gebhart/patrepeval huggingface dataset:
Intersubunit circular permutation of human hemoglobin (2002)

For many years, human hemoglobin (Hb) isolated from erythrocytes has been investigated as a potential oxygen delivery therapeutic. Advantages with respect to the need for blood typing were balanced with various undesirable properties of cell-free Hb, including cost, overall oxygen affinity, alterations in cooperativity, and ready dissociation into toxic dimeric species. The use of total gene synthesis has resulted in very high levels of functional human Hb expression in Escherichia coli, but there remains a desire for effecting the crosslinking of the hemoglobin tetramer and providing for ready means for increasing the globular molecular weight. In this communication, we report a novel method for linking alpha chains. By circularly permuting one alpha sequence, the second alpha chain in the Hb tetramer can be linked with glycine residues to form 2 bridges across the central cavity. The second alpha chain thus presents its amino and carboxyl termini on a solvent exposed surface, providing for additional polymerization of oxygen-carrying subunits or attachment of any other peptide-based therapeutic.
Abstract CN01-03: Immunotherapy of established lesions caused by high-risk HPV (2010)

Abstract Therapeutic vaccination with a synthetic long peptide (SLP@) vaccine mediated the eradication of established human papillomavirus type 16 (HPV16)-positive tumors in mice and controlled wart growth and latent virus infection in rabbits persistently infected with cottontail rabbit papillomavirus. Subsequent phase I/II studies with an HPV16 SLP@ vaccine, consisting of 13 long peptides covering the HPV16 E6 and E7 antigens, in patients with advanced HPV16-positive cervical cancer, revealed that this vaccine was safe and highly immunogenic. The purpose of the current study was to test the clinical efficacy of this HPV16 SLP@ vaccine in HPV16-induced high-grade vulvar intraepithelial neoplasia (VIN3), a premalignant epithelial disorder, spontaneous regression of which occurs in less than 2% of patients and in which recurrence after standard treatment is high. In a phase 2 trial, 20 women with VIN3 were vaccinated three times sc in the limbs with a mix of the HPV16 E6 and E7 synthetic long peptides formulated in Montanide ISA-51. The endpoints were objective clinical responses, defined as reduction of at least 50% in lesion size (partial response) or complete regressions, and HPV16-specific T-cell responses, determined before and after vaccination. The vaccine was safe, as no side effects exceeding CTC grade 2 were observed. At 3 and 12 months after the last vaccination an objective response was observed in 12/20 (60%) and 15/19 (79%) patients respectively. Nine of them showed a complete and durable regression of the lesions at 12 months and at 24 months. The strength of the vaccine-induced HPV16-specific T-cell response was significantly higher in the group of patients with a complete regression of their lesions as compared to nonresponders. This study shows that in women with VIN3 objective clinical responses can be achieved by therapeutic vaccination with synthetic long peptides that is able to induce effective HVP16-specific T-cell responses. Literature: 1. Kenter GG, Welters MJ, Valentijn AR, Lowik MJ, Berends-van der Meer DM, Vloon AP, Essahsah F, Fathers LM, Drijfhout JW, Offringa R,Wafelman AR, Oostendorp J, Fleuren GJ, Burg van der SH, Melief CJ. Vaccination against Human Papillomavirus 16 oncoproteins for vulvar intraepithelial neoplasia. N Engl J Med. 2009 Nov 5;361(19):1838-47. 2. Melief CJ, van der Burg SH. Immunotherapy of established (pre)malignant disease by synthetic long peptide vaccines. Nat Rev Cancer. 2008 May;8(5):351-60. Citation Information: Cancer Prev Res 2010;3(12 Suppl):CN01-03.
Comparative Genomic Analysis of Three Strains of <i>Ehrlichia ruminantium</i> Reveals an Active Process of Genome Size Plasticity (2006)

Ehrlichia ruminantium is the causative agent of heartwater, a major tick-borne disease of livestock in Africa that has been introduced in the Caribbean and is threatening to emerge and spread on the American mainland. We sequenced the complete genomes of two strains of E. ruminantium of differing phenotypes, strains Gardel (Erga; 1,499,920 bp), from the island of Guadeloupe, and Welgevonden (Erwe; 1,512,977 bp), originating in South Africa and maintained in Guadeloupe in a different cell environment. Comparative genomic analysis of these two strains was performed with the recently published parent strain of Erwe (Erwo) and other Rickettsiales (Anaplasma, Wolbachia, and Rickettsia spp.). Gene order is highly conserved between the E. ruminantium strains and with A. marginale. In contrast, there is very little conservation of gene order with members of the Rickettsiaceae. However, gene order may be locally conserved, as illustrated by the tuf operons. Eighteen truncated protein-encoding sequences (CDSs) differentiate Erga from Erwe/Erwo, whereas four other truncated CDSs differentiate Erwe from Erwo. Moreover, E. ruminantium displays the lowest coding ratio observed among bacteria due to unusually long intergenic regions. This is related to an active process of genome expansion/contraction targeted at tandem repeats in noncoding regions and based on the addition or removal of ca. 150-bp tandem units. This process seems to be specific to E. ruminantium and is not observed in the other Rickettsiales.
Continuous density hidden Markov models for speaker-independent recognition of isolated digits (1984)

In a recent report [L. R. Rabiner, S. E. Levinson, and M. M. Sondhi, J. Acoust. Soc. Am. Suppl. 1 74, S17 (1983)], it was shown that the quantization error inherent in discrete-symbol hidden Markov models introduces a small but consistent degradation into speaker-independent isolated word recognition. Our present study demonstrates that this degradation can be eliminated by a number of techniques based on the theory of hidden Markov models with continuous density functions [L. R. Liporace, IEEE Trans. Inform. Theory IT-28, 729–34 (1982)]. By using these methods we have achieved 98% speaker independent recognition accuracy on isolated English digits. This rate is statistically indistinguishable from the best results obtained with the LPC/DTW system [L. R. Rabiner, S. E. Levinson, A. E. Rosenberg, and J. G. Wilpon, IEEE Trans. Acoust. Speech Signal Process. ASSP-27, 134=141 (1979)].
Divalent Metal Cations Increase the Activity of the Antimicrobial Peptide Kappacin (2005)

Kappacin, nonglycosylated kappa-casein(106-169), is a novel antimicrobial peptide produced from kappa-casein found in bovine milk. There are two major genetic forms of kappacin, A and B, and using synthetic peptides corresponding to the active region, kappa-casein(138-158), of these forms, we have shown that the Asp148 to Ala148 substitution is responsible for the lesser antibacterial activity of kappa-casein-B(106-169). Kappacin was shown to have membranolytic action at concentrations above 30 microM at acidic pH when tested against artificial liposomes. There was little membranolytic activity at neutral pH, which is consistent with the lack of antibacterial activity of kappacin against Streptococcus mutans at this pH. Kappacin specifically bound two zinc or calcium ions per mol, and this binding enhanced antibacterial activity at neutral pH. Nuclear magnetic resonance analysis indicated that a kappa-casein-A(138-158) synthetic peptide undergoes a conformational change in the presence of the membrane solvent trifluoroethanol and excess divalent metal ions. This change in conformation is presumably responsible for the increase in antibacterial activity of kappacin detected in the presence of excess zinc or calcium ions at neutral pH. When tested against the oral bacterial pathogen S. mutans cultured as a biofilm in a constant-depth film fermentor, a preparation of 10 g/liter kappacin and 20 mM ZnCl2 reduced bacterial viability by 3 log10 and suppressed recovery of viability. In contrast 20 mM ZnCl2 alone reduced bacterial viability by approximately 1 log10 followed by rapid recovery. In conclusion, kappacin has a membranolytic, antibacterial effect that is enhanced by the presence of divalent cations.
Enantioselective Organocatalytic Michael Addition of Aldehydes to Nitroethylene: Efficient Access to γ<sup>2</sup>-Amino Acids (2008)

Enantioselective organocatalytic Michael addition of aldehydes to nitroethylene catalyzed by (S)-diphenylprolinol silyl ether provides beta-substituted-delta-nitroalcohols in nearly optically pure form (96-99% ee). The Michael adducts bear a single substituent adjacent to the carbonyl and can be efficiently converted to protected gamma2-amino acids, which are essential for the systematic conformational studies of gamma-peptide foldamers.
Relaxer ferroelectric polymers for actuators and transducers (2002)

Ultra-high electrostrictive strains, both longitudinal and transverse strains, were observed in polyvinylidene fluoride-trifluoroethylene (P(VDF-TrFE)) copolymers under a proper electron irradiation treatment. In addition, in DC electric field biased states, the material also exhibits a high effective piezoelectric coefficient, comparable to those in piezoceramic PZT. The material also has a high dielectric constant and relative low dielectric loss. Moreover, these properties can be tailored in a broad range by the processing conditions. These features indicate that the material is attractive for high performance actuators and transducers. In this paper, electrostrictive strain, effective piezocoefficients, elastic, dielectric properties and polarization behavior of the material are reported. We will also show that the material exhibits typical relaxor ferroelectric behavior.
All acrylic-based thermoplastic elastomers with high upper service temperature and superior mechanical properties (2017)

All acrylic-based thermoplastic elastomers (TPEs) offer potential alternatives to the widely-used styrenic TPEs.
Passive transfer models of myasthenia gravis with muscle‐specific kinase antibodies (2018)

Myasthenia gravis (MG) with antibodies to muscle-specific kinase (MuSK) is characterized by fluctuating fatigable weakness. In MuSK MG, involvement of bulbar muscles, neck, and shoulder and respiratory weakness are more prominent than in acetylcholine receptor (AChR) MG. MuSK autoantibodies are mainly of the IgG4 subclass, and as such are unable to activate complement, have low affinity for Fc receptors, and are functionally monovalent. Therefore, the pathogenicity of IgG4 MuSK autoantibodies was initially questioned. A broad collection of in vitro active immunization and passive transfer models has been developed that have shed light on the pathogenicity of MuSK autoantibodies. Passive transfer studies with purified IgG4 from MuSK MG patients confirmed that IgG4 is sufficient to reproduce clear clinical, electrophysiological, and histological signs of myasthenia. In vitro experiments revealed that MuSK IgG4 autoantibodies preferably bind the first Ig-like domain of MuSK, correlate with disease severity, and interfere with the association between MuSK and low-density lipoprotein receptor-related protein 4 and collagen Q. Some patients have additional IgG1 MuSK autoantibodies, but their role in the disease is unclear. Altogether, this provides a rationale for epitope-specific or IgG4-specific treatment strategies for MuSK MG and emphasizes the importance of the development of different experimental models.
Simplified silver protein detection and image enhancement methods in polyacrylamide gels (1982)

Abstract The use of silver for detection of protein in polyacrylamide gels is becoming widespread. An effort has been made to develop a silver stain which minimizes the time to perform the stain, the amount of silver used, and the complexity of the procedures, and which maximizes the sensitivity. This stain is almost 200‐fold more sensitive than the Coomassie Brilliant Blue R‐250 stain. This silver stain procedure has been shown, with eight purified proteins, to generally be linear over a 40‐fold range in concentration, between 0.005 ng/mm 2 to 2.0 ng/mm 2 . For greater sensitivity, a recycling procedure has been developed. This procedure is capable of amplifying trace proteins which could not be visualized with previous silver stain techniques. Analysis of the kinetics of image development revealed that the silver ion was the limiting factor in image formation. By recycling the gel through silver nitrate solutions, silver ions are replenished in the gel, permitting amplification of further details when the gel is treated with a developing solution. A number of problems inherent in silver stain detection of proteins in polyacrylamide gels are discussed with suggested remedies.
Discovering regions of different functions in a city using human mobility and POIs (2012)

The development of a city gradually fosters different functional regions, such as educational areas and business districts. In this paper, we propose a framework (titled DRoF) that Discovers Regions of different Functions in a city using both human mobility among regions and points of interests (POIs) located in a region. Specifically, we segment a city into disjointed regions according to major roads, such as highways and urban express ways. We infer the functions of each region using a topic-based inference model, which regards a region as a document, a function as a topic, categories of POIs (e.g., restaurants and shopping malls) as metadata (like authors, affiliations, and key words), and human mobility patterns (when people reach/leave a region and where people come from and leave for) as words. As a result, a region is represented by a distribution of functions, and a function is featured by a distribution of mobility patterns. We further identify the intensity of each function in different locations. The results generated by our framework can benefit a variety of applications, including urban planning, location choosing for a business, and social recommendations. We evaluated our method using large-scale and real-world datasets, consisting of two POI datasets of Beijing (in 2010 and 2011) and two 3-month GPS trajectory datasets (representing human mobility) generated by over 12,000 taxicabs in Beijing in 2010 and 2011 respectively. The results justify the advantages of our approach over baseline methods solely using POIs or human mobility.
An Inexpensive Simple-to-Use Inverted Fluorescence Microscope: A New Tool for Cellular Analysis (2010)

Advances in laboratory instrumentation often increase the complexity, size, and cost of the device. The resulting complexity and cost, however, then reduce the accessibility of the device to many laboratories. We examine ways to use technological advances to simplify the design of laboratory devices, retaining the essential components that yield sufficient capabilities for routine uses. Inverted fluorescence microscopes, for example, have evolved into large complex instruments with exquisite imaging capability and are loaded with features requiring trained users and costing tens of thousands of dollars. This has limited their potential ubiquity within laboratories. For simple fluorescence microscopy applications, a much smaller and less expensive device with far fewer features would minimize the issues encountered with traditional inverted fluorescence microscopes. Advances in inexpensive complimentary metal-oxide semiconductor sensor technology have allowed its consideration as an alternative to the expensive charge-coupled device cameras currently used. Based on these advances, we have developed a compact, single-color, single-magnification device with a retail price an order of magnitude lower than current benchtop fluorescence microscopes. This device makes routine fluorescence microscopy applications immediately accessible to individual researchers and less well-funded laboratories. Tasks such as determining the presence of cells, their health, confluence, and fluorescent labeling or protein expression are compatible with such a simplified version. The low cost, small size, and ease of use of this device allows fluorescence microscopy to become more accessible for point-of-care medicine and at many points in the research process.
Abstract 2270: Design, synthesis, and functional characterization of new cycle-peptides inhibitors for C-X-C chemokine receptor-4 (CXCR4) (2010)

Abstract Modulation of the axis CXCR4/CXCL12 affected primary tumor growth and secondary lesions development. Moreover, CXCR4 inhibition increases hematopoietic stem cell mobility in patients undergoing autologous transplantation for myeloma and non-Hodgkin lymphoma. Although several CXCR4 inhibitors were described neither one reached satisfactory efficacy, bioavailability and acceptable toxicity. To develop new CXCR4 inhibitors through a rationale design approach, comparative studies were undertaken evaluating the N-terminal structure of the ligand CXCL12 and v-MIP II, an inhibitory chemokine like produced by the herpes virus 8-Kaposi associated. A common amino acidic motif (RFF) was identified in both structures although in inverted orientation. Having as a core this small domain, a new library (20 units) of cycle-peptide molecules was generated. 20 units of cycle-peptide molecules were synthesized that consists of 5 and 7 amino-acid residues cycled by a S-S bridge designed to interact with the receptor CXCR4. The peptides were characterized for functionally CXCR4 interaction through: 1. inhibition of CXCR4 binding; 2. inhibition of migration CXCL12-induced; 3. inhibition of calcium release CXCL12-induced; 4. Inhibition of P-Erk CXCL12-induced. Four peptides were identified as CXCR4 inhibitors. These four CXCR4 inhibitory peptides were further evaluated for the in vivo efficacy through inhibition of metastasis formation. B16 mouse melanoma cells transfected with CXCR4 were injected in the vein tail in C57 Bl mice and peptide treatment followed for 10 days. Dramatic reduction in number and size of lung metastases were registered in mice peptides-treated. Moreover, xenograft of human renal cancer cells SN12C-EGFP were subcutaneously injected and systemic peptides treatment followed for 10 days. Statistically significant decrease in tumor growth was showed in peptides treated mice. Taken together the data define four new CXCR4 inhibitory peptides, designed through innovative strategy, effective in “in vivo” systems deserving further development. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2270.
Unscented guidance (2015)

Unscented guidance combines the concept of the unscented transform with standard optimal control theory to produce an open-loop method to manage uncertainties in nonlinear dynamical systems. The theoretical foundations for this concept can be framed in terms of a low-order semi-discretization of a Lebesgue-Stieltjes optimal control problem. A Zermelo problem subject to parameter uncertainties is used to quantitatively demonstrate the substantial reductions in target error statistics (95% in mean and 70% in the trace of the covariance) through the use of unscented guidance. These ideas generate a tractable approach for solving chance-constrained optimal control problems.
A review on energy harvesting approaches for renewable energies from ambient vibrations and acoustic waves using piezoelectricity (2017)

The principal objective of this article is to categorically review and compare the state of the art vibration based energy harvesting approaches. To evaluate the contemporary methodologies with respect to their physics, average power output and operational frequencies, systematically divided and easy readable tables are presented followed by the description of the energy harvesting methods. Energy harvesting is the process of obtaining electrical energy from the surrounding vibratory mechanical systems through an energy conversion method using smart structures, like, piezoelectric, electrostatic materials. Recent advancements in low power electronic gadgets, micro electro mechanical systems, and wireless sensors have significantly increased local power demand. In order to circumvent the energy demand; to allow limitless power supply, and to avoid chemical waste from conventional batteries, low power local energy harvesters are proposed for harvesting energy from different ambient energy sources. Piezoelectric materials have received tremendous interest in energy harvesting technology due to its unique ability to capitalize the ambient vibrations to generate electric potential. Their crystalline configuration allows the material to convert mechanical strain energy into electrical potential, and vice versa. This article discusses the various approaches in vibration based energy scavenging where piezoelectric materials are employed as the energy conversion medium.
You Will Get Mail!Predicting the Arrival of Future Email (2015)

The majority of Web email is known to be generated by machines even when one excludes spam. Many machine-generated email messages such as invoices or travel itineraries are critical to users. Recent research studies establish that causality relations between certain types of machine-generated email messages exist and can be mined. These relations exhibit a link between a given message to a past message that gave rise to its creation. For example, a shipment notification message can often be linked to a past online purchase message. Instead of studying how an incoming message can be linked to the past, we propose here to focus on predicting future email arrival as implied by causality relations. Such a prediction method has several potential applications, ranging from improved ad targeting in up sell scenarios to reducing false positives in spam detection.
Effects of Structural Modifications on the Activity ofHippelatesEye Gnat1Attractants and Coattractants (1976)

An aqueous mixture of trimethylamine, ammonia, linoleic acid, and indole acidified to p H 6 with acetic acid attracts the eye gnat Hippelates collusor (Townsend). To study the influence of structural modifications of these active components on attractancy, we bioassayed homologs and analogs of the against field populations of the insects. Primary and secondary aliphattc amines either decreased or did not influence the attractancy of a composition containing ammonia, linoleic acid, and indole acidified with acetic acid to p H 6. With the exception of tripropylamine, all tertiary amines tested enhanced the attractancy of the composition. Cyclic amines reduced it. When a low-molecular aliphatic carboxylic acid was used to aCidify a composition containing trimethylamine, ammonia, linoleic acid, and indole to p H 6, those acidified with acetic, propionic, or n -butyric acid showed the greatest attractancy. The addition of linoleic or oleic acid to a composition containing trimethylamme, ammonia, and indole acidified to p H 6 with acetic acid increased the activity of the composition. Saturated fatty acids usually lowered it. Among unsaturated fatty acids tested, only those having 18 carbon atoms with a cis double. bond at the 9 positon or 2 cis double bonds at the 9 and 12 positions were effective in increasing the activity.