gebhart/patrepeval huggingface dataset:
GAGA Factor-dependent Transcription and Establishment of DNase Hypersensitivity Are Independent and Unrelated Events in Vivo (2000)

Using a Drosophila transgenic system we investigated the ability of GAGA factor, a putative anti-repressor, to modulate transcription-related events in the absence or presence of a bona fide activator, the Adf-1 transcription factor. In contrast to previous in vitro and in vivo data linking the binding of GAGA factor to the acquisition of DNase hypersensitivity at heat shock promoters, we observed that inserting multiple GAGA binding motifs adjacent to a minimal alcohol dehydrogenase (Adh) promoter led to strongly elevated embryonic transcription without creation of a promoter-associated DNase-hypersensitive (DH) site. Establishment of DNase hypersensitivity required the presence of both GAGA and Adf-1 binding sites and was accompanied by a further, synergistic increase in transcription. Because Adf-1 is capable neither of establishing a DH site nor of promoting efficient transcription by itself in embryos, it is likely that DH site formation depends on a GAGA factor-mediated binding of Adf-1 to chromatin, perhaps facilitated by a locally remodeled downstream promoter region. More generally we suggest that GAGA factor-binding sequences may operate in a promoter-specific context, with transcriptional activation, polymerase pausing, and/or DH site formation critically dependent on the nature of the sequences (and their binding partners) linked in cis.
Advertisement evaluation using visual saliency based on foveated image (2009)

This paper proposes a novel approach to advertisement evaluation using automatic salient regions. The salient regions are detected using a predicting model, in which the estimation are obtained by the space variant foveated image. The saliency is defined as the difference between the input image and its estimation. Then an advertisement is determined as attractive if the detected salient regions are overlapped with the interested regions of the advertisement. The experimental results on the advertisements data set are encouraging.
Identification of disease genes by whole genome CGH arrays (2005)

Small, submicroscopic, genomic deletions and duplications (1 kb to 10 Mb) constitute up to 15% of all mutations underlying human monogenic diseases. Novel genomic technologies such as microarray-based comparative genomic hybridization (array CGH) allow the mapping of genomic copy number alterations at this submicroscopic level, thereby directly linking disease phenotypes to gene dosage alterations. At present, the entire human genome can be scanned for deletions and duplications at over 30,000 loci simultaneously by array CGH ( approximately 100 kb resolution), thus entailing an attractive gene discovery approach for monogenic conditions, in particular those that are associated with reproductive lethality. Here, we review the present and future potential of microarray-based mapping of genes underlying monogenic diseases and discuss our own experience with the identification of the gene for CHARGE syndrome. We expect that, ultimately, genomic copy number scanning of all 250,000 exons in the human genome will enable immediate disease gene discovery in cases exhibiting single exon duplications and/or deletions.
The 2008 Carl Ludwig Lecture: retrotrapezoid nucleus, CO 2 homeostasis, and breathing automaticity (2008)

The retrotrapezoid nucleus (RTN) contains 2,000 glutamatergic neurons that innervate selectively the respiratory centers of the pontomedullary region. These cells are at the ventral medullary surface in a previously identified chemosensitive region. RTN neurons are highly sensitive to acid in vitro and vigorously activated by inputs from the carotid body and from the hypothalamus in vivo. Mutations of the transcription factor Phox2b cause the congenital hypoventilation syndrome (CCHS), a disease characterized by extremely reduced chemoreflexes and the loss of breathing automaticity during sleep. RTN neurons express Phox2b and develop poorly in a mouse model of CCHS, which lacks chemoreflexes. Based on these and other data, I propose that the RTN is a critical nodal point for the homeostatic regulation of arterial PCO2 and that the nucleus operates as follows. RTN always contributes a major fraction of the tonic excitatory drive to the respiratory centers. RTN neurons derive their activity from two sources: a chemosensory drive (intrinsic chemosensitivity and inputs from the carotid bodies) and synaptic inputs from higher brain centers (non-chemosensory drive). Under anesthesia or non-rapid eye movement sleep, the chemosensory drive to RTN neurons dominates, and, under these circumstances, the excitatory input from RTN to the respiratory controller is required for breathing automaticity. During waking and exercise, RTN contributes a reduced fraction of the total excitatory drive to the respiratory controller, but this fraction remains essential for CO2 homeostasis because of its exquisite chemosensitivity. The working hypothesis could explain the breathing deficits experienced by CCHS patients.
Characterization of Laccases and Peroxidases from Wood-Rotting Fungi (FamilyCoprinaceae) (1998)

ABSTRACT Panaeolus sphinctrinus , Panaeolus papilionaceus , and Coprinus friesii are described as producers of ligninolytic enzymes. P. papilionaceus and P. sphinctrinus both produced a laccase. In addition, P. sphinctrinus produced a manganese peroxidase. C. friesii secreted a laccase and two peroxidases similar to the peroxidase of Coprinus cinereus . The purified laccases and peroxidases were characterized by broad substrate specificities, significant enzyme activities at alkaline pH values, and remarkably high pH optima. The two peroxidases of C. friesii remained active at pH 7.0 and 60°C for up to 60 min of incubation. The peroxidases were inhibited by sodium azide and ethylene glycol-bis(β-aminoethyl ether)- N , N , N ′, N ′-tetraacetic acid (EGTA), whereas the laccases were inhibited by sodium azide and N , N -diethyldithiocarbamic acid. As determined by native polyacrylamide gel electrophoresis and isoelectric focusing, all three fungi produced laccase isoenzymes.
PCR in Bioanalysis (1998)

Application of Nucleic Acid Amplification in Clinical Microbiology Gorm Lisby Detection of Rodent Parvoviruses by PCR David G. Besselsen The SURF Technique: Selective Genetic Analysis of Microscopic Tissue Heterogeneity Darryl Shibata Prenatal and Presymptomatic Diagnosis of Marfan Syndrome Using Fluorescence PCR and an Automated Sequencer Mei Wang and Maurice Godfrey. Measurement of TNF and iNOS mRNA Using cDNA-Equalized Reverse Transcriptase PCR Jay K. Kolls and Jianming Xie PCR Diagnosis of the Bovine Immunodeficiency-Like Virus David L. Suarez and Cecelia A. Whetstone PCR Analysis for the Identification of Porcine Reproductive and Respiratory Syndrome Virus in Boar Semen Jane Christopher-Hennings and Eric A. Nelson Quantitative and Discriminative Detection of Individual HIV-mRNA Subspecies by an RNase Mapping Assay Catherine Mary, Hideo Akaoka, and Bernard Verrier Detection of the Heat-Labile Toxin Coding Gene (LT-Gene) of Enterotoxigenic Escherichia coli Seamus Fanning, Deirdre O'Meara, Lesley Cotter, John O'Mullane, and Bartley Cryan Motif-Dependent Polymerase Chain Reaction (PCR): DNA Fingerprinting Entererotoxigenic Escherichia coli Seamus Fanning, Deirdre O'Meara, Lesley Cotter, Paddy Greer, and Bartley Cryan In Vitro Transcription/Translation Analysis for the Identification of Translation-Terminating Mutations Michael C. Luce, Cameron G. Binnie, Lauren N. W. Kam-Morgan, and Matthew C. Cayouette A Single-Tube Nested RT-PCR for the Detection of Ross River Virus Loryn Sellner Application of PCR to Transgenic Plants Michael Wassenegger Detection of Hepatitis C Virus RNA by Semiquantitative Reverse-Transcription PCR Anderson S. Gaweco and David H. Van Thiel Detection of Legionella Species in Bronchial Fluid by PCR GormLisby Quantitative Measurement of mRNA Expression by Competitive RT-PCR Joe O'Connell, Triona Goode, and Fergus Shanahan PCR Detection of Toxoplasma gondii in Human Fetal Tissues Tamas Toth, Istvan Sziller, and Zoltan Papp Rapid Diagnosis of Pulmonary Tuberculosis Using Roche AMPLICORTM Mycobacterium tuberculosis PCR Test Richard F. D'Amato and Albert Miller The Use of Flow Cytometry and RT-PCR in the Detection of Circulating PSA-Positive Cells in Prostate Cancer Emma J. Fadlon and Freddie C. Hamdy Detection of Chlamydia trachomatis and Trichomonas vaginalis in the Vaginal Introitus, Posterior Vagina, and Endocervix by Polymerase Chain Reaction Jan Jeremias, Vera Tolbert, and Steven S. Witkin Detection and Isolation of Differentially Expressed Genes by PCR John M. Abraham Detection of Transgene Integrants and Homologous Recombinants in Mice by Polymerase Chain Reaction Kristin M. Abraham, Nancy S. Longo, and Judith A. Hewitt Direct Analysis for Familial Adenomatous Polyposis Mutations Steven M. Powell PCR Fingerprinting for Detection of Deleted or Amplified Sequences in Human Cancer Takashi Kohno and Jun Yokota Index
Decreased optical coherence tomography-measured pericentral retinal thickness in patients with diabetes mellitus type 1 with minimal diabetic retinopathy (2007)

In this study a significantly decreased pericentral RT was measured in patients with minimal DR compared to healthy controls. This could be explained by a loss of intraretinal neural tissue in the earliest stage of DR.
[Cloning the gene for vaccinia virus strain L-IVP growth factor in Escherichia coli]. (1993)

The growth factor gene of the vaccinia virus LIVP strain has been primarily cloned in a 4.3 kbp long BamHI-EcoRI fragment and then subcloned in a 440 bp fragment. It was shown that clone 4 of the LIVP strain contains a single copy of this gene while the WR strain contains a repeat. The gene is located on a 4.3 kbp BamHI-EcoRI fragment but not on a 2.2 kbp fragment and has four nucleotide changes, three of which result in amino acid substitutions.
A Novel Sugar Sensing System Designed with a Cooperative Action of a Boronic-Acid-Appended Zinc Porphyrin and a 3-Pyridylboronic Acid Axial Ligand (1997)

Abstract The cooperative action of two boronic acids is indispensable to the selective binding of saccharides in aqueous solution and the binding process can be spectrophotometrically monitored by using porphyrins as a chromophoric probe. It is not so easy, however, to synthesize porphyrins that satisfy these prerequisites, i.e., porphyrins bearing two appropriately-arranged boronic acid groups within a molecule. In this paper, we report that such a diboronic-acid-based porphyrin receptor can be easily designed by utilizing the self-assembling nature of a Zn(II) porphyrin and an axial ligand: That is, a mixture of boronic-acid-appended Zn(II) porphyrin (1-Zn) and 3-pyridylboronic acid (2) self-organizes to create a novel diboronic acid system for saccharide (S) recognition. Thus, the 1-Zn·2·S ternary complexes give the CD spectral pattern inherent to saccharide absolute configuration. The present study is a new example for sugar sensing using a boronic acid-porphyrin self-assembly system.
Genetics of the nephrotic syndrome (2000)

There are a large number of glomerular diseases that may be responsible for a nephrotic syndrome, the most frequent in childhood being minimal change disease. In the past few years, the molecular genetic basis of several conditions that may cause a nephrotic syndrome have been identified. Denys-Drash syndrome and Frasier syndrome are related diseases caused by mutations in the WT1 gene. Familial forms of idiopathic nephrotic syndrome with focal and segmental glomerular sclerosis/hyalinosis have been identified with an autosomal dominant or recessive mode of inheritance and linkage analysis have allowed to localize several genes on chromosomes 1, 11 and 17. The gene responsible for the Finnish type congenital nephrotic syndrome has been identified. This gene, named NPHS1, codes for nephrin, which is located at the slit diaphragm of the glomerular podocytes and is thought to play an essential role in the normal glomerular filtration barrier.
Prolyl Tripeptidyl Peptidase from Porphyromonas gingivalis (1999)

Porphyromonas gingivalis possesses a complex proteolytic system, which is essential for both its growth and evasion of host defense mechanisms. In this report we characterized, both at a protein and genomic level, a novel peptidase of this system with prolyl tripeptidyl peptidase activity. The enzyme was purified to homogeneity, and its enzymatic activity and biochemical properties were investigated. The amino acid sequence at the amino terminus and of internal peptide fragments enabled identification of the gene encoding this enzyme, which we refer to as PtpA for prolyl tripeptidyl peptidase A. The gene encodes an 82-kDa protein, which contains a GWSYGG motif, characteristic for members of the S9 prolyl oligopeptidase family of serine proteases. However, it does not share any structural similarity to other tripeptidyl peptidases, which belong to the subtilisin family. The production of prolyl tripeptidyl peptidase may contribute to the pathogenesis of periodontal tissue destruction through the mutual interaction of this enzyme, host and bacterial collagenases, and dipeptidyl peptidases in the degradation of collagen during the course of infection.
Spleenic Lymphoma and Hemoperitoneum in Jersey Bull: Clinical and Pathological Aspects (2014)

Lymphoma is the most prevalent neoplasia in dairy cattle. The etiology can be viral in animals affected by bovine leukemia virus (BLV) or be classified as primary. Lymphoma can affect several organs and according to the system involved, the clinical signs could manifest themselves in different ways. These tumors can be classified through macroscopic characteristics, histology and immunostaining. This classification can be used to predict prognosis and response to therapy. The aim of this case report was to immunostain and classify the tumor, for which anti-CD4, anti-CD8, anti-CD79 and anti-CD3 markers were used in addition to histopathological findings, in order to classify the tumor. The tumor was positive only for anti-CD3 marker, indicating that it is a tumor of young cells and, in association with histopathology and hematological data, it can be concluded that spleen neoplasia is lymphocytic lymphoma originated from a lymphocytic leukemia.
Oscillation of the human immunodeficiency virus surface receptor is regulated by the state of viral activation in a CD4+ cell model of chronic infection (1991)

We have developed a unique physiologic model of chronic human immunodeficiency virus type 1 (HIV-1) infection, OM-10.1, clonally derived from infected HL-60 promyelocytes and harboring a single integrated provirus. Unlike other models of chronic infection, OM-10.1 cultures remain CD4+ under normal culture conditions, during which less than 10% of the cells constitutively express HIV-1 proteins. However, when treated with tumor necrosis factor alpha (TNF-alpha), OM-10.1 cultures dramatically increased (greater than 35-fold) HIV-1 expression and rapidly down-modulated surface CD4, as greater than 95% of the cells became HIV-1+. The complete loss of surface CD4 following viral activation was neither associated with apparent cytopathicity nor due to a decline of available CD4 mRNA. There was, however, a temporal association between CD4 down-modulation and the accumulation of intracellular HIV-1 gp 160/120; in addition, intracellular CD4-gp 160 complexes were identifiable in OM-10.1 cell lysates at time points following TNF-alpha induction after surface CD4 was no longer detectable. Surface CD4 expression by OM-10.1 cells returned once viral activation ceased and could be repeatedly oscillated upon HIV-1 reactivation. Furthermore, inhibition of protein kinase activity following maximal TNF-alpha stimulation of OM-10.1 cells quickly returned activated HIV-1 to a state of latency, as evidenced by an accelerated return of surface CD4. These results with the new OM-10.1 cell line demonstrate that CD4 surface expression can be maintained during chronic infection and is critically dependent on the state of viral activation, that CD4-gp 160 intracellular complexing is involved in CD4 down-modulation, and that protein kinase pathways not only function in the primary induction of latent HIV-1 but also are required for maintaining the state of viral activation.
Inhibitors of endo-α-mannosidase. Part I. Derivatives of 3-O-(α-D-glucopyranosyl)-D-mannopyranose (1993)

Golgi membrane endo-α-D-mannosidase releases the disaccharide αDGlc(1 → 3)DMan (34) from the GlcMan 9 GlcNAc 2 oligosaccharide of immature N-linked glycoproteins. To convert the hydrolysis product 34 into a potent inhibitor of the enzyme, chemical modifications at the 1- and 2-positions of the mannose unit of 34 were performed. These include replacement of OH-1 by hydrogen (6), fluorine (12), and p-nitrophenoxy (5). Two potent inhibitors resulted, as reported recently, when both OH-1 and OH-2 of 34 were replaced by a double bond (glucal derivative 8) or replaced by hydrogen (1,2-dideoxy 9). 9 proved 40 times stronger as an inhibitor than 1-deoxy 6. However, further modifications at the 4- and 6-positions of 9, namely deoxygenation, methylation, and replacement of OH-6 by an amino group, were now found to largely abolish the activity, demonstrating that OH-4 and OH-6 of 9 are involved in H-bonding with the enzyme.
Novelty and Familiarity Activations in PET Studies of Memory Encoding and Retrieval (1996)

Nine young right-handed men viewed colored pictures of people, scenes, and landscapes. Then, 24 hr later while undergoing PET scanning, they viewed previously studied (OLD) pictures in one type of scan, and previously not seen (NEW) pictures in another. The OLD-NEW subtraction of PET images indicates familiarity, and the NEW-OLD indicates novelty. Familiarity activations, signalling aspects of retrieval, were observed in the left and right frontal areas, and posterior regions bilaterally. Novelty activations were in the right limbic regions, and bilaterally in temporal and parietal regions, including area 37. These latter activations were located similarly to novelty activations in previous PET studies using visual words and auditory sentences, suggesting the existence of brain regions specializing in transmodal novelty assessment. The effects of novelty are seen both behaviorally and in replicable patterns of cortical and subcortical activation. We propose a 'novelty/encoding hypothesis': (1) novelty assessment represents an early stage of long-term memory encoding; (2) elaborate, meaning-based encoding processes operate on the incoming information to the extent of its novelty, and therefore (3) the probability of long-term storage of information varies directly with the novelty of the information.
Automatic Optimisation of Infinite Variable Control Valves (2005)

Abstract This paper discusses the application of an optimisation technique to manage a field consisting of wells with Intelligent Well Technology (IWT) completions that allow the operator to reconfigure well architecture without well intervention. There is currently no generally accepted, efficient, optimisation technique available to optimise the IWT operation so as to maximise well production. The Sequential Quadratic Programming (SQP) candidate technique has previously proved its value in small and large-scale optimisation problems involving large-scale (gas-lifted) well production networks. SQP's ability to solve this new non-linear problem in a relatively reasonable time will be explained in this paper. In the previous publications we used a reservoir simulator controlled by a manual optimisation procedure to develop a value-statement for IWT. This method has proved it could increase value during the plateau period, but efficient optimisation of the decline period was too demanding in terms of engineering time &amp; computer power. This later requires an automatic optimisation tool to be cost effective. The Reservoir simulator has been linked to a (SQP based) Network optimiser so as to set the well and zone so that the production objectives are maximized, subject to the normal constraints (e.g. pressures, flow rates, water cuts etc. frequently imposed on the individual zonal or well production). The cumulative production increase achieved with manual optimisation (compared to the field level control) was doubled once automatic optimisation with zone-level control was implemented for the real-field based example studied previously. Automatic optimisation did significantly improve tail-end production, but delivered its greatest value by extending the plateau period. The results show that the use of automatic optimisation is valuable when building a "value statement" for the implementation of IWT within a particular field. Automatic Production optimisation (using conventional well) in reservoir simulation Production and Injection wells are usually connected together by a surface network contain pipes, chokes, pumps, etc. A number of studies have been performed in order to set the flow rate per well or per group of wells, different tools have been used to meet constraints inherent to this network of these facilities. Reservoir modellers may optimise rate allocation to optimally determine well rate setting so that network objectives and constraints are simultaneously satisfied.
Heterocyclen aus CH‐aciden Nitrilen, VII. 2‐Amino‐thiophene aus α‐Oxo‐mercaptanen und methylenaktiven Nitrilen (1965)

Abstract α‐Oxo‐mercaptane reagieren mit Nitrilen, die in α‐Stellung eine aktive Methylengruppe besitzen, basenkatalysiert zu 2‐Amino‐thiophenen. Diese entstehen auch bei der Einwirkung von Natriumhydrogensulfid auf bestimmte 2.3.4‐trisubstituierte 4‐Halogen‐crotonsäurenitrile.
Erbium-formate frameworks templated by diammonium cations: syntheses, structures, structural transition and magnetic properties (2011)

Two structurally different Er-formate frameworks, one NaCl-like [dmenH(2)][Er(HCOO)(4)](2) (1) and the other pillared-layer type [tmenH(2)][Er(HCOO)(4)](2) (2), were obtained when templated by the corresponding protonated N,N'-dimethylethylenediamine (dmenH(2)) and N,N,N',N'-tetramethyl- ethylenediamine (tmenH(2)). The shape and size of the template cations dictate the different coordination geometries of erbium and consequently the framework topologies, though erbium adopts eight coordination in the two compounds. In the NaCl-like structure of 1, erbium is coordinated by eight anti-anti bridging formates in a square antiprism, while in the pillared-layer structure of 2, it is coordinated by six anti-anti bridging formates and one chelating formate in a pentagonal bipyramid. 2 exhibits a structural phase transition around -70 °C which is related to the disorder-order transition of the template cation. Both compounds behave as paramagnets between 2 and 300 K. However, they display field-dependent ac-susceptibilities with complicated field-induced magnetic relaxation processes, and the major slow ones probably results from spin-lattice relaxation.