gebhart/patrepeval huggingface dataset:
Quantitative mapping of glycoprotein micro‐heterogeneity and macro‐heterogeneity: an evaluation of mass spectrometry signal strengths using synthetic peptides and glycopeptides (2013)

Mass spectrometry (MS) is used to quantify the relative distribution of glycans attached to particular protein glycosylation sites (micro-heterogeneity) and evaluate the molar site occupancy (macro-heterogeneity) in glycoproteomics. However, the accuracy of MS for such quantitative measurements remains to be clarified. As a key step towards this goal, a panel of related tryptic peptides with and without complex, biantennary, disialylated N-glycans was chemically synthesised by solid-phase peptide synthesis. Peptides mimicking those resulting from enzymatic deglycosylation using PNGase F/A and endo D/F/H were synthetically produced, carrying aspartic acid and N-acetylglucosamine-linked asparagine residues, respectively, at the glycosylation site. The MS ionisation/detection strengths of these pure, well-defined and quantified compounds were investigated using various MS ionisation techniques and mass analysers (ESI-IT, ESI-Q-TOF, MALDI-TOF, ESI/MALDI-FT-ICR-MS). Depending on the ion source/mass analyser, glycopeptides carrying complex-type N-glycans exhibited clearly lower signal strengths (10-50% of an unglycosylated peptide) when equimolar amounts were analysed. Less ionisation/detection bias was observed when the glycopeptides were analysed by nano-ESI and medium-pressure MALDI. The position of the glycosylation site within the tryptic peptides also influenced the signal response, in particular if detected as singly or doubly charged signals. This is the first study to systematically and quantitatively address and determine MS glycopeptide ionisation/detection strengths to evaluate glycoprotein micro-heterogeneity and macro-heterogeneity by label-free approaches. These data form a much needed knowledge base for accurate quantitative glycoproteomics.
Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. (1988)

The yeast his3 promoter region contains two distinct classes of "TATA elements," constitutive (TC) and regulatory (TR), that are defined by their interactions with upstream promoter elements, selectivity of initiation sites, and chromatin structure. TC is localized between positions -83 and -53, and TR is localized between positions -55 and -35, regions in which there are several TATA-like sequences. In this study, we used saturation mutagenesis to examine the structural requirements of the his3 TR element necessary for transcriptional induction. To avoid the complications of redundant elements, the phenotypic analysis was carried out by using a gal-his3 hybrid promoter whose function depends on a short oligonucleotide containing the prospective his3 TR element. In this context, an oligonucleotide containing the sequence TATAAA is sufficient for TR function. However, 17 out of the 18 possible single-base substitutions and 9 out of 10 double mutations of this sequence abolish TR function. This strict sequence requirement for TR function strongly suggests that the TR element is a target site for a sequence-specific DNA-binding protein. Further, as the region encoding TC and promoters of certain other yeast genes do not contain a sequence that is compatible with TR function, we suggest that yeast cells contain multiple proteins with distinct sequence specificities that carry out a related "TATA function" and that yeast promoters can be divided into classes based on their downstream promoter elements.
Social Security and the African American Male (A Cash Transfer System) (2005)

All employed workers are required to contribute to the Social Security System; however,a disproportionatep ercentage of African American males never live long enough to collect any benefits from their contributions. On the other hand, the life-expectancy of white males is significantly longer than the life expectancy of African American males, and their collection of Social Security benefits tends to exceed their contributions to the system. The federal government keeps the Social Security system from becoming completely solvent by raiding it of any surplus funds it collects; thereby, preventing the Social Security Fund from developing interest income, and accumulating funds for future generations of retirees.
Cloned hepatitis delta virus cDNA is infectious in the chimpanzee (1989)

A head-to-tail trimer of a full-length cDNA clone of the hepatitis delta virus (HDV) genome was examined for infectivity by direct inoculation into the liver of a chimpanzee that was already infected with hepatitis B virus. Five weeks after inoculation, a marked elevation of serum alanine aminotransferase activity was observed, followed by the appearance of high levels of HDV RNA and antigen in both liver and serum and a high level of viral particles in the serum. A transient suppression of hepatitis B virus replication was evident during the acute phase of HDV infection. Seroconversion for antibodies to delta antigen occurred 3 weeks after the onset of the disease. These results demonstrate that a typical HDV infection can be initiated by inoculation of a susceptible animal with recombinant HDV cDNA.
A pharmacodynamic study of the FLT3 inhibitor KW-2449 yields insight into the basis for clinical response (2008)

Internal tandem duplication mutations of FLT3 (FLT3/ITD mutations) are common in acute myeloid leukemia (AML) and confer a poor prognosis. This would suggest that FLT3 is an ideal therapeutic target, but FLT3 targeted therapy has produced only modest benefits in clinical trials. Due to technical obstacles, the assessment of target inhibition in patients treated with FLT3 inhibitors has been limited and generally only qualitative. KW-2449 is a novel multitargeted kinase inhibitor that induces cytotoxicity in Molm14 cells (which harbor an FLT3/ITD mutation). The cytotoxic effect occurs primarily at concentrations sufficient to inhibit FLT3 autophosphorylation to less than 20% of its baseline. We report here correlative data from a phase 1 trial of KW-2449, a trial in which typical transient reductions in the peripheral blast counts were observed. Using quantitative measurement of FLT3 inhibition over time in these patients, we confirmed that FLT3 was inhibited, but only transiently to less than 20% of baseline. Our results suggest that the failure to fully inhibit FLT3 in sustained fashion may be an underlying reason for the minimal success of FLT3 inhibitors to date, and stress the importance of confirming in vivo target inhibition when taking a targeted agent into the clinical setting.
An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene (2004)

Helix-hairpin-helix DNA glycosylases are typically small proteins that initiate repair of DNA by excising damaged or mispaired bases. An invariant aspartic acid in the active site is involved in catalyzing the excision reaction. Replacement of this critical residue with an asparagine severely reduces catalytic activity but preserves enzyme stability and structure. The Arabidopsis DEMETER (DME) gene encodes a large 1,729-aa polypeptide with a 200-aa DNA glycosylase domain. DME is expressed primarily in the central cell of the female gametophyte. DME activates maternal allele expression of the imprinted MEDEA (MEA) gene in the central cell and is required for seed viability. We mutated the invariant aspartic acid at position 1304 in DME to asparagine (D1304N) to determine whether the catalytic activity of the DNA glycosylase domain is required for DME function in vivo. Transgenes expressing wild-type DME in the central cell rescue seed abortion caused by a mutation in the endogenous DME gene and activate maternal MEA:GFP transcription. However, transgenes expressing the D1304N mutant DME do not rescue seed abortion or activate maternal MEA:GFP transcription. Whereas ectopic expression of the wild-type DME polypeptide in pollen is sufficient to activate ectopic paternal MEA and MEA:GUS expression, equivalent expression of the D1304N mutant DME in pollen failed to do so. These results show that the conserved aspartic acid residue is necessary for DME to function in vivo and suggest that an active DNA glycosylase domain, normally associated with DNA repair, promotes gene transcription that is essential for gene imprinting.
Liver‐Specific Gene Expression in Cultured Human Hematopoietic Stem Cells (2003)

Hematopoietic and hepatic stem cells share characteristic markers such as CD34, c-kit, and Thy1. Based on the recent observations that hepatocytes may originate from bone marrow, we investigated the potential of CD34(+) bone marrow cells to differentiate into hepatocytic cells in vitro. CD34(+) and CD34(-) human bone marrow cells were separated by magnetic cell sorting. Cells were cultured on a collagen matrix in a defined medium containing hepatocyte growth factor. Cell count and size were measured by flow cytometry, and reverse transcription polymerase chain reaction was carried out for the liver-specific markers CK-19 and albumin. During cell culture, CD34(+) cells showed an increasing cell number and proliferative activity as assessed by Ki-67 staining. Under the specified culture conditions, CD34(+) cells expressed albumin RNA and CK-19 RNA after 28 days, whereas CD34(-) cells did not show liver-specific gene expression. The results indicate that CD34(+) adult human bone marrow stem cells can differentiate into hepatocytic cells in vitro.
Chromosome Choreography: The Meiotic Ballet (2003)

The separation of homologous chromosomes during meiosis in eukaryotes is the physical basis of Mendelian inheritance. The core of the meiotic process is a specialized nuclear division (meiosis I) in which homologs pair with each other, recombine, and then segregate from each other. The processes of chromosome alignment and pairing allow for homolog recognition. Reciprocal meiotic recombination ensures meiotic chromosome segregation by converting sister chromatid cohesion into mechanisms that hold homologous chromosomes together. Finally, the ability of sister kinetochores to orient to a single pole at metaphase I allows the separation of homologs to two different daughter cells. Failures to properly accomplish this elegant chromosome dance result in aneuploidy, a major cause of miscarriage and birth defects in human beings.
Directed Movement of Vascular Smooth Muscle Cells on Gradient-Compliant Hydrogels (2003)

Current solutions in the treatment of cardiovascular disease include angioplasty and the insertion of stents, but a large number of these cases result in restenosis. Biomaterial coatings that control vascular smooth muscle cell migration are therefore desirable. In this study, we describe a novel method to create substrata with defined gradients in mechanical compliance using photopolymerization and patterning. Cell speed was found to be 53 ± 2.6 μm/h on a substrate with a Young's modulus of 15 kPa compared to 40 ± 3.1 μm/h for a 28 kPa substratum (P < 0.005). We demonstrate that vascular smooth muscle cells undergo direct migration on radial-gradient-compliant substrata from soft to stiff regions of the substrate and that cells accumulate in the stiff regions after 24 h. Our results show that the pattern of the compliance gradient is important and that substrate compliance may be a key design parameter for modulation of cell migration for vascular tissue engineering applications.
Sociodemographic Trends in the Incidence of Pancreatic and Biliary Tract Cancer in UK Primary Care (2014)

The overall incidence of both cancers is low but increasing. Variations in incidence may reflect changes in coding practice or increased exposure to associated risk factors.
The Mechanism of Long-Range Exciton Diffusion in a Nematically Organized Porphyrin Layer (2008)

The exciton diffusion length in a nematically organized meso-tetra(4-n-butylphenyl)porphyrin (TnBuPP) layer was found to exceed 40 nm at a temperature of 90 K and to be equal to 22 +/- 3 nm at 300 K. The exciton diffusion coefficient decreases from > or = 3.1 x 10(-6) m(2)/s at 90 K to (2.5 +/- 0.5) x 10(-7) m(2)/s at 300 K. This thermal deactivation is attributed to exciton motion via a band mechanism. The motion of an exciton is not limited by polaronic effects; that is, the deformation of the atomic lattice around the exciton. The absence of polaronic self-trapping implies that the exciton diffusion coefficient can be enhanced by improvement of structural order and rigidity of the material.
Duplex Recognition by Oligonucleotides Containing 2‘-Deoxy-2‘-fluoro-d-arabinose and 2‘-Deoxy-2‘-fluoro-d-ribose. Intermolecular 2‘-OH−Phosphate Contacts versus Sugar Puckering in the Stabilization of Triple-Helical Complexes (1999)

To gain insight into the origins of the large binding affinity of RNA toward target duplexes, 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) and 2'-deoxy-2'-fluoroarabinonucleic acid (2'F-ANA) were tested for their ability to recognize duplex DNA, duplex RNA, and RNA-DNA hybrids. 2'F-RNA, 2'F-ANA, and the corresponding control single-stranded (ss) DNA strands were shown to form triple-helical complexes only with duplex DNA and hybrid DNA (Pu)-RNA (Py), but not with duplex RNA and hybrid RNA (Pu)-DNA (Py). In contrast, an RNA third strand recognized all four possible duplexes (DD, DR, RD, and RR) as previously demonstrated by Roberts and Crothers [(1992) Science 258, 1463-1466]. The 2'F-RNA (C3'-endo) strand exhibited significantly reduced affinity for duplexes compared to an unmodified RNA (C3'-endo) strand. These findings are consistent with the intermolecular 2'-OH-phosphate contact mechanism proposed by Escudé et al. [(1993) Nucleic Acids Res. 24, 5547-5553], as a ribo 2'-F atom should not interact with a negatively charged phosphate. In addition, they emphasize the role of the 2'-OH ribose as a general recognition and binding determinant of RNA. The 2'-F arabino modification (2'F-ANA, C2'-endo) led to a considerable increase in the binding affinity for duplex DNA, as compared to those of DNA and 2'F-RNA third strands. This is likely to be the result of a greater population of C2'-endo pucker of the 2'F-ANA compared to DNA. The enhancement observed for 2'F-ANA strands toward duplex DNA is comparable to that observed with 2'-OMe RNA. Since 2'F-ANA has been shown to be more resistant to nuclease degradation than DNA, these results are likely to stimulate experimental work on arabinose derivatives in laboratories concerned with targeting DNA sequences in vivo ("antigene" strategy).
Phase II, Randomized, Multicenter, Double-Blind, Placebo-Controlled Trial of a Polyclonal Anti- Staphylococcus aureus Capsular Polysaccharide Immune Globulin in Treatment of Staphylococcus aureus Bacteremia (2007)

New treatment modalities are needed for the treatment of infections due to multidrug-resistant Staphylococcus aureus. S. aureus capsular polysaccharide immune globulin (Altastaph) is a polyclonal immune globulin preparation that is being developed as adjunctive therapy for persons with S. aureus infections complicated by bacteremia. In a phase II, multicenter, randomized, double-blind, placebo-controlled trial, 40 subjects with documented S. aureus bacteremia received standard therapy plus either Altastaph at 200 mg/kg of body weight in each of two infusions 24 h apart or placebo. During the 42-day observation period, antibody pharmacokinetics and safety were the primary characteristics studied. Information regarding the resolution of bacteremia and fever was also analyzed. Anti-type-5 and anti-type-8 capsular antibody levels peaked after the second infusion at 550 mug/ml and 419 mug/ml, respectively, and remained above 100 mug/ml at day 28. A total of 316 adverse events were noted in 39 of 40 subjects. Infusion-related adverse events in Altastaph recipients were infrequent and similar to those among recipients of commercial intravenously administered immunoglobulin G products. Five of 21 (23%) subjects in the Altastaph group died, whereas 2 of 18 (11%) subjects in the placebo group died (P = 0.42). Compared to the control patients, the Altastaph recipients had a shorter median time to the resolution of fever (2 days and 7 days, respectively; P = 0.09) and a shorter length of hospital stay (9 days and 14 days, respectively; P = 0.03). However, these findings are exploratory, and there were few differences in the other variables measured. High levels of opsonizing antibodies were maintained for the initial 4 weeks. Although the study was not powered to show efficacy, these preliminary findings and safety profile suggest that Altastaph may be an effective adjunct to antibiotics and warrants further investigation (ClinicalTrials.gov number NCT00063089).
Purification and characterization of an extracellular proline iminopeptidase from Arthrobacter nicotianae 9458 (1999)

An extracellular proline iminopeptidase, with a molecular mass of about 53 kDa, was purified from Arthrobacter nicotianae 9458 and characterized. The enzyme had temperature and pH optima of 37°C and 8.0, respectively, was completely inactivated by heating for 1 min at 80°C and showed highest activity on Pro-pNA. The proline iminopeptidase was characterized by activity at low temperature, NaCl concentrations up to 7,5% and by high sensitivity to pH values 6.0, serine enzyme inhibitor PMSF and divalent cations, Fe2+, Sn2+, Cu2+, Zn2+, Hg2+, Co2+ and Ni2+. The extracellular proline iminopeptidase from A. nicotianae 9458 was able to hydrolyze proline-containing peptides at the pH, temperature and NaCl concentration typical of the surface of smear-ripened cheeses and may contribute to proteolysis of these cheeses during ripening.
Introduction of a Composite Parameter to the Pharmacokinetics of Venlafaxine and its Active O‐Desmethyl Metabolite (1992)

Venlafaxine is a structurally novel, nontricyclic compound that is being evaluated for the treatment of various depressive disorders. A randomized three-period crossover study was conducted to obtain pharmacokinetic and dose proportionality data on the drug and its active metabolite, O-desmethylvenlafaxine. Eighteen healthy young men received single doses of venlafaxine 25, 75, and 150 mg followed by 3 days of administration every 8 hours (q8h). Steady-state elimination half-life was 3 to 4 hours for venlafaxine and 10 hours for O-desmethylvenlafaxine; both were independent of dose. Venlafaxine had a high oral-dose clearance, ranging from 0.58 to 2.63 L/hr/kg across doses with the lowest mean clearance, 0.98 L/hr/kg, at the highest dose. The apparent clearance of O-desmethylvenlafaxine was lower than venlafaxine, ranging from 0.21 to 0.66 L/hr/kg, and the lowest mean clearance, 0.33 L/hr/kg, occurred at the lowest dose. The area under the metabolite curve was two to three times greater than that for venlafaxine. Each compound had linear dose proportionality up to 75 mg q8h. A composite parameter incorporating venlafaxine plus O-desmethylvenlafaxine was introduced (i.e., AUC [area under the curve] + activity factor.AUCm), which extended linearity to 150 mg q8h. In summary, venlafaxine is a high-clearance drug that forms a metabolite with almost equal activity and demonstrates linear dose-proportionality.
Relationship between surface-enhanced Raman scattering and the dielectric properties of aggregated silver films (1981)

By using an evaporated silver film that has a continuously varying thickness, we have demonstrated the dependence of surface-enhanced Raman scattering (SERS) on the dielectric properties of the film. These results support local field models that are based on metal-particle resonances for SERS.
How Can Hyperbaric Oxygen Contribute to Treatment? (2001)

Hyperbaric oxygen (HBO2) is used in a sports medicine setting to reduce hypoxia and edema and appears to be particularly effective for treating crush injuries and acute traumatic peripheral ischemias. When used clinically, HBO2 should be considered as an adjunctive therapy as soon as possible after injury diagnosis. Treatment pressures for acute traumatic peripheral ischemia range from 2.0 to 2.5 atmospheres absolute (ATA), with a minimum of 90 minutes for each treatment. Some professional and amateur athletes use HBO2 to aid endurance performance or to speed recovery from exercise-related fatigue; however, research does not yet support these uses. Clinicians and athletes should keep in mind that HBO2 is a medical treatment with associated risks.
5′ Exon replacement and repair by spliceosome-mediated RNA trans-splicing (2003)

Spliceosome-mediated RNA trans-splicing (SMaRT) has been used previously to reprogram mutant endogenous CFTR and factor VIII mRNAs in human epithelial cell and tissue models and knockout mice, respectively. Those studies used 3' exon replacement (3'ER); a process in which the distal portion of RNA is reprogrammed. Here, we also show that the 5' end of mRNA can be completely rewritten by 5'ER. For proof-of-concept, and to test whether 5'ER could generate functional CFTR, we generated a mutant minigene target containing CFTR exons 10-24 (deltaF508) and a mini-intron 10, and a pretrans-splicing molecule (targeted to intron 10) containing CFTR exons 1-10 (+F508), and tested these two constructs in 293T cells for anion efflux transport. Cells cotransfected with target and PTM showed a consistent increase in anion efflux, but there was no response in control cells that received PTM or target alone. Using a LacZ reporter system to accurately quantify trans-splicing efficiency, we tested several unique PTM designs. These studies provided two important findings as follows: (1) efficient trans-splicing can be achieved by binding the PTM to different locations in the target, and (2) relatively few changes in PTM design can have a profound impact on trans-splicing activity. Tethering the PTM close to the target 3' splice site (as opposed to the donor site) and inserting an intron in the PTM coding resulted in a 65-fold enhancement of LacZ activity. These studies demonstrate that (1) SMaRT can be used to reprogram the 5' end of mRNA, and (2) efficiency can be improved substantially.
Static characteristics of a-Si:H dual-gate TFTs (2003)

This paper examines the effect of the top gate on the static characteristics of dual-gate hydrogenated amorphous silicon (a-Si:H) thin-film transistors (TFTs). Both forward and reverse regimes of operation are considered. The top gate has a distinct effect on the threshold voltage, subthreshold slope, drive-current capability, and the leakage current of the TFT. In particular, the threshold voltage is found to linearly decrease with increasing top-gate bias. Specific bias configurations of the dual gate TFT critical to vertical integration of on-pixel electronics for imaging and display applications are also presented.