gebhart/patrepeval huggingface dataset:
Asymmetry in the Structure of the ABC Transporter-Binding Protein Complex BtuCD-BtuF (2007)

BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.
Significance of interferon gamma in the prediction of successful therapy of common warts by intralesional injection of Candida antigen (2017)

Candida antigen is a promising, effective, and safe immunotherapeutic modality for common warts, and IFN-γ may serve as a good predictor of its therapeutic response.
Building Programmable Jigsaw Puzzles with RNA (2004)

One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a variety of complex nanoscopic fabrics with predefined periodic and aperiodic patterns and finite dimensions. This work emphasizes the modular and hierarchical characteristics of RNA by showing that small RNA structural motifs can code the precise topology of large molecular architectures. It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules.
Menin as a hub controlling mixed lineage leukemia (2012)

Mixed lineage leukemia (MLL) fusion protein (FP)-induced acute leukemia is highly aggressive and often refractory to therapy. Recent progress in the field has unraveled novel mechanisms and targets to combat this disease. Menin, a nuclear protein, interacts with wild-type (WT) MLL, MLL-FPs, and other partners such as the chromatin-associated protein LEDGF and the transcription factor C-Myb to promote leukemogenesis. The newly solved co-crystal structure illustrating the menin-MLL interaction, coupled with the role of menin in recruiting both WT MLL and MLL-FPs to target genes, highlights menin as a scaffold protein and a central hub controlling this type of leukemia. The menin/WT MLL/MLL-FP hub may also cooperate with several signaling pathways, including Wnt, GSK3, and bromodomain-containing Brd4-related pathways to sustain MLL-FP-induced leukemogenesis, revealing new therapeutic targets to improve the treatment of MLL-FP leukemias.
Investigation of a known tumor suppressor gene, p161NK4a, in human esophageal squamous cell carcinoma cell lines (2003)

Investigation of a known tumor suppressor gene, p161NK4a, in human esophageal squamous cell carcinoma cell lines by Kwong Fung Mei thesis 2003 xiv, 87 leaves : col. ill. ; 30 cm Esophageal squamous cell carcinoma (ESCC) is the eighth most…Read more ›
Prelamin A and lamin A appear to be dispensable in the nuclear lamina (2006)

Lamin A and lamin C, both products of Lmna, are key components of the nuclear lamina. In the mouse, a deficiency in both lamin A and lamin C leads to slow growth, muscle weakness, and death by 6 weeks of age. Fibroblasts deficient in lamins A and C contain misshapen and structurally weakened nuclei, and emerin is mislocalized away from the nuclear envelope. The physiologic rationale for the existence of the 2 different Lmna products lamin A and lamin C is unclear, although several reports have suggested that lamin A may have particularly important functions, for example in the targeting of emerin and lamin C to the nuclear envelope. Here we report the development of lamin C-only mice (Lmna(LCO/LCO)), which produce lamin C but no lamin A or prelamin A (the precursor to lamin A). Lmna(LCO/LCO) mice were entirely healthy, and Lmna(LCO/LCO) cells displayed normal emerin targeting and exhibited only very minimal alterations in nuclear shape and nuclear deformability. Thus, at least in the mouse, prelamin A and lamin A appear to be dispensable. Nevertheless, an accumulation of farnesyl-prelamin A (as occurs with a deficiency in the prelamin A processing enzyme Zmpste24) caused dramatically misshapen nuclei and progeria-like disease phenotypes. The apparent dispensability of prelamin A suggested that lamin A-related progeroid syndromes might be treated with impunity by reducing prelamin A synthesis. Remarkably, the presence of a single Lmna(LCO) allele eliminated the nuclear shape abnormalities and progeria-like disease phenotypes in Zmpste24-/- mice. Moreover, treating Zmpste24-/- cells with a prelamin A-specific antisense oligonucleotide reduced prelamin A levels and significantly reduced the frequency of misshapen nuclei. These studies suggest a new therapeutic strategy for treating progeria and other lamin A diseases.
Weighted Naive Bayesian Classifier (2007)

The naive Bayesian (NB) classifier is one of the simple yet powerful classification methods. One of the important problems in NB (and many other classifiers) is that it is built using crisp classes assigned to the training data. In this paper, we propose an improvement over the NB classifier by employing emerging patterns (EPs) to weight the training instances. That is, we generalize the NB classifier so that it can take into account weighted classes assigned to the training data. EPs are those itemsets whose frequencies in one class are significantly higher than their frequencies in the other classes. Our experiments prove that our proposed method is superior to the original NB classifier.
Spatial Organization of Transcription Elongation Complex in Escherichia coli (1998)

During RNA synthesis in the ternary elongation complex, RNA polymerase enzyme holds nucleic acids in three contiguous sites: the double-stranded DNA-binding site (DBS) ahead of the transcription bubble, the RNA-DNA heteroduplex-binding site (HBS), and the RNA-binding site (RBS) upstream of HBS. Photochemical cross-linking allowed mapping of the DNA and RNA contacts to specific positions on the amino acid sequence. Unexpectedly, the same protein regions were found to participate in both DBS and RBS. Thus, DNA entry and RNA exit occur close together in the RNA polymerase molecule, suggesting that the three sites constitute a single unit. The results explain how RNA in the integrated unit RBS-HBS-DBS may stabilize the ternary complex, whereas a hairpin in RNA result in its dissociation.
Dynamics of Protamine 1 Binding to Single DNA Molecules (2003)

Protamine molecules bind to and condense DNA in the sperm of most vertebrates, packaging the sperm genome in an inactive state until it can be reactivated following fertilization. By using methods that enable the analysis of protamine binding to individual DNA molecules, we have monitored the kinetics of DNA condensation and decondensation by protamine 1 (P1) and synthetic peptides corresponding to specific segments of the bull P1 DNA binding domain. Our results show that the number of clustered arginine residues present in the DNA binding domain is the most important factor affecting the condensation and stability of the DNA-protamine complex prior to the formation of inter-protamine disulfide cross-links. The high affinity of P1 for DNA is achieved by the coordinated binding of three anchoring domains, which together in bull P1 contain 19 Arg residues. The single DNA molecule experiments show that sequences containing two or more anchoring domains have an off-rate that is at least 3 orders of magnitude slower than those containing a single domain. The use of Arg, rather than Lys residues, and the inclusion of Tyr or Phe residues in the hinge regions between anchoring domains provide additional stability to the complex.
Real-time human pose recognition in parts from single depth images (2013)

We propose a new method to quickly and accurately predict human pose ---the 3D positions of body joints---from a single depth image, without depending on information from preceding frames. Our approach is strongly rooted in current object recognition strategies. By designing an intermediate representation in terms of body parts, the difficult pose estimation problem is transformed into a simpler per-pixel classification problem, for which efficient machine learning techniques exist. By using computer graphics to synthesize a very large dataset of training image pairs, one can train a classifier that estimates body part labels from test images invariant to pose, body shape, clothing, and other irrelevances. Finally, we generate confidence-scored 3D proposals of several body joints by reprojecting the classification result and finding local modes. The system runs in under 5ms on the Xbox 360. Our evaluation shows high accuracy on both synthetic and real test sets, and investigates the effect of several training parameters. We achieve state-of-the-art accuracy in our comparison with related work and demonstrate improved generalization over exact whole-skeleton nearest neighbor matching.
Covalent structure of a human γG-immunoglobulin. VII. Amino acid sequence of heavy-chain cyanogen bromide fragments H1-H4 (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCovalent structure of a human γG-immunoglobulin. VII. Amino acid sequence of heavy-chain cyanogen bromide fragments H1-H4Bruce A. Cunningham, Urs S. Rutishauser, W. Einar Gall, Paul D. Gottlieb, Myron J. Waxdal, and Gerald M. EdelmanCite this: Biochemistry 1970, 9, 16, 3161–3170Publication Date (Print):August 4, 1970Publication History Published online1 May 2002Published inissue 4 August 1970https://pubs.acs.org/doi/10.1021/bi00818a008https://doi.org/10.1021/bi00818a008research-articleACS PublicationsRequest reuse permissionsArticle Views77Altmetric-Citations20LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Mutation and polymorphism of the prion protein gene in Libyan Jews with Creutzfeldt-Jakob disease (CJD). (1993)

The inherited prion diseases are neurodegenerative disorders which are not only genetic but also transmissible. More than a dozen mutations in the prion protein gene that result in nonconservative amino acid substitutions segregate with the inherited prion diseases including familial Creutzfeldt-Jakob disease (CJD). In Israel, the incidence of CJD is about 1 case/10(4) Libyan Jews. A Lys200 substitution segregates with CJD and is reported here to be genetically linked to CJD with a lod score of > 4.8. Some healthy elderly Lys200 carriers > age 65 years were identified, suggesting the possibility of incomplete penetrance. In contrast, no linkage was found between the development of familial CJD and a polymorphism encoding either Met129 or Val129. All Libyan Jewish CJD patients with the Lys200 mutation encode a Met129 on the mutant allele. Homozygosity for Met129 did not correlate with age at disease onset or the duration of illness. The frequency of the Met129 allele was higher in the affected pedigrees than in a control population of Libyan Jews. The frequency of the Met129 and Val129 alleles in the control Libyan population was similar to that found in the general Caucasian population. The identification of three Libyan Jews homozygous for the Lys200 mutation suggests frequent intrafamilial marriages, a custom documented by genealogical investigations.
A theoretical study on laser control of a molecular nonadiabatic process by ultrashort chirped laser pulses (1998)

We have theoretically studied the usefulness of ultrashort chirped laser pulses for laser control of photodissociation dynamics with a one-dimensional model system involving a potential well in the excited electronic state. The molecular system we treat in this paper entails three electronic states, a ground electronic state, and two excited electronic states. The ground electronic state is radiatively dipole-coupled with the lower of the two excited electronic states, while the two excited electronic states are themselves connected by diabatic coupling potential. Previously, we found a single linearly chirped ultrashort (in the order of fs) laser pulse can be employed to control photodissociation dynamics according to the sign of the chirp rate: A positively chirped pulse traps the molecule in the excited state potential well, while a negatively chirped pulse photodissociates the molecule rapidly. In the present paper we take into consideration the influence of the strength of the diabatic coupling and the reduced mass of the molecular system and show such a selectivity works best when the diabatic coupling is moderate and the molecular system is light. We explain these phenomena by a state selective excitation in vibrational states under the condition of adiabatic rapid passage (ARP) population transfer. We solve the integrodifferential equation of the molecular system involving the vibrational states explicitly, which is a quite different approach from that for the atomic case.
Sequential phosphorylation of tau protein by cAMP‐dependent protein kinase and SAPK4/p38δ or JNK2 in the presence of heparin generates the AT100 epitope (2006)

Microtubule-associated protein tau in a hyperphosphorylated state is the major component of the filamentous lesions that define a number of neurodegenerative diseases, including Alzheimer's disease, progressive supranuclear palsy, corticobasal degeneration, Pick's disease, argyrophilic grain disease and frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). Previous work has established that the phosphorylation-dependent anti-tau antibody AT100 is a specific marker for filamentous tau in adult human brain. Here we have identified protein kinases that generate the AT100 epitope in vitro and have used them, in conjunction with site-directed mutagenesis of tau, to map the epitope. We show that the sequential phosphorylation of recombinant tau by cAMP-dependent protein kinase (PKA) and the stress-activated protein kinases SAPK4/p38delta or JNK2 generated the AT100 epitope and that this required phosphorylation of T212, S214 and T217. Tau protein from newborn, but not adult, mouse brain was weakly labelled by AT100. Phosphorylation by PKA and SAPK4/p38delta abolished the ability of tau to promote microtubule assembly, but failed to influence significantly the heparin-induced assembly of tau into filaments.
메타세콰이어, 카담, 물푸레나무 세포내강의 액체이동 (2018)

A study was carried out to observe the 1% aqueous safranine solution flow speed in longitudinal and radial directions of softwood Metasequoia glyptostroboides, diffuse-porous wood Anthocephalus cadamba and ring-porouswood Fraxinus rhynchophylla. In radial direction, ray cells and in longitudinal direction, tracheids, vessel and wood fiber were considered for the measurement of liquid penetration speed at less than 12% moisture contents (MC). The length, lumen diameter, pit diameter, end wall pit diameter and the numbers of end wall pits determined for the flow rate. The liquid flow in the those cells was captured via video and the capillary flow rate in the ones were measured. Vessel in hardwood species and tracheids in softwood was found to facilitate prime role in longitudinal penetration. Anatomical features like the length and diameter, end-wall pit numbers of ray parenchyma were found also responsible fluid flow differences. On the other hand, vessel and fiber structure affected the longitudinal flow of liquids. Therefore, the average liquid penetration depth in longitudinal tracheids of Metasequoia glyptostroboides was found the highest among all cells considered in Anthocephalus cadamba and Fraxinus rhynchophylla In radial direction, ray parenchyma of Metasequoia glyptostroboides was found the highest depth and the one of Fraxinus rhynchophylla was the lowest. The solution was penetrated lowest depth in the wood fiber of Fraxinus rhynchophylla. The large vessel of Fraxinus rhynchophylla was found the lowest depth among the vessels. The solutin was penetrated to the wood fiber of Anthocephalus cadamba higher than the one of Fraxinus rhynchophylla.
Odorant and pheromone binding by aphrodisin, a hamster aphrodisiac protein (2000)

Aphrodisin is a soluble glycoprotein of hamster vaginal discharges, which stimulates male copulatory behavior. Natural aphrodisin was purified and its post-translational modifications characterized by MALDI-MS peptide mapping. To evaluate its ability to bind small volatile ligands, the aphrodisiac protein was expressed in the yeast Pichia pastoris as two major isoforms differing in their glycosylation degree, but close in conformation to the natural protein. Dimeric recombinant aphrodisins were equally able to efficiently bind odors (2-isobutyl-3-methoxypyrazine and methyl thiobutyrate) and a pheromone (dimethyl disulfide), suggesting that they could act as pheromone carriers instead of, or in addition to, direct vomeronasal neuron receptor activators.
Sol−Gel Preparation and Photoluminescence of Size Controlled Germanium Nanoparticles Embedded in a SiO2 Matrix (2003)

Germanium nanoparticles of different sizes in silica glasses were prepared via a sol−gel method, using Cl3−Ge−C2H4−COOH and Si(OC2H5)4 as the starting materials. The size of the germanium nanoparticles decreases as the heat-treatment time in a H2 gas atmosphere increases, and, thus, the optical absorption edge shifts to higher energies. Silica gel glasses doped with germanium nanoparticles showed a strong room-temperature photoluminescence, with peaks at 570, 605, 676, and 730 nm. The peak position of the photoluminescence spectrum scarcely depends on the heat-treatment time. However, the photoluminescence intensity increases sharply as the heat-treatment time is reduced. The photoluminescence arises from germanium clusters <1−2 nm in diameter with a molecular character, instead of from nanocrystalline germanium with the diamond structure.
Prevalence of dental caries among 5-13-year-old children of Mangalore city (2005)

A study of prevalence of dental caries was undertaken in 5-13-year-old children from Mangalore city. A total of 524 children were examined. The sample consisted of 193, 160, and 171 children in the 5-7, 8-10 and 11-13 years of age group, respectively. Dental caries was examined visually and observations were recorded. Silness and L phie plaque index, L phie and Silness gingival index were used to record the periodontal status. The prevalence of dental caries was highest in 5-7-year-age group compared to 8-10 years and 11-13 years age groups. The increasing prevalence of dental caries needs dental health programmes, which target the specific segments of the population.
Synthesis of “Clean” and Well-Dispersive Pd Nanoparticles with Excellent Electrocatalytic Property on Graphene Oxide (2011)

Ultrafine Pd nanoparticles monodispersed on graphene oxide (GO) surfaces were successfully prepared by the redox reaction between PdCl(4)(2-) and GO. The as-made catalyst is very "clean" as a result of the surfactant-free formation process, allowing it to express high electrocatalytic ability in formic acid and ethanol oxidation relative to a commercial Pd/C catalyst. This simple and straightforward method is of significance for the facile preparation metal nanocatalysts with high catalytic activity on proper supporting materials.
Role for FGFR2IIIb-mediated signals in controlling pancreatic endocrine progenitor cell proliferation (2002)

Pancreatic development is a classic example of epithelium-mesenchyme interaction. During embryonic life, signals from the mesenchyme control the proliferation of precursor cells within the pancreatic epithelium and their differentiation into endocrine or acinar cells. It has been shown that signals from the mesenchyme activate epithelial cell proliferation but repress development of the pancreatic epithelium into endocrine cells. Here, experiments with specific inhibitors established that mesenchymal effects on epithelial cell development depended on the mitogen-activated protein kinase pathway. Then we demonstrated that these effects of the mesenchyme were mimicked by fibroblast growth factor 7 (FGF7), a specific ligand of FGFR2IIIb, which is a tyrosine kinase receptor of the FGF-receptor family. When pancreatic epithelium expressing FGFR2IIIb was grown with FGF7, epithelial cell growth occurred in a concentration-dependent manner, whereas endocrine tissue development was repressed. The epithelial cells that proliferated in response to FGF7 were endocrine pancreatic precursor cells, as shown by their differentiation en masse into endocrine cells on FGF7 removal. Thus, efficient propagation of pancreatic progenitor cells can be achieved in vitro by exposure to FGF7, which does not affect their ability to differentiate en masse into endocrine cells on FGF7 removal.
Total Synthesis and Evaluation of iso-Duocarmycin SA and iso-Yatakemycin (2008)

The total synthesis and evaluation of iso-duocarmycin SA (5) and iso-yatakemycin (6), representing key analogues of the corresponding natural products incorporating an isomeric alkylation subunit, are detailed. This pyrrole isomer of the natural alkylation subunit displayed an enhanced reaction regioselectivity and a 2-fold diminished stability. Although still exceptionally potent, the iso-duocarmycin SA derivatives and natural product analogues exhibited a corresponding approximate 3-5-fold reduction in cytotoxic activity [L1210 IC(50) for (+)-iso-duocarmycin SA = 50 pM and for (+)-iso-yatakemycin = 15 pM] consistent with their placement on a parabolic relationship correlating activity with reactivity. The DNA alkylation selectivity of the resulting key natural product analogues was unaltered by the structure modification in spite of the minor-groove presentation of a potential H-bond donor. Additionally, a unique ortho-spirocyclization with such derivatives was explored via the preparation, characterization, and evaluation of 34 that is incapable of the more conventional para-spirocyclization. Although 34 proved sufficiently stable for isolation and characterization, it displayed little stability in protic solvents (t(1/2) = 0.19 h at pH 3, t(1/2) = 0.20 h at pH 7), a pH-independent (H(+) independent) solvolysis rate profile at pH 3/4-7, and a much reduced cytotoxic potency, but a DNA alkylation selectivity and efficiency comparable to those of duocarmycin SA and iso-duocarmycin SA. The implications of these observations on the source of the DNA alkylation selectivity and catalysis for this class of natural products are discussed.