gebhart/patrepeval huggingface dataset:
Interactions of a proteolytically nicked RNA polymerase of bacteriophage T7 with its promoter. (1987)

The association of nicked RNA polymerase of bacteriophage T7 (Ikeda, R. A., and Richardson, C. C. (1987) J. Biol. Chem. 262, 3790-3799) with the T7 phi 10 promoter has been examined by DNA cleavage protection. The phi 10 promoter consists of a 23-base pair consensus sequence that extends from -17 to +6 with respect to the site of the initiation of transcription (+1). Nicked T7 RNA polymerase alone protects 20 bases from -21 to -2 (+/- 1) base at each border. Initiation and synthesis of the trinucleotide r(GGG) expands and shifts the sequence protected by nicked T7 RNA polymerase. Twenty-five bases are protected from -17 to +8 (+/- 1). The polymerization of three additional ribonucleotides, synthesis of the hexamer r(GGGAGA), further expands the protected sequence. Twenty-seven bases are protected from -17-+10 (+/- 1). Finally, the synthesis of a pentadecaribonucleotide transcript, r(GGGAGACCACGG), leads to the formation of a transcription complex that protects 22 bases from -2-+20 (+/- 1). In comparison to the sequences protected by T7 RNA polymerase the sequences protected by the nicked enzyme are shortened at the 5' end and are translocated downstream much earlier during the initiation of transcription. It appears that a portion of the DNA contacts made at the amino terminus of T7 RNA polymerase are disrupted in the small fragment of nicked T7 RNA polymerase. The changes that are observed in the sequences protected by nicked T7 RNA polymerase are reflected in the physical characteristics of the DNA X enzyme complexes. The number of ion pairs formed by the r(GGG)-initiated complex of the nicked enzyme is reduced, and the association constant for the formation of the r(GGG)-initiated complex is decreased as compared to the intact T7 RNA polymerase.
Structural and Electrochemical Properties of La_(15)Fe_(77-x)Ni_xMn_5B_3 (x=55,60,65,70,75) Hydrogen Storage Alloys (2012)

In this paper the La15Fe77-xNixMn5B3(x=55,60,65,70,75) hydrogen storage electrode alloys were prepared by vacuum melting and rapid quenching method.Through XRD,SEM,EDS and electrochemical methods,the structural,P–C isotherms and electrochemical properties of the alloys were studied.The results show that the La15Fe77-xNixMn5B3(x=55,60,65,70,75) alloys exhibit multiphase structure composed of LaNi5 main phase,La3Ni13B2 phase and(Fe,Ni) phase.With increasing Ni content in the alloys,the plateau property for hydrogen desorption becomes better,the maximum discharge capacity increases and the activation numbers decreases,and the high rate discharge(HRD) properties are improved.
IL11 Antagonist Inhibits Uterine Stromal Differentiation, Causing Pregnancy Failure in Mice1 (2009)

Hormonal contraceptives are unsuitable for many women; thus, the development of new, nonhormonal contraceptives is of great interest. In women, uterine epithelial expression of interleukin 11 (IL11) and its receptor (IL11RA) suggests IL11 is critical for blastocyst attachment during implantation. Il11ra-deficient mice are infertile due to a defective decidualization response to the blastocyst, leading to total pregnancy loss. We examined the effect of administering a PEGylated IL11 antagonist, PEGIL11A (where PEG is polyethylene glycol), on pregnancy outcomes in mice and IL11 signaling in human endometrial epithelial cells (HES). PEGIL11A was detected in sera up to 72 h after intraperitoneal (IP) injection versus up to 2 h for the non-PEGylated antagonist. Following IP injection, PEGIL11A localized to uterine decidual cells and reduced immunoreactive cyclin D3 (IL11 decidual target). To inhibit IL11 action during early decidualization, PEGIL11A or control were administered IP on Days 3-6 (beginning just prior to maximal decidual Il11 expression). On Day 6, mesometrial decidualization was disturbed in PEGIL11A-treated animals with regions of hemorrhage visible in the mesometrial decidua. On Day 10, severe decidual destruction was visible: implantation sites contained significant hemorrhage, and the uterine luminal epithelium had reformed, suggesting a return to estrous cycling. These results demonstrate that PEGIL11A blocked IL11 action in the decidua during early decidualization, which totally abolished pregnancy and which is equivalent to the Il11ra(-/-) mouse. PEGIL11A significantly diminished STAT3 phosphorylation in HES cells in vitro (P < or = 0.05). This study provides valuable information for PEGIL11A that could lead to the development of this protein as a nonhormonal contraceptive.
NACM, A cytopathogen from naegleria ameba: purification, production of monoclonal antibody, and immunoreactive material in NACM-treated vertebrate cell cultures (1989)

ABSTRACT An amebic component NACM (Naegleria ameba cytopathogenic material) is obtained from free-living amebae and acts as a cytopathogen in cultured avian and mammalian cells. NACM has been purified and partially characterized using a scheme that includes ammonium sulfate precipitation, liquid chromatographic separations and electrophoretic isolations. The purified NACM product is biologically active. Its properties, revealed by its behavior following treatment with enzymes and during purification, are those of a protein; its size is in the molecular weight range of 36 000 and it has an isoelectric point of pH 4·2. Monoclonal antibodies have been produced to NACM that prevent its cytopathic activity, and, in dot-blot procedures, identify purified NACM-containing fractions. When used as immunostains, NACM antibodies disclose the presence of immunospecific material both in the amebae and in vertebrate cells inoculated with NACM. In the amebae, the immunostain is located at the tips of the pseudopodia and in the peripheral cytoplasm; in the vertebrate cells, it is absent in uninoculated cells and is not observed in the inoculated cells for the first 3–4 days after the addition of the NACM to the culture. Subsequently, in a time course associated with the development of cytopathic changes observed in the light microscope, immunostaining material develops in the perinuclear cytoplasm where it condenses into a large mass before the cells undergo lysis. On the basis of these results, it appears that NACM represents an unprecedented system in which a protein material from an organism, in the course of destroying unrelated cells, causes the production of a cytoplasmic product that is immunologically recognizable as the inoculating amebic material.
A prospective study of the incidence of deep‐vein thrombosis within a defined urban population (1992)

In a prospective study all positive phlebographies within the well-defined population of the city of Malmö, Sweden, during 1987 were studied in order to determine the incidence of deep venous thrombosis (DVT). Epidemiological data were analysed for the detection of patient groups at increased risk of DVT. The incidence was found to be equal for both sexes, i.e. 1.6 per 1000 inhabitants a year. Risk factors were found to be in accordance with earlier studies. The median age for men was 66 years, compared to 72 years for women. At diagnosis of DVT, 19% of subjects had a known malignancy and within 1 year 5% (19 cases) developed a new malignancy. Of the men, 29% had postoperative or post-traumatic (fracture) DVT, compared to 46% of the women. Fewer patients with DVT than expected (39%) belonged to blood group 0 (31%) (P less than 0.005). Pulmonary embolism (PE) was clinically suspected in only 5% of cases, and diagnosis was verified scintigraphically in 2% of cases. None of these died of PE, but of 6 patients who were found to have PE at autopsy, four died about 4 weeks after the DVT was diagnosed.
Strategies for Cancer Vaccine Development (2010)

Treating cancer with vaccines has been a challenging field of investigation since the 1950s. Over the years, the lack of effective active immunotherapies has led to the development of numerous novel strategies. However, the use of therapeutic cancer vaccines may be on the verge of becoming an effective modality. Recent phase II/III clinical trials have achieved hopeful results in terms of overall survival. Yet despite these encouraging successes, in general, very little is known about the basic immunological mechanisms involved in vaccine immunotherapy. Gaining a better understanding of the mechanisms that govern the specific immune responses (i.e., cytotoxic T lymphocytes, CD4 T helper cells, T regulatory cells, cells of innate immunity, tumor escape mechanisms) elicited by each of the various vaccine platforms should be a concern of cancer vaccine clinical trials, along with clinical benefits. This review focuses on current strategies employed by recent clinical trials of therapeutic cancer vaccines and analyzes them both clinically and immunologically.
A family of membrane proteins associated with presenilin expression and γ‐secretase function (2007)

Presenilin 1 (PS1) forms the gamma-secretase complex with at least three components: nicastrin, APH-1, and PEN-2. This complex mediates intramembrane cleavage of amyloid precursor protein (APP) to generate beta-amyloid protein (Abeta) as well as other type 1 transmembrane proteins. Although PS1 mutations linked to familial Alzheimer's disease influence these cleavages, their biological consequences have not been fully understood. In this study, we used mRNA differential display analysis to identify a gene, denoted adoplin-1/ORMDL-1, which displays significantly reduced expression in association with PS1 mutations. Adoplin-1 and two highly homologous genes (adoplin-2, -3) constitute a gene family that encodes transmembrane proteins. The mRNA and protein levels of adoplins (particularly adoplin-1, -2) were markedly elevated in PS-deficient fibroblasts, compared to wild-type cells. Moreover, knockdown of the three adoplins by RNA interference affected maturation of nicastrin and its association with PS1. Adoplin knockdown additionally resulted in elevated levels of APP C-terminal fragments and decreased Abeta production, suggestive of reduced gamma-secretase activity. Our data collectively indicate that adoplins are unique molecules with PS-related expression and functions that may play important role(s) in the maturation and activity of the gamma-secretase complex.
Raman Spectroscopic Investigation of CH4 and N2 Adsorption in Metal−Organic Frameworks (2007)

The adsorption behavior of CH4 and N2 (298 K, 30 bar) in a series of isoreticular metal−organic frameworks (IRMOFs) was investigated by Raman spectroscopy. For CH4, the ν1 vibrational mode shifted to lower frequency by 7.6, 8.4, 11.0, 10.3, and 10.1 cm-1 from 2917 cm-1 when adsorbed to IRMOF-1, -6, -8, -11, and -18, respectively. Along this same series, the adsorbed N2 stretch exhibited smaller shifts of 2.7, 3.1, 4.2, 4.1, and 3.7 cm-1. These shifts arise because of interactions within the framework pores, and not with the outer crystal surface. In all cases, Raman spectra at pressures up to 30 bar showed that saturation of the sorption sites does not occur. The observed shifts of the vibrational modes for each gas indicate different chemical environments within different IRMOFs, pointing to the important role the linkers play in the adsorption of gases.
Optical data storage with electron trapping materials using M-ary data channel coding (1992)

The linear amplitude response of electron trapping optical storage materials provides the capability of utilizing multiple amplitude symbols in the data channel code sets. M-ary channel coding has received much interest from information theorists but, has had little acceptance for practical storage systems. Conventional optical and magnetic storage devices are limited by the marking process to codes requiring no more than two, or possibly three, symbol amplitudes. Electron trapping materials offer an excellent opportunity to exploit the increased capacity and transfer rates characteristic of M-ary code sets.
Biochemistry of Na,K-ATPase (2002)

The Na,K-ATPase or sodium pump carries out the coupled extrusion and uptake of Na and K ions across the plasma membranes of cells of most higher eukaryotes. It is a member of the P-type ATPase superfamily. This heterodimeric integral membrane protein is composed of a 100-kDa alpha-subunit with ten transmembrane segments and a heavily glycosylated beta subunit of about 55 kDa, which is a type II membrane protein. Current ideas on how the protein achieves active transport are based on a fusion of results of transport physiology, protein chemistry, and heterologous expression of mutant proteins. Recently acquired high resolution structural information provides an important new avenue for a more complete understanding of this protein. In this review, the current status of knowledge of Na,K-ATPase is discussed, and areas where there is still considerable uncertainty are highlighted.
Development of a New Material: Monolithic Ti4O7 Ebonex Ceramic (2002)

Towards an Electrically Conductive Ceramic The Properties of Titanium Suboxide & Associated Processes Applications - I Applications - II Is Ti4O7 an Optimum Ceramic Electrode Choice? Conclusions and Epilogue References and Further Reading Index.
Inhibition of Sham Feeding-Induced Gastric Secretion and Serum Hormonal Responses by Analogs of (pyro)Glu-His-Gly-OH (1982)

The effects of intravenous infusion of analogs of (pyro)Glu-His-Gly-OH on secretion of gastric acid and elevation of serum gastrin and insulin levels induced by sham feeding were evaluated in conscious dogs. Tripeptides (pyro)Glu-3Me-His-Gly-OH, (pyro)Glu-His-D-Ala-OH, D-(pyro)Glu-His-Gly-OH, (pyro)Glu-His-Trp-NH2, (pyro)Glu-His-Gly-NH2, and (pyro)Glu-His-Gly-ethylamide, but not control peptides Glu-His-Pro-OH or Leu-Arg-Phe-OH, significantly suppressed the cephalic phase rise in serum insulin and gastrin as compared to saline-infused controls and lowered these hormonal levels below basal values. Analogs (pyro)Glu-3Me-His-Gly-OH, D-(pyro)Glu-His-Gly-OH, and (pyro)Glu-His-D-Ala-OH also significantly inhibited the gastric acid response to sham feeding. The reductions in gastric acid caused by (pyro)Glu-His-Gly-NH2 or (pyro)Glu-His-Gly-ethylamide were less intense. Statistical analyses of food intake in 86 sham feeding experiments in seven dogs showed that the reduction during the infusion of (pyro)Glu-His-Gly-OH and its analogs was not significant by Duncan's multiple range test, and only that induced in (pyro)Glu-3Me-His-Gly-OH was significant by Student's t-test as compared to saline control. Our findings suggest that some analogs of (pyro)Glu-His-Gly-OH are more powerful inhibitors of the hormonal and gastric secretory responses during the cephalic phase stimulation than the original tripeptide.
Characterization of Superantigen-Induced Clonal Deletion with a Novel Clan III-Restricted Avian Monoclonal Antibody: Exploiting Evolutionary Distance to Create Antibodies Specific for a Conserved VH Region Surface (2000)

Evolution of the Ab system has yielded three clans of VH region genes that are represented in almost every known higher species with an adaptive immune system. These clans are defined by sequence homologies primarily in highly conserved framework (FR) subdomains, which serve a scaffolding function maintaining the conformation of loops responsible for Ag binding. Structural analyses indicate that the VH FR1 and FR3 form a conserved composite exposed surface, which has been implicated in interactions with B cell superantigens. To directly investigate the expression of clan-defined supraclonal sets, we exploited the evolutionary distance of the chicken immune system and the selection power of phage display, to derive Abs diagnostic for clan III Ig. Using a specially tailored immunization and selection strategy, we created recombinant avian single chain Fv Abs specific for the clan III products, including those from the human VH3 family, and the analogous murine 7183, S107, J606, X24, and DNA4 families, and binding was competitive with natural B cell superantigens. The archetype, LJ-26, was demonstrated to recognize a clan-specific surface expressed in diverse mammalian, and also the Xenopus and chicken, immune systems. In flow-cytometric studies with LJ-26, we found that treatment of heterozygous T15i transgenic mice with a model B cell superantigen induced a clan III-restricted clonal deletion. These studies demonstrate the utility of a novel recombinant serologic reagent to study the composition of the B cell compartment and also the consequences of B cell superantigen exposure.
Characterization of inhibition of M2 ion channel activity by BL-1743, an inhibitor of influenza A virus (1996)

The influenza A virus M2 integral membrane protein has ion channel activity that can be inhibited by the antiviral drug amantadine. Recently, a spirene-containing compound, BL-1743 (2-[3-azaspiro (5,5)undecanol]-2-imidazoline), that inhibits influenza virus growth was identified (S. Kurtz, G. Lao, K. M. Hahnenberger, C. Brooks, O. Gecha, K. Ingalls, K.-I. Numata, and M. Krystal, Antimicrob. Agents Chemother. 39:2204-2209, 1995). We have examined the ability of BL-1743 to inhibit the M2 ion channel when expressed in oocytes of Xenopus laevis. BL-1743 inhibition is complete as far as can be measured by electrophysiological methods and is reversible, with a reverse reaction rate constant of 4.0 x 10(-3) s(-1). In contrast, amantadine inhibition is irreversible within the time frame of the experiment. However, BL-1743 inhibition and amantadine inhibition have similar properties. The majority of isolated influenza viruses resistant to BL-1743 are also amantadine resistant. In addition, all known amino acid changes which result in amantadine resistance also confer BL-1743 resistance. However, one BL-1743-resistant virus isolated, designated M2-I35T, contained the change Ile-35-->Thr. This virus is >70-fold more resistant to BL-1743 and only 10-fold more resistant to amantadine than the wild-type virus. When the ion channel activity of M2-I35T was examined in oocytes, it was found that M2-I35T is BL-1743 resistant but is reversibly inhibited by amantadine. These findings suggest that these two drugs interact differently with the M2 protein transmembrane pore region.
Sodium channels accumulate at the tips of injured axons (1994)

The axolemmal distribution of voltage-gated sodium channels largely determines the regions of axonal electrical excitability. Using a well-characterized anti-sodium channel antibody, we examined peripheral nerve fibers focally injured by exposure to the neurotoxic agent, potassium tellurite (K2TeO3). Immunocytochemical and radioimmunoassay data showed a focal accumulation of sodium channels within the tips of injured axons. The major increase in sodium channel concentration occurred between 7 and 11 days after toxin exposure; however, immunocytochemically, excess sodium channels persisted in several axonal endings for a much longer time. The accumulation of sodium channels at injured axonal tips may be responsible, in part, for ectopic axonal excitability and the resulting abnormal sensory phenomena (especially pain and paresthesias) which frequently complicate peripheral nerve injury in humans.
An adaptive multimodal interface for wireless applications (2002)

In this paper we present an adaptive multimodal interface for wireless computing applications. The system optimizes its performance by dynamically selecting its network service based on cost and performance requirements. We describe a prototype system and its application to demonstrate the proposed concept.
A disposable DNA sample preparation microfluidic chip for nucleic acid probe assay (2003)

A new DNA sample preparation microfluidic chip for Nucleic Acid (NA) probe assay has been proposed. The proposed microfluidic chip is composed of three parts: microfilter, micromixer and DNA purification chip. We have fabricated a microsieve type filter with an array of 2.2 /spl mu/m diameter holes. We have also demonstrated the mixing can be successfully achieved for low Reynolds number below 50 by using the fabricated micromixer. The fabricated DNA purification chip has shown a binding capacity of 15 ng/cm/sup 2/ and a minimum extractable input concentration of 100 copies/200 /spl mu/L. The proposed microfluidic chip can be applied for low-cost, disposable sample preparation of NA probe assays.
Scopolamine model of dementia: electroencephalogram findings and cognitive performance (1998)

Scopolamine produces similar memory deficits seen in the elderly, but the drug cannot induce the full range of deficits seen in patients with Alzheimer's disease. Various aspects of memory were unaffected by scopolamine administration. Memory improvements in elderly subjects can be achieved after cholinergic stimulation.
Chemical Arsenal for the Study of O-GlcNAc (2011)

The concepts of both protein glycosylation and cellular signaling have been influenced by O-linked-β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) on the hydroxyl group of serine or threonine residues. Unlike conventional protein glycosylation, O-GlcNAcylation is localized in the nucleocytoplasm and its cycling is a dynamic process that operates in a highly regulated manner in response to various cellular stimuli. These characteristics render O-GlcNAcylation similar to phosphorylation, which has long been considered a major regulatory mechanism in cellular processes. Various efficient chemical approaches and novel mass spectrometric (MS) techniques have uncovered numerous O-GlcNAcylated proteins that are involved in the regulation of many important cellular events. These discoveries imply that O-GlcNAcylation is another major regulator of cellular signaling. However, in contrast to phosphorylation, which is regulated by hundreds of kinases and phosphatases, dynamic O-GlcNAc cycling is catalyzed by only two enzymes: uridine diphospho-N-acetyl-glucosamine:polypeptide β-N-acetylglucosaminyl transferase (OGT) and β-D-N-acetylglucosaminidase (OGA). Many useful chemical tools have recently been used to greatly expand our understanding of the extensive crosstalk between O-GlcNAcylation and phosphorylation and hence of cellular signaling. This review article describes the various useful chemical tools that have been developed and discusses the considerable advances made in the O-GlcNAc field.
Direct Josephson coupling between superconducting flux qubits (2005)

We have demonstrated strong antiferromagnetic coupling between two three-junction flux qubits based on a shared Josephson junction, and therefore not limited by the small inductances of the qubit loops. The coupling sign and magnitude were measured by coupling the system to a high-quality superconducting tank circuit. Design modifications allowing to continuously tune the coupling strength and/or make the coupling ferromagnetic are discussed.
Data synchronization protocol in mobile computing environment using yncML (2003)

The popularity of mobile computing and communications devices can be traced to their ability to deliver information to users when needed. Users want anywhere, anytime access to information and applications from the device in hand, and they want to access and update this information. The ability to use applications and information on one mobile device, then to synchronize any updates with the applications and information back at the office, or on the network, is key to the utility and popularity of this pervasive, disconnected way of computing. Rather, there is a proliferation of different, proprietary data synchronization protocols for mobile devices. Each of these protocols is only available for selected transports, implemented on a selected subset of devices, and able to access a small set of networked data. The absence of a single synchronization standard poses many problems for end users, device manufacturers, application developers, and service providers. We analyze the SyncML architecture and protocol of synchronization technique, and represent the server architecture.