gebhart/patrepeval huggingface dataset:
Characterization of a unique glycoprotein antigen expressed on the surface of human neuroblastoma cells. (1986)

In order to develop a molecular probe to delineate chemical and biological characteristics of human neuroblastoma cells, a murine monoclonal antibody (Mab 5G3) was produced that is directed to a glycoprotein, preferentially expressed on the surface of such cells. This antibody is of IgG2a isotype, has an association constant of 8 X 10(9) M-1, and reacts preferentially with human neuroblastoma cell lines and fresh frozen tissue sections in enzyme-linked immunosorbent assay and immunoperoxidase assays, respectively. Minimal reactivity is observed with a variety of lymphoblastoid cell lines and normal fetal and adult tissues. Mab 5G3 specifically recognizes a neuroblastoma target glycoprotein antigen of 215 kDa that is derived from a 200-kDa precursor, as evident from pulse-chase biosynthetic studies. Treatment with tunicamycin revealed that both molecules contain N-asparagine-linked oligosaccharides; however, only the 215-kDa species is resistant to treatment with endo-beta-N-acetylglucosaminidase H and sensitive to neuraminidase, indicating that it contains trimmed and terminally sialylated oligosaccharides of the "complex" type. In contrast, the 200-kDa precursor is sensitive to endo-beta-N-acetylglucosaminidase H and resistant to neuraminidase treatment indicating that it contains high-mannose non-processed oligosaccharides. The 215-kDa molecule is sulfated, phosphorylated at serine residues, and expressed on the cell surface. A molecule of 200 kDa is detected by Mab 5G3 in spent culture medium of human neuroblastoma cells which is neither sulfated nor phosphorylated.
Specific inhibition of herpes simplex virus DNA polymerase by helical peptides corresponding to the subunit interface. (1995)

The herpes simplex virus DNA polymerase consists of two subunits--a catalytic subunit and an accessory subunit, UL42, that increases processivity. Mutations affecting the extreme C terminus of the catalytic subunit specifically disrupt subunit interactions and ablate virus replication, suggesting that new antiviral drugs could be rationally designed to interfere with polymerase heterodimerization. To aid design, we performed circular dichroism (CD) spectroscopy and analytical ultracentrifugation studies, which revealed that a 36-residue peptide corresponding to the C terminus of the catalytic subunit folds into a monomeric structure with partial alpha-helical character. CD studies of shorter peptides were consistent with a model where two separate regions of alpha-helix interact to form a hairpin-like structure. The 36-residue peptide and a shorter peptide corresponding to the C-terminal 18 residues blocked UL42-dependent long-chain DNA synthesis at concentrations that had no effect on synthesis by the catalytic subunit alone or by calf thymus DNA polymerase delta and its processivity factor. These peptides, therefore, represent a class of specific inhibitors of herpes simplex virus DNA polymerase that act by blocking accessory-subunit-dependent synthesis. These peptides or their structures may form the basis for the synthesis of clinically effective drugs.
RAIM with Optimal Integrity and Continuity Allocations Under Multiple Failures (2010)

Among the receiver autonomous integrity monitoring (RAIM) algorithms treating multiple failures, multiple hypothesis solution separation algorithms (MHSS) - a type of solution separation algorithm - offer several advantages: First, the link between threat model, upper bound on the position error - the protection level and probability of hazardously misleading information is an easy and straightforward one; second, the calculation of the protection level does not involve complex steps. One of the critical steps in this algorithm is the allocation of the integrity and continuity budgets among the failure modes, as it determines the overall performance of the algorithm. After describing the baseline MHSS approach, we present an algorithm that simultaneously allocates the integrity and continuity budget among the failure modes to obtain the minimum protection level per satellite geometry. Then, we show how slope-based RAIM and solution separation RAIM are related through a little-known formula, which both unifies and highlights the differences between the two approaches. Finally, we apply the algorithm to evaluate the performance of RAIM for vertical guidance for a dual constellation, and find that even with a very large prior probability of satellite failure, vertical guidance can be achieved worldwide with high availability.
Inhibition of Herpesvirus Replication by Hexadecyloxypropyl Esters of Purine- and Pyrimidine-Based Phosphonomethoxyethyl Nucleoside Phosphonates (2008)

Patients infected with human immunodeficiency virus (HIV) often suffer from herpesvirus infections as a result of immunosuppression. These infections can occur while patients are receiving antiretroviral therapy, and additional drugs required to treat their infection can adversely affect compliance. It would be useful to have antivirals with a broader spectrum of activity that included both HIV and the herpesviruses. We reported previously that alkoxyalkyl ester prodrugs of cidofovir are up to 3 orders of magnitude more active against herpesvirus replication and may be less toxic than the unmodified drug. To determine if this strategy would be effective for certain phosphonomethoxyethyl nucleoside phosphonates which are also active against HIV infections, the hexadecyloxypropyl (HDP) esters of 1-(phosphonomethoxyethyl)-cytosine, 1-(phosphonomethoxyethyl)-5-bromo-cytosine (PME-5BrC), 1-(phosphonomethoxyethyl)-5-fluoro-cytosine, 9-(phosphonomethoxyethyl)-2,6-diaminopurine (PME-DAP), and 9-(phosphonomethoxyethyl)-2-amino-6-cyclopropylaminopurine (PME-cPrDAP) were evaluated for activity against herpesvirus replication. The HDP esters were substantially more active than the unmodified acyclic nucleoside phosphonates, indicating that esterification with alkoxyalkyl groups increases the antiviral activity of many acyclic nucleoside phosphonates. The most interesting compounds included HDP-PME-cPrDAP and HDP-PME-DAP, which were 12- to 43-fold more active than the parent nucleoside phosphonates against herpes simplex virus and cytomegalovirus, and HDP-PME-cPrDAP and HDP-PME-5BrC which were especially active against Epstein-Barr virus. The results presented here indicate that HDP-esterified acyclic nucleoside phosphonates with antiviral activity against HIV also inhibit the replication of some herpesviruses and can extend the spectrum of activity for these compounds.
Photoaffinity labeling of A1-adenosine receptors. (1985)

The ligand-binding subunit of the A1-adenosine receptor has been identified by photoaffinity labeling. A photolabile derivative of R-N6-phenylisopropyladenosine, R-2-azido-N6-p-hydroxyphenylisopropyladenosine (R-AHPIA), has been synthesized as a covalent specific ligand for A1-adenosine receptors. In adenylate cyclase studies with membranes of rat fat cells and human platelets, R-AHPIA has adenosine receptor agonist activity with a more than 60-fold selectivity for the A1-subtype. It competes for [3H]N6-phenylisopropyladenosine binding to A1-receptors of rat brain membranes with a Ki value of 1.6 nM. After UV irradiation, R-AHPIA binds irreversibly to the receptor, as indicated by a loss of [3H]N6-phenylisopropyladenosine binding after extensive washing; the Ki value for this photoinactivation is 1.3 nM. The p-hydroxyphenyl substituent of R-AHPIA can be directly radioiodinated to give a photoaffinity label of high specific radioactivity (125I-AHPIA). This compound has a KD value of about 1.5 nM as assessed from saturation and kinetic experiments. Adenosine analogues compete for 125I-AHPIA binding to rat brain membranes with an order of potency characteristic for A1-adenosine receptors. Dissociation curves following UV irradiation at equilibrium demonstrate 30-40% irreversible specific binding. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicates that the probe is photoincorporated into a single peptide of Mr = 35,000. Labeling of this peptide can be blocked specifically and stereoselectively by adenosine receptor agonists and antagonists in a manner which is typical for the A1-subtype. The results indicate that 125I-AHPIA identifies the ligand-binding subunit of the A1-adenosine receptor, which is a peptide with Mr = 35,000.
Role of the M2-1 Transcription Antitermination Protein of Respiratory Syncytial Virus in Sequential Transcription (1999)

M2-1 protein of human respiratory syncytial virus (RSV) is a transcription antitermination factor that is important for the efficient synthesis of full-length mRNAs as well as for the synthesis of polycistronic readthrough mRNAs, which are characteristic of nonsegmented negative-strand RNA viruses. The contributions of these effects to RSV sequential transcription were investigated with minigenomes which contained one to five genes which were either foreign marker genes or authentic RSV genes. When evaluated on a promoter-proximal gene, the effect of M2-1 on the synthesis of full-length mRNA was much greater for a long (1,212- or 1,780-nucleotide) gene (up to a 615-fold increase) than for a short (274-nucleotide) gene (less than a 2-fold increase). This was independent of whether the gene contained non-RSV or RSV-specific sequence. Once the polymerase had terminated prematurely, it was unable to reinitiate at a downstream gene. These studies also confirmed that M2-1 enhances the synthesis of polycistronic mRNAs and that the magnitude of this effect varied greatly among different naturally occurring gene junctions. The synthesis of polycistronic mRNAs, which presumably involves antitermination at the gene-end signal, required a higher level of M2-1 than did the synthesis of the corresponding monocistronic mRNAs. M2-1 did not have a comparable antitermination effect at the junction between the leader region and the first gene. In a minigenome containing the NS1 and NS2 genes in their authentic sequence context, synthesis of full-length NS1 and NS2 mRNAs in the absence of M2-1 was remarkably high (36 and 57%, respectively, of the maximum levels observed in the presence of M2-1). In contrast, synthesis of mRNA from additional downstream genes was highly dependent on M2-1. Thus, RSV has the potential for two transcription programs: one in the absence of M2-1, in which only the NS1 and NS2 genes are transcribed, and one in the presence of M2-1, in which sequential transcription of the complete genome occurs. The dependence on M2-1 for transcription was greater for a gene in the fifth position from the promoter than for one in the third position. This indicates that under conditions where M2-1 is limiting, its concentration affects the gradient of transcription. Although M2-1 was found to have profound effects on transcription, it had no effect on replication of any minigenome tested, suggesting that it is not an active participant in RNA replication or regulation of RNA replication. Finally, since a permissive RSV infection is marked by a gradual increase in the intracellular accumulation of viral proteins including M2-1, we examined the relative abundances of various mRNAs during RSV infection for evidence of temporal regulation of transcription. None was found, implying that the availability of M2-1 during a permissive infection is sufficient at all times such that its concentration does not mediate temporal regulation of gene transcription.
Pressure-Assisted Synthesis of HKUST-1 Thin Film on Polymer Hollow Fiber at Room Temperature toward Gas Separation (2014)

The scalable fabrication of continuous and defect-free metal-organic framework (MOF) films on the surface of polymeric hollow fibers, departing from ceramic supported or dense composite membranes, is a huge challenge. The critical way is to reduce the growth temperature of MOFs in aqueous or ethanol solvents. In the present work, a pressure-assisted room temperature growth strategy was carried out to fabricate continuous and well-intergrown HKUST-1 films on a polymer hollow fiber by using solid copper hydroxide nanostrands as the copper source within 40 min. These HKUST-1 films/polyvinylidenefluoride (PVDF) hollow fiber composite membranes exhibit good separation performance for binary gases with selectivity 116% higher than Knudsen values via both inside-out and outside-in modes. This provides a new way to enable for scale-up preparation of HKUST-1/polymer hollow fiber membranes, due to its superior economic and ecological advantages.
Hyperinsulinaemia and Alzheimer's Disease (1994)

Because the aetiology of Alzheimer's disease (AD) remains unclear, and fasting hyperinsulinaemia has been incriminated in several human diseases, we examined the relationship between AD, fasting plasma insulin, glucose, body mass index and waist: hip ratio in 24 men and 24 women aged 58-90 years of whom half had probable AD. AD patients were randomly selected from the Bristol Memory Disorders Clinic, while controls were chosen from patients' spouses and the local community. Women with AD, compared with controls, have higher plasma insulin (p = 0.04), higher glucose (p = 0.04), and higher body mass index (p = 0.01). Similar differences were present in men but were not statistically significant except for body mass index (p = 0.03). We conclude that patients with AD have hyperinsulinaemia and insulin resistance, and this may be secondary to being overweight but a causal relationship cannot be excluded.
Beyond convex relaxation: A polynomial-time non-convex optimization approach to network localization (2013)

The successful deployment and operation of location-aware networks, which have recently found many applications, depends crucially on the accurate localization of the nodes. Currently, a powerful approach to localization is that of convex relaxation. In a typical application of this approach, the localization problem is first formulated as a rank-constrained semidefinite program (SDP), where the rank corresponds to the target dimension in which the nodes should be localized. Then, the non-convex rank constraint is either dropped or replaced by a convex surrogate, thus resulting in a convex optimization problem. In this paper, we explore the use of a non-convex surrogate of the rank function, namely the so-called Schatten quasi- norm, in network localization. Although the resulting optimization problem is non-convex, we show, for the first time, that a first- order critical point can be approximated to arbitrary accuracy in polynomial time by an interior-point algorithm. Moreover, we show that such a first-order point is already sufficient for recovering the node locations in the target dimension if the input instance satisfies certain established uniqueness properties in the literature. Finally, our simulation results show that in many cases, the proposed algorithm can achieve more accurate localization results than standard SDP relaxations of the problem.
Genetic markers for early detection of lung cancer and outcome measures for response to chemoprevention (1997)

Lung cancer is one of the leading causes of cancer death in the world. The high mortality rate for lung cancer probably results, at least in part, from the absence of standard clinical procedures for diagnosis of the disease at early and more treatable stages compared to breast, prostate, and colon cancers. The delineation of genetic alterations that occur in lung tumorigenesis may aid in both developing molecular markers for early detection and predicting of response to chemoprevention/chemotherapy. Cytogenetic and molecular genetic studies have shown that mutations in protooncogenes and tumor suppressor genes (TSGs) are critical in the multi-step development and progression of lung tumors. Inactivation of TSGs are by far the most common mutational events documented during the development of lung cancer. For example, loss of function of the Rb and/or p53 genes has been detected in both small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). In addition, allelic loss analyses have implicated the existence of other tumor suppressor gene loci on 9p as well as on 3p, 5q, 8p, 9q, 11p, 11q, and 17q. We examined the short arm of chromosomes 3 and 9 for TSG loci by analyzing 23 squamous cell carcinomas of the lung with numerous microsatellite markers. On chromosome 9p, loss of heterozygosity was detected in all of the 23 tumors and homozygous deletions of the p16/CDKN2 locus were detected in 6 of the 23 (26%) tumors. In addition, a novel region of homozygous deletion was detected in 6 of the tumors (26%) at D9S126. The homozygous deletion of D9S126 was confirmed by fluorescent in situ hybridization (FISH) analysis of tumor tissue touch preparations and isolated nuclei using P1 and cosmid probes that contain D9S126. Only one tumor harbored a homozygous deletion at both the p16/CDKN2 locus and the D9S126 locus. The data identify a region of homozygous loss on the short arm of chromosome 9, suggesting the presence of a novel TSG locus approximately 2.5 cM proximal to p16/CDKN2. On chromosome 3p, a similar high percentage of the tumors exhibited loss of heterozygosity. Also, homozygous deletions were detected in several tumors at 3p21.3. Thus, FISH analysis with probes containing the D9S126 or p16 locus could be used as molecular markers to assay sputum samples for premalignant cells exfoliated from the bronchial epithelium. Probes from other chromosome regions such as 3p21 could be used in a similar manner. J. Cell. Biochem. Suppls. 28/29:64–73. © 1998 Wiley-Liss, Inc.
Laboratory investigation of hemorrhagic colitis outbreaks associated with a rare Escherichia coli serotype (1983)

Two outbreaks of hemorrhagic colitis, a newly recognized syndrome characterized by bloody diarrhea, severe abdominal pain, and little or no fever, occurred in 1982. No previously recognized pathogens were recovered from stool specimens from persons in either outbreak. However, a rare E. coli serotype, O157:H7, was isolated from 9 of 20 cases and from no controls. It was also recovered from a meat patty from the implicated lot eaten by persons in one outbreak. No recovery of this organism was made from stools collected 7 or more days after onset of illness; whereas 9 of 12 culture-positive stools had been collected within 4 days of onset of illness. The isolate was not invasive or toxigenic by standard tests, and all strains has a unique biotype. Plasmid profile analysis indicates that all outbreak-associated E. coli O157:H7 isolates are closely related. These results suggest that E. coli O157:H7 was the causative agent of illness in the two outbreaks.
Role of potassium in acid secretion (2005)

Potassium (K+) ions are critical for the activation and catalytic cycle of the gastric H+, K(+)-ATPase, resulting in the secretion of hydrochloric acid into the parietal cell canaliculus. As both symptom, severity and esophageal mucosal damage in gastro-esophageal reflux disease (GERD) are related to the degree of acid exposure, K+ is a logical target for approaches to inhibit acid production. The probable K+ binding site on the gastric H+, K(+)-ATPase has recently been described and studies are elucidating how K+ activates the enzyme. K+ channels in the apical membrane of the parietal cell are implicated in the recycling of K+ and, to date, three potential K+ channels (KCNQ1, Kir2.1 and Kir4.1) have been identified. The channels represent theoretical sites for agents to control acid secretion but it will be difficult to develop selective blockers. An alternative strategy is to prevent K+ from activating gastric H+, K(+)-ATPase; the potassium-competitive acid blocker (P-CAB) class inhibits acid secretion by binding at or near the K+ binding site. Ongoing research is further defining the role of K+ in the functioning of the gastric H+, K(+)-ATPase, as well as determining the clinical utility of agents directed toward this important cation.
Regulation of Clock and NPAS2 DNA Binding by the Redox State of NAD Cofactors (2001)

Clock:BMAL1 and NPAS2:BMAL1 are heterodimeric transcription factors that control gene expression as a function of the light-dark cycle. Although built to fluctuate at or near a 24-hour cycle, the clock can be entrained by light, activity, or food. Here we show that the DNA-binding activity of the Clock:BMAL1 and NPAS2:BMAL1 heterodimers is regulated by the redox state of nicotinamide adenine dinucleotide (NAD) cofactors in a purified system. The reduced forms of the redox cofactors, NAD(H) and NADP(H), strongly enhance DNA binding of the Clock:BMAL1 and NPAS2:BMAL1 heterodimers, whereas the oxidized forms inhibit. These observations raise the possibility that food, neuronal activity, or both may entrain the circadian clock by direct modulation of cellular redox state.
Optimal Location of Charging Stations for Electric Vehicles in a Neighborhood in Lisbon, Portugal (2011)

Growing concerns about environmental issues have led to the consideration of alternatives to current mobility. Electric mobility is one such alternative that is receiving a great deal of attention in Europe. In particular, a new legal framework for the introduction of an electric mobility system in Portugal has recently been set up by the government. A key issue in this system is recharging the batteries and, consequently, the location of charging stations. This paper presents a study on the location of electric-vehicle charging stations for an area of Lisbon, the capital city of Portugal, characterized with a strong concentration of population and employment. This type of area is appropriate for slow charging because vehicles stay parked for several hours within a 24-h period. The methodology used here is based on a maximal covering model to optimize the demand covered within an acceptable level of service and to define the number and capacity of the stations to be installed. The results clearly indicate that this methodology can be useful in the future planning of electric mobility systems.
A novel role for mitochondria in regulating epigenetic modifications in the nucleus (2008)

Epigenetic modification in the nuclear genome plays a key role in human tumorigenesis. In this paper, we investigated whether changes in the mtDNA copy number frequently reported to vary in a number of human tumors induce methylation changes in the nucleus. We utilized the Restriction Landmark Genomic Scanning (RLGS) to identify genes that undergo changes in their methylation status in response to the depletion and repletion of mtDNA. Our study demonstrates that depletion of mtDNA results in significant changes in methylation pattern of a number of genes. Furthermore, our study suggests that methylation changes are reversed by the restoration of mtDNA in cells otherwise lacking the entire mitochondrial genome. These studies provide the first direct evidence that mitochondria regulate epigenetic modification in the nucleus that may contribute to tumorigenesis.
Modified Vaccinia Ankara: Potential as an Alternative Smallpox Vaccine (2004)

Despite the declaration of smallpox eradication in 1980, the existence of variola stockpiles and the threat of bioterrorism demand that immunity to smallpox through vaccination be maintained. Although the currently available vaccine was used for the most successful medical intervention ever accomplished, it also is associated with side effects that are difficult to accept in a vaccine for a disease that has not been present for >25 years. Herein, we review alternative approaches to maintaining immunity to smallpox through vaccination with attenuated poxviruses, and we suggest modified vaccinia Ankara (MVA) as a leading candidate for an alternative smallpox vaccine.