gebhart/patrepeval huggingface dataset:
Abnormal Solvent Effects on Hydrogen Atom Abstraction. 2. Resolution of the Curcumin Antioxidant Controversy. The Role of Sequential Proton Loss Electron Transfer (2004)

The rates of reaction of 1,1-diphenyl-2-picrylhydrazyl (dpph•) radicals with curcumin (CU, 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione), dehydrozingerone (DHZ, “half-curcumin”), and isoeugenol (IE) have been measured in methanol and ethanol and in two non-hydroxylic solvents, dioxane and ethyl acetate, which have about the same hydrogen-bond-accepting abilities as the alcohols. The reactions of all three substrates are orders of magnitude faster in the alcohols, but these high rates can be suppressed to values essentially equal to those in the two non-hydroxylic solvents by the addition of acetic acid. The fast reactions in alcohols are attributed to the reaction of dpph• with the CU, DHZ, and IE anions (see J. Org. Chem. 2003, 68, 3433), a process which we herein name sequential proton loss electron transfer (SPLET). The most acidic group in CU is the central keto−enol moiety. Following CU's ionization to a monoanion, ET from the [−(O)CCHC(O)−]- moiety to dpph• yields the neutral [−(O)CCHC(O)−]• radical moiety which will be strongly electron withdrawing. Consequently, a phenolic proton is quickly lost into the alcohol solvent. The phenoxide anion so formed undergoes charge migration to produce a neutral phenoxyl radical and the keto−enol anion, i.e., the same product as would be formed by a hydrogen atom transfer (HAT) from the phenolic group of the CU monoanion. The SPLET process cannot occur in a nonionizing solvent. The controversy as to whether the central keto−enol moiety or the peripheral phenolic hydroxyl groups of CU are involved in its radical trapping (antioxidant) activity is therefore resolved. In ionizing solvents, electron-deficient radicals will react with CU by a rapid SPLET process but in nonionizing solvents, or in the presence of acid, they will react by a slower HAT process involving one of the phenolic hydroxyl groups.
Translocation of the precursor of 5- enol pyruvylshikimate-3-phosphate synthase into chloroplasts of higher plants in vitro (1986)

5-enolPyruvylshikimate-3-phosphate synthase (EPSP synthase; 3-phosphoshikimate 1-carboxyvinyl-transferase; EC 2.5.1.19) is a chloroplast-localized enzyme of the shikimate pathway in plants. This enzyme is the target for the nonselective herbicide glyphosate (N-phosphonomethylglycine). We have previously isolated a full-length cDNA clone of EPSP synthase from Petunia hybrida. DNA sequence analysis suggested that the enzyme is synthesized as a cytosolic precursor (pre-EPSP synthase) with an amino-terminal transit peptide. Based on the known amino terminus of the mature enzyme, and the 5' open reading frame of the cDNA, the transit peptide of pre-EPSP synthase would be maximally 72 amino acids long. To confirm this prediction and to assay directly for translocation of pre-EPSP synthase into chloroplasts in vitro, we cloned the full-length cDNA into an SP6 transcription system to produce large amounts of mRNA for in vitro translation. The translation products, when analyzed by NaDodSO(4)/PAGE autoradiography, indicate a relative molecular mass for pre-EPSP synthase of approximately 55 kDa. Uptake studies with intact chloroplasts, in vitro, indicate that pre-EPSP synthase was rapidly taken up into chloroplasts and proteolytically cleaved to the mature approximately 48-kDa enzyme. The transit peptide was shown to be essential for import of the precursor enzyme into the chloroplast. To our knowledge, post-translational import into chloroplasts of a precursor enzyme involved in amino acid biosynthesis has not been reported previously. Furthermore, enzymatic analysis of translation products indicates that pre-EPSP synthase is catalytically active and has a similar sensitivity to the herbicide glyphosate as the mature enzyme. To our knowledge, pre-EPSP synthase represents the only example of a catalytically competent chloroplast-precursor enzyme.
Stabilization of Polyolefins to Gamma Irradiation (1991)

The initial, atypical peroxyl radicals which start the free-radical chain oxidations have been identified in γ-irradiated polyolefins. These radicals were quantified in total by electron spin resonance and trapped by reaction with nitric oxide at -78°C to give nitrates which could be individually identified by infrared spectroscopy. Loss in physical properties was correlated with the accumulation of oxidation products formed during post-irradiation storage for polypropylene containing several stabilizer combinations. The best retention of impact strength corresponded to the minimum formation of oxidation products although none of the stabilizer combinations was able to completely suppress the oxidation processes.
Conformations of Signal Peptides Induced by Lipids Suggest Initial Steps in Protein Export (1986)

Despite the requirement for a functional signal sequence in protein export, little is known of the conformational properties and membrane interactions of these highly hydrophobic amino terminal extensions on nearly all exported proteins. The Escherichia coli lambda phage receptor signal sequence was studied in phospholipid monolayers by circular dichroism and Fourier transform infrared spectroscopy; the signal peptide was shown to prefer an alpha-helical conformation when inserted into the lipid phase. However, interaction with the lipid surface without insertion induced the signal sequence, which is unstructured in bulk aqueous solution, to adopt a beta structure. These observations are combined in a model for the initial steps in signal sequence-membrane interaction in vivo.
Serum One-Carbon Metabolites and Risk of Cervical Cancer (2014)

Most cases of cervical cancer are associated with human papilloma virus (HPV) infection of high risk types. In folate deficiency, heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) interferes with HPV16 viral capsid protein synthesis. We aimed to study the importance of 1-carbon metabolism in cervical carcinogenesis by examining serum vitamin B12 (cobalamin), homocysteine, folate levels, and the RNA and protein expression of HPV16 L1, L2, E6, E7, and to correlate them with hnRNP-E1 expression and HPV infection in normals, squamous intraepithelial lesions (SILs), and cervical cancer subjects. Serum cobalamin, folate, and homocysteine were estimated using kits, RNA by real time PCR and proteins by Western blotting. We observed that lower folate and vitamin B12 levels were associated with HPV infection. hnRNP-E1 progressively decreased from normals (100%) to SILs (75%) to cervical cancer (52.6%). The findings show that HPV16 E6 and E7 are overexpresed whereas HPV16 L1 and L2 are downregulated at mRNA and protein levels in cervical cancer as compared to normals and SILs. The results indicate that perhaps the reduced expression of hnRNP-E1 might be involved with the cervical cancer pathogenesis, with folate playing a role in the natural history of HPV infection.
SARS-CoV-2 Vaccines and the Growing Threat of Viral Variants (2021)

Wenjuan Zhang, PhD; Brian D. Davis, BSc; Stephanie S. Chen, BSc; Jorge M. Sincuir Martinez, BS; Jasmine T. Plummer, PhD; Eric Vail, MD
Structure of the Insulin Receptor of Rat Adipocytes: The Three Interconvertible Redox Forms (1983)

Isolated intact rat adipocytes were photoaffinity labeled with radioactive and photoreactive N alpha B1-monoazidobenzoyl insulin (B1-MABI) or N epsilon B29-monoazidobenzoyl insulin (B29-MABI). Polyacrylamide gel electrophoresis of the labeled plasma membranes solubilized in sodium dodecyl sulfate revealed the specific labeling of three receptor species of 380 kDa, 300 kDa, and 230 kDa. Reduction of each species individually produced the subunits of 130 kDa, 90 kDa, and 40 kDa. Exposure of the adipocytes or plasma membranes after photolabeling to sulfhydryl alkylating agents such as N-ethylmaleimide or p-chloromercuriphenylsulfonate resulted in the appearance of the receptor quantitatively in the 380-kDa form. The effect of the sulfhydryl reagent was concentration dependent and in the case of p-chloromercuriphenylsulfonate the three receptor species reappeared when high concentrations of the reagent were used. Incubation of the adipocytes with low concentrations of dithiothreitol before photolabeling reduced these receptors to discrete lower-molecular-weight forms. In addition, an 85-kDa subunit was now photolabeled by B1-MABI. This subunit was demonstrated to be different from the 90-kDa subunit normally labeled by B29-MABI. We conclude that on the cell surface of the adipocyte, there is one molecular-weight form of insulin receptor of 380 kDa composed of one 130-kDa, one 90-kDa, one 85-kDa, and two 40-kDa subunits. The 300 kDa and 230 kDa are partially reduced forms of the 380-kDa species. We further postulate that a membrane factor or factors sensitive to sulfhydryl alkylating reagents may be involved in the partial reduction and oxidation of these three redox receptor species. The distribution of these redox receptor species may be related to the cellular or tissue sensitivity to insulin.
Preparation of copper‐indium sulfide thin films by single‐source OMCVD: Mass‐spectral investigation of decomposition path of the organometallic sources (1992)

Abstract In order to prepare high‐quality CuInS 2 thin films vapor phase decomposition patterns of three copper‐indium binuclear complexes, equation image and equation image as candidates for source materials were investigated using EI MS. The complex 1c showed series of intensive peaks due to the fragmentation of M + . For 1a, only a fragmentation pattern starting from BuIn(S 2 CNBu 2 ) 2 was detectable. This should suggest that 1a decomposed into BuIn(S 2 CNBu 2 ) 2 and copper sulfide before vaporization. In addition an ambiguous feature could be observed for 1b, viz. two fragmentation paths. Consequently, we judge that 1c is a suitable source complex to prepare CuInS 2 thin films via a single‐source OMCVD process. Thus chalcopyrite CuIns 2 thin films were successfully prepared via single‐source OMCVD using 1c as a source complex, with T substrate 400°C, T source 80°C, base pressure 0.7 Torr and carrier (nitrogen) flow rate 0.8 L min −1 . Fragmentation of two copper dithiocarbmates, Cu(S 2 CNBu 2 ) 2 and Cu[S 2 CN(i‐Pr) 2 ] 2 , and two butylindium thiolates, Bu 2 InS(i‐Pr) and BuIn[S(i‐Pr)] 2 , as components of 1 is additionally discussed.
Adsorption of polyethylene from thermodynamically good solvents on a zeolite stationary phase (2003)

Abstract Adsorption of linear polyethylene and isotactic polypropylene on columns packed with zeolites ZSM‐5, Y, and silicalite was studied using high‐temperature liquid phase chromatography. Linear polyethylene was fully retained on a column packed with ZSM‐5 zeolite from non‐polar solvents, such as 1,1,2,2‐tetrachloroethane and 1,3,5‐trimethylbenzene at a temperature of 140°C. Partial adsorption on ZSM‐5 zeolite was found for polyethylene in 1,2,4‐trichlorobenzene and on silicalite from 1,2,4‐trichlorobenzene and 1,3,5‐trimethylbenzene. On the other hand, adsorption of polyethylene was not found from polar liquids, such as 2‐ethylhexyl acetate, cyclohexyl acetate, and cyclohexanone. Isotactic polypropylene was not adsorbed on any tested sorbent.
Gastric antisecretory activity of telenzepine, a new M1-selective muscarinic antagonist: comparison with pirenzepine. (1990)

The new M1-receptor antagonist telenzepine has been studied for its antisecretory effect in different in vitro and in vivo experimental models in comparison with pirenzepine. Telenzepine was found to be from 3 to 10 times more potent than pirenzepine in inhibiting bethanechol-, pentagastrin- and dimaprit-induced acid secretion in the conscious gastric fistula cat. Also, in the lumen-perfused stomach of the anaesthetized rat, telenzepine was more active than pirenzepine as an inhibitor of bethanechol-induced acid secretion; the inhibitory effect of telenzepine lasted more than 3 hr, while that of pirenzepine disappeared within 1 hr. In the isolated gastric fundus from immature rats, telenzepine and pirenzepine did not modify the spontaneous acid secretion, whereas both drugs caused a competitive inhibition of bethanechol-induced acid secretion (pA2 values were 7.96 and 6.81 for telenzepine and pirenzepine, respectively). These data indicate that telenzepine is a potent antisecretory agent both in vitro and in vivo.
Decreased β-Amyloid1-42and Increased Tau Levels in Cerebrospinal Fluid of Patients With Alzheimer Disease (2003)

Alzheimer disease is associated with a significant decrease in CSF beta-amyloid1-42 levels along with an increase in CSF tau levels. These findings suggest that the 2 measures are biological markers of AD pathophysiology. While these CSF measures may have a potential clinical utility as biomarkers of disease, the preliminary and retrospective nature of the findings, the absence of assay standardization, and the lack of comparison patient populations must be addressed in future studies testing the usefulness of these CSF measures for predictive, diagnostic, or treatment evaluation purposes.
Possible Mechanism for in Vitro Complement Activation in Blood and Plasma Samples: Futhan/EDTA Controls in Vitro Complement Activation (1999)

The combination of Futhan (0.1 g/L) and EDTA (1 g/L) eliminates in vitro C activation.
T lymphocytes coexpressing CCR4 and a chimeric antigen receptor targeting CD30 have improved homing and antitumor activity in a Hodgkin tumor model (2009)

For the adoptive transfer of tumor-directed T lymphocytes to prove effective, there will probably need to be a match between the chemokines the tumor produces and the chemokine receptors the effector T cells express. The Reed-Stemberg cells of Hodgkin lymphoma (HL) predominantly produce thymus- and activation-regulated chemokine/CC chemokine ligand 17 (TARC/CCL17) and macrophage-derived chemokine (MDC/CCL22), which preferentially attract type 2 T helper (Th2) cells and regulatory T cells (Tregs) that express the TARC/MDC-specific chemokine receptor CCR4, thus generating an immunosuppressed tumor environment. By contrast, effector CD8(+) T cells lack CCR4, are nonresponsive to these chemokines and are rarely detected at the tumor site. We now show that forced expression of CCR4 by effector T cells enhances their migration to HL cells. Furthermore, T lymphocytes expressing both CCR4 and a chimeric antigen receptor directed to the HL associated antigen CD30 sustain their cytotoxic function and cytokine secretion in vitro, and produce enhanced tumor control when infused intravenously in mice engrafted with human HL. This approach may be of value in patients affected by HL.
Mitogen-Activated Protein Kinases in Heart Development and Diseases (2007)

Mitogen-activated protein (MAP) kinases belong to a highly conserved family of Ser-Thr protein kinases in the human kinome and have diverse roles in broad physiological functions. The 4 best-characterized MAP kinase pathways, ERK1/2, JNK, p38, and ERK5, have been implicated in different aspects of cardiac regulation, from development to pathological remodeling. Recent advancements in the development of kinase-specific inhibitors and genetically engineered animal models have revealed significant new insights about MAP kinase pathways in the heart. However, this explosive body of new information also has yielded many controversies about the functional role of specific MAP kinases as either detrimental promoters or critical protectors of the heart during cardiac pathological processes. These uncertainties have raised questions on whether/how MAP kinases can be targeted to develop effective therapies against heart diseases. In this review, recent studies examining the role of MAP kinase subfamilies in cardiac development, hypertrophy, and survival are summarized.
Overcoming catastrophic forgetting in neural networks (2017)

The ability to learn tasks in a sequential fashion is crucial to the development of artificial intelligence. Until now neural networks have not been capable of this and it has been widely thought that catastrophic forgetting is an inevitable feature of connectionist models. We show that it is possible to overcome this limitation and train networks that can maintain expertise on tasks that they have not experienced for a long time. Our approach remembers old tasks by selectively slowing down learning on the weights important for those tasks. We demonstrate our approach is scalable and effective by solving a set of classification tasks based on a hand-written digit dataset and by learning several Atari 2600 games sequentially.
Role of the deletion of polymorphism of the angiotensin converting enzyme gene in the progression and therapeutic responsiveness of IgA nephropathy. (1995)

Studies conducted over the last decade demonstrated variable therapeutic efficacy of angiotensin converting enzyme (ACE) inhibitor on the progression of glomerular diseases, including IgA nephropathy. In this study, among patients with biopsy-proven IgA nephropathy, 53 patients in whom creatinine clearance had been monitored over 5 yr were recruited for study. These patients were classified into two groups according to whether or not renal function had declined as determined by the slope of creatinine clearance against time: group 1 had stable renal function; group 2 had declining renal function (average: -6.7 +/- 1.3 ml/min/yr). 21 of 53 patients were treated with ACE inhibitor and followed for 48 wk. Gene polymorphism consisting of insertion (I) or deletion (D) of a 287-bp DNA fragment (presumed to be a silencer element) of the ACE gene was determined by PCR. 46 age-matched individuals without history of proteinuria were analyzed as controls. The DD genotype was significantly more frequent in group 2 (43%) than in controls (7%) or group 1 patients with stable renal function (16%). 48 wk after ACE inhibitor administration, proteinuria significantly decreased in patients with DD genotype but not in those with ID or II genotypes. The results indicate that deletion polymorphism in the ACE gene, particularly the homozygote DD, is a risk factor for progression to chronic renal failure in IgA nephropathy. Moreover, this deletion polymorphism predicts the therapeutic efficacy of ACE inhibition on proteinuria and, potentially, on progressive deterioration of renal function.
CATMA: a complete Arabidopsis GST database (2003)

The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a complete reannotation of the genome using uniform parameters. The database is searchable by sequence name, sequence homology or direct SQL query, and is available through the CATMA website at http://www.catma.org/.
Deficiency in the Repair of DNA Damage by Homologous Recombination and Sensitivity to Poly(ADP-Ribose) Polymerase Inhibition (2006)

Deficiency in either of the breast cancer susceptibility proteins BRCA1 or BRCA2 induces profound cellular sensitivity to the inhibition of poly(ADP-ribose) polymerase (PARP) activity. We hypothesized that the critical role of BRCA1 and BRCA2 in the repair of double-strand breaks by homologous recombination (HR) was the underlying reason for this sensitivity. Here, we examine the effects of deficiency of several proteins involved in HR on sensitivity to PARP inhibition. We show that deficiency of RAD51, RAD54, DSS1, RPA1, NBS1, ATR, ATM, CHK1, CHK2, FANCD2, FANCA, or FANCC induces such sensitivity. This suggests that BRCA-deficient cells are, at least in part, sensitive to PARP inhibition because of HR deficiency. These results indicate that PARP inhibition might be a useful therapeutic strategy not only for the treatment of BRCA mutation-associated tumors but also for the treatment of a wider range of tumors bearing a variety of deficiencies in the HR pathway or displaying properties of 'BRCAness.'
Mitotic partitioning of transcription factors (2008)

Mitosis is a highly orchestrated process involving numerous protein kinases and phosphatases. At the onset of mitosis, the chromatin condensation into metaphase chromosomes is correlated with global phosphorylation of histone H3. The bulk of transcription is silenced while many of the transcription-associated proteins, including transcription and chromatin remodeling factors, are excluded from chromatin, typically as a consequence of their phosphorylation. Components of the transcription machinery and regulatory proteins are recycled and equally partitioned between newly divided cells by mechanisms that may involve microtubules, microfilaments or intermediate filaments. However, as demonstrated in the case of Runx2, a subset of transcription factors involved in lineage-specific control, likely remain associated with their target genes to direct the deposition or removal of epigenetic marks. The displacement and re-entry into daughter cells of transcription and chromatin remodeling factors are temporally defined and regulated. Reformation of daughter nuclei is a critical time to re-establish the proper gene expression pattern. The mechanisms involved in the marking and re-establishment of gene expression has been elucidated for few genes. The elucidation of how the memory of a programmed expression profile is transmitted to daughter cells represents a challenge.
Mass Spectrometry of Self-Assembled Monolayers: A New Tool for Molecular Surface Science (2008)

Most reactions can be performed in solution and on a surface, yet the challenges faced in applying known reactions or in developing entirely new reactions for modifying surfaces remain formidable. The products of many reactions performed in solution can be characterized in minutes, and even products having complex structures can be characterized in hours. When performed on surfaces, even the most basic reactions require a substantial effort--requiring several weeks--to characterize the yields and structures of the products. This contrast stems from the lack of convenient analytical tools that provide rapid information on the structures of molecules attached to a surface. This review describes recent work that has established mass spectrometry as a powerful method for developing and characterizing a broad range of chemical reactions of molecules attached to self-assembled monolayers of alkanethiolates on gold. The SAMDI-TOF mass spectrometry technique will enable a next generation of applications of molecularly defined surfaces to problems in chemistry and biology.
Identification of novel rhodopsin mutations associated with retinitis pigmentosa by GC-clamped denaturing gradient gel electrophoresis. (1991)

Retinitis pigmentosa (RP) is a group of disorders characterized by progressive degeneration of the outer retina, resulting in night blindness, visual field loss, an abnormal electroretinogram, and characteristic retinal pigmentary changes. An important step in the understanding of RP has been the recognition that some cases of autosomal dominant RP (ADRP) are caused by mutations in the rhodopsin gene. Multiple different point mutations within the coding sequence of the rhodopsin gene have been associated with ADRP. We have developed a GC-clamped denaturing-gradient-gel electrophoresis (DGGE) assay for the coding region of the rhodopsin gene and have used this assay to screen ADRP patients for mutations. The assay consists of amplifying with PCR the five exons of the rhodopsin gene and then analyzing each PCR product by DGGE. We have used this assay to detect three previously unreported rhodopsin base substitutions associated with ADRP. The use of this assay to identify ADRP patients who have various rhodopsin mutations has allowed us to begin studies seeking to correlate molecular genotype with clinical phenotype. Furthermore, GC-clamped DGGE has allowed us to identify families with ADRP not caused by a rhodopsin mutation. Such families will be important in the search for other genes involved in ADRP.