gebhart/patrepeval huggingface dataset:
A class of fast cyclic convolution algorithms based on block pseudocirculants (1995)

Pseudocirculant matrices have been studied in the past in the context of FIR filtering, block filtering, polyphase networks and others. For completeness, their relation to cyclic convolution, stride permutations, circulant matrices, and to certain permutations of the Fourier matrix is explicitly established in this work. Within this process, a class of highly regular fast cyclic convolution algorithms, based on block pseudocirculant matrices, is obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Surface passivation dependent photoluminescence from silicon quantum dot phosphors (2012)

We demonstrate wavelength-tunable, air-stable and nontoxic phosphor materials based on silicon quantum dots (SiQDs). The phosphors, which are composed of micrometer-size silicon particles with attached SiQDs, are synthesized by an electrochemical etching method under ambient conditions. The photoluminescence (PL) peak wavelength can be controlled by the SiQD size due to quantum confinement effect, as well as the surface passivation chemistry of SiQDs. The red-emitting phosphors have PL quantum yield equal to 17%. The SiQD-phosphors can be embedded in polymers and efficiently excited by 405 nm light-emitting diodes for potential general lighting applications.
Hiponatremia e hidratación: hidratación adecuada para corredores de distancia : auto-test para estimar la hidratación (2003)

Avian influenza, listed by the World Organization for Animal Health (OIE), has become a disease of great importance for animal and human health. Several aspects of the disease lack scientific information, which has hampered the management of some recent crises. Millions of animals have died, and concern is growing over the loss of human lives and management of the pandemic potential. On the basis of data generated in recent outbreaks and in light of new OIE regulations and maintenance of animal welfare, we review the available control methods for avian influenza infections in poultry, from stamping out to prevention through emergency and prophylactic vaccination.
Friendship Selection in the Social Internet of Things: Challenges and Possible Strategies (2014)

The Internet of Things (IoT) is expected to be overpopulated by a very large number of objects, with intensive interactions, heterogeneous communications, and millions of services. Consequently, scalability issues will arise from the search of the right object that can provide the desired service. A new paradigm known as Social Internet of Things (SIoT) has been introduced and proposes the integration of social networking concepts into the Internet of Things. The underneath idea is that every object can look for the desired service using its friendships, in a distributed manner, with only local information. In the SIoT it is very important to set appropriate rules in the objects to select the right friends as these impact the performance of services developed on top of this social network. In this work, we addressed this issue by analyzing possible strategies for the benefit of overall network navigability. We first propose five heuristics, which are based on local network properties and that are expected to have an impact on the overall network structure. We then perform extensive experiments, which are intended to analyze the performance in terms of giant components, average degree of connections, local clustering, and average path length. Unexpectedly, we discovered that minimizing the local clustering in the network allowed for achieving the best results in terms of average path length. We have conducted further analysis to understand the potential causes, which have been found to be linked to the number of hubs in the network.
Gene expression profiling of mouse postnatal cerebellar development (2000)

Expression patterns of 1,869 genes were determined using adapter-tagged competitive PCR (ATAC-PCR) at 6 time points during mouse postnatal cerebellar development. The expression patterns were classified into 12 clusters that were further assembled into 3 groups by hierarchical cluster analysis. Among the 1,869 genes, 1,053 known genes were assigned to 90 functional categories. Statistically significant correlation between the clusters or groups of gene expression and the functional categories was ascertained. Genes involved in oncogenesis or protein synthesis were highly expressed during the earlier stages of development. Those responsible for brain functions such as neurotransmitter receptor and synapse components were more active during the later stages of development. Many other genes also showed expression patterns in accordance with literature information. The gene expression patterns and the inferred functions were in good agreement with anatomical as well as physiological observations made during the developmental process.
The phycobilisome, a light-harvesting complex responsive to environmental conditions. (1993)

Photosynthetic organisms can acclimate to their environment by changing many cellular processes, including the biosynthesis of the photosynthetic apparatus. In this article we discuss the phycobilisome, the light-harvesting apparatus of cyanobacteria and red algae. Unlike most light-harvesting antenna complexes, the phycobilisome is not an integral membrane complex but is attached to the surface of the photosynthetic membranes. It is composed of both the pigmented phycobiliproteins and the nonpigmented linker polypeptides; the former are important for absorbing light energy, while the latter are important for stability and assembly of the complex. The composition of the phycobilisome is very sensitive to a number of different environmental factors. Some of the filamentous cyanobacteria can alter the composition of the phycobilisome in response to the prevalent wavelengths of light in the environment. This process, called complementary chromatic adaptation, allows these organisms to efficiently utilize available light energy to drive photosynthetic electron transport and CO2 fixation. Under conditions of macronutrient limitation, many cyanobacteria degrade their phycobilisomes in a rapid and orderly fashion. Since the phycobilisome is an abundant component of the cell, its degradation may provide a substantial amount of nitrogen to nitrogen-limited cells. Furthermore, degradation of the phycobilisome during nutrient-limited growth may prevent photodamage that would occur if the cells were to absorb light under conditions of metabolic arrest. The interplay of various environmental parameters in determining the number of phycobilisomes and their structural characteristics and the ways in which these parameters control phycobilisome biosynthesis are fertile areas for investigation.
The Purification and Characterization of Escherichia coli Enolase (1971)

Enolase has been purified from aqueous extracts of Escherichia coli acetone powder by (a) heat treatment, (b) fractionation with acetone, (c) TEAE-cellulose chromatography, (d) Sephadex G-100 chromatography, and (e) crystallization. The purified, crystalline enzyme migrates as a single band in disc gel electrophoresis and is homogeneous by ultracentrifugal analysis. The molecular weight of the enzyme is approximately 90,000, as determined by sedimentation velocity and sedimentation equilibrium experiments. The subunit molecular weight estimated by electrophoresis in polyacrylamide gels containing sodium dodecyl sulfate is 46,000, suggesting that the enzyme is composed of two subunits of equal size. Functionally there are many similarities between E. coli enolase and other enolases studied. Thus, the dependence on Mg2+ for activity and the inhibition by fluoride in the presence of phosphate are quantitatively very similar for all enolases. Other catalytic parameters (Km, Vmax, and pH optimum) are also similar, but minor quantitative distinction indicates that E. coli enolase is more closely related to yeast enolase than to enolases from vertebrate muscle.
In vitro Sortagging of an Antibody Fab Fragment: Overcoming Unproductive Reactions of Sortase with Water and Lysine Side Chains (2011)

Sortase A from Staphylococcus aureus attracts growing interest for its use in biotechnological protein modification. This enzyme binds to a short signal sequence at the C terminus of a target protein, cleaves it by formation of an acyl-enzyme intermediate, and subsequently attaches an oligoglycine with a peptide bond. In this work, we explored its usability for the modification of the L19 Fab fragment (specific for fibronectin ED-B), a promising candidate for antibody-based cancer therapy. The Fab fragment was expressed with a sortase signal sequence attached to its light chain, and was successfully modified with a fluorescent oligoglycine probe in good yield. Our interest focused on performance under conditions of limited oligoglycine concentrations. Two unproductive side reactions of sortase were observed. The first was hydrolysis of the acyl-enzyme intermediate; in the second, sortase accepted the ε-amino group of lysine as substrate, thereby resulting in polypeptide crosslinking. In case of the L19 Fab fragment, it led to the covalent connection of the heavy and light chains. Both side reactions were effectively suppressed by sufficient concentrations of the oligoglycine probe.
Chimeras of the Rat and Human FSH Receptors (FSHRs) Identify Residues that Permit or Suppress Transmembrane 6 Mutation-Induced Constitutive Activation of the FSHR via Rearrangements of Hydrophobic Interactions Between Helices 6 and 7 (2002)

Although a large number of naturally occurring activating mutations of the human LH receptor (hLHR) and human TSH receptor (hTSHR) have been identified, only one activating mutation of the human FSH receptor (hFSHR) has been found. Furthermore, mutations of several residues within the i3/transmembrane domain (TM) 6 region of the hFSHR that were done based upon known constitutively activating mutations of the human LHR were found to have no effect on hFSHR signaling. One of the hFSHR mutations examined in this context was the substitution of a highly conserved aspartate (D581) in TM6 with glycine. We show herein that although the basal activity of the rat FSHR (rFSHR) is similar to the hFSHR, mutation of the comparable residue (D580) in the rFSHR causes marked constitutive activation. Taking advantage of the high degree of amino acid identity between the rat and human FSHRs, we have used chimeras and point substitutions to determine the precise residues that suppress or permit constitutive activity by the D580/581G mutation. Thus, the simultaneous substitution of M576 in TM6 and H615 in TM7 of the hFSHR with the cognate rFSHR residues (threonine and tyrosine, respectively) now renders the hFSHR(D581G) mutant constitutively active. Conversely, the substitution of Y614 of the rFSHR with the cognate hFSHR residue (histidine) fully suppresses the constitutive activity of the rFSHR (D580G) mutant. Computer models of the human and rat FSHRs and mutants thereof were created based upon the crystal structure of rhodopsin. These models suggest that differences in hydrophobic interactions between TMs 6 and 7 of the rat and human FSHRs may account for the ability of TM6 of the rat, but not human, FSHR to adopt an active conformation as a result of the D580/581G mutation.
Antibody guided diagnosis and therapy of brain gliomas using radiolabeled monoclonal antibodies against epidermal growth factor receptor and placental alkaline phosphatase. (1989)

Twenty-seven patients with brain glioma were scanned using 123I-labeled monoclonal antibodies against epidermal growth factor receptor (EGFR1) or placental alkaline phosphatase (H17E2). Successful localization was achieved in 18 out of 27 patients. Eleven out of 27 patients were also studied using a nonspecific control antibody (11.4.1) of the same immunoglobulin subclass and observable tumor localization was also achieved in five patients. The specificity of targeting was assessed by comparing images obtained with specific and nonspecific antibodies and by examining tumor and normal tissue biopsies after dual antibody administration. Ten patients with recurrent grade III or IV glioma who showed good localization of radiolabeled antibody were treated with 40-140 mCi of 131I-labeled antibody delivered to the tumor area intravenously (n = 5) or by infusion into the internal carotid artery (n = 5). Six patients showed clinical improvement lasting from 6 mo to 3 yr. One patient continues in remission (3 yr after therapy), but the other five who responded initially relapsed 6-9 mo after therapy and died. No major toxicity was attributable to antibody-guided irradiation. Targeted irradiation by monoclonal antibody may be clinically useful and should be explored further in the treatment of brain gliomas resistant to conventional forms of treatment.
Cloning of ten distinct DNA fragments of Clostridium thermocellum coding for cellulases (1985)

Ten distinct Eco RI fragments of Clostridum thermocellum DNA have been cloned in Escherichia coli and shown to express enzymatic activities related to cellulose degradation. Two of the cloned fragments appeared to carry the previously characterized celA and celB genes, which code for the endoglucanases (EG) A and B. Five other cloned fragments code for hitherto unidentified EGs, which can be detected by the Congo red test for hydrolysis of carboxymethylcellulose (CMC). In addition, three separate clones hydrolyzed methylumbelliferyl-β-cellobioside (MUC) but not CMC, hinting that they may express three different cellobiohydrolase genes.
Kinetics of a Reversible Covalent-Bond-Forming Reaction Observed at the Single-Molecule Level (2002)

Arsenic, currents, and pores: Reversible covalent-bond-forming reactions are monitored by single-molecule detection. One reactant, a thiol group, is present on the wall of a protein pore, while the second, an organoarsenic(III) compound is in solution (see scheme). The reaction is detected by observing the current flowing through the pore (see trace), which allows the determination of rate constants with microsecond time resolution.
Structure of the Rat Platelet Factor 4 Gene: A Marker for Megakaryocyte Differentiation (1987)

A rat platelet factor 4 (PF4) cDNA has been isolated by immunoscreening a g lambda 11 rat megakaryocyte cDNA expression library. Sequence analysis of the rat PF4 cDNA revealed that this megakaryocyte protein is composed of a leader sequence of 29 amino acid residues and a mature protein sequence of 76 amino acid residues. The structure of rat PF4 derived from its cDNA shows a marked homology with the amino acid sequence of human PF4 obtained by classical protein chemistry techniques. This observation is particularly striking with regard to the carboxy-terminal region of rat and human PF4, where 28 of the last 31 C-terminal residues are identical. The rat PF4 gene was obtained from a rat genomic library by using rat PF4 cDNA as a hybridization probe. Sequence analysis showed that the gene is constructed of three exons and two short introns. The transcriptional start site is located 73 base pairs upstream of the translational start codon as judged by S1 nuclease mapping and primer extension. The 5' noncoding region of the gene also exhibited a sequence homologous to the TATA box at -31, as well as a series of direct and inverted repeat sequences and a cluster of 26 T residues at -155 to -218. This latter domain may be involved in regulating PF4 gene expression during megakaryocytopoiesis.
Specific covalent binding of platelet-derived growth factor to human plasma alpha 2-macroglobulin. (1984)

Attempts to measure the platelet-derived growth factor (PDGF) in human plasma resulted in the discovery of a specific plasma binding protein. The 125I-labeled PDGF (125I-PDGF)-plasma binding protein complex retained mitogenic activity but lost reactivity against rabbit anti-PDGF antiserum. Copurification of the plasma binding protein and alpha 2-macroglobulin (alpha 2M) in human plasma, the formation of a complex between 125I-PDGF and purified alpha 2M, and the comigration of the 125I-PDGF-plasma binding protein complex and the 125I-PDGF-alpha 2M complex in NaDodSO4/polyacrylamide gel electrophoresis and in pore-limiting polyacrylamide gel electrophoresis strongly suggested that alpha 2M is the plasma binding protein for 125I-PDGF. Immunoprecipitation of 125I-PDGF-alpha 2M and 125I-PDGF-plasma binding protein complexes by anti-human alpha 2M antiserum further established that alpha 2M and the plasma binding protein are the same molecule. Approximately 20% of 125I-PDGF is complexed by alpha 2M; further 125I-PDGF is complexed if the remaining 125I-PDGF is incubated with additional alpha 2M. Complex formation of 125I-PDGF with plasma or with alpha 2M was completely inhibited by 0.2 mM p-chloromercuric benzoate or 0.2 mM N-ethylmaleimide. The 125I-PDGF-alpha 2M complex or 125I-PDGF-plasma binding protein complex was not dissociated by 8 M urea, 1 M acetic acid, 0.1 M NaOH, or 1% NaDodSO4 but was dissociated by 2-mercaptoethanol, suggesting that the covalent binding of 125I-PDGF to alpha 2M occurs through a disulfide/sulfhydryl exchange reaction. The 125I-PDGF-alpha 2M complex (780,000 daltons) appears to contain two molecules of 125I-PDGF and two dimers of alpha 2M. The precise physiological role of the 125I-PDGF-alpha 2M interaction is unknown. alpha 2M may serve to limit PDGF released locally at sites of blood vessel injury. Alternatively, because of the nearly complete homology between the partial amino acid sequence of PDGF and the predicted amino acid sequence of the transforming protein of the simian sarcoma virus, p28sis, alpha 2M may play an important role in limiting the activity of a PDGF-like activity expressed by virus-transformed cells.
Matrix Metalloproteinases in Brain Injury (1995)

Proteolytic remodeling of the extracellular matrix occurs normally during development and pathologically in arthritis, tumor metastasis, wound healing, and angiogenesis. The major extracellular matrix-degrading proteinases belong to the matrix metalloproteinase (MMP) and plasminogen activator gene families. Intracerebral injection of 72-kDa type IV collagenase (gelatinase A) opens the blood-brain barrier. During hemorrhagic brain injury or intracerebral injection of proinflammatory cytokines, endogenous production of 92-kDa type IV collagenase (gelatinase B) occurs. The gelatinase B gene contains a phorbol ester responsive region (TRE) that binds AP-1 proteins, including c-Fos/c-Jun dimer, the early immediate response gene products. Maximum production of gelatinase B in injury occurs between 16 and 24 h, making this a late effector gene. The serine proteinase, urokinase-type plasminogen activator (uPA), is also produced at that time. Gelatinases and plasminogen activators work in concert to disrupt basement membranes proteolytically. A similar process opens the blood-brain barrier after ischemic and hemorrhagic brain injury, leading to secondary vasogenic brain edema. Delayed damage by proteolytic cascade enzymes provides opportunities for treatment much later than had been thought possible. Potential treatments possible in this second therapeutic window include interfering with the genes that produce the MMPs or inhibiting the action of the gene products.
Calcium binding to phosphatidylcholine bilayers as studied by deuterium magnetic resonance. Evidence for the formation of a calcium complex with two phospholipid molecules (1984)

The binding of Ca2+ to bilayer membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was investigated with atomic absorption spectroscopy and deuterium magnetic resonance, leading to the following conclusions. Atomic absorption spectroscopy allowed the determination of the amount of Ca2+ bound to the membrane surface (Cb) at low Ca2+ concentrations (3-100 mM). Simultaneous measurements of the deuterium magnetic resonance spectra of POPC with specifically deuterated choline head groups revealed a linear relationship between the quadrupole splitting and the amount of bound Ca2+. With this calibration, the amount of bound Ca2+ could be determined from the deuterium spectra under conditions where atomic absorption spectroscopy was technically not feasible, i.e., in the concentration range of 0.1-5 M CaCl2. The Ca2+ binding isotherm exhibited saturation behavior. The quadrupole splitting at the saturation limit corresponded to a binding stoichiometry of one Ca2+ per two POPC molecules. The surface charge density (sigma) could be evaluated from the amount of bound Ca2+ and the surface area per POPC molecule. By employing the Gouy-Chapman theory, it was then possible to determine the surface potential (psi 0) and the Ca2+ concentration immediately at the lipid-water interface (CI). With this set of experimental parameters, various models for the mode of Ca2+ binding were tested. A simple partition equilibrium or a Langmuir absorption model could be ruled out. However, a very good fit to the experimental data was obtained by applying the law of mass action in the form Cb/(1 - 2Cb)2 = KCI in which K is the only adjustable parameter.(ABSTRACT TRUNCATED AT 250 WORDS)
Quantification of Immunotoxin Number for Complete Therapeutic Response (2003)

Radiolabeled antibodies are commonly administered to patients, and their biodistribution to tumor and normal tissues is routinely quantitated by nuclear medicine scanning for dosimetry (). Only a few studies have examined the uptake of radiolabeled immunotoxins into tumors or normal tissues (, , , , , ). These studies used toxin-ligand chemical conjugates and determined uptake by percentage of injected dose per gram of tissue (%id/g). The present review details the methods involved in determining the uptake of the recombinant immunotoxin LMB-2, and the calculations necessary to convert %id/g to the number of molecules binding specifically to each tumor cell. These methods can also be used for any radiolabeled ligand, including monoclonal antibodies (MAbs), to determine numbers of molecules per cell that bind to the target antigen in vivo. With immunotoxins, however, one can compare the number of molecules per cell needed for complete tumor regression with the need for eradication of tumor cells in monolayer culture.
The ubiquitin-specific protease USP2a enhances tumor progression by targeting cyclin A1 in bladder cancer (2012)

The deubiquitinating enzyme USP2a has shown oncogenic properties in many cancer types by impairing ubiquitination of FASN, MDM2, MDMX or Aurora A. Aberrant expression of USP2a has been linked to progression of human tumors, particularly prostate cancer. However, little is known about the role of USP2a or its mechanism of action in bladder cancer. Here, we provide evidence that USP2a is an oncoprotein in bladder cancer cells. Enforced expression of USP2a caused enhanced proliferation, invasion, migration and resistance to several chemotherapeutic reagents, while USP2a loss resulted in slower proliferation, greater chemosensitivity and reduced migratory/invasive capability compared with control cells. USP2a, but not a catalytically inactive mutant, enhanced proliferation in immortalized TRT-HU1 normal human bladder epithelial cells. USP2a bound to cyclin A1 and prevented cyclin A1 ubiquitination, leading to accumulation of cyclin A1 by a block in degradation. Enforced expression of wild type USP2a, but not an inactive USP2a mutant, resulted in cyclin A1 accumulation and increased cell proliferation. We conclude that USP2a impairs ubiquitination and stabilizes an important cell cycle regulator, cyclin A1, raising the possibility of USP2a targeting as a therapeutic strategy against bladder tumors in combination with chemotherapy.