gebhart/patrepeval huggingface dataset:
Loss of the p53/p63 Regulated Desmosomal Protein Perp Promotes Tumorigenesis (2010)

Dysregulated cell-cell adhesion plays a critical role in epithelial cancer development. Studies of human and mouse cancers have indicated that loss of adhesion complexes known as adherens junctions contributes to tumor progression and metastasis. In contrast, little is known regarding the role of the related cell-cell adhesion junction, the desmosome, during cancer development. Studies analyzing expression of desmosome components during human cancer progression have yielded conflicting results, and therefore genetic studies using knockout mice to examine the functional consequence of desmosome inactivation for tumorigenesis are essential for elucidating the role of desmosomes in cancer development. Here, we investigate the consequences of desmosome loss for carcinogenesis by analyzing conditional knockout mice lacking Perp, a p53/p63 regulated gene that encodes an important component of desmosomes. Analysis of Perp-deficient mice in a UVB-induced squamous cell skin carcinoma model reveals that Perp ablation promotes both tumor initiation and progression. Tumor development is associated with inactivation of both of Perp's known functions, in apoptosis and cell-cell adhesion. Interestingly, Perp-deficient tumors exhibit widespread downregulation of desmosomal constituents while adherens junctions remain intact, suggesting that desmosome loss is a specific event important for tumorigenesis rather than a reflection of a general change in differentiation status. Similarly, human squamous cell carcinomas display loss of PERP expression with retention of adherens junctions components, indicating that this is a relevant stage of human cancer development. Using gene expression profiling, we show further that Perp loss induces a set of inflammation-related genes that could stimulate tumorigenesis. Together, these studies suggest that Perp-deficiency promotes cancer by enhancing cell survival, desmosome loss, and inflammation, and they highlight a fundamental role for Perp and desmosomes in tumor suppression. An understanding of the factors affecting cancer progression is important for ultimately improving the diagnosis, prognostication, and treatment of cancer.
Lack of protection against gastric helicobacter infection following immunisation with jack bean urease: The rejection of a novel hypothesis (1994)

The common mucosal immune system was stimulated by oral immunisation with jack bean urease and the adjuvant cholera toxin. A high level of local antibody and serum antibody was induced in mice following hyperimmunisation with this combination. No cross-reacting antibody was found against either Helicobacter pylori or Helicobacter felis. No protection was observed against oral challenge of immunised mice with living H. felis thus disproving the interesting hypothesis of Pallen and Clayton that plant urease might induce a protective immunity against helicobacter infection.
A PHOTOMETRIC ADAPTATION OF THE SOMOGYI METHOD FOR THE DETERMINATION OF GLUCOSE (1944)

The reliability of the various Somogyi-Shaffer-Hartmann (1, 2) copper reagents for glucose determination in biological material has been established. Adaptation of these reagents to calorimetric use may be accomplished by omission of the iodide and iodate in their preparation, since these interfere with the molybdate color reagents. This omission produces no especial change in the character of the reagents. KI, however, inhibits the autoreduction of the copper and in its absence an unstable reagent results. Nevertheless, if the copper is added to the rest of the reagent on the day of its use, this difficulty is avoided. When the Somogyi micro reagent (2) is used in this way with almost any of the various phosphomolybdate reagents, very satisfactory proportionality is found between color density and glucose taken over a wide range of values. However, all of the phosphomolybdate reagents tried left much to be desired in reproducibility from time to time and lacked the desired stability of color. We therefore tried various color reagents, which led to the development of a new arsenomolybdate reagent. When this reagent was used with Somogyi’s micro reagent, it gave satisfactory stability and reproducibility of color. By this means it has been possible to utilize the copper reagents in a photometric procedure for practically all the uses to which the titrimetric procedures are adapted. These include tissue sugar, glycogen, urine reduction equivalent, maltose, glucuronic acid, etc. However, diastase determinations have not been successful because of the effect of the undigested starch on the clarity of the final colored solution. The reactions involved in the molybdenum blue reaction are uncertain and beyond the scope of this report. Woods and Mellon (3) discuss and give references to the various interpretations of the reaction. Reagents-Analytical reagent grade or the equivalent. 1. Copper Reagent A. Dissolve 25 gm. of N&C03 (anhydrous), 25 gm. of Rochelle salt, 20 gm. of NaHCOs, and 200 gm. of NaiSOa (anhydrous) in about 800 ml. of water and dilute to 1 liter. Filter if necessary.’ This
Joint source-channel decoding of correlated sources over noisy channels (2002)

We consider the case of two correlated binary information sequences. Instead of compressing the information using source coding, both sequences are independently channel encoded, and transmitted over an AWGN channel. The correlation between both sequences is exploited at the receiver, allowing reliable communications at signal to noise ratios very close to the theoretical limits established by the combination of Shannon and Slepian-Wolf theorems.
Topography of the Duchenne muscular dystrophy (DMD) gene: FIGE and cDNA analysis of 194 cases reveals 115 deletions and 13 duplications. (1989)

We have studied 34 Becker and 160 Duchenne muscular dystrophy (DMD) patients with the dystrophin cDNA, using conventional blots and FIGE analysis. One hundred twenty-eight mutations (65%) were found, 115 deletions and 13 duplications, of which 106 deletions and 11 duplications could be precisely mapped in relation to both the mRNA and the major and minor mutation hot spots. Junction fragments, ideal markers for carrier detection, were found in 23 (17%) of the 128 cases. We identified eight new cDNA RFLPs within the DMD gene. With the use of cDNA probes we have completed the long-range map of the DMD gene, by the identification of a 680-kb SfiI fragment containing the gene's 3' end. The size of the DMD gene is now determined to be about 2.3 million basepairs. The combination of cDNA hybridizations with long-range analysis of deletion and duplication patients yields a global picture of the exon spacing within the dystrophin gene. The gene shows a large variability of intron size, ranging from only a few kilobases to 160-180 kb for the P20 intron.
[Cloning,expression and activity identification of human innate immune protein apolipoprotein B mRNA editing enzyme catalytic subunit 3A(APOBEC3A)]. (2017)

The study constructed successfully APOBEC3 A eukaryotic expression vector,identified the differential expression of APOBEC3 A protein in HEK293 T and Hep G2 cells,and confirmed that the APOBEC3 A protein had cytosine deaminase activity.
AP-2δ Is a Crucial Transcriptional Regulator of the Posterior Midbrain (2011)

Ap-2 transcription factors comprise a family of 5 closely related sequence-specific DNA binding proteins that play pivotal and non-redundant roles in embryonic organogenesis. To investigate the function of Ap-2δ, wδe analyzed its expression during embryogenesis and generated Ap-2δ-deficient mice. In line with the specific expression pattern of Ap-2δ in the mesencephalic tectum and the dorsal midbrain, Ap-2δ-deficient mice failed to maintain the colliculus inferior, a derivative of the dorsal midbrain, as a consequence of increased apoptotic cell death. To identify specific Ap-2δ target genes in cells of the developing dorsal midbrain, we performed whole genome analysis of cDNA expression levels. This approach identified a set of 12 putative target genes being expressed in the developing midbrain, including the transcription factors Pitx2, Mef2c, Bhlhb4 and Pou4f3. Using chromatin immunoprecipitation (CHIP) we showed that some of these genes are direct targets of Ap-2δ. Consistently, we demonstrate that Ap-2δ occupies and activates the Pou4f3 and Bhlhb4 promoters. In addition, known Pou4f3 target genes were downregulated in the posterior midbrain of Ap-2δ-deficient mice. Despite the absence of a central part of the auditory pathway, the presence of neuronal responses to sounds in the neocortex of Ap-2δ-deficient mice indicates that auditory information from the brainstem still reaches the neocortex. In summary, our data define Ap-2δ as an important transcription factor, specifying gene expression patterns required for the development of the posterior midbrain.
Effects of Repetitive Transcranial Magnetic Stimulation on Movement-related Cortical Activity in Humans (2000)

Several lines of evidence suggest that low-rate repetitive transcranial magnetic stimulation (rTMS) of the motor cortex at 1 Hz reduces the excitability of the motor cortex and produces metabolic changes under and at a distance from the stimulated side. Therefore, it has been suggested that rTMS may have beneficial effects on motor performance in patients with movement disorders. However, it is still unknown in what way these effects can be produced. The aim of the present study is to investigate whether rTMS of the motor cortex (15 min at 1 Hz) is able to modify the voluntary movement related cortical activity, as reflected in the Beretischaftspotential (BP), and if these changes are functionally relevant for the final motor performance. The cortical movement-related activity in a typical BP paradigm of five healthy volunteers has been recorded using 61 scalp electrodes, while subjects performed self-paced right thumb oppositions every 8-20 s. After a basal recording, the BP was recorded in three different conditions, counterbalanced across subjects: after rTMS stimulation of the left primary motor area (M1) (15 min, 1 Hz, 10% above motor threshold), after 15 min of sham rTMS stimulation and following 15 min of voluntary movements performed with spatio-temporal characteristics similar to those induced by TMS. The tapping test was used to assess motor performance before and after each condition. Only movement-related trials with similar electromyographic (onset from muscular 'silence') and accelerometric patterns (same initial direction and similar amplitudes) were selected for computing BP waveforms. TMS- evoked and self-paced thumb movements had the same directional accelerometric pattern but different amplitudes. In all subjects, the real rTMS, but neither sham stimulation nor prolonged voluntary movements, produced a significant amplitude decrement of the negative slope of the BP; there was also a shortening of the BP onset time in four subjects. The effect was topographically restricted to cortical areas which were active in the basal condition, irrespective of the basal degree of activation at every single electrode. No changes in the tapping test occurred. These findings suggest that rTMS of the motor cortex at 1 Hz may interfere with the movement related brain activity, probably through influence on cortical inhibitory networks.
Physiologic role of nitric oxide and nitric oxide synthase in female lower urinary tract (2004)

NO plays an important role in the micturition process and in disorders of the lower urinary tract. Improved understanding of the pathophysiologic role of NO/NOS system and of the L-arginine-NO-cGMP pathway may allow us to identify suitable therapeutic targets for lower urinary tract disorders. However, there is a need for further investigation to determine the precise function of NO in human lower urinary tract because most work thus far has been done in animal models.
The proform of eosinophil major basic protein: a new maternal serum marker for Down syndrome (1999)

The proform of eosinophil major basic protein (proMBP), the most abundant protein in the eosinophil specific granule, is synthesized by the placenta and secreted into the maternal circulation, where it is found complex-bound to pregnancy-associated plasma protein-A (PAPP-A) and other proteins. We examined the potential of proMBP as a maternal serum marker for fetal Down syndrome (DS) by determining its maternal serum concentration (MSpMBP) in 25 Down syndrome (DS) pregnancies and 152 control pregnancies in the first trimester, and in 105 DS pregnancies and 156 control pregnancies in the second trimester. The median (95 per cent confidence interval) MSpMBP MoM in DS pregnancies (n=15) was 0.66 (0.49-0.79) in gestational weeks 5-9; 1.06 (0.71-1.97) in weeks 10-12 (n=10) and 1.62 (1.18-1.98) in weeks 14-20 (n=105). Using parameterized receiver operator characteristics analysis for proMBP as a single marker for DS, detection rates (DRs) of 22 per cent and 38 per cent, for false-positive rates (FPRs) of 5 per cent, were found in weeks 5-9 (using MSpMBP</=cut-off) and weeks 14-20 (using MSpMBP>/=cut-off), respectively. When age and MSpMBP were used as markers in combination, a DR of 36.8 per cent for an FPR of 5.5 per cent was obtained in weeks 5-9 using a risk cut-off of 1:250. In weeks 14-20 the DR was 48.4 per cent for an FPR of 5.3 per cent using the same risk cut-off. This makes proMBP a marker comparable in diagnostic efficiency to human chorionic gonadotrophin (hCG), and exceeding that of alpha-fetoprotein (AFP) and unconjugated oestriol (uE3), in the second trimester.
PMD fundamentals: Polarization mode dispersion in optical fibers (2000)

This paper reviews the fundamental concepts and basic theory of polarization mode dispersion (PMD) in optical fibers. It introduces a unified notation and methodology to link the various views and concepts in Jones space and Stokes space. The discussion includes the relation between Jones vectors and Stokes vectors, rotation matrices, the definition and representation of PMD vectors, the laws of infinitesimal rotation, and the rules for PMD vector concatenation.
A single source approach to the synthesis of CdSe nanocrystallites (1996)

Synthetic routes to semiconductor nanocrystallites have become of particular interest since nanoparticle devices have been constructed. The route reported here for CdSe uses a single source in tri‐ n ‐octylphosphine oxide instead of the hazardous metal alkyls conventionally employed. The characterization of the nanocrystallites (see figure) shows that they are crystalline, approximately spherical, and close to monodispersed. magnified image
A Review of Natural and Modified Betulinic, Ursolic and Echinocystic Acid Derivatives as Potential Antitumor and Anti-HIV Agents (2003)

The aim of this review is to update current knowledge on the betulinic, ursolic and echinocystic acids and their natural and semisynthetic analogs, focussing on their cytotoxic and anti-HIV activities. Then, the last results of the authors' team on unusual semisynthetic derivatives of these triterpenoids will be presented in order to establish structure/activity relationships.
Collective Intelligence for Smarter API Recommendations in Python - eScholarship (2016)

Software developers use Application Programming Interfaces (APIs) of libraries and frameworks extensively while writing programs. In this context, the recommendations provided in code completion tools help developers choose the desired methods. The candidate lists recommended by these tools, however, tend to be large, ordered alphabetically and sometimes even incomplete. A fair amount of work has been done recently to improve the relevance of these code completion results, especially for statically typed languages like Java. However, these proposed techniques rely on the static type of the object and are therefore inapplicable for a dynamically typed language like Python.In this thesis, I present PyReco, an intelligent code completion system for Python which uses the mined API usages from open source repositories to order the results based on relevance rather than the conventional alphabetic order. To recommend suggestions that are relevant for a working context, a nearest neighbor classifier is used to identify the best matching usage among all the extracted usage patterns.To evaluate the effectiveness of our system, the code completion queries are automatically extracted from projects and tested quantitatively using a ten-fold cross validation technique. The evaluation shows that our approach outperforms the alphabetically ordered API recommendation systems in recommending APIs for standard, as well as, third-party libraries.
A bi-conical multibeam antenna for space division multiple access (2002)

Bi-conical horn antennas are commonly used as high bandwidth omni-directional antennas for vertical polarisation. They are excited by a TEM-mode in the coaxial feed of the bi-conical antenna, which results in a field distribution in the aperture surface that is independent of the azimuth angle. In a new approach the bi-conical horn antenna is excited by a mixture of TEM- and TE/sub n1/-modes. Single directional beams can be radiated, and the use of multiple feed connectors allows simple and inexpensive implementation of space division multiple access (SDMA). Also, adaptive antenna pattern synthesis, that was not available up to now, is realised by this set-up. For the excitation of the additional higher modes the coaxial waveguide feeding the bi-conical antenna is overmoded. In the special case shown the cut-off frequencies for some of the higher modes are given, with an outer radius chosen as 20 mm. Linear superposition of the modes in the coaxial waveguide results in angle dependent electromagnetic fields in the radiating aperture as well. As the field distribution in this surface determines the far-field radiation pattern of the antenna, pattern synthesis can be realised by adequate mode mixing.
“Green” Atom Transfer Radical Polymerization:  From Process Design to Preparation of Well-Defined Environmentally Friendly Polymeric Materials (2007)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT"Green" Atom Transfer Radical Polymerization: From Process Design to Preparation of Well-Defined Environmentally Friendly Polymeric MaterialsNicolay V. Tsarevsky and Krzysztof MatyjaszewskiView Author Information Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213 Cite this: Chem. Rev. 2007, 107, 6, 2270–2299Publication Date (Web):May 27, 2007Publication History Received10 August 2006Published online27 May 2007Published inissue 1 June 2007https://pubs.acs.org/doi/10.1021/cr050947phttps://doi.org/10.1021/cr050947presearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views13565Altmetric-Citations1189LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Catalysts,Ligands,Monomers,Polymers,Radical polymerization Get e-Alerts
Integrin α5 controls osteoblastic proliferation and differentiation responses to titanium substrates presenting different roughness characteristics in a roughness independent manner (2006)

Integrin alpha(5)beta(1) regulates osteoblast proliferation and differentiation on smooth synthetic surfaces presenting different chemistries, but it is not known whether this integrin controls osteoblast behavior on surfaces that have micron-scale rough topographies. We cultured MG63 human osteoblast-like cells on titanium substrates with three different roughness characteristics: chemically polished (PT), grit blasted and acid etched with a complex topography consisting of 20-100 mum craters and 0.5-2 mum micropits (SLA), and plasma-sprayed Ti with irregular projections (TPS). Cells spread well on PT but displayed a smaller footprint on SLA or TPS. Nuclei were larger on PT as well. alpha(5)beta(1) binding and FAK phosphorylation were greater on the rougher surfaces (TPS > SLA > PT). Antibodies against the alpha(5)beta(1) binding site on fibronectin had no effect on cell number at 3 days, but [(3)H]-thymidine incorporation was increased, suggesting that binding to fibronectin was necessary for cell cycle regulation. Antibodies to the alpha(5) subunit reduced cell number at 3 days on PT and TPS and reduced DNA synthesis on all substrates in a surface microstructure-independent manner. At 7 days, cell numbers were reduced on PT, and DNA synthesis was reduced by 50% on all surfaces. At 7 days, anti-alpha(5) antibodies caused a partial reduction in alkaline phosphatase enzyme activity on all surfaces, but this effect was independent of surface microstructure. These results indicate that surface micron-scale topography modulates alpha(5)beta(1) integrin binding and FAK activation. Signaling via alpha(5)-dependent mechanisms is required for DNA synthesis and regulation of alkaline phosphatase, but this effect is independent of surface microstructure.