gebhart/patrepeval huggingface dataset:
Triacylglycerol synthesis in the oleaginous yeastCandida curvata D (1991)

Low rates of triacylglycerol (TAG) biosynthesis were observed in cell-free extracts of Candida curvata, but rates were increased up to 10-fold by adding either alpha- or beta-cyclodextrins. Spheroplasts, whole or gently disrupted, had higher rates of incorporation of both [U-14C]glycerol 3-phosphate or [1-14C]oleate into triacylglycerol and the intermediates of its biosynthesis: lysophosphatic acid, phosphatidic acid and diacylglycerol. Fatty acyl-CoA synthetase was highest with palmitate, oleate and linoleate but was some 6- to 8-fold lower with stearate. Stearate and stearoyl-CoA were poorly incorporated into lipids. Subcellular fractionation of the spheroplasts into mitochondrial, microsomal, lipid bodies and supernatant fractions diminished the rates of 14C incorporation of oleate into triacylglycerol. By comparing the relative specific activities for each activity in each fraction, the fatty acyl-CoA synthetase activity appeared mainly in the lipid bodies, and that for phosphatidic acid formation was mainly in the mitochondrion; other activities were too weak and too dispersed for accurate assessment of their location. Recombining all the subcellular fractions restored triacylglycerol synthesizing activity. Omitting any single fraction from the mixture did not result in restoration of triacylglycerol synthesizing activity. Starvation of the yeast, which leads to utilization of the endogenous lipid reserves, stimulated fatty acyl-CoA synthetase activity, but diminished phosphatidic acid and triacylglycerol biosynthesis indicating probable induction of beta-oxidation in the peroxisomes and repression of lipid biosynthesis.
The Group Lasso for Logistic Regression (2008)

Summary The group lasso is an extension of the lasso to do variable selection on (predefined) groups of variables in linear regression models. The estimates have the attractive property of being invariant under groupwise orthogonal reparameterizations. We extend the group lasso to logistic regression models and present an efficient algorithm, that is especially suitable for high dimensional problems, which can also be applied to generalized linear models to solve the corresponding convex optimization problem. The group lasso estimator for logistic regression is shown to be statistically consistent even if the number of predictors is much larger than sample size but with sparse true underlying structure. We further use a two-stage procedure which aims for sparser models than the group lasso, leading to improved prediction performance for some cases. Moreover, owing to the two-stage nature, the estimates can be constructed to be hierarchical. The methods are used on simulated and real data sets about splice site detection in DNA sequences.
Human C3 and C5: Subunit Structure and Modifications by Trypsin and C42-C423 (1975)

The subunit composition of human C3 and C5 was analyzed. Acrylamide gel electrophoresis of the fully reduced and dissociated proteins disclosed a similar structure, consisting of one alpha and beta subunit, linked together by one or more disulfide bonds. The approximate molecular weights for the alpha and beta subunits of C3 as well as C5 were 140,000 and 80,000 respectively. C42 caused cleavage solely of C3alpha, whereas trypsin affected both C3alpha as well as C3beta. A characteristic subunit modification by both enzmes indicated that C3alpha constitutes the source of C3a. C423 as well as trypsin exclusively affect C5alpha. C5a therefore appears to originate from the C5alpha subunit. The mode of primary cleavage by C423 and trypsin differs, giving rise to different forms of C5b. The questions is raised if multiple forms of C5a also exist. It appeared from our studies that certain forms of C5b may retain portions of the alpha subunit, which could potentially release some biologically active split products following secondary cleavage by the appropriate enzyme.
Formation of covalent complexes between humanO6alkyltransferase and BCNU-treated defined length synthetic oligodeoxynucleotides (1988)

Repair of chloroethylnitrosourea (CENU)-induced precursors of DNA interstrand cross-links by O6-alkylguanine-DNA alkyltransferase (GAT or GATase) appears to be a factor in tumor resistance to therapy with this class of antineoplastic drugs. Since human GAT is highly specific for O6-guanine, yet the probable cross-link structure is N'-Guanine N3-cytosine ethane, rearrangement of the initial O6-guanine adduct via O6,N1ethanoguanine has been proposed. We suggested that GAT reaction with this intermediate would produce DNA covalently linked to protein through an ethane link from N1-guanine to the alkylacceptor site on GAT. In preliminary studies we demonstrated a covalent complex between GAT and carmustine (BCNU)-treated DNA by a precipitation assay method. We have now developed a method for isolating the reaction product of BCNU-treated synthetic 14-mer [32P]-labeled oligodeoxynucleotide and GAT using polyacrylamide gel electrophoresis. This approach can be used to characterize the adducts induced by CENUs that lead to complex formation with GAT. Results obtained to date are consistent with these adducts being precursors of DNA interstrand cross-links.
Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2 (2005)

The molecular regulation of methane oxidation in the first fully authenticated facultative methanotroph Methylocella silvestris BL2 was assessed during growth on methane and acetate. Problems of poor growth of Methylocella spp. in small-scale batch culture were overcome by growth in fermentor culture. The genes encoding soluble methane monooxygenase were cloned and sequenced, which revealed that the structural genes for soluble methane monooxygenase, mmoXYBZDC, were adjacent to two genes, mmoR and mmoG, encoding a sigma54 transcriptional activator and a putative GroEL-like chaperone, located downstream (3') of mmoC. Transcriptional analysis revealed that the genes were all cotranscribed from a sigma54-dependent promoter located upstream (5') of mmo X. The transcriptional start site was mapped. Transcriptional analysis of soluble methane monooxygenase genes and expression studies on fermentor grown cultures showed that acetate repressed transcription of sMMO in M. silvestris BL2. The possibility of the presence of a particulate, membrane-bound methane monooxygenase enzyme in M. silvestris BL2 and the copper-mediated regulation of soluble methane monooxygenase was investigated. Both were shown to be absent. A promoter probe vector was constructed and used to assay transcription of the promoter of the soluble methane monoxygenase genes of M. silvestris BL2 grown under various conditions and with different substrates. These data represent the first insights into the molecular physiology of a facultative methanotroph.
Inhibition of anandamide hydrolysis in rat brain tissue by (E)‐6‐(bromomethylene) tetrahydro‐3‐(1‐naphthalenyl)‐2H‐pyran‐2‐one (1997)

Anandamide, an endogenous canabinoid substance, is hydrolyzed by an amidohydrolase activity present in rat brain and liver. We report that the bromoenol lactone, (E)-6-(bromomethylene) tetrahydro-3-(1-naphthalenyl)-2H-pyran-2-one (BTNP), is a potent inhibitor of this enzyme activity. BTNP prevented anandamide hydrolysis in rat brain microsomes with an IC50 of 0.8 +/- 0.3 microM. Kinetic and dialysis experiments indicated that this effect was non-competitive and irreversible. After chromatographic fractionation of the enzyme activity, BTNP was still effective, suggesting that it interacts directly with the enzyme. Anandamide hydrolysis was 12-fold greater in rat cortical neurons (1.94 +/- 0.1 pmol/min/mg protein) than in cortical astrocytes (0.16 +/- 0.01 pmol/min/mg protein) and, in either cell type, it was inhibited by BTNP (IC50 = 0.1 microM in neurons). These results suggest that BTNP may provide a useful lead for the development of novel inhibitors of anandamide hydrolysis.
Maternal Hypercholesterolemia During Pregnancy Promotes Early Atherogenesis in LDL Receptor-Deficient Mice and Alters Aortic Gene Expression Determined by Microarray (2002)

These findings establish an atherogenic effect of maternal hypercholesterolemia in genetically uniform mice and indicate that changes in aortic gene expression persist long after fetal exposure to hypercholesterolemia. In addition to elucidating pathogenic mechanisms initiated during fetal development, this approach may identify genes in morphologically normal arteries that influence the susceptibility to classical risk factors of atherosclerosis.
Hemophilia B caused by five different nondeletion mutations in the protease domain of factor IX (1992)

Factor IX is a multidomain protein and is the proenzyme of a serine protease, factor IXa, essential for hemostasis. In this report, we describe the molecular basis of hemophilia B (deficiency of factor IX activity) in five patients who have neither deletions nor rearrangements of the factor IX gene. By enzymatic amplification and sequencing of all exons and promoter regions, the following causative mutation in the protease domain of factor IX was identified in each patient: IXSchmallenberg: nucleotide 31,215G----T, Ser365Ile; IXVarel: nucleotide 31,214A----G, Ser365Gly; IXMechtal: nucleotide 31,211G----C, Asp364His; IXDreihacken: nucleotide 30,864G----A, Arg248Gln; and IXMonschau: nucleotide 30,855A----T, Glu245Val. In IXVarel, nucleotide 31,213T was also replaced by C, which results in a silent mutation (GAT----GAC) at Asp-364. Thus, this patient has a double base-pair substitution of TA to CG at nucleotides 31,213 and 31,214 but only a single amino acid change of Ser-365 to Gly. This patient also developed an antibody to factor IX during replacement therapy, which suggests that deletion of the factor IX gene is not necessary for development of the antibody in hemophilia B patients. The levels of plasma factor IX antigen in the patients ranged from 40% to 100% except for IXDreihacken (Arg248Gln), in which case it was approximately 4% of normal. The Ser365Gly and Ser365Ile mutants are nonfunctional because of lack of the active site serine residue. Mutant Asp364His is inactive because it cannot form the hydrogen bond between the carboxylate group of Asp-364 and the alpha-amino group of Val-181 generated after activation. As observed in other homologous serine proteases, this hydrogen bond is essential for maintaining the correct active site conformation in normal factor IXa (IXaN). Purified Arg248Gln had approximately 41% and Glu245Val had approximately 17% of the activity of normal factor IX (IXN) in a partial thromboplastin time (aPTT) assay. In immunodot blot experiments, the isolated Glu245Val mutant did and the Arg248Gln mutant did not bind to an anti-IXN monoclonal antibody that has been shown previously to inhibit the interaction of factor VIIIa with factor IXaN. We have recently shown that a high-affinity calcium binding site exists in the protease domain of IXN; among the proposed Ca(2+)-binding ligands is the carboxyl group of Glu-245. Further, a part of the epitope for the above antibody was shown to be contained in the 231 to 265 residue segment of factor IX.(ABSTRACT TRUNCATED AT 400 WORDS)
Hypomethylation: One Side of a Larger Picture (2003)

Hypomethylation signifies one end of a spectrum of DNA methylation states. In most cases hypomethylation refers to a relative state that represents a change from the "normal" methylation level. Hypomethylation, when approached from a topographical perspective, has been used to describe either overall decreases in the methylation status of the entire genome (global hypomethylation) or more localized relative demethylation of specific subsets of the genome, such as the promoter regions of protooncogenes or normally highly methylated repetitive sequences. Global hypomethylation accompanied by gene-specific hypermethylation is observed in at least two important settings: cancer and aging. Global hypomethylation is generally reflective of decreased methylation in CpGs dispersed throughout repetitive sequences as well as the bodies of genes. Hypomethylation of repetitive and parasitic DNA sequences correlates with a number of adverse outcomes. For example, decreased methylation of repetitive sequences in the satellite DNA of the pericentric region of chromosomes is associated with increased chromosomal rearrangements, a hallmark of cancer. Decreased methylation of proviral sequences can lead to reactivation and increased infectivity. However, hypomethylation in cancer can also affect the CpGs in the promoters of specific genes-namely, protooncogenes-leading to their overexpression and resulting in the functional outcome of increased cell proliferation. Thus, hypomethylation, in a variety of settings in which it represents a deviation from "normal," appears to correlate with progression to cancer and offers potential mechanisms to explain the carcinogenic process.
Functional Analysis of cDNAs for Two Types of Human Heme Oxygenase and Evidence for Their Separate Regulation1 (1993)

We cloned a cDNA coding for a putative human heme oxygenase isozyme, designated type 2 (HO-2), and analyzed its function by transient expression assays. HeLa cells transfected with either HO-2 cDNAs or a cDNA coding for authentic heme oxygenase (HO-1) expressed the activity of heme oxygenase, although no activity was detected in the mock transfected cells. Using specific anti-HO-1 antibody, we showed that expression of a HO-1 cDNA resulted in the increase in its protein levels, but HO-1 protein was not detectable in the cells expressing HO-2 cDNAs. We thus confirmed the functional identity of HO-1 and HO-2. Then, we analyzed their expression in an erythroid cell line, YN-1-0-A. Treatment with hem in or by heat shock (42°C) led to a remarkable increase in the HO-1 mRNA levels, while HO-2 mRNA expression was not induced at all, suggesting that they are under separate regulation.
OX40 triggering blocks suppression by regulatory T cells and facilitates tumor rejection (2008)

Regulatory T (T reg) cells are the major obstacle to cancer immunotherapy, and their depletion promptly induces conversion of peripheral precursors into T reg cells. We show that T reg cells can be functionally inactivated by OX40 triggering. In tumors, the vast majority of CD4+ T cells are Foxp3+ and OX40bright. However, intratumor injection of the agonist anti-OX40 monoclonal antibody (mAb) OX86, but not anti-CD25 mAb, induces tumor rejection in 80% of mice, an effect that is abrogated by CD8 depletion. Upon intratumor OX40 triggering, increased numbers of infiltrating dendritic cells (DCs) migrate to draining lymph nodes and generate a new wave of tumor-specific cytotoxic T lymphocytes, as detected by tetramer and CD44 staining of node CD8+ T lymphocytes. Tumor-bearing Rag1-knockout (KO) mice reconstituted with OX40-deficient T reg cells and wild-type (WT) effector T cells, or the reciprocal combination, showed that both T reg and effector T cells must be triggered via OX40 for the tumor to be rejected. Accordingly, WT but not OX40-KO mice receiving intratumor coinjection of OX86 and ovalbumin protein were able to revert tumor-induced tolerization of adoptively transferred OX40-competent OTII T lymphocytes. In conclusion, OX40-mediated inactivation of T reg cell function unleashes nearby DCs, allowing them to induce an adaptive immune response. In addition, the known OX40-dependent delivery of fitness signals to activated T cells is boosted by concurrent T reg cell inhibition. OX40 triggering thus has multiple effects that converge to mediate tumor rejection.
LDL Receptor-Related Protein 1: Unique Tissue-Specific Functions Revealed by Selective Gene Knockout Studies (2008)

The LDL receptor-related protein (originally called LRP, but now referred to as LRP1) is a large endocytic receptor that is widely expressed in several tissues. LRP1 is a member of the LDL receptor family that plays diverse roles in various biological processes including lipoprotein metabolism, degradation of proteases, activation of lysosomal enzymes, and cellular entry of bacterial toxins and viruses. Deletion of the LRP1 gene leads to lethality in mice, revealing a critical, but as of yet, undefined role in development. Tissue-specific gene deletion studies reveal an important contribution of LRP1 in the vasculature, central nervous system, macrophages, and adipocytes. Three important properties of LRP1 dictate its diverse role in physiology: 1) its ability to recognize more than 30 distinct ligands, 2) its ability to bind a large number of cytoplasmic adaptor proteins via determinants located on its cytoplasmic domain in a phosphorylation-specific manner, and 3) its ability to associate with and modulate the activity of other transmembrane receptors such as integrins and receptor tyrosine kinases.
Brush‐first and Click: Efficient Synthesis of Nanoparticles that Degrade and Release Doxorubicin in Response to Light (2013)

New strategies for the synthesis of multifunctional particles that respond to external stimuli and release biologically relevant agents will enable the discovery of new formulations for drug delivery. In this article, we combine two powerful methods: brush-first ring-opening metathesis polymerization and copper-catalyzed azide-alkyne cycloaddition click chemistry, for the synthesis of a novel class of brush-arm star polymers (BASPs) that simultaneously degrade and release the anticancer drug doxorubicin (DOX) in response to 365 nm light. In vitro cell viability studies were performed to study the toxicity of azide- and DOX-loaded BASPs. The former were completely nontoxic. The latter showed minimal toxicity in the absence of light; UV-triggered DOX release led to IC50 values that were similar to that of free DOX.
Peptide .alpha.-keto ester, .alpha.-keto amide, and .alpha.-keto acid inhibitors of calpains and other cysteine proteases (1993)

A series of dipeptidyl and tripeptidyl alpha-keto esters, alpha-keto amides, and alpha-keto acids having leucine in the P2 position were synthesized and evaluated as inhibitors for the cysteine proteases calpain I, calpain II, cathepsin B, and papain. In general, peptidyl alpha-keto acids were more inhibitory toward calpain I and II than alpha-keto amides, which in turn were more effective than alpha-keto esters. In the series Z-Leu-AA-COOEt, the inhibitory potency decreased in the order: Met (lowest KI) > Nva > Phe > 4-Cl-Phe > Abu > Nle (highest KI) with calpain I, while almost the reverse order was observed for calpain II. Extending the dipeptide alpha-keto ester to a tripeptide alpha-keto ester yielded significant enhancement in the inhibitory potency toward cathepsin B, but smaller changes toward the calpains. Changing the ester group in the alpha-keto esters did not substantially decrease KI values for calpain I and calpain II. N-Monosubstituted alpha-keto amides were better inhibitors than the corresponding alpha-keto esters. alpha-Keto amides with hydrophobic alkyl groups or alkyl groups with an attached phenyl group had the lower KI values. N,N-Disubstituted alpha-keto amides were much less potent inhibitors than the corresponding N-monosubstituted peptide alpha-keto amides. The peptide alpha-keto acid Z-Leu-Phe-COOH was the best inhibitor for calpain I (KI = 0.0085 microM) and calpain II (KI = 0.0057 microM) discovered in this study. It is likely that the inhibitors are transition-state analogs and form tetrahedral adducts with the active site cysteine of cysteine proteases and form hydrogen bonds with the active site histidine and possibly another hydrogen bond donor in the case of monosubstituted amides. Several inhibitors prevented spectrin degradation in a platelet membrane permeability assay and may be useful for the treatment of diseases which involve neurodegeneration.
Housing Construction in Earthquake-prone Places: Perspectives, Priorities and Projections for Development (2003)

It can no longer be assumed for all earthquake areas, as it was thirty years ago, that all architects and engineers are both accessible and competent for earthquake-resistant housing. There is a long-overdue requirement for urban multi-storey and self-build small buildings to improve the standard of their construction. After almost every urban earthquake, the call goes out for building construction to be improved. But what are the requirements for improving building construction, and how can they be achieved; and are there other housing strategies to be considered for the achievement of earthquake disaster reduction as an integral part of sustainable development ? Continued attention to rural small buildings is not disputed, but there is now also a need for redress of an imbalance in the strategy, to reflect the need that clearly exists for more attention to all kinds of urban housing - but it is not only shortcomings in the application of building construction technology that is responsible for these circumstances; so are planning, management, administration and integrity. All forms of building construction involve a process of legitimate physical covering over of each stage of construction. As each stage is completed, it becomes concealed by a subsequent stage - from foundations under the ground through to the last coat of paint. For there to be as much certainty as possible, from stage to stage, in the achievement of construction quality, periodic, even constant, independent inspection of buildings under construction is necessary. Legislation does exist in the form of building regulations, codes, standards and guidelines in most countries, but legislation is insufficient without regular, strategic, informed and reliable inspection to ensure its enforcement. Earthquake-responsible development can achieve more by adopting earthquake awareness through all sectors; micro-zoning of earthquake risk can be used to modify population occupancy and to modify construction standards. Peru is an example of the practice and Turkey is an example of the need.