gebhart/patrepeval huggingface dataset:
Double-Lanthanide-Binding Tags:  Design, Photophysical Properties, and NMR Applications (2007)

Lanthanide-binding tags (LBTs) are peptide sequences of up to 20 encoded amino acids that tightly and selectively complex lanthanide ions and can sensitize terbium (Tb3+) luminescence. On the basis of these properties, it was predicted that increasing the number of bound lanthanides would improve the capabilities of these tags. Therefore, using a structurally well-characterized single-LBT sequence as a starting point, a "double-LBT" (dLBT), which concatenates two lanthanide-binding motifs, was designed. Herein we report the generation of dLBT peptides and luminescence and NMR studies on a dLBT-tagged ubiquitin fusion protein. These lanthanide-bound constructs are shown to be improved luminescent tags with avid lanthanide binding and up to 3-fold greater luminescence intensity. NMR experiments were conducted on the ubiquitin construct, wherein bound paramagnetic lanthanides were used as alignment-inducing agents to gain residual dipolar couplings, which are valuable restraints for macromolecular structure determination. Together, these results indicate that dLBTs will be valuable chemical tools for biophysical applications leading to new approaches for studying the structure, function, and dynamics of proteins.
Regulation of the concentration of pre.beta. high-density lipoprotein in normal plasma by cell membranes and lecithin-cholesterol acyltransferase activity (1992)

A minor fraction of plasma high-density lipoprotein (pre beta-1 HDL) has been shown to promote cholesterol efflux from peripheral cell membranes [Castro, G. R., & Fielding, C. J. (1988) Biochemistry 27, 25-29]. When isolated native plasma is incubated at 37 degrees C, this fraction is specifically decreased. On the other hand, the level of plasma pre beta-1 HDL is fully protected in the presence of even very low levels of fibroblasts, vascular smooth muscle cells, or macrophages. Blood cells were completely inactive in maintaining plasma pre beta-1 HDL levels in the absence of peripheral cells, even at the relatively high levels present in whole blood. The loss of pre beta-1 observed in isolated plasma was dependent upon lecithin-cholesterol acyltransferase (LCAT) activity. These data suggest that reverse cholesterol transport catalyzed by pre beta-1 HDL, and subsequent LCAT-mediated cholesterol esterification, is directly dependent upon the interaction between this HDL species and competent peripheral cells.
Simulation study of the glass transition temperature in poly(methyl methacrylate) (2002)

The glass transition in syndiotactic poly (methyl methacrylate) has been studied through atomistic molecular dynamics simulations performed at temperatures in the range from 297 K to 684 K. The mean squared deviations of atoms, monomers, and molecules from their initial positions were analyzed by means of a technique that separates the effects of diffusive motion from the underlying vibrational motion. The diffusive motion shows a novel power-law variation with time, with an exponent that varies continuously from 0.5 below the glass transition temperature T(g) to 1 at high temperatures. The self part of the van Hove correlation functions for both hydrogen atoms and monomers shows structural arrest at the lowest temperature studied. A second peak in the atomic van Hove correlation is attributed to rotation of the CH3 group.
Micro-doppler effect in radar: phenomenon, model, and simulation study (2006)

When, in addition to the constant Doppler frequency shift induced by the bulk motion of a radar target, the target or any structure on the target undergoes micro-motion dynamics, such as mechanical vibrations or rotations, the micro-motion dynamics induce Doppler modulations on the returned signal, referred to as the micro-Doppler effect. We introduce the micro-Doppler phenomenon in radar, develop a model of Doppler modulations, derive formulas of micro-Doppler induced by targets with vibration, rotation, tumbling and coning motions, and verify them by simulation studies, analyze time-varying micro-Doppler features using high-resolution time-frequency transforms, and demonstrate the micro-Doppler effect observed in real radar data.
Vector–Hexamer PCR Isolation of All Insert Ends from a YAC Contig of the MouseIgh Locus (1998)

We have developed a simple PCR strategy, termed vector–hexamer PCR, that is unique in its ability to easily recover every insert end from large insert clones in YAC and BAC vectors. We used this method to amplify and isolate all insert ends from a YAC contig covering the mouse Igh locus. Seventy-seven ends were amplified and sequenced from 36 YAC clones from four libraries in the pYAC4 vector. Unexpectedly, 40% of the insert ends of these YACs were LINE1 repeats. Nonrepetitive ends were suitable for use as probes on Southern blots of digested YACs to identify overlaps and construct a contig. The same strategy was used successfully to amplify insert ends from YACs in the pRML vector from the Whitehead Institute/MIT-820 mouse YAC library and from BACs in pBeloBAC11. The simplicity of this technique and its ability to isolate every end from large insert clones are of great utility in genomic investigation. [The nucleotide sequence data reported in this paper are accessible in GenBank under accession nos. B07512 – B07598 .]
The Family of Connexin Genes (2008)

The connexin genes code for a family of proteins that form intercellular gap junction channels. There are 21 connexin genes in the human genome and 20 in the mouse genome. Most connexin genes contain the protein coding region in a single exon. Variations in promoter usage and splicing of 5’-untranslated exons contribute to regulation of connexin expression. Connexin gene promoters contain binding sites for both cell type–independent and cell type–specific transcription factors that regulate connexin transcription and intercellular communication in many different cell types. Connexin transcription is also influenced by epigenetic mechanisms such as DNA methylation and histone acetylation. RNA stability and translation are influenced by binding of microRNAs and by utilization of internal ribosome entry sites. Mutations in connexin genes have been identified as associated with a variety of inherited diseases. These mutations can cause alterations in intercellular communication by affecting various processes of the connexin life cycle or channel function. The recent progress in connexin genetics has had a significant impact in elucidating the mechanisms leading to mutant connexin-associated diseases. These advances will provide the basis for future therapeutic interventions.
Model studies related to the cofactor of oxomolybdoenzymes. Part 4. Reduction of the pyrazine ring in quinoxalines and pteridines (1992)

Reduction of quinoxalines and pteridines with sodium borohydride or sodium cyanoborohydride in the presence of benzyl chloroformate gives N-benzyloxycarbonyl- or N,N′-bisbenzyloxycarbonyl tetrahydro derivatives.
Stroke Treatment Economic Model (STEM) (1999)

Linking functional recovery at the end of short-term treatment with patients' treatment and residential locations allows this model to estimate the long-term economic impact of stroke interventions. Using patient location instead of the more common natural history as the model foundation allows quantification of the long-term impact to become data driven and hence increases confidence in the results.
Channel formation properties of synthetic pardaxin and analogues (1990)

Six analogues of teh 33-residue shark repellent neurotoxin pardaxin were synthesized by the solid phase method: [Ala13]pardaxin, [Gly14,Gly15]pardaxin, des[1----9]pardaxin, [N1-succinamido]pardaxin, C33-dihydroxyethylamido]pardaxin, and C33-[diaminoethylamido]pardaxin. The spectroscopic and functional characterizations of the analogues are described. The peptides were characterized spectroscopically by circular dichroism (CD) before and after binding to soybean vesicles. They were characterized functionally by measuring their potential to evoke the dissipation of diffusion potential and calcein release from sonicated unilamellar soybean liposomes, by determining their ability to create single channels in planar bilayers, and by measuring their cytolytic activity on human erythrocytes. The behavior of the analogues modified at the C terminus is similar to that of pardaxin. [N'-succinamido]Pardaxin, however, reveals an increase in alpha-helicity both alone and in the presence of liposomes. It has the same potency as pardaxin to dissipate diffusion potential, to evoke calcein release and to produce single channels in lipid bilayers, but at a slower rate than that of pardaxin. It has more than 70-fold less cytolytic activity than pardaxin. [Ala13] Pardaxin has twice the alpha-helical content than pardaxin, both alone and in the presence of vesicles, yet it has less effect on the diffusion potential and calcein release, and it does not have cytolytic activity on human erythrocytes. Both [Gly14,Gly15]pardaxin and des[1----9]pardaxin are much less potent than pardaxin in all effects. However des[1----9]pardaxin exhibits a slight change in alpha-helicity upon binding to vesicles, whereas [Gly14,Gly15]pardaxin does not. The results support a model in which pardaxin is composed of two putative alpha-helices separated by proline. The N-terminal alpha-helix is important for the insertion of the peptide to the lipid bilayer, and the C-terminal amphiphilic alpha-helix is the ion channel lining segment of pardaxin.
Room Temperature, High-Yield Synthesis of Multiple Shapes of Gold Nanoparticles in Aqueous Solution (2004)

A seed-mediated growth method was used to control the morphology and dimensions of Au nanocrystals by the manipulation of the experimental parameters in aqueous solution at room temperature. This chemical route produces various structural architectures with rod-, rectangle-, hexagon-, cube-, triangle-, and starlike profiles and branched (such as bi-, tri-, tetra-, and multipod) Au nanocrystals of various dimensions in high yield in the presence of a single surfactant, cetyltrimethylammonium bromide.
Glucagon: Role in the Hyperglycemia of Diabetes Mellitus (1975)

Glucagon suppression by somatostatin reduces or abolishes hyperglycemia in dogs made insulin-deficient by somatostatin, alloxan, or total pancreatectomy. This suggests that the development of severe diabetic hyperglycemia requires the presence of glucagon, whether secreted by pancreatic or newly identified gastrointestinal A cells, as well as a lack of insulin. Glucagon suppression could improve therapeutic glucoregulation in diabetes.
Identification of an Inhibitor of hsc70-mediated Protein Translocation and ATP Hydrolysis (2001)

Members of the hsc70 family of molecular chaperones are critical players in the folding and quality control of cellular proteins. Because several human diseases arise from defects in protein folding, the activity of hsc70 chaperones is a potential therapeutic target for these disorders. By using a known hsc70 modulator, 15-deoxyspergualin, as a seed, we identified a novel inhibitor of hsc70 activity. This compound, R/1, inhibits the endogenous and DnaJ-stimulated ATPase activity of hsc70 by 48 and 51%, respectively, and blocks the hsc70-mediated translocation of a preprotein into yeast endoplasmic reticulum-derived microsomal vesicles. Biochemical studies demonstrate that R/1 most likely exerts these effects by altering the oligomeric state of hsc70.
A novel sub–1 V high speed circuit design technique in partially depleted SOI–CMOS technology with ultra low–leakage power (2002)

As supply voltage is scaled to below 1 V, leakage power becomes significant in CMOS ICs. This paper proposes a new circuit style in PD-SOI technology to reduce standby power in the sub-1 V regime by over three orders of magnitude while maintaining circuit speed and with minimal overhead. It makes use of dual-V TH transistors to suppress leakage current in standby mode but uses a simple positive body biasing technique in active mode to reduce VTH and boost circuit speed. This scheme can be applied to both static and dynamic logic circuits in a variety of ways and is illustrated in this paper. Simulation results obtained using process parameters from an IBM 0.13 µm PD-SOI technology show considerable improvement over previously proposed methods as supply voltage is scaled to 0.5 V.
什么是科学说明 萨尔蒙S-R说明模型初探 (1988)

科学说明是科学的最重要特征之一,因而也是科学哲学的重要课题。长期以来,科学哲学家提出了形形色色的科学说明理论,彼此之间展开了热烈而持久的争论。这种争论在近十余年来似乎变得越来越尖锐,分歧也越来越大,这部分地是由于科学哲学家开始认识到科学说明本身的极端复杂性,部分地则是因为说明研究者各自的哲学立场和倾向大不相同。我们刊登选译的几位科学哲学家有代表性的对科学说明的不同看法。我们希望通过这组文章能够勾画出这场争论的轮廓,有助于国内对这方面问题的研究。本组文章主要是在武汉大学江天骥教授指导下选编的,陆健体负责具体选编工作,责任编辑鲁旭东。
Targeting primary human Ph(+) B-cell precursor leukemia-engrafted SCID mice using radiolabeled anti-CD19 monoclonal antibodies. (2003)

The radiolabeled anti-CD19 antibody showed specific targeting and rapid internalization in ALL cell-engrafted SCID mice and may also be used for selective intracellular delivery of cytotoxic radionuclides with beta-, Auger, or alpha-emissions.
Fusion to Listeriolysin O and Delivery by Listeria monocytogenes Enhances the Immunogenicity of HER-2/neu and Reveals Subdominant Epitopes in the FVB/N Mouse (2005)

Five overlapping fragments of rat HER-2/neu have been expressed in recombinant Listeria monocytogenes. Each fragment of HER-2/neu is secreted as a fusion protein with a truncated, nonhemolytic form of listeriolysin O (LLO). Lm-LLO-EC1, Lm-LLO-EC2, and Lm-LLO-EC3 overlap the extracellular domain of HER-2/neu, whereas Lm-LLO-IC1 and Lm-LLO-IC2 span the intracellular domain. All five strains controlled the growth of established NT-2 tumors, a rat HER-2/neu-expressing tumor line derived from a spontaneously arising mammary tumor in a FVB/N HER-2/neu-transgenic mouse. The antitumor effect of each of these vaccine constructs was abrogated by the in vivo depletion of CD8(+) T cells, although only one known epitope has been defined previously and is present in Lm-LLO-EC2. Anti-HER-2/neu CTL responses were generated by each of the rLm vaccine constructs. With the use of a panel of 3T3 cell lines expressing overlapping fragments of HER-2/neu, regions of HER-2/neu with potential CD8(+) T cell epitopes have been defined. DNA vaccines expressing either a fragment or full-length HER-2/neu were constructed in LLO-fused and non-LLO-fused forms. CTL analysis of the DNA vaccines revealed a broadening in the regions of HER-2/neu recognizable as targets when the target Ag is fused to LLO. These studies show the efficacy of L. monocytogenes-based HER-2/neu vaccines in a murine model of breast cancer and also that the immunogenicity of self-Ags can be increased by fusion to LLO and delivery by L. monocytogenes revealing subdominant epitopes.
Real-time posture and activity recognition (2003)

We propose an algorithm for human posture and activity recognition for uncompressed and compressed (MPEG) video inputs. A real-time compression domain technique is developed to recognize different postures such as standing, pointing left/right, opening arms, etc. by using an eigenspace representation of human silhouettes obtained from AC-DCT coefficients. The system stores frames with specific postures and finds the global activity of the human body in the compressed domain. In the uncompressed domain, this information is used as an input for the activity/gesture recognition algorithm. The first part of our approach is invariant to changes in intensity, color and textures and has the advantage of using the available data in the standard compression algorithms. The second part of the system can recognize activities in a set of frames starting with a recognized posture that is classified as a reference movement by the system. A prototype system has been developed with two camera nodes; each consists of a standard camera and a video processing board.
Short-segment Pedicle Instrumentation (1996)

Supplemental offset hooks significantly increase construct stiffness without sacrificing principles of short-segment pedicle instrumentation, and absorb some part of the construct strain, thereby reducing pedicle screw bending moments and the likelihood of postyield deformation and clinical failure.
Generalization of Multi-Channel Linear Prediction Methods for Blind MIMO Impulse Response Shortening (2012)

The performance of many microphone array processing techniques deteriorates in the presence of reverberation. To provide a widely applicable solution to this longstanding problem, this paper generalizes existing dereverberation methods using subband-domain multi-channel linear prediction filters so that the resultant generalized algorithm can blindly shorten a multiple-input multiple-output (MIMO) room impulse response between a set of unknown number of sources and a microphone array. Unlike existing dereverberation methods, the presented algorithm is developed without assuming specific acoustic conditions, and provides a firm theoretical underpinning for the applicability of the subband-domain multi-channel linear prediction methods. The generalization is achieved by using a new cost function for estimating the prediction filter and an efficient optimization algorithm. The proposed generalized algorithm makes it easier to understand the common background underlying different dereverberation methods and future technical development. Indeed, this paper also derives two alternative dereverberation methods from the proposed algorithm, which are advantageous in terms of computational complexity. Experimental results are reported, showing that the proposed generalized algorithm effectively achieves blind MIMO impulse response shortening especially in a mid-to-high frequency range.
Ligament Tissue Engineering Using Synthetic Biodegradable Fiber Scaffolds (1999)

Tissue engineering offers the possibility of replacing damaged human ligaments with engineered ligament tissues. Hence, we attempted to culture in vitro ligament tissues by seeding human anterior cruciate ligament (ACL) and medial collateral ligament (MCL) cells onto synthetic biodegradable polymer fiber scaffolds. The ACL and MCL cells readily attached to the scaffold fibers. These cells and their secreted matrix soon surrounded the scaffold fibers and bridged the gaps in between. Beginning at 2 weeks, portions of the scaffolds were completely filled with tissue matrix. By 5 weeks, the scaffolds became single bundles of tissue. Thus the cell/fiber system appears to be a viable system for culturing ligament tissues. Additionally, cell proliferation under mechanical and biochemical stimuli was studied for up to 4 days. Whereas mechanical stimulus and transforming growth factor enhanced proliferation, inflammatory agents (lipopolysaccharide and complement C5a) had a negative effect. This work can thus contribute to a sound strategy for culturing replacement ligament tissues in vitro.
Clinical Immunity to Plasmodium falciparum Malaria Is Associated with Serum Antibodies to the 19-kDa C-Terminal Fragment of the Merozoite Surface Antigen, PfMSP-l (1996)

The development of an effective malaria vaccine depends upon identification of antigens that are targets of protective immune responses. An immunoepidemiologic approach has been used to investigate the relationship between antibody responses to a defined region of the major merozoite surface protein of Plasmodium falciparum (PfMSP-1 19) and resistance to clinical malaria in 2 populations of children from West Africa. After allowing for the confounding effects of age, antibodies to PfMSP-1 19 were shown the provide 40% protection against clinical malaria in children in Sierra Leone. In Gambian children, antibodies to one of the epidermal growth factor-like motifs of PfMSP-1 19 were strongly associated with resistance to both clinical malaria and high levels of parasitemia.
The single-stranded DNA-binding protein of Escherichia coli (1990)

The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.
cORF and RcRE, the Rev/Rex and RRE/RxRE Homologues of the Human Endogenous Retrovirus Family HTDV/HERV-K (1999)

cORF, a protein encoded by the human endogenous retrovirus family HTDV/HERV-K, contains amino acid motifs which resemble the nuclear import and export signals of the viral regulatory proteins Rev (human immunodeficiency virus) and Rex (human T-cell leukemia virus [HTLV]). In this study, we demonstrated that cORF indeed has a Rev-like function and mapped the cORF-responsive RNA element to a sequence in the 3' long terminal repeat, a localization similar to RxRE, the responsive element in HTLV type 1. Accordingly, we have given the element the designation RcRE. cORF and RcRE stabilize unspliced and incompletely spliced viral transcripts and enhance their nuclear export via the CRM1 export pathway. So far, HTDV/HERV-K is the only endogenous retrovirus family with a complex regulation at the posttranscriptional level. It may be regarded as an intermediate in the evolution from simple to complex retroviruses.
Induction of the cytokine signal regulator SOCS3/CIS3 as a therapeutic strategy for treating inflammatory arthritis (2001)

Immune and inflammatory systems are controlled by multiple cytokines, including ILs and INFs. These cytokines exert their biological functions through Janus tyrosine kinases and STAT transcription factors. One such cytokine, IL-6, has been proposed to contribute to the development of rheumatoid arthritis (RA). We found that STAT3 was strongly tyrosine phosphorylated in synovial tissue of RA patients, but not those with osteoarthritis. Blockade of the IL-6-gp130-JAK-STAT3-signaling pathway might therefore be beneficial in the treatment of RA. We show here that the mRNA for the endogenous cytokine signaling repressor CIS3/SOCS3 is abundantly expressed in RA patients. To determine whether CIS3 is effective in treating experimental arthritis, a recombinant adenovirus carrying the CIS3 cDNA was injected periarticularly into the ankle joints of mice with antigen-induced arthritis or collagen-induced arthritis (CIA). Periarticular injection of CIS3 adenovirus drastically reduced the severity of arthritis and joint swelling compared with control groups. CIS3 was more effective than a dominant-negative form of STAT3 in the CIA model. Thus, induction of CIS3 could represent a new approach for effective treatment of RA.