gebhart/patrepeval huggingface dataset:
<title>Single Mode Fiber Recirculating Delay Line</title> (1982)

Recirculating delay lines have been made using loops of single mode fiber that are closed, without splices, using one or more single mode fiber directional couplers. The use of an all single mode fiber system allows the accurate storage of high frequency analog or digital signals for long delay periods. Such devices can be used as wideband transient or buffer memories. Recirculating fiber loops are also useful as transversal filters that can exhibit uniform notch and bandpass filter characteristics over a wide range of frequencies from 1 MHz to 1.3 GHz.
Cytokines regulating hematopoietic stem cell function (2008)

The study of genetically modified mice and improvements in the in-vitro hematopoietic stem cell culture system will be powerful tools to elucidate the functions of cytokines that regulate hematopoietic stem cell function. These will further reveal the complex nature of the mechanisms by which extrinsic factors regulate signal transduction and cell-fate decisions of hematopoietic stem cells.
Cell-Free Protein Preparation Through Prokaryotic Transcription–Translation Methods (2009)

We have been developing and using an Escherichia coli cell extract-based coupled transcription-translation cell-free system. The development includes many different issues such as cell extract preparation, template construction, reaction condition, reaction format, and automation. These developments improved the efficiency, productivity, and throughput of our prokaryotic cell-free system, enabling us to use the system as one of the standard expression methods in our group. Our system certainly has the largest successful applications especially to the protein production for the structure determination, among the existing cell-free protein synthesis systems.
Enantioselective Michael Reaction of Malonates to Nitroolefins Catalyzed by Bifunctional Organocatalysts (2003)

Michael reaction of malonates to nitroolefins with chiral bifunctional organocatalysts, bearing both a thiourea and tertiary amino group, afforded Michael adducts with high yields and enantioselectivities (up to 95%, up to 93% ee).
Direct Cloning and Sequence Analysis of Enzymatically Amplified Genomic Sequences (1986)

A method is described for directly cloning enzymatically amplified segments of genomic DNA into an M13 vector for sequence analysis. A 110-base pair fragment of the human beta-globin gene and a 242-base pair fragment of the human leukocyte antigen DQ alpha locus were amplified by the polymerase chain reaction method, a procedure based on repeated cycles of denaturation, primer annealing, and extension by DNA polymerase I. Oligonucleotide primers with restriction endonuclease sites added to their 5' ends were used to facilitate the cloning of the amplified DNA. The analysis of cloned products allowed the quantitative evaluation of the amplification method's specificity and fidelity. Given the low frequency of sequence errors observed, this approach promises to be a rapid method for obtaining reliable genomic sequences from nanogram amounts of DNA.
Access to cellulose limits the efficiency of enzymatic hydrolysis: the role of amorphogenesis (2010)

The efficient enzymatic saccharification of cellulose at low cellulase (protein) loadings continues to be a challenge for commercialization of a process for bioconversion of lignocellulose to ethanol. Currently, effective pretreatment followed by high enzyme loading is needed to overcome several substrate and enzyme factors that limit rapid and complete hydrolysis of the cellulosic fraction of biomass substrates. One of the major barriers faced by cellulase enzymes is their limited access to much of the cellulose that is buried within the highly ordered and tightly packed fibrillar architecture of the cellulose microfibrils. Rather than a sequential 'shaving' or 'planing' of the cellulose fibrils from the outside, it has been suggested that these inaccessible regions are disrupted or loosened by non-hydrolytic proteins, thereby increasing the cellulose surface area and making it more accessible to the cellulase enzyme complex. This initial stage in enzymatic saccharification of cellulose has been termed amorphogenesis. In this review, we describe the various amorphogenesis-inducing agents that have been suggested, and their possible role in enhancing the enzymatic hydrolysis of cellulose.
Postoperative Nausea and Vomiting (1992)

In a recent editorial, Kapur described perioperative nausea and vomiting as "the big 'little problem' following ambulatory surgery."257 Although the actual morbidity associated with nausea is relatively low in health outpatients, it should not be considered an unavoidable part of the perioperative experience. The availability of an emesis basin for every patient in the postanesthesia recovery unit is a reflection of the limited success with the available therapeutic techniques.257 There had been little change in the incidence of postoperative emesis since the introduction of halothane into clinical practice in 1956. However, newer anesthetic drugs (e.g. propofol) appear to have contributed to a recent decline in the incidence of emesis. Factors associated with an increased risk of postoperative emesis include age, gender (menses), obesity, previous history of motion sickness or postoperative vomiting, anxiety, gastroparesis, and type and duration of the surgical procedure (e.g., laparoscopy, strabismus, middle ear procedures). Anesthesiologists have little, if any, control over these surgical factors. However, they do have control over many other factors that influence postoperative emesis (e.g., preanesthetic medication, anesthetic drugs and techniques, and postoperative pain management). Although routine antiemetic prophylaxis is clearly unjustified, patients at high risk for postoperative emesis should receive special considerations with respect to the prophylactic use of antiemetic drugs. Minimally effective doses of antiemetic drugs can be administered to reduce the incidence of sedation and other deleterious side effects. Potent nonopioid analgesics (e.g., ketorolac) can be used to control pain while avoiding some of the opioid-related side effects. Gentle handling in the immediate postoperative period is also essential. If emesis does occur, aggressive intravenous hydration and pain management are important components of the therapeutic regimen, along with antiemetic drugs. If one antiemetic does not appear to be effective, another drug with a different site of action should be considered. With the availability of new antiserotonin drugs, the incidence of recurrent (intractable) emesis could be further decreased. Research into the mechanisms of this common postoperative complication may help in improving the management of emetic sequelae in the future. As suggested in a recent editorial, improvement in antiemetic therapy could have a major impact for surgical patients, particularly after ambulatory surgery. Patients as well as those involved in their postoperative care look forward to a time when the routine offering of an emesis basin after surgery becomes a historical practice.
Antivascular approaches to solid tumour therapy: evaluation of tubulin binding agents. (1996)

We have assessed the vascular effects of vinblastine and four other tubulin binding agents (dolastatin 10, dolastatin 15, combretastatin A1 and combretastatin A4), which are awaiting clinical evaluation. All five agents induce a reduction in tumour blood flow as measured by uptake of RbCI 24 h post drug administration. The degree of reduction ranged from 50% with combretastatin A1 to 90% with dolastatin 10. These reductions were similar to that seen with flavone acetic acid (FAA) and indicate that antivascular effects are a common feature of tubulin binding agents. We subsequently evaluated whether the blood flow reductions, induced by FAA and vinblastine, could be used to enhance the activity of the bioreductive drug tirapazamine. Since the kinetics and extent of blood flow reductions induced by the agents is comparable, similar therapeutic response was expected. Potentiation was only evident with FAA, indicating that this effect is not directly related to killing of hypoxic tumour cells induced as a consequence of blood flow reduction.
FIXATION OF CARBON DIOXIDE IN OXALACETATE BY PIGEON LIVER (1945)

The fixation of CO2 in oxalacetate as shown in Reaction 1 has previously been demonstrated with a bacterial preparation.'PO2 + CHI-CO.COOH = C'300H.CH~.CO.COOH (1)A similar attempt with pigeon liver failed,2 although fixation of CO, in Lu-ketoglutarate3s4 and in fumarate and lactate2s4 with this tissue had been well established.We have found that in the presence of adenosine triphosphate (ATP), Reaction 1 occurs readily with liver extracts, thus demonstrating the primary fixation reaction in animal tissue.In the table it is shown that some Cl302 is fixed in the carboxyl adjacent to the methylene group in oxalacetate without ATP but that addition of the latter greatly increases the Cl3 fixed.In this experiment, an undialyzed extract obtained from an acetone powder of pigeon liver similar to that described by Evans et aL6 was used.The extract was incubated with oxalacetate, pyruvate, MnClz, and NaHC303 until about one-half of the oxalacetate had been decarboxylated.Occasionally, undialysed preparations may be quite active in fixation even in the absence of ATP, but ATP is always necessary for effective fixation with dialyzed preparations.According to Reaction 1, C302 should be found only in the carboxyl adjacent to the methylene group in oxalacetate unless the latter compound is in equilibrium with a symmetrical substance such as fumarate.Since the Cl3 was fixed only in the one position, the possibility is eliminated that the initial fixation reaction involved fumarate or any substance in equilibrium with fumarate.The carboxyl adjacent to the methylene groups was obtained by acid heat decarboxylation and the second carboxyl, along with the pyruvate carboxyl, by treatment with ceric sulfate.The effectiveness of the removal of residual Cl302 preliminary t.o the degradation of oxalacetate is attested by the low Cl3 values of the CO, collect,ed from the last.portion of the CO2 rinse used in removal of Cl302 from the medium.
Reconstructing Human Exposures Using Biomarkers and other “Clues” (2011)

Biomonitoring is the process by which biomarkers are measured in human tissues and specimens to evaluate exposures. Given the growing number of population-based biomonitoring surveys, there is now an escalated interest in using biomarker data to reconstruct exposures for supporting risk assessment and risk management. While detection of biomarkers is de facto evidence of exposure and absorption, biomarker data cannot be used to reconstruct exposure unless other information is available to establish the external exposure-biomarker concentration relationship. In this review, the process of using biomarker data and other information to reconstruct human exposures is examined. Information that is essential to the exposure reconstruction process includes (1) the type of biomarker based on its origin (e.g., endogenous vs. exogenous), (2) the purpose/design of the biomonitoring study (e.g., occupational monitoring), (3) exposure information (including product/chemical use scenarios and reasons for expected contact, the physicochemical properties of the chemical and nature of the residues, and likely exposure scenarios), and (4) an understanding of the biological system and mechanisms of clearance. This review also presents the use of exposure modeling, pharmacokinetic modeling, and molecular modeling to assist in integrating these various types of information.
Cytokine Responses to LTP Induction in the Rat Hippocampus: A Comparison of In Vitro and In Vivo Techniques (2000)

Because exogenous application of a number of cytokines and growth factors can alter synaptic properties, we sought to determine if endogenous cytokine expression is affected by neuronal activity. In addition, we examined whether cytokine expression is altered by the techniques used to stimulate and record from hippocampal neurons. Using semi-quantitative RNase protection and RT-PCR assays, we studied the expression of 18 cytokine, growth factor, and receptor genes in the hippocampus following the induction of Schaffer collateral-CA1 long-term potentiation (LTP). We found that various cytokines are dramatically induced following preparation of slices for in vitro recording and as a result of injury following acute electrode placement in vivo. These increases can be overcome in vivo, however, using permanent electrodes implanted three weeks prior to testing. Using this chronic preparation, we found that interleukin-6 (IL-6) mRNA was upregulated nearly 20-fold by LTP induction in vivo, marking the first demonstration of endogenous regulation of this cytokine in response to LTP. In situ hybridization for IL-6 revealed that upregulation is tightly localized near the site of stimulation and is detected only in non-neuronal cells, identified as GFAP+ astrocytes and GFAP- cells within proximal blood vessels. Coupled with previous results showing that exogenously applied IL-6 can prevent the induction of LTP, this finding suggests a mechanism by which the local release of a cytokine could regulate LTP at nearby sites.
The TWIN-E Project in Emotional Wellbeing: Study Protocol and Preliminary Heritability Results Across Four MRI and DTI Measures (2012)

Despite the significant advancements being made in the neurogenetics for mental health, the identification and validation of potential endophenotype markers of risk and resilience remain to be confirmed. The TWIN-E study (The Twin study in Wellbeing using Integrative Neuroscience of Emotion) aims to validate endophenotype markers of mental health across cognitive, brain, and autonomic measures by testing the heritability, clinical plausibility, and reliability of each of these measures in a large adult twin cohort. The specific gene and environmental mechanisms that moderate prospective links between endophenotype-phenotype markers and the final outcome of wellbeing will also be identified. TWIN-E is a national prospective study with three phases: I) baseline testing on a battery of online questionnaires and cognitive tasks, and EEG, MRI, and autonomic testing; II) 12-month follow-up testing on the online assessments; and III) randomized controlled trial of brain training. Minimum target numbers include 1,500 male/female twins (18–65 years) for the online assessments (Phase I and II), 300 twins for the EEG testing component, and 244 twins for the MRI testing component. For Phase III, each twin out of the pair will be randomized to either the treatment or waitlist control group to test the effects of brain training on mental health over a 30-day period, and to confirm the gene–environment and endophenotype contributions to treatment response. Preliminary heritability results are provided for the first 50% of the MRI subgroup ( n = 142) for the grey matter volume, thickness, and surface area measures, and white matter diffuse tensor imaging fractional anisotropy.
Regulation of basal tyrosine phosphorylation of the B cell antigen receptor complex by the protein tyrosine phosphatase, CD45 (1992)

Signal transduction via the B cell AgR complex has recently been shown to be dependent on the activation of one or more protein tyrosine kinases. Similarly, it has been found that signal transduction requires the expression of the protein tyrosine phosphatase CD45. Thus, transduction of a signal after AgR cross-linking must involve the coordinate interaction of these two enzymatic activities. It is therefore logical to hypothesize that the competence of the B cell to respond to ligands that bind the AgR may be dependent on the maintenance of an equilibrium between the tyrosine phosphorylation and dephosphorylation of specific signal transduction components. We have demonstrated in the present study that in resting B cells, the basal level of AgR complex tyrosine phosphorylation is regulated by cellular protein tyrosine phosphatases. Treatment of cells with the protein tyrosine phosphatase inhibitor, Na3VO4, resulted in rapid hyperphosphorylation of the receptor complex. Based on this observation, experiments were designed to examine the role of CD45 in regulation of AgR complex phosphorylation. Treatment of B cells with anti-CD45 mAb alone was found to have no effect on cytoskeletal association of CD45 or on its distribution within the membrane. Addition of a secondary cross-linking reagent, however, induced the association of CD45 with the cytoskeleton and caused capping. Subsequent studies demonstrated that increased tyrosine phosphorylation of the mIg-associated proteins MB-1 and B29 could be induced after incubating cells with anti-CD45 mAb and a secondary cross-linker, but not after the addition of anti-CD45 mAb alone. Changes in tyrosine phosphorylation of MB-1 and B29 were found to correlate with the cytoskeletal association of CD45. Interestingly, although cross-linking CD45 induced alterations in its association with the cytoskeleton and in its distribution within the membrane, no significant change in the level of protein tyrosine phosphatase activity could be detected under these conditions. These findings support the possibility that ligand binding to CD45 can induce biochemical and/or physical alterations in the molecule that presumably inhibit its ability to interact with specific substrates in the cell, thereby shifting the established equilibrium between tyrosine-specific phosphorylation and dephosphorylation.
Origins of domestication and polyploidy in oca (Oxalis Tuberosa: Oxalidaceae). 2. Chloroplast‐expressed glutamine synthetase data (2002)

In continuing study of the origins of the octoploid tuber crop oca, Oxalis tuberosa Molina, we used phylogenetic analysis of DNA sequences of the chloroplast-active (nuclear encoded) isozyme of glutamine synthetase (ncpGS) from cultivated oca, its allies in the "Oxalis tuberosa alliance," and other Andean Oxalis. Multiple ncpGS sequences found within individuals of both the cultigen and a yet unnamed wild tuber-bearing taxon of Bolivia were separated by molecular cloning, but some cloned sequences appeared to be artifacts of polymerase chain reaction (PCR) recombination and/or Taq error. Nonetheless, three classes of nonrecombinant sequences each joined a different part of the O. tuberosa alliance clade on the ncpGS gene tree. Octoploid oca shares two sequence classes with the Bolivian tuber-bearing taxon (of unknown ploidy level). Fixed heterozygosity of these two sequence classes in all ocas sampled suggests that they represent homeologous loci and that oca is allopolyploid. A third sequence class, found in eight of nine oca plants sampled, might represent a third homeologous locus, suggesting that oca may be autoallopolyploid, and is shared with another wild tuber-bearing species, tetraploid O. picchensis of southern Peru. Thus, ncpGS data identify these two taxa as the best candidates as progenitors of cultivated oca.
Antibodies to liposomes, phospholipids, and cholesterol: implications for autoimmunity, atherosclerosis, and aging. (1990)

Abstract : It is often stated that lipids are are nonimmunogenic; however, this idea is now known to be a false presumption. Polyclonal antibodies having considerable specificity for individual phospholipid constituents of liposomes have now also been developed (Wassef et al., 1989; Banerji and Alving, 1989). After developing immunoassay procedures (complement-dependent assays and solid- phase immunosorbent assays) for detecting antibodies to lipids, we and others discovered that naturally-occurring autoantibodies to various phospholipids are widespread and occur in most adult animal or human sera.
Polymerase Chain Reaction in High Surface-to-Volume Ratio SiO2 Microstructures (2004)

We have performed the Taqman beta-actin PCR system in high-surface-to-volume ratio (0.02-0.13 microm(-1)) SiO2 microchannels and observed the reaction yield and uniformity. The concentrations of the enzyme, magnesium chloride, and reaction template were varied in the reaction mix, and PCR amplification was performed in devices of various surface-to-volume ratios. We found that microchannels with higher surface-to-volume ratios required higher enzyme concentrations to achieve the same amplification efficiency. We investigated the possibility that the observed reaction nonuniformity was related to the specific adsorption of magnesium ions to the negatively charged SiO2 surface. The effect of several modifications to the reaction chemistry, the addition of the caged-magnesium dye DM-Nitrophen, the replacement of human DNA template with PCR product, and the coating of the microchannel surface with Teflon were all studied. These modifications resulted in improved reaction uniformity in the microchannels and present opportunities for further studies on enhancing the efficiency and uniformity of PCR in high surface-to-volume ratio SiO2 microchannels.
Efficient UV and visible generation using a pulsed, Yb-doped fiber amplifier (2003)

We report efficient generation of the second, third, fourth, and fifth harmonics of a double-clad, Yb-doped fiber amplifier seeded by a pulsed Nd:YAG microchip laser. Up to 18 mW at 213 nm was obtained.
Maximum-likelihood estimation of Rician distribution parameters (1998)

The problem of parameter estimation from Rician distributed data (e.g., magnitude magnetic resonance images) is addressed. The properties of conventional estimation methods are discussed and compared to maximum-likelihood (ML) estimation which is known to yield optimal results asymptotically. In contrast to previously proposed methods, ML estimation is demonstrated to be unbiased for high signal-to-noise ratio (SNR) and to yield physical relevant results for low SNR.
Expression of K homology domain Containing protein Overexpressed in cancer in pancreatic FNA for diagnosing adenocarcinoma of pancreas (2007)

We evaluated the immunocytochemical (ICC) expression of K homology domain containing protein overexpressed in cancer (KOC) in pancreatic endoscopic ultrasound-guided fine needle aspirates (EUS-FNAs) to assess its potential use as an adjunct in differentiating nonneoplastic (GI epithelium) and benign neoplastic epithelia (benign epithelial pancreatic neoplasms) from pancreatic adenocarcinoma cells. Forty-eight cases of EUS-FNAs with histological and/or clinical follow-up data were selected for this study. Alcohol-fixed and PAP-stained slides were stained with monoclonal antibody to KOC/L523S (clone 69.1). Results were recorded as negative or positive. KOC expression was present in 35/40 (88%) of adenocarcinomas (Ac) and was negative in all eight benign cases. The sensitivity and specificity were as follows: cytology 85 and 100%, KOC 88 and 100%; combination of cytology and KOC 95 and 100%. We conclude that KOC ICC expression on alcohol-fixed smears along with cytology improves the sensitivity of EUS-FNAs in the diagnosis of pancreatic Ac, and KOC reactivity is especially useful in differentiating Ac from nonneoplastic gastrointestinal epithelium and benign neoplastic epithelia.
Bench-to-bedside review: Inhaled nitric oxide therapy in adults (2009)

Nitric oxide (NO) is an endogenous mediator of vascular tone and host defence. Inhaled nitric oxide (iNO) results in preferential pulmonary vasodilatation and lowers pulmonary vascular resistance. The route of administration delivers NO selectively to ventilated lung units so that its effect augments that of hypoxic pulmonary vasoconstriction and improves oxygenation. This 'Bench-to-bedside' review focuses on the mechanisms of action of iNO and its clinical applications, with emphasis on acute lung injury and the acute respiratory distress syndrome. Developments in our understanding of the cellular and molecular actions of NO may help to explain the hitherto disappointing results of randomised controlled trials of iNO.