gebhart/patrepeval huggingface dataset:
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. (1992)

A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field of pattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm.
Deformation in nanocrystalline metals (2006)

It is now possible to synthesize polycrystalline metals made up of grains that average less than 100 nm in size. Such nanocrystalline metals contain a significant volume fraction of interfacial regions separated by nearly perfect crystals. The small sizes involved limit the conventional operation of dislocation sources and thus a fundamental question arises: how do these materials deform plastically? We review the current views on deformation mechanisms in nanocrystalline, face-centered cubic metals based on insights gained by atomistic computer simulations. These insights are discussed with reference to recent striking experimental observations that can be compared with predictions made by the simulations.
Targeted Delivery of Saporin Toxin by Monoclonal Antibody to the Transcobalamin Receptor, TCblR/CD320 (2010)

Cellular uptake of cobalamin (Cbl) occurs by endocytosis of transcobalamin saturated with Cbl by the transcobalamin receptor (TCblR/CD320). The cell cycle-associated overexpression of this receptor in many cancer cells provides a suitable target for delivering chemotherapeutic drugs and cytotoxic molecules to these cells while minimizing the effect on the normal cell population. We have used monoclonal antibodies to the extracellular domain of TCblR to deliver saporin-conjugated secondary antibody to various cell lines propagating in culture. A molar ratio of 2.5:10 nmol/L of primary:secondary antibody concentration was identified as the lowest concentration needed to produce the optimum cytotoxic effect. The effect was more pronounced when cells were seeded at lower density, suggesting lack of cell division in a fraction of the cells at higher density as the likely explanation. Cells in suspension culture, such as K562 and U266 cells, were more severely affected than adherent cultures, such as SW48 and KB cells. This differential effect of the anti-TCblR-saporin antibody conjugate and the ability of an anti-TCblR antibody to target proliferating cells were further evident by the virtual lack of any effect on primary skin fibroblasts and minimal effect on bone marrow cells. These results indicate that preferential targeting of some cancer cells could be accomplished through the TCblR.
Distance-Dependent Electron Transfer in DNA Hairpins (1997)

The distance dependence of photoinduced electron transfer in duplex DNA was determined for a family of synthetic DNA hairpins in which a stilbene dicarboxamide forms a bridge connecting two oligonucleotide arms. Investigation of the fluorescence and transient absorption spectra of these hairpins established that no photoinduced electron transfer occurs for a hairpin that has six deoxyadenosine-deoxythymidine base pairs. However, the introduction of a single deoxyguanosine-deoxycytidine base pair resulted in distance-dependent fluorescence quenching and the formation of the stilbene anion radical. Kinetic analysis suggests that duplex DNA is somewhat more effective than proteins as a medium for electron transfer but that it does not function as a molecular wire.
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability (2002)

Here we present a novel method that resolves this problem by analyzing a set of bootstrap trees instead of the optimal tree. The frequency of orthology assignments in the bootstrap trees can be interpreted as a support value for the possible orthology of the sequences. Our method is efficient enough to analyze data in the scale of whole genomes. It is implemented in Java and calculates orthology support levels for all pairwise combinations of homologous sequences of two species. The method was tested on simulated datasets and on real data of homologous proteins.
Safety and tolerability of multiple doses of imipenem/cilastatin (1985)

The safety and tolerability of 1 gm imipenem and cilastatin given together every 6 hours for 10 days was evaluated in a randomized, double-blind, placebo-controlled trial in normal subjects. Nausea was more common in the drug-treated group (five of six subjects) than in the control group (two of six subjects). No consistent changes in hepatic function indices were noted. Although beta 2-microglobulin excretion showed a significant trend of rising over time in the drug group, there were no differences between groups with regard to 24-hour urinary excretion of either N-acetyl-beta-glucosaminidase or beta 2-microglobulin. Urinalysis did not reveal any casts and serial creatinine clearance determinations showed no change in renal function in either the drug- or placebo-treated groups. Pure tone audiograms were performed before and after dosing in 11 of 12 subjects; no changes were noted. We conclude that the combination of imipenem and cilastatin was well tolerated and safe.
Slow release of anticancer drugs from porous calcium hydroxyapatite ceramic (1992)

We have developed a new delivery system for sustained release of an anticancer drug (cis-platinum) by enclosure into blocks of porous calcium hydroxyapatite ceramic. The slow release of this drug from this system was confirmed in in vitro experiments. When this system was implanted into normal back muscle, or the tibia, sustained release of cis-platinum was observed during a 12-week period after implantation. The diffusion rate of cis-platinum into blood and other organs (liver, kidney, brain) was less than 10% of that at the implanted site. This delivery system placed into experimental tumors of mice also showed a uniform release of anticancer drug for more than 3 months. Inhibition of tumor growth was more marked after local implantation of this system than after intraperitoneal administration of cis-platinum. These results indicate that this new approach to a drug delivery system may well have an important role in cancer chemotherapy. In bone tumors it is attractive because the mechanical strength of calcium hydroxyapatite ceramic permits partial surgical excision and replacement of the bone defect at the same time.
Are stingless bees the primary vector in spread of banana Xanthomonas wilt in Central Uganda (2014)

Stingless bees were speculated to be the primary vectors in the spread of the bacterial agent responsible for banana Xanthomonas wilt (BXW) in Uganda. It was hypothesized that the vector entered the banana plant through the male flowers. We therefore determined the likely role of the bees in spread of Xanthomonas campestris pv. musacearum that causes BXW. We first documented species of stingless bees present in the banana farms, their nesting sites and foraging behavior. Then we documented the foraging behavior of Hypotrigona gribodoi - Magretti and Plebeina hildebrandti Friese reared in wooden observation hives where we offered banana sap, bacterial ooze and nectar. We then measured sugar concentration in Pisang Awak, the banana variety reported to be most susceptible to Xanthomonas. We tested how far stingless bees&#13;\nwould fly to collect banana nectar through indirect recruitment experiments to experimental feeders with 11, 33, 48 and 54% sugar solutions. Our findings were: four species of stingless bees, Hypotrigona gribodoi, Plebeina hildebrandti, Meliponula ferruginea Lepeletier and Meliponula sp. foraged and nested within the banana farms. They collected nectar from both male and female banana flowers but spent more time on&#13;\nfemale flowers than on male flowers. They did not collect banana sap and bacterial ooze from scars of recently dehisced male flowers and at the nest entrance of the observation hives. The foraging distance of workers of P. hildebrandti was 1050 and 1215 m when sugar solutions 11 and 33% were offered, respectively. The foragers would therefore fly less than 1215 m from the nest to collect Pisang Awak nectar which had an average sugar concentration of 12.5%. Thus stingless bees were likely to get accidental&#13;\ncontamination with Xanthomonas campestris pv. musacearum just like any other moving object or insects. If the bees got accidentally contaminated with Xanthomonas, saps and resins within the nest would decontaminate them.
Fatal Leukemia in Interleukin 15 Transgenic Mice Follows Early Expansions in Natural Killer and Memory Phenotype Cd8+ T Cells (2001)

Inflammation likely has a role in the early genesis of certain malignancies. Interleukin (IL)-15, a proinflammatory cytokine and growth factor, is required for lymphocyte homeostasis. Intriguingly, the expression of IL-15 protein is tightly controlled by multiple posttranscriptional mechanisms. Here, we engineered a transgenic mouse to overexpress IL-15 by eliminating these posttranscriptional checkpoints. IL-15 transgenic mice have early expansions in natural killer (NK) and CD8+ T lymphocytes. Later, these mice develop fatal lymphocytic leukemia with a T-NK phenotype. These data provide novel evidence that leukemia, like certain other cancers, can arise as the result of chronic stimulation by a proinflammatory cytokine.
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454 (2010)

We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.
The effect of subthreshold continuous electrical stimulation on the facial function of patients with Bell’s palsy (2015)

The overall rate of patient recovery among those treated with prednisolone or/and acyclovir plus electrical stimulation (96%) was significantly better (p < 0.05) than the rate among those treated with only prednisolone or/and acyclovir (88%).
Characterization of cDNA Clones Selected by the GeneMark Analysis from Size-Fractionated cDNA Libraries from Human Brain (1999)

We have conducted a sequencing project of human cDNAs which encode large proteins in brain. For selection of cDNA clones to be sequenced in this project, cDNA clones have been experimentally examined by in vitro transcription/translation prior to sequencing. In this study, we tested an alternative approach for picking up cDNA clones having a high probability of carrying protein coding region. This approach exploited 5'-end single-pass sequence data and the GeneMark program for assessing protein-coding potential, and allowed us to select 74 clones out of 14,804 redundant cDNA clones. The complete sequence data of these 74 clones revealed that 45% of them encoded proteins consisting of more than 500 amino acid residues while all the clones thus selected carried possible protein coding sequences as expected. The results indicated that the GeneMark analysis of 5'-end sequences of cDNAs offered us a simple and effective means to select cDNA clones with protein-coding potential although the sizes of the encoded proteins could not be predicted.
Influence of CYP2D6 activity on the pharmacokinetics and pharmacodynamics of a single 20 mg dose of ibogaine in healthy volunteers (2015)

Conversion of ibogaine to its active metabolite noribogaine appears to be mediated primarily by CYP2D6. We compared 168 hours pharmacokinetic profiles of both analytes after a single oral 20 mg dose of ibogaine in 21 healthy subjects who had been pretreated for 6 days with placebo or the CYP2D6 inhibitor paroxetine. In placebo-pretreated subjects, ibogaine was rapidly converted to noribogaine. Median peak noribogaine concentrations occurred at 4 hours. Compared with placebo-pretreated subjects, paroxetine-pretreated subjects had rapid (Tmax = 1.5 hours) and substantial absorption of ibogaine, with detectable levels out to 72 hours, and an elimination half-life of 10.2 hours. In this group, ibogaine was also rapidly converted to noribogaine with a median Tmax of 3 hours. Extent of noribogaine exposure was similar in both groups. CYP2D6 phenotype was robustly correlated with ibogaine AUC0-t (r = 0.82) and Cmax (r = 0.77). Active moiety (ibogaine plus noribogaine) exposure was ∼2-fold higher in paroxetine-pretreated subjects. Single 20 mg ibogaine doses were safe and well tolerated in all subjects. The doubling of exposure to active moiety in subjects with reduced CYP2D6 activity suggests it may be prudent to genotype patients awaiting ibogaine treatment, and to at least halve the intended dose of ibogaine in CYP2D6 poor metabolizers.
Photochemical primary process of xanthene dyes. 7. Xanthene dyes as probes for the characterization of anionic micelles (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemical primary process of xanthene dyes. 7. Xanthene dyes as probes for the characterization of anionic micellesE. Fanghaenel, W. Ortman, K. Behrmann, S. Willscher, N. J. Turro, and I. R. GouldCite this: J. Phys. Chem. 1987, 91, 13, 3700–3703Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://pubs.acs.org/doi/10.1021/j100297a048https://doi.org/10.1021/j100297a048research-articleACS PublicationsRequest reuse permissionsArticle Views146Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Purification and characterization of a new recombinant factor VIII (N8) (2009)

A new recombinant factor VIII (FVIII), N8, has been produced in Chinese hamster ovary (CHO) cells. The molecule consists of a heavy chain of 88 kDa including a 21 amino acid residue truncated B-domain and a light chain of 79 kDa. The two chains are held together by non-covalent interactions. The four-step purification includes capture, affinity purification using a monoclonal recombinant antibody, anion exchange chromatography and gel filtration. The specific clotting activity of N8 was 8800-9800 IU mg(-1). Sequence and mass spectrometry analysis revealed two variants of the light chain, corresponding to two alternative N-terminal sequences also known from plasma FVIII. Two variants of the heavy chain are present in the purified product, namely with and without the B-domain linker attached. This linker is removed upon thrombin activation of N8 rendering an activated FVIII (FVIIIa) molecule similar to plasma FVIIIa. All six known tyrosine sulphations of FVIII were confirmed in N8. Two N-linked glycosylations are present in the A3 and C1 domain of the light chain and two in the A1 domain of the heavy chain. The majority of the N-linked glycans are sialylated bi-antennary structures. An O-glycosylation site is present in the B-domain linker region. This site was glycosylated with a doubly sialylated GalNAc-Gal structure in approximately 65% of the product. In conclusion, the present data show that N8 is a pure and well-characterized FVIII product with biochemical properties that equal other FVIII products.
Inhibin A Is an Endocrine Stimulator of Bone Mass and Strength (2006)

Gonadal function plays a major role in bone homeostasis. It is widely held that the skeletal consequences of hypogonadism are solely due to a loss of sex steroids; however, increases in bone turnover begin during perimenopause before decreases in serum estradiol levels. These data and our demonstration that inhibins acutely regulate bone cell differentiation in vitro led us to test whether inhibin A (InhA) regulates bone mass in vivo. Using a transgenic model of inducible human InhA expression, InhA increased total body bone mineral density, increased bone volume, and improved biomechanical properties at the proximal tibia in intact mice and also prevented the loss of BMD and bone volume and strength associated with gonadectomy at both the spine and proximal tibia. In addition, InhA increased mineral apposition rate, double-labeled surface, and serum osteocalcin levels in vivo and osteoblastogenesis ex vivo without affecting osteoclast number or activity. Together these results demonstrate novel stimulatory effects of InhA on the skeleton in vivo. These studies provide in vivo evidence demonstrating that gonadal factors other than sex steroids play an important role in regulating bone mass and strength and, combined with our previous clinical data, suggest that gonadal InhA may be a component of the normal endocrine repertoire that regulates bone quality in both the axial and appendicular skeleton.
The Translation Initiation Factor eIF3-p48 Subunit Is Encoded byint-6, a Site of Frequent Integration by the Mouse Mammary Tumor Virus Genome (1997)

Translation initiation factor eIF3 is a large, multisubunit protein complex that plays a central role in the pathway of initiation by promoting the binding of both methionyl-tRNAi and mRNA to the 40S ribosomal subunit. As part of a broad effort to elucidate the structure of eIF3, we have cloned and sequenced the human cDNA encoding the 48-kDa subunit, eIF3-p48. The recombinant protein comigrates with the authentic p48 subunit in purified eIF3 and coprecipitates with affinity-purified antibodies to the p170 subunit of eIF3. A search of the data base indicates that the mouse gene encoding eIF3-p48 had previously been identified and characterized by others as int-6. The int-6 gene is the site of frequent integration of mouse mammary tumor virus DNA into chromosomes, implicating the gene in the regulation of cell proliferation. In addition, it was shown elsewhere that the homologous human int-6 gene product binds to the human T-cell leukemia virus type I Tax protein, leading to the translocation of Int-6 to the cytoplasm. We discuss how the cytosolic function of eIF3-p48 (Int-6) in protein synthesis may account for oncogenesis caused by these two viruses.
A Consideration of Alternative Models for the Initiation of Translation in Eukaryotes (1992)

Although recent biochemical and genetic investigations have produced some insights into the mechanism of initiation of translation in eukaryotic cells, two aspects of the initiation process remain controversial. One unsettled issue concerns a variety of functions that have been proposed for mRNA binding proteins, including some initiation factors. The need to distinguish between specific and nonspecific binding of proteins to mRNA is discussed herein. The possibility that certain initiation factors might act as RNA helicases is evaluated along with other ideas about the functions of mRNA- and ATP-binding factors. A second controversial issue concerns the universality of the scanning mechanism for initiation of translation. According to the conventional scanning model, the initial contact between eukaryotic ribosomes and mRNA occurs exclusively at the 5' terminus of the message, which is usually capped. The existence of uncapped mRNAs among a few plant and animal viruses has prompted a vigorous search for other modes of initiation. An "internal initiation" mechanism, first proposed for picornaviruses, has received considerable attention. Although a large body of evidence has been adduced in support of such a mechanism, many of the experiments appear flawed or inconclusive. Some suggestions are given for improving experiments designed to test the internal initiation hypothesis.
Clinical importance of minimal residual disease in childhood acute lymphoblastic leukemia (2000)

By using rapid flow cytometric techniques capable of detecting one leukemic cell in 10(4) normal cells, we prospectively studied minimal residual disease (MRD) in 195 children with newly diagnosed acute lymphoblastic leukemia (ALL) in clinical remission. Bone marrow aspirates (n = 629) were collected at the end of remission induction therapy and at 3 intervals thereafter. Detectable MRD (ie, > or = 0.01% leukemic mononuclear cells) at each time point was associated with a higher relapse rate (P < .001); patients with high levels of MRD at the end of the induction phase (> or = 1%) or at week 14 of continuation therapy (> or = 0.1%) had a particularly poor outcome. The predictive strength of MRD remained significant even after adjusting for adverse presenting features, excluding patients at very high or very low risk of relapse from the analysis, and considering levels of peripheral blood lymphoblasts at day 7 and day 10 of induction therapy. The incidence of relapse among patients with MRD at the end of the induction phase was 68% +/- 16% (SE) if they remained with MRD through week 14 of continuation therapy, compared with 7% +/- 7% if MRD became undetectable (P = .035). The persistence of MRD until week 32 was highly predictive of relapse (all 4 MRD(+) patients relapsed vs 2 of the 8 who converted to undetectable MRD status; P = .021). Sequential monitoring of MRD by the method described here provides highly significant, independent prognostic information in children with ALL. Recent improvements in this flow cytometric assay have made it applicable to more than 90% of all new patients. (Blood. 2000;96:2691-2696)