gebhart/patrepeval huggingface dataset:
Cutting Off Functional Loops from Homodimeric Enzyme Superoxide Dismutase 1 (SOD1) Leaves Monomeric β-Barrels (2011)

Demetallation of the homodimeric enzyme Cu/Zn-superoxide dismutase (SOD1) is known to unleash pronounced dynamic motions in the long active-site loops that comprise almost a third of the folded structure. The resulting apo species, which shows increased propensity to aggregate, stands out as the prime disease precursor in amyotrophic lateral sclerosis (ALS). Even so, the detailed structural properties of the apoSOD1 framework have remained elusive and controversial. In this study, we examine the structural interplay between the central apoSOD1 barrel and the active-site loops by simply cutting them off; loops IV and VII were substituted with short Gly-Ala-Gly linkers. The results show that loop removal breaks the dimer interface and leads to soluble, monomeric β-barrels with high structural integrity. NMR-detected nuclear Overhauser effects are found between all of the constituent β-strands, confirming ordered interactions across the whole barrel. Moreover, the breathing motions of the SOD1 barrel are overall insensitive to loop removal and yield hydrogen/deuterium protection factors typical for cooperatively folded proteins (i.e. the active-site loops act as a "bolt-on" domain with little dynamic influence on its structural foundation). The sole exceptions are the relatively low protection factors in β-strand 5 and the turn around Gly-93, a hot spot for ALS-provoking mutations, which decrease even further upon loop removal. Taken together, these data suggest that the cytotoxic function of apoSOD1 does not emerge from its folded ground state but from a high energy intermediate or even from the denatured ensemble.
Effect of Xylooligosaccharide on the Growth of Bifidobacteria (1990)

Xylooligosaccharide was found to have a favorable effect on human intestinal flora. Xylooligosaccharide was utilized by bifidobacteria, but it was not utilized by Escherichia coli and Clostridium spp. in vitro. In vivo, xylooligosaccharide (5 g/day) promoted the growth of bifidobacteria, lowered fecal pH and helped to maintain the fecal water content within normal range. These results showed that xylooligosaccharide can selectively promote the growth of bifidobacteria and help to establish favorable environmental conditions in the intestines.
Retroviral DNA Integration (1999)

DNA integration is a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by the virus-encoded integrase (IN). The mechanism involves a series of nucleophilic attacks, the first of which removes the terminal 2 bases from the 3' ends of the long terminal repeats and of the second which inserts the viral DNA into the host genome. IN specifically recognizes the DNA sequences at the termini of the viral DNA, juxtaposing both ends in an enzyme complex that inserts the viral DNA into a single site in a concerted manner. Small duplications of the host DNA, characteristic of the viral IN, are found at the sites of insertion. At least two host proteins, HMG-I(Y) and BAF, have been shown to increase the efficiency of the integration reaction.
Amino acid sequences of α-helical segments from S-carboxymethylkerateine-A. Complete sequence of a type-II segment (1978)

1. The helical fragments obtained by partial chymotryptic digestion of S-carboxymethylkeratine-A, the low-sulphur fraction from wool, were fractionated into type-I and type-II helical segments in aqueous urea under conditions limiting carbamoylation. 2. The amino acid sequence of a 109-residue type-II segment was completed by using the sequenator. 3. When the data were incorporated into a helical model of 3.6 residues per turn the hydrophobic residues generated a band aligned at a slight angle to the helical axis. This result is in accord with the postulated coiled-coil structure of the crystalline regions of alpha-keratin.
Scaling Law for Entropic Effects at Interfaces between Grafted Layers and Polymer Melts (1998)

We consider surfaces protected by polymer chains of N monomers grafted at a density σ, that are immersed in a melt of chemically similar chains of polymerization index P. We have used the self-consistent field approximation to analyze the practically useful (but analytically untractable) case of moderately long melt chains and moderately stretched grafted chains. We have confirmed previous analyses of concentration profiles, but we have also arrived at new features by looking in a systematic way at the interaction energy between two grafted surfaces: (i) we have found a general scaling criterion that an entropic attraction between two such surfaces exists if > (N/P)2, which differs from predictions obtained for very stretched brushes; (ii) this work also demonstrates the existence of an attraction for sparsely grafted layers ( < 1) provided that P is large enough. These subtle entropic effects should be of direct consequence for “macroscopic” phenomena such as wetting of protected surfaces and colloidal stabilization.
dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics (1998)

PCR-based detection of single nucleotide polymorphisms is a powerful tool for the plant geneticist. Cleaved amplified polymorphic sequence analysis is the most widely used approach for the detection of single nucleotide polymorphisms. However, this technique is limited to mutations which create or disrupt a restriction enzyme recognition site. This paper presents a modification of this technique where mismatches in a PCR primer are used to create a polymorphism based on the target mutation. This technique is useful for following known mutations in segregating populations and genetic mapping of isolated DNAs used for positional based cloning of new genes. In addition, a computer program has been developed that facilitates the design of these PCR primers.
Vaccine and adjuvant design for emerging viruses (2011)

Vaccination is currently the most effective strategy to medically control viral diseases. However, developing vaccines is a long and expensive process, and traditional methods, such as attenuating wild-type viruses by serial passage, may not be suitable for all viruses and may lead to vaccine safety considerations, particularly in the case of the vaccination of particular patient groups, such as the immunocompromised and the elderly. In particular, developing vaccines against emerging viral pathogens adds a further level of complexity, as they may only be administered to small groups of people or only in response to a specific event or threat, limiting our ability to study and evaluate responses. In this commentary, we discuss how novel techniques may be used to engineer a new generation of vaccine candidates as we move toward a more targeted vaccine design strategy, driven by our understanding of the mechanisms of viral pathogenesis, attenuation and the signaling events which are required to develop a lasting, protective immunity. We will also briefly discuss the potential future role of vaccine adjuvants, which could be used to bridge the gap between vaccine safety, and lasting immunity from a single vaccination.
Development of NGR peptide-based agents for tumor imaging. (2011)

Molecular imaging allows direct visualization of targets and characterization of cellular pathways, as long as a high signal/background ratio can be achieved, which requires a sufficient amount of probes to accumulate in the imaging region. The Asn-Gly-Arg (NGR) tripeptide selected by phage display can specifically target tumor vasculature. Recognizing the aminopeptidase N (APN or CD13) receptor on the membrane of tumor cells, the peptide can be further internalized into cytoplasma by the endosomal pathway. Hence NGR can serve as an ideal candidate for tumor imaging, once it is conjugated with fluorescent or radiolabeled imaging probes. Herein, we highlight some recent developments of NGR peptide based imaging of tumors. Although still in the preliminary stage, some NGR probes have shown potential as promising agents in future clinical applications.
A New Adaptive Focus Measure for Shape From Focus (2008)

This paper proposes a new focus measure operator for Shape From Focus to recover a dense depth map of a scene. The method can handle depth discontinuities effectively by using adaptively shaped and weighted support windows. The support window shapes and weights are determined from the image characteristics of the all-focused image of the scene. Similar and closer pixels in the support window get higher weights, which inhibits the problems caused by the depth discontinuities. The size of the support window can be increased conveniently for a more robust depth estimation without introducing any window size related Shape From Focus problems. The large support window sizes also addresses the edge bleeding problem. The experiments on the real and synthetically refocused images show that the introduced ideas work effectively and efficiently in real world applications.
Function of specific 2'-hydroxyl groups of guanosines in a hammerhead ribozyme probed by 2' modifications. (1992)

The importance of the 2'-hydroxyl group of several guanosine residues for the catalytic efficiency of a hammerhead ribozyme has been investigated. Five ribozymes in which single guanosine residues were substituted with 2'-amino-, 2'-fluoro-, or 2'-deoxyguanosine were chemically synthesized. The comparison of the catalytic activity of the three 2' modifications at a specific position allows conclusions about the functional role of the parent 2'-hydroxyl group. Substitutions of nonconserved nucleotides within the ribozyme caused little alteration in the catalytic activity relative to that obtained with the unmodified ribozyme. In contrast, when either of the guanosines within the single-stranded loop between stem I and stem II of the ribozyme was replaced by 2'-deoxyguanosine or 2'-fluoro-2'-deoxyguanosine, the catalytic activities of the resulting ribozymes were reduced by factors of at least 150. The catalytic activities of the corresponding ribozymes containing 2'-amino-2'-deoxyguanosine substitutions at these positions, however, were both reduced by factors of 15. These effects resulted from decreases in the respective kcat values, whereas variations in the Km values were comparatively small. A different pattern of reactivity of the three 2' modifications was observed at the guanosine immediately 3' to stem II of the ribozyme. Whereas both 2'-deoxyguanosine and 2'-amino-2'-deoxyguanosine at this position showed catalytic activity similar to that of the unmodified ribozyme, the activity of the corresponding 2'-fluoro-2'-deoxyguanosine-containing ribozyme was reduced by a factor of 15. The implications of these substitution-specific reactivities on the functional role of the native 2'-hydroxyl groups are discussed.
Natural serum bactericidal activity against Neisseria gonorrhoeae isolates from disseminated, locally invasive, and uncomplicated disease. (1980)

Abstract Fresh frozen sera obtained from 10 normal human volunteers were each repetitively tested in a bactericidal assay against different strains of Neisseria gonorrhoeae isolated from patients in Boston with disseminated infection (DGI), and women with uncomplicated infection (UC) and pelvic inflammatory disease (PID). DGI strains isolated from patients with only dermatitis and arthralgia (DA) were significantly more serum resistant than either UC or PID strains. DGI patients with suppurative arthritis (SA), however, more consistently developed bactericidal antibodies (measured in their whole sera against the homologous infecting strain) in convalescence (91%) than patients with only dermatitis and arthralgias (DA) (18%) and strains causing SA were significantly more sensitive to normal volunteer sera than strains causing only DA. PID strains that caused severe illness were significantly more sensitive to normal volunteer sera than PID strains causing mild or moderate disease. Likewise, PD3 and DGI strains that promoted the development of bactericidal antibodies in infected hosts were also more sensitive to volunteer sera; these strains were by and large the same strains that caused severe PID or suppurative arthritis. UC strains associated with homologous bactericidal activity in infected hosts were also more sensitive to volunteer sera, but length of gonococcal carriage was also more prolonged in hosts infected with these strains. Serum sensitivity of N. gonorrhoeae to normal serum was mediated by IgM and complement. These experiments suggest that bactericidal reactivity as expressed in normal and patient sera may be an important predictor of the specific interactions of gonococci with the human host.
Molecular Staging in Stage II and III Melanoma Patients and Its Effect on Long-Term Survival (2005)

Our study shows a strong association between PCR and disease-specific survival time. Detection of tyrosinase mRNA in peripheral blood may be of similar importance for the clinical course of melanoma as the detection of micrometastatic disease in the sentinel lymph node. Whether a combination of these two factors leads to a better definition of the prognosis of melanoma patients is under investigation in current studies.
Recombinant Factor VIla in Joint and Muscle Bleeding Episodes (1996)

Recombinant factor VIIa (rFVIIa) improves haemostasis and eliminates the risk of transmission of blood-borne infection in haemophilia patients with inhibitors, acquired inhibitors to factor VIII or IX or FVII deficiency. rFVIIa has been available on a compassionate use basis since 1988 and has been administered to 111 patients for a total of 494 joint and muscle bleeding episodes. Seventy-nine percent of joint and 65% of muscle bleeding episodes were evaluated by the investigator as having an excellent/effective response. rFVIIa is also an effective treatment for joint and muscle bleeding episodes in patients undergoing immune tolerance regimens and does not affect the inhibitor titre level.
The cAMP effectors Epac and protein kinase a (PKA) are involved in the hepatic cystogenesis of an animal model of autosomal recessive polycystic kidney disease (ARPKD)† (2008)

Our data provide strong evidence that both cAMP effectors, Epac and PKA, and the levels of intracellular calcium are involved in the hepatic cystogenesis of ARPKD.
Adaptive transmission protocols for frequency-hop radio networks (2002)

The focus of this paper is on the performance of an adaptive transmission protocol for frequency-hop (FH) radio networks in which the radios can adjust the power in the transmitted signal and the rate of a Reed-Solomon code to respond to variations in partial-band interference and propagation loss. The adaptation is based on side information from the FH receiver and on information derived from the decoder. The results presented in this paper are obtained from a simulation of a wireless FH radio network in which the characteristics of the links are time-varying. These results demonstrate that the adaptive transmission protocol can improve the quality of a link by adapting to variations in both path-loss and interference to take advantage of favorable channel conditions.
What we know so far: COVID-19 current clinical knowledge and research (2020)

In December 2019, health authorities in Wuhan, China, identified a cluster of pneumonia cases of unknown aetiology linked to the city's South China Seafood Market. Subsequent investigations revealed a novel coronavirus, SARS-CoV-2, as the causative agent now at the heart of a major outbreak. The rising case numbers have been accompanied by unprecedented public health action, including the wholesale isolation of Wuhan. Alongside this has been a robust scientific response, including early publication of the pathogen genome, and rapid development of highly specific diagnostics. This article will review the new knowledge of SARS-CoV-2 COVID-19 acute respiratory disease, and summarise its clinical features.
A highly prevalent and genetically diversified Picornaviridae genus in South Asian children (2008)

Viral metagenomics focused on particle-protected nucleic acids was used on the stools of South Asian children with nonpolio acute flaccid paralysis (AFP). We identified sequences distantly related to Seneca Valley virus and cardioviruses that were then used as genetic footholds to characterize multiple viral species within a previously unreported genus of the Picornaviridae family. The picornaviruses were detected in the stools of >40% of AFP and healthy Pakistani children. A genetically diverse and highly prevalent enteric viral infection, characteristics similar to the Enterovirus genus, was therefore identified substantially expanding the genetic diversity of the RNA viral flora commonly found in children.
Tissue Oxygen Perfusion and Pressure Ulcer Healing (2000)

Diabetes mellitus is known to retard wound healing. This study of 35 subjects with pressure ulcers found that carbon dioxide levels were negatively correlated to healing rates. Transcutaneous oxygen levels of peri ulcer was not statistically significantly related to healing rates.
The 31-kDa precursor of interleukin 1 alpha is myristoylated on specific lysines within the 16-kDa N-terminal propiece. (1993)

The cytokine interleukin 1 alpha (IL-1 alpha) is a critical mediator of the immune and inflammatory responses. A unique determinant of its activity as compared with IL-1 beta may be its association with the plasma membrane. While the biologic activity of "membrane IL-1" has been extensively reported, the mechanism of membrane binding remains unclear. We report that the N terminus of the 31-kDa IL-1 alpha precursor is myristoylated on specific internal lysine residues. Immunoprecipitation of [3H]myristic acid-radiolabeled human monocyte lysates with IgG antibodies to the 31-kDa IL-1 alpha precursor recovered a protein with the physicochemical properties of the IL-1 alpha N-terminal propiece (16 kDa, pI 4.45). Glycyl N-myristoylation of this protein is precluded by the absence of a glycine residue at position 2, suggesting that the propiece is myristoylated on epsilon-amino groups of lysine. To determine which lysine(s) are acylated, a series of synthetic peptides containing all lysines found in the IL-1 alpha N-terminal propiece were used in an in vitro myristoylation assay containing peptide, myristoyl-CoA, and monocyte lysate as enzyme source. Analysis of the reaction products by reverse-phase HPLC and gas-phase sequencing demonstrated the specific myristoylation of Lys-82 and Lys-83, yielding predominantly monoacylated product. A conserved sequence in the IL-1 beta propiece was myristoylated with at least 8-fold less efficiency. Acylation of the IL-1 alpha precursor by a previously unrecognized lysyl epsilon-amino N-myristoyl-transferase activity may facilitate its specific membrane targeting.
Remote atmospheric breakdown for standoff detection by using an intense short laser pulse (2005)

A remote atmospheric breakdown is a very rich source of UV and broadband visible light that could provide an early warning of the presence of chemical-biological warfare agents at extended standoff distances. A negatively chirped laser pulse propagating in air compresses in time and focuses transversely, which results in a rapid laser intensity increase and ionization near the focal region that can be located kilometers away from the laser system. Proof-of-principle laboratory experiments are performed on the generation of remote atmospheric breakdown and the spectroscopic detection of mock biological warfare agents. We have generated third harmonics at 267 nm and UV broadband radiation in air from the compression and focusing of femtosecond laser pulses. Fluorescence emission from albumin aerosols as they were illuminated by the femtosecond laser pulse has been observed.
Automated Quantification of Atherosclerosis in CTA of Carotid Arteries (2012)

How is the human body built and how does it function? What are the causes of\ndisease, and where is disease located? Throughout the history of mankind these\nquestions were answered by the use of invasive methods that included the\n“opening” of the human body, mainly cadavers. Thanks to these invasive\ntechniques the first precise and complete anatomy works started to appear in\nthe 16th century. The most influential works were published by Leonardo da\nVinci and the anatomist and physician Andreas Vesalius.\nThe discovery of X-rays in 1895, and their use for medical applications,\nintroduced a new era, in which non-invasive imaging of the functioning human\nbody became feasible. Nowadays, medical imaging includes many different\nimaging modalities, such as X-ray, computed tomography (CT), magnetic\nresonance imaging (MRI), ultrasound (US), nuclear and optical imaging, and\nhas become an indispensable diagnostic tool for a wide range of applications.\nInitially, the application of medical imaging focused on the visualization of\nanatomy and on the detection and localization of disease. However, with the\ndevelopment of different modalities it has evolved into a much more versatile\ntool providing important information on e.g. physiology and organ function,\nbiochemistry and metabolism using nuclear imaging (mainly positron emission\ntomography (PET) imaging), molecular and processes on the molecular\nand cellular level using molecular imaging techniques.
Reaction of Thiaxanthydrol With Compounds Containing Active Hydrogen1 (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of Thiaxanthydrol With Compounds Containing Active Hydrogen1EUGENE SAWICKI and VINCENT T. OLIVERIOCite this: J. Org. Chem. 1956, 21, 2, 183–189Publication Date (Print):February 1, 1956Publication History Published online1 May 2002Published inissue 1 February 1956https://pubs.acs.org/doi/10.1021/jo01108a009https://doi.org/10.1021/jo01108a009research-articleACS PublicationsRequest reuse permissionsArticle Views282Altmetric-Citations12LEARN 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
Deamidation of human proteins (2001)

Deamidation of asparaginyl and glutaminyl residues causes time-dependent changes in charge and conformation of peptides and proteins. Quantitative and experimentally verified predictive calculations of the deamidation rates of 1,371 asparaginyl residues in a representative collection of 126 human proteins have been performed. These rates suggest that deamidation is a biologically relevant phenomenon in a remarkably large percentage of human proteins.
Mechanisms of Protein Folding: Molecular Chaperones and Their Application in Biotechnology (2002)

To fold or not to fold! Molecular chaperones are highly versatile molecules assisting a large variety of protein folding events during the entire lifespan of proteins. Knowledge about the network and functions of bacterial chaperones offers new prospects to improve the yield of properly folded recombinant proteins, perhaps boosting biotechnology.