gebhart/patrepeval huggingface dataset:
TAXONOMIC STUDIES ON CORYNEFORM BACTERIA (1972)

Morphological, cultural, biochemical, and physiological characteristics of 112 strains of coryneform bacteria were examined. Coryneform bacteria were taxonomically divided into seven groups on the basis of the combination of the characteristics of gram-stain, motility, presence of metachromatic granules, pleomorphism, effect of citrate on cell form, acid formation from carbohydrates, assimilation of organic acids, hydrolysis of gelatin, extracellular DNase, urease, and cell wall composition.
Prostate-specific antigen as a measure of disease outcome in metastatic hormone-refractory prostate cancer. (1993)

The results suggest that posttherapy PSA declines can be used as a surrogate end point to evaluate new agents in hormone-refractory prostate cancer. The criteria for response need prospective validation in phase III trials.
Structural Basis of Constitutive Activity and a Unique Nucleotide Binding Mode of Human Pim-1 Kinase (2004)

Pim-1 kinase is a member of a distinct class of serine/threonine kinases consisting of Pim-1, Pim-2, and Pim-3. Pim kinases are highly homologous to one another and share a unique consensus hinge region sequence, ER-PXPX, with its two proline residues separated by a non-conserved residue, but they (Pim kinases) have <30% sequence identity with other kinases. Pim-1 has been implicated in both cytokine-induced signal transduction and the development of lymphoid malignancies. We have determined the crystal structures of apo Pim-1 kinase and its AMP-PNP (5'-adenylyl-beta,gamma-imidodiphosphate) complex to 2.1-angstroms resolutions. The structures reveal the following. 1) The kinase adopts a constitutively active conformation, and extensive hydrophobic and hydrogen bond interactions between the activation loop and the catalytic loop might be the structural basis for maintaining such a conformation. 2) The hinge region has a novel architecture and hydrogen-bonding pattern, which not only expand the ATP pocket but also serve to establish unambiguously the alignment of the Pim-1 hinge region with that of other kinases. 3) The binding mode of AMP-PNP to Pim-1 kinase is unique and does not involve a critical hinge region hydrogen bond interaction. Analysis of the reported Pim-1 kinase-domain structures leads to a hypothesis as to how Pim kinase activity might be regulated in vivo.
Prehydrolysis in Softwood Pulping Produces a Valuable Biorefinery Fraction for Material Utilization (2012)

A scaled-up prehydrolysis process was elaborated to demonstrate an industrially feasible operation step in a pulping process that generates a valuable side product in addition to the cellulose pulp. The valuable side product is aqueous process liquor, a softwood hydrolysate (SWH) herein produced in 60 L batches, and its components were recovered and utilized as materials. The process parameters were shown to influence the yield, composition, and quality of the obtained hydrolysates. Furthermore, the process conditions were shown to influence the ability of SWHs to form free-standing, foldable films in blends with either microfibrillated cellulose (MFC) or carboxymethyl cellulose (CMC). Films with oxygen permeabilities (OP) as low as 0.35 cm(3) μm day(-1) m(-2) kPa(-1) at 50% relative humidity, were produced from aqueous solutions providing a viable and green alternative to petroleum-based packaging barriers. The OPs were very low regardless of SWH film composition and upgrading conditions, whereas the films' tensile performance was directly controlled by the ratio of SWH to cocomponent.
Intestinal absorption and stability of morphine 6-glucuronide in different physiological compartments of the rat. (1998)

Morphine 6-glucuronide (M6G) is an active metabolite of morphine that could be used as a drug, but its hydrolysis into morphine remains controversial. We investigated the acidic hydrolysis of M6G and found that the recovery of morphine did not exceed 5%. The stability of M6G was studied in different physiological compartments of male Sprague-Dawley rats. The formation of morphine after M6G incubation in feces was under 2% in the small intestine, whereas the formation of morphine in colon feces represented 85.6 +/- 12.9% of the initial concentration of M6G. The stability of M6G was also determined ex vivo using the isolated perfused rat liver. The hepatic extraction ratio of M6G was very low (0.04 +/- 0.02), but 88. 7 +/- 11.2% of the dose was excreted in bile. The elimination half-life of M6G in the perfusate (66.4 +/- 20.6 min) was higher than the elimination half-life in bile (18.6 +/- 2.5 min). The hydrolysis of M6G was low, with only 7.7% and 0.03% of morphine in the perfusate and bile, respectively. The perfusate level of morphine 3-glucuronide (M3G) resulting from morphine conjugation was 4.9 +/- 3.6%. An in vivo experiment demonstrated that after oral administration, M6G was absorbed per se in the proximal intestine, and the process was prolonged over the 24-hr experiment due to its reabsorption following enterohepatic recirculation. Finally, 10.5 +/- 4.3% of morphine and 12.9 +/- 5.1% of M3G compared with M6G AUCs were found in plasma. These results show that M6G is weakly converted into morphine when orally absorbed, with a kinetic profile similar to a slow release formulation.
Flow cytometric analysis of heterogeneity in blood group-related antigen expression in a human urinary bladder carcinoma cell line, 647V. (1985)

Previous immunohistological studies showed a relationship between expression of blood group-related antigens (BG-Ag) and invasive potential in human urinary bladder carcinoma, but the marked variability of antigen staining within many individual tumors has obscured the biological basis of this finding. We studied the expression of the A, H, and T (Thomsen-Friedenreich) BG-Ag by flow cytometry in a human bladder carcinoma cell line (647V) using fluoresceinated BG-Ag-specific lectins (Dolichos bifloris, Ulex europaeus, and Arachis hypogaea). Cell cycle compartments were quantitated by flow cytometry using propidium iodide staining. Expression of all three antigens was highly variable, but staining for each antigen produced a distinct profile. T antigen expression appeared independent of A or H antigen expression. Cell populations sorted by T antigen expression showed heritable antigenic differences persistent over many weeks in culture. However, much of the T antigen variability was nonheritable, since the stable staining profiles of the sorted cells were intermediate between the parental and the profiles obtained immediately after sorting. The nonheritable antigenic variation did not appear entirely explainable by cell size or cell cycle fluctuation. These results were confirmed by isolating 64 clones from the dim part of the T antigen staining profile, 19 of which had a persistently dim phenotype. The variability of BG-Ag expression by human bladder carcinoma cells in vitro may explain the staining patterns observed in the study of antigen expression in resected human bladder carcinomas.
The enzymatic mechanisms for deoxythymidine synthesis in human leukocytes (1969)

(1) Synthesis of deoxythymidine by either direct transfer of deoxyribosyl to thymine (pyrimidine deoxyribosyltransferase) or by a coupled deoxynucleoside phosphorylase mechanism is approximately twofold greater with normal leukocyte extracts (55 to 88% granulocytes) than with extracts prepared from leukocytes obtained from patients with chronic myelogenous leukemia. Activities in lymphocytes (normal or leukemic) are one-fifth the activity of normal granulocytes.(2) The lower activity in chronic myelogenous leukemia remains at 50% of normal even when patients are in hematologic remission with a normal per cent mature granulocytes in the peripheral blood.(3) The leukemic enzyme could not be distinguished from the normal by pH optima, thermal stability, or kinetic properties. The Km's for the deoxyribosyl acceptor and deoxyribosyl donors were identical for both enzymes. Both are subject to substrate inhibition by thymine and to inhibition by purine bases with similar Ki's. In addition, the transferase component of both the leukemic and the normal cell enzyme is activated by phosphate and arsenate. It appears, therefore, that there is no qualitative difference between the enzyme obtained from leukocytes of patients with chronic myelogenous leukemia and the enzyme obtained from normal leukocytes, suggesting that the difference in total cell activity is due to an actual decrease in amount of enzyme in chronic myelogenous leukemia or to a mixed cell population, one with a normal quantity of enzyme and the other with little or no active enzyme.(4) In both the normal cell and the leukemic cell extracts, transferase and phosphorylase activities could not be separated. The ratio of the two activities remained constant over a 140- and a 230-fold purification in normal and leukemic cell extracts, respectively. These and other observations indicate that transferase and phosphorylase activities are associated with the same protein.(5) The metabolism of pyrimidine and purine deoxynucleosides is similar for normal and leukemic cells. Catabolism of all deoxynucleosides tested was by direct phosphorolysis, except for deoxyadenosine which required initial deamination to deoxyinosine before phosphorolysis. In contrast to the greater rates of pyrimidine deoxynucleoside synthesis and cleavage with normal leukocyte extracts, the rates of purine deoxynucleoside synthesis and cleavage were approximately twofold greater with extracts prepared from cells of patients with chronic myelogenous leukemia. There was no significant difference in the rate of phosphorolytic cleavage of pyrimidine nucleosides (uridine) between the CML and normal leukocyte extracts.
Bioactive Suture (2004)

This is the first report to demonstrate that bioactive surgical sutures can generate a prolonged T(H)1 immune response and expand flu-specific T cells. Bioactive sutures, which are primarily a T-cell stimulant, also stimulated other cells to secrete IL-12 and prolonged the immune response. Sutures may provide a novel in situ stimulating strategy for enhancing the immune system of cancer patients.
Inducible Expression of Tau Repeat Domain in Cell Models of Tauopathy (2005)

We generated several cell models of tauopathy in order to study the mechanisms of neurodegeneration in diseases involving abnormal changes of tau protein. N2a neuroblastoma cell lines were created that inducibly express different variants of the repeat domain of tau (tau(RD)) when exposed to doxycycline (Tet-On system). The following three constructs were chosen: (i) the repeat domain of tau that coincides with the core of Alzheimer paired helical filaments; (ii) the repeat domain with the deletion mutation DeltaK280 known from frontotemporal dementia and highly prone to spontaneous aggregation; and (iii) the repeat domain with DeltaK280 and two proline point mutations that inhibit aggregation. The comparison of wild-type, pro-aggregation, and anti-aggregation mutants shows the following. (a) Aggregation of tau(RD) is toxic to cells. (b) The degree of aggregation and toxicity depends on the propensity for beta-structure. (c) Soluble mutants of tau(RD) that cannot aggregate are not toxic. (d) Aggregation is preceded by fragmentation. (e) Fragmentation of tau(RD) in cells is initially due to a thrombin-like protease activity. (f) Phosphorylation of tau(RD) (at KXGS motifs) precedes aggregation but is not correlated with the degree of aggregation. (g) Aggregates of tau(RD) disappear when the expression is silenced, showing that aggregation is reversible. (h) Aggregation can be prevented by drugs and even pre-formed aggregates can be dissolved again by drugs. Thus, the cell models open up new insights into the relationship between the structure, expression, phosphorylation, aggregation, and toxicity of tau(RD) that can be used to test current hypotheses on tauopathy and to develop drugs that prevent the aggregation and degeneration of cells.
Synthesis of Model Network Hydrogels via Tetrazine‐Olefin Inverse Electron Demand Diels‐Alder Cycloaddition (2013)

Summary The formation of poly(etheylene glycol) (PEG) model network hydrogels via an A 2 + B 3 inverse‐electron‐demand tetrazine‐olefin Diels‐Alder cycloaddition is reported. This method provides an efficient, additive‐free, colorimetric gelation reaction that will complement other “click chemistry” approaches to model network synthesis.
Advanced techniques for target discrimination using laser speckle (1992)

II A new high-resolution imaging technique known as wavelength decorrelation is demonstrated in the laboratory for measuring target shape and estimating surface-scattering properties. In these demonstrations, the target is flood illuminated with a frequency-scanning Ti:sapphire ring laser. As the laser frequency changes, the speckle pattern in the backscattered light appears to boil; the time-varying intensity at a point in this pattern carries information about the target&amp;apos;s range-resolved laser radar cross section U(z). A range resolution of better than 1 mm is demonstrated. A theoretical analysis ofwavelength decorre1ation is also presented, including the mathematical framework for predicting wavelength-decorrelation signatures. An additional technique known as speckle tracking is described for measuring a target&amp;apos;s angular dynamics. THE LASER SPECKLE LABORATORY at Lincoln Laboratory was established in 1990 to study high-resolution discrimination techniques based on laser speckle. These techniques allow us to
Microvessel count predicts survival in uveal melanoma. (1996)

Microvessel density has become established as an important prognostic indicator for many tumor types. This study investigates the microvessel density as a prognostic factor for survival in patients with uveal melanoma, which is the commonest intraocular tumor and has a clear tendency for metastatic spread to the liver. Factor VIII-related antigen was identified immunohistochemically in bleached sections from 123 tumors. Maximum blood vessel density in an area of 0.25 mm2 was recorded, along with other accepted prognostic information. Microvessel density was the single most important prognostic factor on univariate testing, and in a Cox proportional hazard model, tumor size was the only other variable to be entered. No other accepted prognostic factor entered the model. We conclude that microvessel density is an important prognostic factor for survival in patients with uveal melanoma and allows the identification of high-risk patients for whom adjuvant therapy should be considered.
Effects of Interface Trap Generation and Annihilation on the Data Retention Characteristics of Flash Memory Cells (2004)

It is revealed that the interface trap generation rate increases by Fowler-Nordheim current stressing on the tunnel oxide as the channel width of shallow-trench isolation (STI)-isolated NAND flash cells shrinks. Furthermore, we argue that the interface trap annihilation phenomenon during retention mode becomes a major failure mechanism of the data retention characteristics of sub-100-nm cells in addition to the conventional charge loss mechanism. A new interface trap analysis method using the hysteresis of the I/sub d/--V/sub g/ curve is proposed and shows that the interface traps consist of fast traps and slow traps.
TheIn VivoResponse of Invariant Natural Killer T Cells to Glycolipid Antigens (2007)

Invariant natural killer T (iNKT) cells are a subset of T lymphocytes that recognizes glycolipid antigens presented by the major histocompatibility complex class I-related protein CD1d. Although iNKT cells have received a lot of attention as targets for the development of immunotherapies, few studies have investigated the in vivo response of iNKT cells to glycolipid antigen activation. Accumulating evidence indicates that iNKT cells generate a dynamic response to in vivo activation by glycolipid antigens that is characterized by surface receptor downmodulation, expansion, cytokine production, cross talk with other cells, homeostatic contraction, and acquisition of an anergic phenotype. These studies provide new insight into the biology of iNKT cells and have important implications for designing safe and effective iNKT cell-based vaccines and therapies.
p-Type Cu−Ti−O Nanotube Arrays and Their Use in Self-Biased Heterojunction Photoelectrochemical Diodes for Hydrogen Generation (2008)

Copper and titanium remain relatively plentiful in the earth's crust; hence, their use for large-scale solar energy conversion technologies is of significant interest. We describe fabrication of vertically oriented p-type Cu-Ti-O nanotube array films by anodization of copper rich (60% to 74%) Ti metal films cosputtered onto fluorine doped tin oxide (FTO) coated glass. Cu-Ti-O nanotube array films 1 mum thick exhibit external quantum efficiencies up to 11%, with a spectral photoresponse indicating that the complete visible spectrum, 380 to 885 nm, contributes significantly to the photocurrent generation. Water-splitting photoelectrochemical pn-junction diodes are fabricated using p-type Cu-Ti-O nanotube array films in combination with n-type TiO 2 nanotube array films. With the glass substrates oriented back-to-back, light is incident upon the UV absorbing n-TiO 2 side, with the visible light passing to the p-Cu-Ti-O side. In a manner analogous to photosynthesis, photocatalytic reactions are powered only by the incident light to generate fuel with oxygen evolved from the n-TiO 2 side of the diode and hydrogen from the p-Cu-Ti-O side. To date, we find under global AM 1.5 illumination that such photocorrosion-stable diodes generate a photocurrent of approximately 0.25 mA/cm (2), at a photoconversion efficiency of 0.30%.
A Family of Rat CRMP Genes Is Differentially Expressed in the Nervous System (1996)

Members of the collapsin/semaphorin family play an important role in creating the complex pattern of neuronal connectivity. Inhibition of growth cone motility by chick collapsin is mediated by the intraneuronal protein CRMP-62. We have now isolated four rat sequences that are highly related to chick CRMP-62. All four genes are expressed exclusively in the nervous system and primarily during development. Rat CRMP-2/TOAD-64 is most closely related to chick CRMP-62 and is the most widely expressed CRMP within the nervous system. Rat CRMP-1 and CRMP-4/rUlip are expressed during discrete periods of neuronal development and are not found in the adult nervous system. Rat CRMP-3 has a distinct distribution, being expressed transiently in developing spinal cord and selectively in the postnatal cerebellum. The differential expression of these genes suggests that CRMPs may transduce signals from different semaphorins and that semaphorins may regulate the plasticity of the adult nervous system.
Procedure To Evaluate the Stability during Processing and Storage of a Medicated Premix and Medicated Farm Feed:  Erythromycin Thiocyanate (2001)

In this paper, a stability study of a medicated premix and medicated farm feed containing erythromycin thiocyanate was planned. No drug degradation was detected during the medicated farm feed processing. In the medicated premix stability study, significant drug degradation was detected only at 40 degrees C and 75% relative humidity. Because after 2 years of storage at 25 degrees C and 60% relative humidity no degradation of erythromycin thiocyanate was detected, this period of time is proposed as the premix shelf life. In the medicated farm feed stability study, drug degradation was detected under accelerated conditions, but it was not detected under long-term storage conditions for 3 months. Therefore, the proposed shelf life of the medicated farm feed is 3 months, as this is time enough to be consumed. The planned stability study-storage conditions, testing frequency, and proposed data evaluation-allowed an easy and reliable evaluation of veterinary medicine stability.
Rab GTPase Prenylation Hierarchy and Its Potential Role in Choroideremia Disease (2013)

Protein prenylation is a widespread post-translational modification in eukaryotes that plays a crucial role in membrane targeting and signal transduction. RabGTPases is the largest group of post-translationally C-terminally geranylgeranylated. All Rabs are processed by Rab geranylgeranyl-transferase and Rab escort protein (REP). Human genetic defects resulting in the loss one of two REP isoforms REP-1, lead to underprenylation of RabGTPases that manifests in retinal degradation and blindness known as choroideremia. In this study we used a combination of microinjections and chemo-enzymatic tagging to establish whether Rab GTPases are prenylated and delivered to their target cellular membranes with the same rate. We demonstrate that although all tested Rab GTPases display the same rate of membrane delivery, the extent of Rab prenylation in 5 hour time window vary by more than an order of magnitude. We found that Rab27a, Rab27b, Rab38 and Rab42 display the slowest prenylation in vivo and in the cell. Our work points to possible contribution of Rab38 to the emergence of choroideremia in addition to Rab27a and Rab27b.
A bacterial cell–cell communication signal with cross‐kingdom structural analogues (2003)

Extracellular signals are the key components of microbial cell-cell communication systems. This report identified a diffusible signal factor (DSF), which regulates virulence in Xanthomonas campestris pv. campestris, as cis-11-methyl-2-dodecenoic acid, an alpha,beta unsaturated fatty acid. Analysis of DSF derivatives established the double bond at the alpha,beta positions as the most important structural feature for DSF biological activity. A range of bacterial pathogens, including several Mycobacterium species, also displayed DSF-like activity. Furthermore, DSF is structurally and functionally related to farnesoic acid (FA), which regulates morphological transition and virulence by Candida albicans, a fungal pathogen. Similar to FA, which is also an alpha,beta unsaturated fatty acid, DSF inhibits the dimorphic transition of C. albicans at a physiologically relevant concentration. We conclude that alpha,beta unsaturated fatty acids represent a new class of extracellular signals for bacterial and fungal cell-cell communications. As prokaryote-eukaryote interactions are ubiquitous, such cross-kingdom conservation in cell-cell communication systems might have significant ecological and economic importance.
Barley Lunasin Suppresses ras-Induced Colony Formation and Inhibits Core Histone Acetylation in Mammalian Cells (2002)

Lunasin is a novel peptide originally identified in soybean that suppresses chemical carcinogen-induced transformation in mammalian cells and skin carcinogenesis in mice. Since the lunasin gene was cloned from soybean and the chemically synthesized form of the lunasin peptide has been used in experiments conducted so far, the isolation of lunasin from other natural sources and testing of its biological properties have not been carried out. We report here the isolation, purification, and biological assay of lunasin from barley, a newly found rich source of the peptide. The identity of lunasin was established by Western blot analysis and mass spectrometric peptide mapping of the in-gel tryptic digest of the putative protein band. Lunasin was partially purified with anion exchange and immunoaffinity chromatography. The crude and partially purified lunasin from barley suppressed colony formation in stably ras-transfected mouse fibroblast cells induced with IPTG. These fractions also inhibited histone acetylation in mouse fibroblast NIH 3T3 and human breast MCF-7 cells in the presence of the histone deacetylase inhibitor sodium butyrate.