gebhart/patrepeval huggingface dataset:
Insulin Treatment Improves the Systemic Inflammatory Reaction to Severe Trauma (2004)

Insulin attenuates the inflammatory response by decreasing the pro-inflammatory and increasing the anti-inflammatory cascade, thus restoring systemic homeostasis, which has been shown critical for organ function and survival in critically ill patients.
Knowledge-based updating of maps by interpretation of aerial images (2002)

The aim of this paper is to present our approach for interpretation of aerial images in the context of map updating. We describe concepts for the design of a top-down process that generates goals for detection of changed and new objects. The complexity of aerial photographs requires the use of context. We show that contextual reasoning provides a mechanism to generate goals to search objects by their optional or essential spatial relationship with objects already recognized. Each goal operates on a restricted search area and uses an image processing technique with parameters tailored to the searched object type. Furthermore, a priori knowledge about adaptation of the search area and the parameter setting for image processing is provided. The outcome of each goal is matched with a priori knowledge about properties of the searched object type. The concepts are illustrated by a case study for updating of a road map.
The design of inhibitors of protein kinase C; the solution conformation of staurosporine (1991)

NMR spectra in several solvents show that the conformation of the tetrahydropyran ring in Staurosporine changes from a chair form in the free base to a boat conformation on protonation, mainly owing to the increased solvation requirement of –NH2Me+vs.–NHMe; implications for the bioactive conformation are discussed.
A blueprint for the prevention of preterm birth: vaginal progesterone in women with a short cervix (2013)

Preterm birth is the leading cause of perinatal morbidity and mortality worldwide, and is the most important challenge to modern obstetrics. A major obstacle has been that preterm birth is treated (implicitly or explicitly) as a single condition. Two thirds of preterm births occur after the spontaneous onset of labor, and the remaining one third after "indicated" preterm birth; however, the causes of spontaneous preterm labor and "indicated" preterm birth are different. Spontaneous preterm birth is a syndrome caused by multiple etiologies, one of which is a decline in progesterone action, which induces cervical ripening. A sonographic short cervix (identified in the midtrimester) is a powerful predictor of spontaneous preterm delivery. Randomized clinical trials and individual patient meta-analyses have shown that vaginal progesterone reduces the rate of preterm delivery at <33 weeks of gestation by 44%, along with the rate of admission to the neonatal intensive care unit, respiratory distress syndrome, requirement for mechanical ventilation, and composite neonatal morbidity/mortality score. There is no evidence that 17-α-hydroxyprogesterone caproate can reduce the rate of preterm delivery in women with a short cervix, and therefore, the compound of choice is natural progesterone (not the synthetic progestin). Routine assessment of the risk of preterm birth with cervical ultrasound coupled with vaginal progesterone for women with a short cervix is cost-effective, and the implementation of such a policy is urgently needed. Vaginal progesterone is as effective as cervical cerclage in reducing the rate of preterm delivery in women with a singleton gestation, history of preterm birth, and a short cervix (<25 mm).
Modeling and control of electromagnetic brakes for enhanced braking capabilities for automated highway systems (2002)

In automatic highway systems, a faster response and a robust braking system are crucial part of the overall automatic control of the vehicle. This paper describes electromagnetic brakes as a supplementary system for regular brakes. This system provides better time for emergency situations, and in general keeps the friction brake working longer and safer. A modified mathematical model for electromagnetic brakes is proposed to describe their static characteristics (angular speed versus brake torque). The performance of the modified mathematical model is better than the other three models available in the literature. To control the brakes, a robust sliding mode controller is designed to maintain the wheel slip at a given value. Simulations show that the controller designed is capable of controlling the vehicle with parameter deviations and disturbances.
Cutting-edge technologies in colon-targeted drug delivery systems (2011)

Oral colon-targeted drug delivery systems have gained enormous attention among researchers in the last two decades. The significance of this site-specific drug delivery system can be measured by its usefulness for delivering a variety of therapeutic agents, both for the treatment of local diseases or for systemic therapies. With the arrival of newer innovations, a large number of breakthrough technologies have emerged for targeting a drug molecule to the colon. Researchers have attempted various approaches in the development of these formulation technologies, such as pH-dependent, time-dependent and microflora-activated systems. Recently, a number of approaches have been proposed that utilize a novel concept of di-dependent drug delivery systems, that is, the systems in which the drug release is controlled by two factors: pH and time, and pH and microflora of the colon. This Editorial article is not intended to offer a comprehensive review on drug delivery, but shall familiarize the readers with the formulation technologies that have been developed for attaining colon-specific drug delivery.
Differential expression of hydrogenase isoenzymes in Escherichia coli K-12: evidence for a third isoenzyme (1985)

The cellular contents of the nickel-containing, membrane-bound hydrogenase isoenzymes 1 and 2 (hydrogenases 1 and 2) were analyzed by crossed immunoelectrophoresis. Their expression was differentially influenced by nutritional and genetic factors. Hydrogenase 2 content was enhanced after growth with either hydrogen and fumarate or glycerol and fumarate and correlated reasonably with cellular hydrogen uptake capacity. Hydrogenase 1 content was negligible under the above conditions but was enhanced by exogenous formate. Its expression was greatly reduced in a pfl mutant, which is unable to synthesise formate, but was restored to normal levels when the growth medium included formate. A mutation in the anaerobic regulatory gene, fnr, led to low overall hydrogenase activity and greatly reduced levels of both isoenzymes and abolished the formate enhancement of hydrogenase 1 content. Formate hydrogenlyase activity was similarly reduced in the fnr strain but, in contrast, was restored, as was overall hydrogenase activity, to normal levels by growth in the presence of formate. Low H2 uptake activity was found for the fnr strain under all growth conditions examined. Hydrogenase 1 content, therefore, does not correlate with formate hydrogenlyase activity and its role is unclear. A third hydrogenase isoenzyme, immunologically distinct from hydrogenases 1 and 2, whose expression is enhanced by formate, is present and forms part of the formate hydrogenlyase. We suggest that the effect of the fnr gene product on formate hydrogenlyase expression is mediated via internal formate.
Thermoinducible filamentation in Escherichia coli due to an altered RNA polymerase beta subunit is suppressed by high levels of ppGpp (1994)

The Escherichia coli strain known as GC2553, FB8, UTH1038, or K12S (Luria), considered an F- lambda- wild-type strain, is shown here to carry a cryptic mutation, ftsR1, causing nonlethal filamentation during exponential growth in Luria-Bertani (LB) broth at 42 degrees C and the inability to grow in salt-free LB broth at 42 degrees C. The ftsR1 mutation is completely suppressed in genetic backgrounds which increase RelA-dependent synthesis of the nucleotide ppGpp, i.e., argS201 (Mecr) and alaS21 (Mecr) mutations, affecting aminoacyl-tRNA synthetases, or the presence of a plac-relA' plasmid. These backgrounds also confer resistance in LB broth to the beta-lactam mecillinam, an antibiotic which specifically inhibits penicillin-binding protein 2 and, in wild-type cells, causes an indirect block in cell division. Furthermore, the ftsR1 mutant (but not an isogenic ftsR+ strain) is sensitive to mecillinam in minimal glucose medium at 37 degrees C. Since the division block caused by mecillinam can be overcome by overproduction of the cell division protein FtsZ, we tested the effect of plasmid pZAQ (carrying the ftsZ, ftsA, and ftsQ genes) on the ftsR1 mutant; it suppressed the filamentation in LB broth and the mecillinam sensitivity on minimal glucose medium at 37 degrees C but not the growth defect in salt-free LB broth at 42 degrees C. Genetic analysis indicated that the full phenotype of the ftsR1 mutant is due to a single mutation in the rpoB gene (90 min), coding for the beta subunit of RNA polymerase; we call this allele rpoB369(Fts). We propose that the rpoB369(Fts) mutation alters the specificity of the polymerase and that the mutant enzyme can recover normal activity in the presence of high salt concentrations or via interaction with the nucleotide ppGpp.
Antibody like peptidomimetics as large scale immunodetection probes. (2003)

Antibodies are often used to study the molecular basis of physiologic processes. Despite the widespread applications of monoclonal antibodies (mAb) from basic science to successful therapeutics in clinical settings their use is limited. Production of mAb is often cumbersome and creating diverse and therapeutic amounts of useful mAb is difficult. We have developed a methodology to reduce an antibody into much smaller peptidomimetics and have engineered the mimetics for increased serum half life and affinity. The novel species are termed "antibody like binding peptidomimetics" (ABiP). We developed the Anti-Her2/neu peptidomimetic (AHNP) which is a mimic of Herceptin, a mAb used for advanced breast cancer therapy. The AHNP has been used as a defining tool to develop immunodetection probes that exemplify a general process application. AHNP has been expressed as an oligomeric fusion protein with streptavidin. These Herceptin like ABiPs were used to detect the Her2/neu antigen at extremely low concentrations using the immunodetection amplification technique (IDAT) which our laboratory has also developed. A fully developed highly diverse library of ABiPs represents an alternative for panels of monoclonal antibodies and may also be useful for target validation, antigen detection, therapeutics and as a platform for drug development.
The outcomes of hypoglossal nerve stimulation in the management of OSA: A systematic review and meta‐analysis (2018)

HNS is a safe and effective treatment for CPAP refractory OSA. Further study comparing HNS to other therapies is required.
Polo-like Kinase 1 (Plk1) Inhibits p53 Function by Physical Interaction and Phosphorylation (2004)

Polo-like kinase 1 (Plk1) has an important role in the regulation of M phase of the cell cycle. In addition to its cell cycle-regulatory function, Plk1 has a potential role in tumorigenesis. Here we found for the first time that Plk1 physically binds to the tumor suppressor p53 in mammalian cultured cells, and inhibits its transactivation activity as well as its pro-apoptotic function. During the cisplatin-induced apoptosis in human neuroblastoma SH-SY5Y cells, the expression level of Plk1 was significantly decreased both at mRNA and protein levels, whereas cisplatin treatment caused a remarkable stabilization of p53. Systematic immunoprecipitation analyses using a series of deletion mutants of p53 revealed that a sequence-specific DNA-binding region of p53 is required and sufficient for the physical interaction with Plk1. The ectopically overexpressed Plk1 was co-localized with the endogenous p53 in mammalian cell nucleus, as shown by confocal laser microscopy. Expression of exogenous Plk1 and p53 in p53-deficient lung carcinoma H1299 cells greatly decreased the p53-mediated transcription from the p53-responsive p21(WAF1), MDM2, and BAX promoters, whereas the kinase-deficient mutant form of Plk1 failed to reduce the transcriptional activity of p53. Consistent with the luciferase reporter analysis, Plk1 had an ability to block the p53-dependent induction of the endogenous p21(WAF1). In addition, Plk1 inhibited the pro-apoptotic function of p53 in H1299 cells. Intriguingly, Plk1-mediated repression of p53 was attenuated with ATM. Thus, our present findings strongly suggest that p53 is a critical target of Plk1, and its function is abrogated through the physical interaction with Plk1.
Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy (2013)

Removal of introns from nascent transcripts (pre-mRNAs) by the spliceosome is an essential step in eukaryotic gene expression. Previous studies have suggested that the earliest steps in spliceosome assembly in yeast are highly ordered and the stable recruitment of U1 small nuclear ribonucleoprotein particle (snRNP) to the 5' splice site necessarily precedes recruitment of U2 snRNP to the branch site to form the "prespliceosome." Here, using colocalization single-molecule spectroscopy to follow initial spliceosome assembly on eight different S. cerevisiae pre-mRNAs, we demonstrate that active yeast spliceosomes can form by both U1-first and U2-first pathways. Both assembly pathways yield prespliceosomes functionally equivalent for subsequent U5·U4/U6 tri-snRNP recruitment and for intron excision. Although fractional flux through the two pathways varies on different introns, both are operational on all introns studied. Thus, multiple pathways exist for assembling functional spliceosomes. These observations provide insight into the mechanisms of cross-intron coordination of initial spliceosome assembly.
Design and physicochemical characterisation of novel dissolving polymeric microneedle arrays for transdermal delivery of high dose, low molecular weight drugs (2014)

We describe formulation and evaluation of novel dissolving polymeric microneedle (MN) arrays for the facilitated delivery of low molecular weight, high dose drugs. Ibuprofen sodium was used as the model here and was successfully formulated at approximately 50% w/w in the dry state using the copolymer poly(methylvinylether/maleic acid). These MNs were robust and effectively penetrated skin in vitro, dissolving rapidly to deliver the incorporated drug. The delivery of 1.5mg ibuprofen sodium, the theoretical mass of ibuprofen sodium contained within the dry MN alone, was vastly exceeded, indicating extensive delivery of the drug loaded into the baseplates. Indeed in in vitro transdermal delivery studies, approximately 33mg (90%) of the drug initially loaded into the arrays was delivered over 24h. Iontophoresis produced no meaningful increase in delivery. Biocompatibility studies and in vivo rat skin tolerance experiments raised no concerns. The blood plasma ibuprofen sodium concentrations achieved in rats (263μgml(-1) at the 24h time point) were approximately 20 times greater than the human therapeutic plasma level. By simplistic extrapolation of average weights from rats to humans, a MN patch design of no greater than 10cm(2) could cautiously be estimated to deliver therapeutically-relevant concentrations of ibuprofen sodium in humans. This work, therefore, represents a significant progression in exploitation of MN for successful transdermal delivery of a much wider range of drugs.
Experimental evaluation of a new composite mesh with the selective property of incorporation to the abdominal wall without adhering to the intestines (1994)

This preliminary study examined the possibility of preventing intestinal adhesions to biomaterials while preserving their incorporation with the abdominal wall. White New Zealand rabbits received intraperitoneal implants of different biomaterials for repair of defects created on the abdominal wall. The following biomaterials were used: polypropylene, polyester, expanded polytetraflueroethylene, polypropylene mesh/polypropylene sheeting (polypropylene mesh covered with polypropylene sheeting on the peritoneal side), polypropylene/silastic, polypropylene/polyglactin, polypropylene/polyglycolic acid, and polypropylene/fibrin. All biomaterials evaluated caused adhesions to the intestines except for polypropylene mesh/polypropylene sheeting and polypropylene mesh/silastic composites. Because adhesion of the intestine to the biomaterial is the first stage of biomaterial-related intestinal fistula, its prevention is logical for the elimination of this complication. Composites with the selective property of adhering to the abdominal wall, yet sparing the viscera, would facilitate thoracic and abdominal wall surgeries, as well as intraperitoneal laparoscopic hernioplasties.
Benzophenone Photophores in Biochemistry (1994)

The photoactivatable aryl ketone derivatives have been rediscovered as biochemical probes in the last 5 years. The expanding use of benzophenone (BP) photoprobes can be attributed to three distinct chemical and biochemical advantages. First, BPs are chemically more stable than diazo esters, aryl azides, and diazirines. Second, BPs can be manipulated in ambient light and can be activated at 350-360 nm, avoiding protein-damaging wavelengths. Third, BPs react preferentially with unreactive C-H bonds, even in the presence of solvent water and bulk nucleophiles. These three properties combine to produce highly efficient covalent modifications of macromolecules, frequently with remarkable site specificity. This Perspectives includes a brief review of BP photochemistry and a selection of specific applications of these photoprobes, which address questions in protein, nucleic acid, and lipid biochemistry.
MYC rearrangement and translocations involving band 8q24 in diffuse large cell lymphomas (1991)

The configuration of the MYC gene in diffuse large cell lymphomas (DLCL) with translocations involving band 8q24 [t(8q24)] has not been systematically studied. We collected cytogenetic and clinical data on 171 consecutive cases of DLCL, including cleaved, noncleaved, and immunoblastic types, of which 96 had DNA available and 124 had abnormal karyotypes. The cases with DNA available were evaluated for MYC rearrangement (MYC-R) by Southern hybridization of EcoRI-digested tumor DNA using an exon-1 probe, a combination of probe and enzyme known to detect over 85% of breaks in sporadic Burkitt's lymphoma. In cases studied at diagnosis, MYC-R, t(8;14)(q24;q32), or other t(8q24) were not prognostically significant. Among the 124 cases with karyotypic abnormalities, seropositivity for human immunodeficiency virus was significantly more common in cases with a t(8q24) (72%) than in cases without it (9%) (P less than .05). Of the four cases with an MYC -R, two had a t(8;14), one had a t(7;8;14)(p15;q24;q32), and one had a t(8;?)(q24;?) and a del(8)(q24). In the three previous cases with translocations involving 8q24 and 14q32, comigration of the rearranged MYC band with either the J region or the switch-mu region of the Ig heavy chain gene could not be demonstrated, leaving the 14q32 breakpoint undefined at the molecular level. Among the remaining 72 cases where both an abnormal karyotype and molecular data were available, 11 had a t(8q24), either t(8;14) or t(8;22)(q24;q11), in the absence of an MYC-R. In these cases, the 8q24 break was presumably located outside of the EcoRI MYC fragment. All 15 cases with a t(8q24) were also screened for point mutations in the PvuII site in the first exon of MYC; two cases that were not MYC-R showed loss of this restriction site. These results indicate that in most DLCL with t(8;14) or other t(8q24), the 8q24 breakpoint lies away from the MYC gene; in a minority of these cases, point mutations in regulatory noncoding regions were detected.
Is chronic inflammation a determinant of blood pressure in the elderly? (2003)

These results suggest that chronic inflammation may play a role in the modulation of arterial BP.
A modular PROTAC design for target destruction using a degradation signal based on a single amino acid (2019)

Proteolysis targeting chimeras (PROTACs) are bivalent molecules that bring a cellular protein to a ubiquitin ligase E3 for ubiquitination and subsequent degradation. Although PROTAC has emerged as a promising therapeutic means for cancers as it rewires the ubiquitin pathway to destroy key cancer regulators, the degradation signals/pathways for PROTACs remain underdeveloped. Here we append single amino acids, the simplest degradation signal, to a ligand specific for estrogen-related receptor α (ERRα) and demonstrate their utility in ERRα knockdown via the N-end rule pathway and also their efficiency in the growth inhibition of breast cancer cells. The modular design described offers unique advantages including smaller molecular size with shortest degradation sequences and degradation speed modulation with different amino acids. Our study expands the repertoire of limited ubiquitin pathways currently available for PROTACs and could be easily adapted for broad use in targeted protein degradation.
Refolding and Oxidation of Recombinant Human Stem Cell Factor Produced in Escherichia coli (1996)

Oxidative folding of recombinant human stem cell factor (rhSCF) produced in Escherichia coli was investigated in vitro. Folding of denatured and reduced rhSCF involves at least five intermediate forms, I-1 to I-5, detectable by their differences in hydrophobicity using reverse-phase high performance liquid chromatography. Both I-1 and I-2 contain a native-like disulfide bond, Cys4-Cys89 and Cys43-Cys138, respectively, and I-3 forms a mispaired disulfide, Cys43-Cys89. These forms appear to reach steady state equilibrium and are important folding intermediates. I-1 was found to be the prominent intermediate that directly folds into native rhSCF (N); and the thermodynamically less stable I-2 favors rearrangment into I-1. I-3 may serve as an intermediate for disulfide rearrangment between I-1 and I-2. I-4 and I-5, which are disulfide-linked dimers, are in equilibrium with reduced rhSCF and other intermediates and may not play an important role in rhSCF folding. Both trifluoroacetic acid-trapped I-1 and I-2, after isolation by high performance liquid chromatography, proceed with the remaining oxidative folding process after reconstitution. Iodoacetate-trapped I-1 and I-2 contain low alpha-helical content and some tertiary structure, while I-3 and reduced rhSCF have little ordered structure. Gel filtration/light-scattering experiments indicate that reduced rhSCF and iodoacetate-trapped I-1, I-2, and I-3 exist as dimeric forms, indicating that rhSCF dimerization precedes formation of disulfide bonds. I-1, I-2, I-3, and the C43,138A analog lacking Cys43-Cys138 bond are not biologically active or exhibit significantly lower activity. The two disulfide bonds in rhSCF seem to be essential for the molecule to maintain an active conformation required for its receptor binding and biological activities.
Immunological Similarity between Low Molecular Weight Trypsin-Chymotrypsin Inhibitors from Human Bronchial Secretion and Seminal Plasma (1976)

Article Immunological Similarity between Low Molecular Weight Trypsin-Chymotrypsin Inhibitors from Human Bronchial Secretion and Seminal Plasma was published on January 1, 1976 in the journal Biological Chemistry (volume 357, issue 2).
aS,7S‐absolute configuration of natural (−)‐colchicine and allocongeners (1990)

The aS,7S-absolute configuration of (-)-colchicine (1) and (-)-N-acetylcolchinol methyl ether (3, NCME) suggested on the basis of 1H NMR data and negative Cotton effects at about 260 nm (EtOH) is firmly established by an X-ray analysis of urea 5, a compound derived from 3. Binding of these compounds to tubulin requires an aS-configuration of the biaryl system.