gebhart/patrepeval huggingface dataset:
Causes and Prevention of Temperature-Dependent Bubbles in Silicon Wafer Bonding (1991)

Unbonded areas or bubbles generated at the interface of bonded silicon wafers in the temperature range of 200-800°C have been investigated. Experiments described in this paper demonstrate that the desorption of hydrocarbon contamination at the silicon wafer surfaces appears to be a necessary condition for the formation of these bubbles. SIMS data also indicate the existence of hydrocarbons at the bonding interface. It is speculated that hydrocarbon gas such as CH 4 is required for bubble nucleation and that either CH 4 or H 2 itself or a mixture of both gases is contained in these bubbles. Finally, methods to prevent the formation of these bubbles are presented.
Pantropic retroviral vector integration, expression, and germline transmission in medaka (Oryzias latipes). (1997)

Pantropic retroviral vectors were used to introduce transgenes into Japanese medaka (Oryzias latipes). These vectors contain the long terminal repeat (LTR) sequence of Moloney murine leukemia virus (Mo-MLV) and a reporter gene (neo or lacZ) regulated by the LTR sequence of rous sarcoma virus (RSV). Because these pseudotyped retroviral vectors contain the vesicular stomatitis virus envelope glycoprotein (VSV-G), they have an extremely broad host cell range and can infect many no mammalian species. Newly fertilized medaka eggs (intact or dechorionated) were electroporated at different voltage settings in the presence of 4 x 10(4) cfu of pantropic retroviral vector. The survival rates of the pantropic retroviral vector-treated embryos ranged from 65% to 20% with increasing amplitude of electroporation. Dechorionation did not substantially affect the survival rate of embryos. PCR amplification demonstrated proviral sequences in up to 60% of the 2-month-old fish. The efficiency of gene transfer was enhanced by dechorionation. Furthermore, overnight incubation of dechorionated embryos with pantropic retroviral vectors without electroporation also resulted in proviral integration in 60% of the embryos without compromising survival rate. Southern blot analysis of DNA samples isolated from polymerase chain reaction (PCR) as positive F1 reaction animals confirmed the integration of a single copy of the provirus into the host genome. Three P1 transgenic females transmitted the proviral sequence to 50% of their F1 progeny in a back cross with wild-type males, suggesting that the entire germline of these P1 fish was transformed by the pantropic retroviral vector. Expression of the neomycin phosphotranferase transgene in F1 transgenic individuals was detected by reverse transcription (RT)-PCR amplification of the neo mRNA sequence. Furthermore, expression of a beta-galactosidase transgene was also observed in 4-day-old F1 transgenic individuals. Thus, pantropic retroviral vectors provide a convenient method to stably introduce and express foreign genes in medaka.
Rapid Retreat and Acceleration of Helheim Glacier, East Greenland (2009)

This chapter contains sections titled: Introduction Methods Results Analysis Conclusions References
On Improvement of Cloud Virtual Machine Availability with Virtualization Fault Tolerance Mechanism (2011)

Virtualization is a common strategy to improve the existing computing resources, particularly in cloud computing field. Hadoop, one of Apache projects, is designed to scale up from single servers to thousands of machines, and each offer local computation and storage. However, how to guarantee stability and reliability have become great study topics. In this article, we use current open-source based on software and platform to reach our goal. For instance, Xen-Hyper visor virtualization technology, Open Nebula virtual machines management tool, and so on. After extending component capabilities, we developed a mechanism to support our idea and reached Hadoop High Availability which called Virtualization Fault Tolerance (VFT). We consider a practical problem that occurs frequently in our system, and the results in this paper also confirm the downtime time can be shortened if failure occurred. In this case, it is not only for the Hadoop applications, but also extended to more areas of cluster-based systems.
Neutralizing antiidiotypic antibodies to factor VIII inhibitors after desensitization in patients with hemophilia A. (1996)

Hemophilia A patients producing antibodies towards FVIII are usually treated with infusions of high doses of FVIII in an attempt to "desensitize" them. To examine the mechanisms by which such desensitization operates, sequential plasma samples of two unrelated inhibitor patients were analyzed for anti-FVIII and antiidiotypic antibodies before and during infusions of high doses of FVIII. Anti-FVIII antibodies were separated from antiidiotypic antibodies by immunoaffinity chromatography before analysis. We show in the present study that the concentration of anti-FVIII antibodies did not change during a successful desensitization and that antibodies maintained their capacity to inhibit the procoagulant function of FVIII, even though the number of Bethesda units in plasma was reduced to undetectable levels. Using a competition assay with mAbs, we further show that the specificity of human antibodies did not vary significantly during therapy. Finally, we show that the treatment elicited antiidiotypic antibodies, which neutralized the inhibitory capacity of anti-FVIII antibodies. Inhibitor antibodies can therefore not be accurately evaluated in plasma, as their function appears to be neutralized by antiidiotypic antibodies. These findings could have implications for the design of new therapies for hemophilia A patients with inhibitors.
Metagenomics - a guide from sampling to data analysis (2012)

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.
Review: Chemotherapy-induced diarrhea: pathophysiology, frequency and guideline-based management (2009)

Diarrhea is one of the main drawbacks for cancer patients. Possible etiologies could be radiotherapy, chemotherapeutic agents, decreased physical performance, graft versus host disease and infections. Chemotherapy-induced diarrhea (CID) is a common problem, especially in patients with advanced cancer. The incidence of CID has been reported to be as high as 50-80% of treated patients (≥30% CTC grade 3-5), especially with 5-fluorouracil bolus or some combination therapies of irinotecan and fluoropyrimidines (IFL, XELIRI). Regardless of the molecular targeted approach of tyrosine kinase inhibitors and antibodies, diarrhea is a common side effect in up to 60% of patients with up to 10% having severe diarrhea. Furthermore, the underlying pathophysiology is still under investigation. Despite the number of clinical trials evaluating therapeutic or prophylactic measures in CID, there are just three drugs recommended in current guidelines: loperamide, deodorized tincture of opium and octreotide. Newer strategies and more effective agents are being developed to reduce the morbidity and mortality associated with CID. Recent research focusing on the prophylactic use of antibiotics, budesonide, probiotics or activated charcoal still have to define the role of these drugs in the routine clinical setting. Whereas therapeutic management and clinical work-up of patients presenting with diarrhea after chemotherapy are rather well defined, prediction and prevention of CID is an evolving field. Current research focuses on establishing predictive factors for CID like uridine diphosphate glucuronosyltransferase-1A1 polymorphisms for irinotecan or dihydropyrimidine-dehydrogenase insufficiency for fluoropyrimidines.
Thermochemotherapy: synergism between hyperthermia (42-43 degrees) and adriamycin (of bleomycin) in mammalian cell inactivation. (1975)

The sensitivity of cells exposed in vitro to the antibiotics bleomycin or adriamycin is only mildly increased at 41 degrees over that seen at 37 degrees. However, at 43 degrees a marked synergism between the effects of hyperthermia and drug is observed. This synergism can also be demonstrated to occur in solid tumors in vivo. Cells after bleomycin exposure at 37 degrees repair potentially lethal damage, and 43 degrees inhibits this repair. This inhibition may in part account also for the observed sensitization of the cells to bleomycin, but not to adriamycin, since for the latter no repair can be demonstrated. However, fluorescence measurements show that at 43 degrees much more adriamycin is able to enter the cells than at 37 degrees. The possible implications of the results for cancer treatment are discussed.
Enantioselektive Katalyse, 4. Synthese N‐substituierter (R,R)‐3,4‐Bis(diphenylphosphino)‐pyrrolidine und Anwendung ihrer Rhodiumkomplexe zur asymmetrischen Hydrierung von α‐(Acylamino)acrylsäure‐Derivaten (1986)

Abstract Eine einfache Synthese von ( R , R )‐3,4‐Bis(diphenylphosphino)pyrrolidin ( 6a ) und verschiedenen N ‐substituierten Derivaten 6b–m wird beschrieben. 61 und 6m sind optisch aktive Tetraphosphane, die aus zwei ( R , R )‐3,4‐Bis(diphenylphosphino)pyrrolidin‐Einheiten und einem Dicarbonsäure‐Rest zusammengesetzt sind. Die Struktur der Stammverbindung 6a wurde durch Röntgenstrukturanalyse bestimmt. Von den Phosphanen 6a–m wurden die kationischen 1,5‐Cyclooctadien‐bisphosphan‐Rhodiumkomplexe 7a–m dargestellt. Die Komplexe 71 und 7m sind über den Liganden verbrückte Bis(rhodium)‐Dikationen. Die Komplexe 7a–m wurden zur asymmetrischen katalytischen Hydrierung verschiedener α‐(Acylamino)acrylsäuren 9a–l eingesetzt. Die erzielten optischen Ausbeuten betragen bis zu 100% und sind im Bereich von 1 bis 70 at vom Wasserstoffdruck unabhängig. Das Substrat/Katalysator‐Verhältnis kann bis 50000/1 betragen.
Rituximab (Anti‐CD20) Therapy of B‐Cell Lymphomas: Direct Complement Killing is Superior to Cellular Effector Mechanisms (2000)

Rituximab (IDEC-C2B8, Mabthera(R)) is a chimeric (human-mouse) monoclonal antibody (MoAb) against the B-cell specific CD20-antigen. It has been used for the clinical treatment of non-Hodgkin's lymphomas, but variable clinical results suggest that some lymphoma cells remain resistant. In the present study we have evaluated the relative efficiencies of humoral and cell-mediated effector mechanisms complement-dependent cytotoxicity (CDC), antibody-(ADCC), complement-(CDCC) dependent cellular cytotoxicity and apoptosis on lymphoma cell killing by rituximab. Rituximab activated the cytolytic complement (C) cascade and induced a strong CDC, but the rituximab-triggered ADCC and CDCC were relatively ineffective. The CDC was strongly enhanced by antibodies against the C inhibitor CD59 (protectin). Neutralization of CD55 (DAF) and CD46 (MCP) had a similar but weaker effect. Rituximab also induced apoptosis but in a cell line-dependent fashion. The results strongly emphasize the role of direct CDC as the major, fast and efficient effector mechanism of rituximab. In the immunotherapeutic treatment of B-cell lymphomas, it is important to consider the role of C-regulatory proteins as an escape mechanism of the malignant cells. Our results suggest that the effect of rituximab therapy could be enhanced by combining it with neutralization of CD59.
Sulfate contributes to the negative charge of podocalyxin, the major sialoglycoprotein of the glomerular filtration slits. (1991)

Podocalyxin is the major sialoprotein of the rat glomerulus. Its function is to maintain the filtration slits of the glomerular epithelium open by virtue of its high net negative charge. We have used biosynthetic labeling and oligosaccharide analysis to characterize the anionic-charge-carrying moieties on this protein. Kidney slices from 2-day-old rats were biosynthetically labeled with [35S]Cys, [3H]Man, [3H]GlcN, and 35SO4, after which podocalyxin was immunoprecipitated and purified by SDS/PAGE. All these labels were incorporated into podocalyxin. Immunoprecipitates were subjected to digestion with specific glycosidases or digested with Pronase followed by chromatographic analysis of the released glycopeptides. Podocalyxin was susceptible to digestion with N-Glycanase and O-Glycanase, indicating the presence of both N- and O-linked oligosaccharides. Approximately 30% of the [3H]GlcN-labeled glycopeptides bound to Con A, confirming the presence of high mannose, hybrid, or biantennary N-linked structures; alkaline borohydride treatment confirmed the presence of O-linked oligosaccharides. Analysis of the 35SO4-labeled glycopeptides indicated that both the N- and O-linked structures were sulfated. We conclude that in newborn rat kidney (i) podocalyxin contains both O- and N-linked oligosaccharides [high mannose or hybrid type, biantennary, and complex (sialylated) type], (ii) podocalyxin is sulfated, and (iii) sulfate is located on both O-linked oligosaccharides and on glycopeptides carrying tri- or tetrantennary N-linked structures. These results indicate that the net negative charge of podocalyxin is most likely derived from sulfate as well as from sialic acid residues.
Triple modular redundancy (2007)

In computing, triple modular redundancy (TMR) is a fault tolerant form of N-modular redundancy, in which three systems perform a process and that result is processed by a voting system to produce a single output. If any one of the three systems fails, the other two systems can correct and mask the fault. If the voter fails then the complete system will fail. However, in a good TMR system the voter is much more reliable than the other TMR components. Alternatively, if there is another stage of TMR logic following the current one (for example, in systems such as the Saturn Launch Vehicle Digital Computer), then three voters are used - one for each copy of the next stage of logic.
Inductive electron heating revisited (1997)

The induced rf magnetic fields of low-frequency inductively coupled plasmas are measured and modeled [M. Tuszewski, Phys. Rev. Lett. 77, 1286 (1996)]. The fields penetrate deep into the discharges, in contrast with existing predictions of field decay within a thin skin layer. Fluid calculations suggest that the enhanced rf penetration is due to a reduction of the plasma conductivity by the induced magnetic fields. In this paper, new oxygen and argon data concerning rf power absorption are reported and a general description of inductive electron heating is suggested.
Phase 1 Clinical Trial of Apical Membrane Antigen 1: an Asexual Blood-Stage Vaccine for Plasmodium falciparum Malaria (2005)

Apical membrane antigen 1 (AMA1), a polymorphic merozoite surface protein, is a leading blood-stage malaria vaccine candidate. A phase 1 trial was conducted with 30 malaria-naive volunteers to assess the safety and immunogenicity of the AMA1-C1 malaria vaccine. AMA1-C1 contains an equal mixture of recombinant proteins based on sequences from the FVO and 3D7 clones of Plasmodium falciparum. The proteins were expressed in Pichia pastoris and adsorbed on Alhydrogel. Ten volunteers in each of three dose groups (5 mug, 20 mug, and 80 mug) were vaccinated in an open-label study at 0, 28, and 180 days. The vaccine was well tolerated, with pain at the injection site being the most commonly observed reaction. Anti-AMA1 immunoglobulin G (IgG) was detected by enzyme-linked immunosorbent assay (ELISA) in 15/28 (54%) volunteers after the second immunization and in 23/25 (92%) after the third immunization, with equal reactivity to both AMA1-FVO and AMA1-3D7 vaccine components. A significant dose-response relationship between antigen dose and antibody response by ELISA was observed, and the antibodies were predominantly of the IgG1 isotype. Confocal microscopic evaluation of sera from vaccinated volunteers demonstrated reactivity with P. falciparum schizonts in a pattern similar to native parasite AMA1. Antigen-specific in vitro inhibition of both FVO and 3D7 parasites was achieved with IgG purified from sera of vaccinees, demonstrating biological activity of the antibodies. To our knowledge, this is the first AMA1 vaccine candidate to elicit functional immune responses in malaria-naive humans, and our results support the further development of this vaccine.
High-Throughput One-Bead-One-Compound Approach to Peptide-Encoded Combinatorial Libraries:  MALDI-MS Analysis of Single TentaGel Beads (2003)

The identification of pharmacologically promising compounds (lead compounds) from combinatorial libraries is frequently limited by the throughput of the analytical technique employed. Fourier transform mass spectrometry (FTMS) offers high sensitivity, mass accuracy (m/Deltam > 500 000), and sequencing capabilities. A rapid and efficient method for high-throughput analysis of single beads from peptide-encoded combinatorial libraries with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. Encoding peptides on single beads are identified and structurally characterized by MALDI time-of-flight (TOF) and ultrahigh-resolution MALDI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. A strategy of on-probe sample preparation is developed to minimize handling of the beads.
The Performance Evaluation Model of Intel SGX-Based Data Protection (2018)

The hardware-level security protection method represented by SGX is the main trend of security guarantee for data processing of cloud tenants. However, different protection strategies have a great impact on the application performance of the tenants. How to make effective balance between the protection cost and the security enhancement has become the key problem in the decision of the data processing hardware security protection. Aiming at this problem, we will study an effective method to balance SGX application performance overhead and security enhancements, which is based on multi-objective optimization. Because there are many factors that cause performance losses in SGX applications, the performance of CPU intensive programs and concurrent programs is difficult to accurately estimate. We analyze the invisible relationship between performance factors and performance losses with deep learning theory, then we build a high precision SGX application performance loss estimation model which can adapt to different application scenarios.
Physical and Functional Interactions between Type I Transforming Growth Factor β Receptors and Bα, a WD-40 Repeat Subunit of Phosphatase 2A (1998)

We have previously shown that a WD-40 repeat protein, TRIP-1, associates with the type II transforming growth factor beta (TGF-beta) receptor. In this report, we show that another WD-40 repeat protein, the Balpha subunit of protein phosphatase 2A, associates with the cytoplasmic domain of type I TGF-beta receptors. This association depends on the kinase activity of the type I receptor, is increased by coexpression of the type II receptor, which is known to phosphorylate and activate the type I receptor, and allows the type I receptor to phosphorylate Balpha. Furthermore, Balpha enhances the growth inhibition activity of TGF-beta in a receptor-dependent manner. Because Balpha has been characterized as a regulator of phosphatase 2A activity, our observations suggest possible functional interactions between the TGF-beta receptor complex and the regulation of protein phosphatase 2A.
Dressings for venous leg ulcers: systematic review and meta-analysis (2007)

The type of dressing applied beneath compression was not shown to affect ulcer healing. The results of the meta-analysis showed that applying hydrocolloid dressings beneath compression produced no benefit in terms of ulcer healing compared with applying simple low adherent dressings. No conclusive recommendations can be made as to which type of dressing is most cost effective. Decisions on which dressing to apply should be based on the local costs of dressings and the preferences of the practitioner or patient.
Tumor pretargeting: role of avidin/streptavidin on monoclonal antibody internalization. (1997)

The internalization ability of avidin suggests its potential clinical application for delivering toxic agents in a two-step approach (biotinylated MAb + avidin conjugate). The suitability of a given MAb for three-step clinical applications (biotinylated MAb + avidin + biotin) should be previously investigated by using appropriate in vitro experiments.
Sensorimotor neuropathy resembling CIDP in patients receiving FK506 (1994)

FK506 is an important immunosuppressant that has shown great promise in the treatment of autoimmune diseases. Approximately 5% of patients receiving FK506 develop major central nervous system toxicity, but the peripheral nerves are usually spared. During 1990-1991, some 1000 patients received liver transplants under FK506 immunosuppression. Of these, 3 patients developed severe multifocal demyelinating sensorimotor polyneuropathy 2-10 weeks after initiation of FK506 therapy. Improvement followed plasmapheresis or intravenous immunoglobulin (IVIG), suggesting an immune-mediated cause. Although autoimmune neuropathy has been previously reported in immune-deficient states such as Hodgkin's disease and AIDS, it is not an expected complication of immunosuppressive therapy. However, others have shown that this phenomenon can be produced in rats with cyclosporine A (CsA), whose effects on T-cell subsets are similar to those seen with FK506. These T-cell subset changes may have precipitated this dysimmune neuropathy in our patients.
Piasma Neopterin/C-Reactive Protein Ratio as an Adjunct to the Assessment of Infection and Cancer Cachexia (1995)

Neopterin (NPT), a pteridine intermediate metabolite in the biopterine synthetic pathway, is synthesized and secreted by monocytes/macrophages upon stimulation, mainly by gamma-interferon produced by activated T cells. C-reactive protein (CRP) is one of the major acute-phase reactants and its release is thought to be mediated by interleukin-6. Plasma concentrations of NPT and CRP were synchronously analyzed in 25 determinations of 5 patients with severe infectious complications and 50 determinations of 10 cancer-burden patients representing cachexia. The mean value of NPT (pmol/ml) was 201.6 in the infection group and 16.5 in the cancer cachexia group. The mean value of CRP (mg/dl) was 12.5 in the infection group and 3.4 in the cancer cachexia group. The number of samples in which NPT alone exceeded the cut-off level were 0/25 (0%) in the infection group and 38/50 (76.0%) in the cancer cachexia group. The number of samples in which both NPT and CRP exceeded the cut-off level was 25/25 (100%) in the infection group and 12/50 (24.0%) in the cancer cachexia group. The mean ratio of NPT to CRP was 11.3 in the infection group and 30.7 in the cancer cachexia group, respectively. These results suggest that gamma-interferon could play the principal role in the pathogenesis of cancer cachexia and that interleukin-6 modified the disease status. Interleukin-6 would be the critical mediator of host responses in infectious complications.