gebhart/patrepeval huggingface dataset:
Lipids in Human Milk and Infant Formulas (1992)

About 50 metabolically important fatty acids can be identified in human milk. The extent of absorption of milk fatty acids varies considerably from infant to infant, particularly in pre-term infants, and requires more study. Human milk provides sufficient vitamins A and E for the term infant, but supplementation with vitamins D and K may be necessary. More research is needed on the amounts of the fat-soluble vitamins in human milk, the efficiency of transfer from mother to infant, the reasons for variation in different women, and the consequences to breast-fed infants of inadequate intake of vitamins D and K. Breast milk contains the PUFA needed by term infants who are able to synthesize the long-chain PUFA soon after birth. Pre-term infants fed formulae need supplementation with n3 and n6 long-chain PUFA, since formulas currently do not contain these acids. More work is needed to determine the requirements for n3 and n6 fatty acids, expressed as weights per kilogram. A larger data base using improved analytical procedures to study the nature and content of lipids in human milk is needed. The impact of maternal genetics and diet on fatty acids in milk should be studied, as well as the effect of maternal diet on eicosanoids secreted by the mammary gland. Information on the structure and function of the milk fat globule and its membrane is needed. Little is known about the effect of milk banking on milk lipids. The reader of this review will no doubt find other gaps in our knowledge of the lipid composition and nutritional value of milk that require additional investigation.
Phase I Study of Oral CI-994 in Combination with Gemcitabine in Treatment of Patients with Advanced Cancer (2003)

The 6-mg/m2 dose of CI-994 (p.o. x 21 days) was defined as the maximum tolerated dose that could safely be administered in combination with gemcitabine (1,000 mg/m2 i.v. on days 1, 8, and 15) during a 28-day cycle.
Tissue-Specific Expression in Transgenic Mice of a Fused Gene Containing RSV Terminal Sequences (1986)

Transgenic mice were generated with pRSV-CAT, a chimeric gene construct containing the long terminal repeat of Rous sarcoma virus (RSV) linked to the bacterial gene encoding chloramphenicol acetyltransferase (CAT). CAT expression, detected in adult animals of five independent strains, was preferentially directed to organs rich in tendon, bone, and muscle. This pattern reflects the disease specificity of the intact virus and suggests that the tissue tropism of RSV is determined at least in part by the presence of endogenous tissue-specific factors that can promote expression of genetic information linked to the long terminal repeat. In two of the mouse strains, insertion of the pRSV-CAT DNA resulted in developmental abnormalities. One of these strains was characterized by a dominant trait of embryonic lethality, the other by a recessive trait of fused toes in all four feet.
Inhibition of Parathyroid Hormone Bioactivity by Human Parathyroid Hormone (PTH)-(3–84) and PTH (8–84) Synthesized in Escherichia coli* (1988)

Human PTH (hPTH)-(3-84) and hPTH-(8-84) were synthesized in Escherichia (E.) coli when the cells were transformed with a multicopy plasmid in which the transcription of human preproPTH cDNA is directed by the E. coli lac promoter. PTH fragments were extracted from cells and purified by reverse phase HPLC. PTH bioactivity and PTH antagonist activity were estimated in a renal cytochemical bioassay. hPTH-(3-84) and hPTH-(8-84) exhibited less than 1% and less than 0.1%, respectively, of the biological activity of synthetic hPTH-(1-84). hPTH-(8-84) had 1% of the PTH inhibitory activity of synthetic [Nle8,18,Tyr34]bovine PTH-(3-34)amide, whereas hPTH-(3-84) was 100 times more active as a PTH inhibitor than the synthetic bovine PTH-(3-34) analog. The latter has so far been recognized as the most potent PTH antagonist in vitro. A 5-fold molar excess of hPTH-(3-84) over hPTH-(1-84) completely blocked the biological action of intact hPTH-(1-84) in the renal cytochemical bioassay. These findings suggest that the carboxyl-terminal portion of the intact hPTH-(1-84) molecule contributes importantly to inhibitor potency.
DECREASE IN BLADDER OVERACTIVITY WITH REN1820 IN RATS WITH CYCLOPHOSPHAMIDE INDUCED CYSTITIS (2005)

These studies demonstrate that the use of the NGF sequestering protein REN1820 in rats with CYP induced cystitis decreases bladder overactivity. This is characterized by 1) a decrease in the number and amplitude of nonvoiding contractions and 2) decreased voiding frequency. Rats treated with REN1820 showed greater mobility and normal resting postures, which may reflect improved overall health or well-being. REN1820 may prove to be a novel therapeutic in individuals with the chronic inflammatory bladder syndrome interstitial cystitis.
Visualizing instrument vibrations and sound fields (2002)

A review is given of recent applications of modern optical techniques to visualize structural vibrations and sound fields in musical instruments. The advantage of optical techniques in this context is that they give an image of the measured quantity without disturbing the measurements. The techniques considered are usually referred to as TV holography (also called Digital or Electronic Speckle Pattern Interferometry, abbreviated ESPI or DSPI), phase modulated TV holography, pulsed TV holography (pulsed holographic interferometry) and scanning Laser Doppler Vibrometry (LDV).
Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA (2015)

With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.
A series of yeast shuttle vectors for expression of cDNAs and other DNA sequences (1993)

Expression/shuttle vectors for the yeast Saccharomyces cerevisiae have usually been large plasmids with only one or a small number of sites that are suitable for cloning and expression. We report here the construction and properties of a series of 12 expression vectors with multiple (four to eight) unique sites in their polylinkers which allow directional cloning and expression of DNA sequences under four different promoters. Eleven of these plasmids replicate at high copy number in Escherichia coli, and all have the yeast TRP1 gene, and the 2 microns origin including REP3 sequence, allowing selection and high copy number replication in yeast. Six of the plasmids are designed for the construction and selection and high copy number replication in yeast. Six of the plasmids are designed for the construction and selection of cDNA libraries from various eukaryotic organisms, allowing directional cloning and expression of cDNAs. All of these six have similar polylinkers containing a unique promoter proximal EcoRI site and a unique promoter distal XhoI site, allowing for directional cloning and expression of 'ZAP'-type cDNAs. cDNAs that complement a wide variety of yeast mutants can be selected from libraries constructed in this way. The four alternative promoters, ADH2, PGK, GAL10 and SV40 were compared for their relative activity, both in E. coli and in yeast. All yeast promoters showed substantial activity in E. coli with ADH2 showing the highest activity. ADH2 also was well-regulated in yeast, showing very high relative activity under derepressing conditions. cDNAs selected by genetic complementation from libraries constructed in these vectors should be easily subclonable into other vectors, allowing expression in different eukaryotic organisms, DNA sequencing or site-directed mutagenesis.
Osteocalcin cluster: Implications for functional studies (1995)

Osteocalcin is a skeletal member of the family of extracellular mineral binding Gla protein. Osteocalcin is synthesized only by the osteoblast and it is secreted into the bone matrix at the time of bone mineralization. The mineral binding properties of osteocalcin as well as its spatial and temporal pattern of expression suggest that it plays a role during bone mineralization, however until now its biological function is unclear. To understand osteocalcin function during skeletogenesis we mutated the two osteocalcin genes by homologous recombination in embryonic stem (ES) cells. Eight targeted clones were identified by Southern analysis using external probes. One of these clones contributed to the germ line of mouse chimera. Interbreeding of heterozygotes is currently in progress. Mutant mice will be useful to understand osteocalcin function in vivo.
Notch activity synergizes with B-cell–receptor and CD40 signaling to enhance B-cell activation (2006)

How diverse environmental cues are integrated to regulate B-cell activation and development remains poorly understood. Here we show that Notch activity synergizes with B-cell receptor (BCR) and/or CD40 signaling to enhance several aspects of B-cell activation and function. We find that costimulation of follicular B cells with the Notch ligand Delta-like-1 leads to significant increases in BCR- and CD40-mediated proliferation and enhances production of IgG1(+) cells in vitro and in vivo. We further find that coengagement of Notch and the BCR results in increased activation of the MAPK pathway, and MAPK and Notch inhibitors prevent B-cell activation events mediated by coengagement of Notch and the BCR. These data suggest that the BCR and CD40 signaling pathways collaborate with the Notch pathway to optimize B-cell activation.
RMD-1, a novel microtubule-associated protein, functions in chromosome segregation in Caenorhabditis elegans (2007)

For proper chromosome segregation, the sister kinetochores must attach to microtubules extending from the opposite spindle poles. Any errors in microtubule attachment can induce aneuploidy. In this study, we identify a novel conserved Caenorhabditis elegans microtubule-associated protein, regulator of microtubule dynamics 1 (RMD-1), that localizes to spindle microtubules and spindle poles. Depletion of RMD-1 induces severe defects in chromosome segregation, probably through merotelic attachments between microtubules and chromosomes. Although rmd-1 embryos also have a mild defect in microtubule growth, we find that mutants of the microtubule growth regulator XMAP215/ZYG-9 show much weaker segregation defects. This suggests that the microtubule growth defect in rmd-1 embryos does not cause abnormal chromosome segregation. We also see that RMD-1 interacts with aurora B in vitro. Our results suggest that RMD-1 functions in chromosome segregation in C. elegans embryos, possibly through the aurora B–mediated pathway. Human homologues of RMD-1 could also bind microtubules, which would suggest a function for these proteins in chromosome segregation during mitosis in other organisms as well.
Terminal modifications inhibit proteolytic degradation of an immunogenic mart-127-35 peptide: Implications for peptide vaccines (1999)

Peptide epitopes for tumor-reactive cytotoxic T-lymphocytes (CTL) have been identified on human cancers and are being used in tumor vaccine trials. However, the pharmacokinetics and pharmacodynamics of such peptides have been inadequately studied. It is predicted that immunogenic tumor peptides would have short half-lives in vivo. The goal of the present work was to evaluate the stability of the immunogenic peptide MART-1(27-35) in fresh normal human plasma (NHP) and to identify modifications that convey protection against enzymatic destruction without loss of immunogenicity. We evaluated the stability of the MART-1(27-35) peptide (AAGIGILTV) and modified forms of that peptide for stability and immune recognition in an in vitro model. The peptides were incubated in plasma for varied time intervals and evaluated for their ability to reconstitute the epitope for MART-1(27-35)-reactive CTL. Loss of CTL reactivity signaled loss of immunoreactive peptide. When 1 microM MART-1(27-35) peptide was incubated in plasma prior to pulsing on target cells, CTL reactivity was lost within 3 hr, and the calculated half-life of this peptide was 22 sec. This degradation was mediated by peptidases. The stability of MART-1(27-35) was markedly prolonged by C-terminal amidation and/or N-terminal acetylation (peptide capping), or by polyethylene-glycol modification (PEGylation) of the C-terminus. These modified peptides were recognized by CTL. The MART-1(27-35) peptide is very unstable in plasma. It is probable that it and other immunogenic peptides will be similarly unstable in vivo. Immunogenicity of these peptides might be enhanced by creating modifications that enhance stability.
A Component of the Chloroplast Protein Import Apparatus Functions in Bacteria (1997)

Toc36 is a family of 44-kDa envelope polypeptides previously identified as components of the chloroplast protein import apparatus by virtue of their close physical proximity to translocating proteins. An indication of their function thus remains at large. A heterologous in vivo approach for studying the function of Toc36 was developed in this study by introducing a member of Toc36 into E. coli to assess its effect on bacterial protein translocation. The presence of Toc36 enhances the translocation of two bacterial periplasmic proteins in a manner resembling the chloroplast system. Translocation of the two bacterial periplasmic proteins was less sensitive to sodium azide, resembling more the azide-insensitive nature of the chloroplast protein import process. Mutated Toc36 proteins were not capable of causing the same effect as that observed for unaltered Toc36. Toc36 was also capable of complementing bacterial strains with temperature-sensitive secA mutations that affected protein translocation. The combined results provide evidence that Toc36 plays a central role in the chloroplast protein translocation process.
Net‐shaped hydroxyapatite implants for release of agents modulating periodontal‐like tissues (1997)

Periodontal-like tissues and, in particular, alveolar bone- and root cementum-like material can theoretically be modulated by release of biochemical agents such as bisphosphonate (PCP), growth hormone (GH) and alkaline phosphatase (ALP) from the implant surface. The present research focused on porous ceramic hydroxyapatite (PCHA) implants. In the past the PCHA implants were machined on a lathe out of simple blocks of PCHA ceramic. This was a tedious and cumbersome method, often resulting in implants with undesirable characteristics: different porosities, cracks and fractures. Therefore a moulding technique was developed to sinter near-net-shaped PCHA implants at 2 different sintering temperatures: 1170 degrees C and 1280 degrees C, resulting in PCHA implants with porosities of 62.06% (PCHA type 1) and 40.74% (PCHA type 2), respectively. After 1 h incubation in a 10(-2) M solution of PCP, the total amounts adsorbed onto PCHA type 1 and type 2 were 114.9 +/- 2.1 micrograms and 46.1 +/- 1.5 micrograms, respectively. This was approximately 5 times higher than after incubation for 1 wk in a 10(-4) M solution of PCP. The total amounts of PCP released after the observation period of 75 d from PCHA type 1 and type 2 after incubation in the 10(-2) M solution were 103.1 +/- 1.8 micrograms and 42.8 +/- 1.5 micrograms, respectively. The total amounts released from type 1 and 2 after incubation in the 10(-4) M solution were 7.4 +/- 0.4 micrograms and 4.1 +/- 0.1 micrograms, respectively. After 2 wk of incubation in a liver/bone/kidney ALP solution the total amount of ALP adsorbed onto PCHA type 1 implants was 5039 +/- 412 mU/ml. The total amounts of ALP released were 4674 +/- 438 mU/ml and 53 +/- 20 mU/ml after 1 and 2 wk, respectively. The release of ALP was high at the beginning but slowed down thereafter. It was evident that despite the well-known high bonding affinity of PCP to HA the release of PCP occurred steadily, over a long period of time in vitro.
Functional studies of corticosterone receptors in neuronal membranes. (1995)

This work reviews evidence that some physiological and behavioral responses to steroid hormones use membrane-associated receptors. The review emphasizes research with an amphibian model, Taricha granulosa, but also cites examples from mammalian research. Many studies document steroid responses that occur within a time frame of a few milliseconds or minutes. In Taricha, corticosterone rapidly inhibits reproductive behaviors and causes site-specific changes in neurotransmitter concentrations and neuronal activity. Ligand binding assays using radiolabeled corticosterone and neuronal membranes from Taricha (and other animals) provide evidence that there are high-affinity steroid receptors in neuronal membranes. Subcellular fractionation, autoradiography, and immunocytochemistry add support to the conclusion that there are steroid receptors in neuronal membranes. Other studies indicate that, in Taricha and other animals, there are two types of membrane-associated steroid receptors--ligand-gated ion channels (specifically, the GABAA receptor) and G-protein coupled receptors.
Incorporating non-local information into information extraction systems by Gibbs sampling (2005)

Most current statistical natural language processing models use only local features so as to permit dynamic programming in inference, but this makes them unable to fully account for the long distance structure that is prevalent in language use. We show how to solve this dilemma with Gibbs sampling, a simple Monte Carlo method used to perform approximate inference in factored probabilistic models. By using simulated annealing in place of Viterbi decoding in sequence models such as HMMs, CMMs, and CRFs, it is possible to incorporate non-local structure while preserving tractable inference. We use this technique to augment an existing CRF-based information extraction system with long-distance dependency models, enforcing label consistency and extraction template consistency constraints. This technique results in an error reduction of up to 9% over state-of-the-art systems on two established information extraction tasks.
An alternatively spliced region of the human hexabrachion contains a repeat of potential N-glycosylation sites. (1989)

We have cloned and sequenced two cDNA molecules that code for parts of two forms of human hexabrachion. The smaller clone has a sequence that corresponds to the previously published sequence of a cDNA clone coding for a part of chicken hexabrachion [Jones, F. S., Burgoon, M. P., Hoffman, S., Crossin, K. L., Cunningham, B. A. & Edelman, G. M. (1988) Proc. Natl. Acad. Sci. USA 85, 2186-2190]. It has eight consecutive domains similar to the type III homology units from fibronectin, several epidermal growth factor repeats, and a domain similar to the beta and gamma chains of fibrinogen. The larger clone has 5' and 3' ends that are identical to the smaller clone but also has an alternatively spliced 1.9-kilobase internal segment. The unique segment contains remarkable repeats of potential glycosylation sites and an additional seven type III homology units.
Aminotransferase Activity of α-Aminoisobutyric Acid Decomposing Enzyme (1972)

Journal Article Aminotransferase Activity of α-Aminoisobutyric Acid Decomposing Enzyme Get access Mamoru Honma, Mamoru Honma Department of Agricultural Chemistry, Hokkaido University, Sapporo, Japan Search for other works by this author on: Oxford Academic Google Scholar Makoto Ikeda, Makoto Ikeda Department of Agricultural Chemistry, Hokkaido University, Sapporo, Japan Search for other works by this author on: Oxford Academic Google Scholar Tokuji Shimomura Tokuji Shimomura Department of Agricultural Chemistry, Hokkaido University, Sapporo, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 36, Issue 10, 1 October 1972, Pages 1661–1666, https://doi.org/10.1080/00021369.1972.10860462 Published: 01 October 1972 Article history Received: 01 October 1971 Published: 01 October 1972
Cutting Edge: Essential Role of Hypoxia Inducible Factor-1α in Development of Lipopolysaccharide-Induced Sepsis (2007)

Sepsis, the leading cause of death in intensive care units, reflects a detrimental host response to infection in which bacteria or LPS act as potent activators of immune cells, including monocytes and macrophages. In this report, we show that LPS raises the level of the transcriptional regulator hypoxia-inducible factor-1alpha (HIF-1alpha) in macrophages, increasing HIF-1alpha and decreasing prolyl hydroxylase mRNA production in a TLR4-dependent fashion. Using murine conditional gene targeting of HIF-1alpha in the myeloid lineage, we demonstrate that HIF-1alpha is a critical determinant of the sepsis phenotype. HIF-1alpha promotes the production of inflammatory cytokines, including TNF-alpha, IL-1, IL-4, IL-6, and IL-12, that reach harmful levels in the host during early sepsis. HIF-1alpha deletion in macrophages is protective against LPS-induced mortality and blocks the development of clinical markers including hypotension and hypothermia. Inhibition of HIF-1alpha activity may thus represent a novel therapeutic target for LPS-induced sepsis.
Antibiotic Susceptibility Among Aerobic Gram-negative Bacilli in Intensive Care Units in 5 European Countries (1999)

The high incidence of reduced antibiotic susceptibility among gram-negative bacteria in these ICUs suggests that more effective strategies are needed to control the selection and spread of resistant organisms.
Site-Specific Pegylation of G-CSF by Reversible Denaturation (2007)

A new strategy has been developed for extending the possibility of poly(ethylene glycol) (PEG) modification to accessible thiol groups of biologically active proteins. In particular, thiol-reactive PEGs have been coupled to the cysteine 17 of granulocyte colony stimulating factor (G-CSF), which is known to be partially buried in a hydrophobic protein pocket. The PEG linking was accomplished by partial protein denaturation with 3 M guanidine.HCl in the absence of any reducing agent in order to preserve the native protein's disulfide bridges. PEG coupling occurred also, but at a lower degree, by using a 3 M solution of urea as the denaturing agent. Following the PEGylation, which was carried out in the unfolded state, the conjugated protein was refolded using dialysis or gel filtration chromatography to eliminate the denaturant. Different thiol-reactive PEGs and polymer molecular weights (5, 10, or 20 kDa) were investigated for G-CSF conjugation under denaturation. The secondary structure of the protein in the G-CSF-PEG conjugates, evaluated using circular dichroism and biological activity assay in cell culture, was maintained with respect to the native protein. Unexpectedly, conjugation enhanced the G-CSF tendency to aggregate, a problem that was overcome by a proper formulation.