Blockchain is an underlying technology that could help organizations to improve access control systems through consensus mechanisms, and underlying features of immutability, transparency, auditability, and cryptography. In this work, we propose a MELs orchestration approach through a Software Defined Membrane (SDMem) that leverages Blockchain facilities obeying the osmosis principles.
Effects of interleukin-1 on hematopoietic progenitors: evidence of stimulatory and inhibitory activities in a primate model (1989)

The effects of recombinant human interleukin-1 rhIL-1 beta (rhIL-1b) on hematopoietic recovery following chemotherapy in a primate model were investigated. Cynomolgus monkeys received 1 microgram/kg/day rhIL-1b intravenously for 2, 7, and 14 days following 5-Fluorouracil (5-FU) treatment (75 mg/kg x 2 days). Compared with controls, a significantly shortened time to achieve an absolute neutrophil (ANC) count over 500/microL was observed in animals receiving 2- and 7-day courses of rhIL-1b (17 v 30 days), while animals receiving a 14-day course of rhIL-1b achieved an ANC over 500/microL by 23 days. Concomitantly, a marked increase in granulocyte-macrophage colonies (CFU-GM) was observed at 14 days following 5-FU in animals receiving 2- and 7-day rhIL-1b courses. In animals receiving a 14-day rhIL-1b course, a significant increase in CFU-GM relative to control was not seen until 21 days post 5-FU. Utilizing a serum-free colony assay system, a 50% inhibition of normal marrow CFU-GM growth was observed with the addition of sera obtained on day 9 post 5-FU from animals receiving rhIL-1b for 14 days. Sera obtained at any time from animals receiving 2- and 7-day rhIL-1b treatment did not show any growth inhibition. Addition of antibodies to TNFa to the coculture assay abrogated the CFU-GM growth inhibition. TNFa levels in sera with the inhibitory activity was relatively high (918 pg/mL). Our data indicate that rhIL-1b enhances hematopoietic recovery following 5-FU if administered for short periods of time (less than 7 days), whereas prolonged administration has a counterproductive effect that is due in part to the induction of TNFa production.
Zur Rolle der “Epidermoid Formations” in der Pathogenese des kongenitalen Cholesteatoms - eine aktuelle Übersicht * (1999)

It is widely accepted that congenital cholesteatomas may originate from the postpartum persistence of epidermoid formations. Nevertheless, a clear transition from epidermoid formation to congenital cholesteatoma has yet to be confirmed.
BIOASSAY OF HYPOPHYSEAL GROWTH HORMONE IN HYPOPHYSECTOMIZED MICE BY THE TIBIA TEST1 (1957)

THE intact mouse has been found to be quite unresponsive to exogenously administered growth hormone (1, 2). No data, however, have heretofore been published on the effects of growth hormone in the hypophysectomized mouse; in the studies reported here, the responsiveness of hypophysectomized female mice of the C3H, A/He, BALB/c, and C57 BL strains has been assessed on the basis of increases in the width of the proximal epiphyseal cartilage of the tibia and of increases in body weight. Wherever possible, comparisons have been made between the results obtained in the hypophysectomized mouse and those reported for the hypophysectomized rat.
Percentages of ash, total sulfur, and sulfur forms in U. S. A. coals. [8 refs] (1958)

The frequency distributions of ash and sulfur percentages for coals of the United States are presented graphically, including coals from the various coal producing counties and coal beds of 30 states plus Alaska. Coals of all ranks are included. The range of ash and sulfur percentages and their relative frequency are shown by the graphs. The percentages of pyritic, organic and sulfate sulfur are shown versus total sulfur, for coals of Ohio and Illinois.
Effects of defolliculation on membrane current responses of Xenopus oocytes. (1989)

1. Catecholamines, adenosine, gonadotrophins, vasoactive intestinal peptide (VIP) and E-series prostaglandins all elicit K+ currents in follicle-enclosed Xenopus oocytes. Evidence suggests that cyclic nucleotides act as intracellular messengers in the activation of this K+ conductance. Muscarinic agonists and some divalent cations (e.g. Co2+, Mn2+, Ni2+ and Cd2+) elicit slow oscillatory Cl- currents, which are activated through hydrolysis of inositol phospholipids and mobilization of intracellular calcium by inositol phosphates. 2. We investigated whether these membrane current responses were generated in the oocyte itself or in enveloping follicular cells which are coupled to the oocyte by gap junctions. Oocytes were defolliculated, either enzymatically using collagenase, or by manual dissection combined with rolling over poly-L-lysine-coated slides. Removal of follicular cells was checked using scanning electron microscopy. Membrane current responses of defolliculated oocytes were compared with responses seen in follicle-enclosed oocytes taken from the same ovary. 3. The K+ responses evoked by all the various hormones/neurotransmitters were either drastically reduced (greater than 90%) or abolished by defolliculation. K+ currents generated by the adenylate cyclase activator forskolin and by intraoocyte injection of adenosine 3',5'-cyclic monophosphate (cyclic AMP), or guanosine 3',5'-cyclic monophosphate were similarly reduced in defolliculated oocytes. In contrast, oscillatory Cl- currents to acetylcholine and divalent cations were selectively preserved through defolliculation. 4. Injection of cyclic AMP (1-20 pmol) into defolliculated oocytes had little or no effect on oscillatory Cl- currents elicited by ACh. However, the calcium-dependent transient Cl- current, activated by depolarization of the oocyte membrane, was consistently potentiated (100-900%) by injections of cyclic AMP (1-10 pmol). 5. These experiments suggest that cyclic nucleotide-activated K+ currents arise essentially in follicular cells and are monitored within the oocyte through electrical coupling by gap junctions. Oscillatory Cl- responses evoked by ACh and divalent cations are produced largely or wholly in the oocyte itself.
Phenotype-genotype association grid: a convenient method for summarizing multiple association analyses (2006)

The PGA grid, which permits interactive exploration of large numbers of association test results, can serve as an easily adapted common and useful display format for large-scale genetic studies. Doing so would reduce the problem of publication bias, and would simplify the task of summarizing large-scale association studies.
Optimal chip sizing for multi-chip modules (1994)

The functions of a complex electronic system will be partitioned across multiple chips. An optimal system using PWB technology will contain just a few chips in order to minimize the inter-chip delays. However, the area delay penalty for inter-die interconnects is much lower for MCM technology, and different partitioning options should be considered. This paper develops a criteria for optimal MCM chip sizing based upon system quality level, cost and silicon efficiency. The criteria are then applied to a 500,000 gate MCM case study.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A smartphone intervention that enhances real-world memory and promotes differentiation of hippocampal activity in older adults (2022)

The act of remembering an everyday experience influences how we interpret the world, how we think about the future, and how we perceive ourselves. It also enhances long-term retention of the recalled content, increasing the likelihood that it will be recalled again. Unfortunately, the ability to recollect event-specific details tends to decline with age, resulting in an impoverished ability to mentally re-experience the past. This shift has been linked to a corresponding decline in the distinctiveness of hippocampal memory representations. Despite these well-established changes, there are few effective cognitive behavioral interventions that target real-world episodic memory. We addressed this gap by developing a smartphone-based application called HippoCamera that allows participants to record labelled videos of everyday events and subsequently replay standardized, high-fidelity autobiographical memory cues. In two experiments, we found that older adults were able to easily integrate this non-invasive intervention into their daily lives. Using HippoCamera to repeatedly reactivate memories for real-world events improved episodic recollection and it evoked more positive autobiographical sentiment at the time of retrieval. In both experiments, these benefits were observed shortly after the intervention and again after a 3-month delay. Moreover, more detailed recollection was associated with more differentiated memory signals in the hippocampus. We conclude that using this smartphone application to systematically reactivate memories for recent real-world experiences can help to maintain a bridge between the present and past self in older adults.
Special Issue: Characterization of Crystal Growing Surface by "In-Situ Photon-Probing". In Situ Observation of As Desorption Processes from GaAs Surfaces in Hydrogen by the Surface Photo Absoption Method. (1993)

Arsenic desorption processes from GaAs surfaces with various crystallographic orientations were studied in the MOVPE reactor under H2 atmosphere (13.3 kPa) by the surface photo-absorption (SPA) method. We found two desorption processes (fast and slow processes) on the GaAs (001) surface. The real part of the refractive index of the surface layer which is removed during the fast As desorption process, is different from that of the GaAs substrate. Both the real and the imaginary parts of the refractive index of the layer which is removed during the slow As desorption process, are different from those of the GaAs substrate. We observed single As desorption processes on the GaAs (111) A and (111) B surfaces. We also studied SPA signals while AsH3 and TMG were being alternately supplied to those surfaces. We observed the ALE process on the (001) surface around 480°C. Growth rates were less than one monolayer per cycle on (111) A within the entire temperature range of our experiments (from 420°C to 550°C).
Confocal microscopy and passive staining with the styryl dye FM1-43: a convenient method to evaluate morphometric changes in nodes of Ranvier of single living myelinated axons (2017)

International audience
EFFICACY OF LIVER TRANSPLANTATION IN THE TREATMENT OF MALIGNANT LIVER DISEASES - A SINGLE CENTER EXPIRIENCE (1999)

753 Liver transplantation (OLT) is the only curative therapeutic option for patients with malignant liver diseases. Early reports showed that the efficacy of OLT is limited by high tumor-recurrence rates. Recent studies, however, demonstrated that outcome is highly dependent on tumor stage and patients with early stages have survival rates comparable to those of patients transplanted for benign liver diseases. In this retrospective study we analyzed data of patients who were transplanted for malignant liver diseases at our center. Between 4/85 and 3/97 70 out of 292 patients (24%) with malignant liver diseases underwent OLT. In 54 patients a hepatocellular carcinoma (HCC) was diagnosed, 9 patients had a cholangiocarcinoma (CCa) and 7 patients a metastatic liver disease of a neuroendocrine tumor. Mean follow-up of all patients was 23 months. The actuarial patient survival of all patients at 1, 3, 5, and 10-years were 72.9%, 53.9%, 32.2% and 19.3%, respectively. These rates are significantly reduced compared to those of patients transplanted for benign liver diseases. The main causes of death were tumor recurrence (n=19) and infection-related (n=8). In 4 patients reOLT was necessary. No difference in overall outcome was seen between patients transplanted for HCC, CCa and neuroendocrine tumor. Regarding patients with HCC survival was significantly dependent on tumor stage. Patients with stage I/II (n=12) and stage III (n=17) tumors, according to UICC criteria, had 1, 3 and 5-year survival rates of 90.9%, 78.8%, 78.8% and 93.3%, 67.9% and 60.5%, respectively. These rates did not differ significantly from those of benign liver diseases (p>0.05). Chemoembolisation (TACE) was applied to 24 patients prior to OLT. TACE showed a slight positive effect on overall survival, but this difference did not reach statistical significance. No difference was found concerning the etiology of liver disease. The median survival of patients with CCa was 1.9 years. Most of these patients died due to tumor-recurrence. Although all patients with neuroendocrine tumor and liver metastases developed tumor recurrence, the median survival was 2.6 years. Our data showed that OLT is effective in the treatment of malignant liver diseases. Especially patients with low stage HCCs demonstrated survival rates equal to those of patients with benign liver cirrhosis which is consistent with previous reports (Hepatology 1997)
PLA/POSS Nanofibers: A Novel System for the Immobilization of Metal Nanoparticles (2013)

In this work, a novel catalytic system is developed, consisting of palladium nanoclusters homogenously dispersed on the surface of nanostructured polymer nanofibers based on poly(L-lactic acid) (PLLA) and polyhedral oligomeric silsesquioxanes (POSS). Indeed, PLLA nanofibers containing amino-functionalized silsesquioxane molecules (POSS-NH2), potentially capable of interacting with the metal precursor, are prepared by means of electrospinning. Conversely to the polymer matrix, which does not show any tendency to retain the metal precursor, the submicrometric dispersion of POSS-NH2 in the PLLA nanofibers, as demonstrated by SEM-EDS analysis, turns out to promote the formation of metal nanoclusters. TEM measurements show a uniform distribution of Pd nanoparticles, characterized by an average dimension of ca. 4 nm, along the fibers. The prepared system proves a relevant catalytic activity toward the hydrogenation of stilbene under heterogeneous conditions. Moreover, as demonstrated by XPS measurements, the support is capable of retaining the catalyst during the hydrogenation reaction, thus preventing its leaching.
Interactions of DNA with a new electron‐deficient tentacle porphyrin: meso‐Tetrakis[2,3,5,6‐tetrafluoro‐4‐(2‐trimethylammoniumethylamine)phenyl]porphyrin (1997)

A new electron-deficient tentacle porphyrin meso-tetrakis[2,3,5,6-tetrafluoro-4-(2-trimethylammoniumethylamine)phenyl]porphyrin (TθF4TAP) has been synthesized. The binding interactions of TθF4TAP with DNA polymers were studied for comparison to those of an electron-deficient tentacle porphyrin and an electron-rich tentacle porphyrin; these previously studied porphyrins bind to DNA primarily by intercalative and outside-binding modes, respectively. The three tentacle porphyrins have similar size and shape. The basicity of TθF4TAP indicated that it has electronic characteristics similar to those of the intercalating electron-deficient tentacle porphyrin. However, TθF4TAP binds to calf thymus DNA, [poly(dA-dT)]2, and [poly(dG-dC)]2 in a self-stacking, outside-binding manner under all conditions. Evidence for this binding mode included a significant hypochromicity of the Soret band, a conservative induced CD spectrum, and the absence of an increase in DNA solution viscosity. As found previously for the electron-rich porphyrin, the results suggest that combinations of closely related self-stacked forms coexist. The mix of forms depended on the DNA and the solution conditions. There are probably differences in the detailed features of the self-stacking adducts for the two types of tentacle porphyrins, especially at high R (ratio of porphyrin to DNA). At low R values, the induced CD signal of TθF4TAP/CT DNA resembled that of TθF4TAP/[poly(dA-dT)]2, suggesting that TθF4TAP binds preferentially at AT regions. Competitive binding experiments gave evidence that TθF4TAP binds preferentially to [poly(dA-dT)]2 over [poly(dG-dC)]2. Thus, despite the long, positively charged, flexible substituents on the porphyrin, the binding of TθF4TAP is significantly affected by base-pair composition. Similar characteristics were found previously for the electron-rich tentacle porphyrin. Thus, significant changes in electron richness have relatively minor effects on this outside binding selectivity for AT regions. TθF4TAP is the first porphyrin with electron deficiency and shape similar to intercalating porphyrins that does not appear to intercalate. All porphyrins reported to intercalate have had pyridinium substituents. Thus, the electronic distribution in the porphyrin ring, not just the overall electron richness, may play a role in facilitating intercalation. © 1997 John Wiley & Sons, Inc. Biopoly 42: 203–217, 1997
Design Study for a Superconducting Proton Linac From 20 to 100 MeV (1994)

Advances in superconducting radiofrequency technology during the past 15 years have made possible the large-scale application of superconducting niobium accelerators. So far this development has been restricted to rather low-current electron and heavy-ion accelerators. In addition to the power savings, the improved capability of superconducting cavities to provide acceleration of high currents with low beam losses, which follows from the ability to use larger beam apertures without a large economic penalty from increased rf losses, could make superconducting proton linacs very attractive for high-intensity applications, where activation of the accelerator is a major concern. During the past year, at Los Alamos, the authors have been looking at a possible upgrade to the 800-MeV LAMPF proton accelerator, to provide higher intensity injection into a new storage ring for a new high-intensity pulsed neutron source. As part of this upgrade to the LAMPF accelerator, the entire linac below 100 MeV would be rebuilt to provide improved beam quality, improved reliability, and to include funneling at 20 MeV for higher beam currents. Both a room-temperature and a superconducting option are being considered for the section from 20 to 100 MeV. At present, this section is a 201.25 MHz room-temperature copper drift-tube linac (DTL). For this new upgrade scenario the frequency from 20 to 100 MeV was fixed at 805 MHz. The new duty factor is assumed to be 7.2%, and the authors show some results at two currents, 30 mA and 150 mA, that span the range of interest. Their superconducting linac concept consists of individual multicell cavities, each driven by a klystrode. Focusing would be provided by superconducting quadrupole lenses between cavities. In the remainder of the paper they describe their study to evaluate the potential of a superconducting proton linac section for this application, and address some of the many design choices.