gebhart/patrepeval huggingface dataset:
A random sequencing approach for placing markers on the physical map of<i>Mycoplasma genitalium</i> (1991)

A physical map of the Mycoplasma genitalium genome has been prepared using pulsed-field gel electrophoresis. This report details recent efforts made to add markers or specific loci to this map in the absence of any mutants or system of genetic exchange. A total of 44 random clones were partially sequenced. Computer analysis was performed in an attempt to identify homologies with genes already recorded in the DNA sequence database. Clones with a large extent of homology to genes from other microorganisms have been assigned to specific loci on the M. genitalium map by hybridization to selected restriction digests. The additional data has facilitated an updated version of the physical map, and verified this random sequencing method as a useful mapping procedure as well as offering new insight into the physiological processes of this fastidious organism.
Atypical Teratoid Rhabdoid Tumor: Current Therapy and Future Directions (2012)

Atypical teratoid rhabdoid tumors (ATRTs) are rare central nervous system tumors that comprise approximately 1-2% of all pediatric brain tumors; however, in patients less than 3 years of age this tumor accounts for up to 20% of cases. ATRT is characterized by loss of the long arm of chromosome 22 which results in loss of the hSNF5/INI-1 gene. INI1, a member of the SWI/SNF chromatin remodeling complex, is important in maintenance of the mitotic spindle and cell cycle control. Overall survival in ATRT is poor with median survival around 17 months. Radiation is an effective component of therapy but is avoided in patients younger than 3 years of age due to long term neurocognitive sequelae. Most long term survivors undergo radiation therapy as a part of their upfront or salvage therapy, and there is a suggestion that sequencing the radiation earlier in therapy may improve outcome. There is no standard curative chemotherapeutic regimen, but anecdotal reports advocate the use of intensive therapy with alkylating agents, high-dose methotrexate, or therapy that includes high-dose chemotherapy with stem cell rescue. Due to the rarity of this tumor and the lack of randomized controlled trials it has been challenging to define optimal therapy and advance treatment. Recent laboratory investigations have identified aberrant function and/or regulation of cyclin D1, aurora kinase, and insulin-like growth factor pathways in ATRT. There has been significant interest in identifying and testing therapeutic agents that target these pathways.
Study on Finger-Articular Back Texture recognition (2008)

Human’s finger-articular back texture(FABT), as a novel biometric identification pattern, has been studied. As a basis set of FABT space, eigenjoints are extracted by principle component analysis. The features of each Finger-Articular Back Texture are computed by projecting on the related eigenjoint space. In matching stage, the decision are made by using nearest neighbor classifier based on Mahalanobis distance. The results show that: back finger- joint texture has high uniqueness in terms of high recognition accuracy rate (97.57 percent); the inter-class and intra-class have good separability; and recognition speed is fast enough for real time identification.
Expression of Na-P(i) cotransport in rat kidney: localization by RT-PCR and immunohistochemistry (1994)

We have recently identified a rat kidney cortex Na-dependent transport system for phosphate (P(i)) by expression cloning (NaP(i)-2) (S. Magagnin, A. Werner, D. Markovich, V. Sorribas, G. Stange, J. Biber, and H. Murer. Proc. Natl. Acad. Sci. USA 90: 5979, 1993). In this study we have used reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemistry to establish the sites of expression of the NaP(i)-2-related mRNA and protein. RT-PCR was performed with single microdissected nephron segments. From these experiments we conclude that NaP(i)-2 mRNA is predominantly expressed in the proximal tubules of superficial and deep nephrons. No NaP(i)-2 mRNA was detected in the thick ascending limb of Henle's loop; however, faint NaP(i)-2 related PCR products were also observed in collecting ducts. Expression of the NaP(i)-2 protein was examined with the use of polyclonal antibodies raised against synthetic NaP(i)-2-derived peptides. Strong specific anti-NaP(i)-2 antiserum-mediated immunofluorescence was found in the convoluted part of proximal tubules and gradually decreased along the straight part. Immunofluorescence indicated that the NaP(i)-2 protein is present in the brush border of proximal tubular cells. In addition, NaP(i)-2-specific immunofluorescence was also observed in subapical vesicles. The described distribution of the NaP(i)-2 protein is in agreement with previously described nephron sites of P(i) reabsorption in the rat kidney and therefore suggests that the NaP(i)-2 transport system represents an Na-P(i) cotransporter involved in proximal tubular apical transport of phosphate.
The Evidence Framework Applied to Classification Networks (1992)

Three Bayesian ideas are presented for supervised adaptive classifiers. First, it is argued that the output of a classifier should be obtained by marginalizing over the posterior distribution of the parameters; a simple approximation to this integral is proposed and demonstrated. This involves a "moderation" of the most probable classifier's outputs, and yields improved performance. Second, it is demonstrated that the Bayesian framework for model comparison described for regression models in MacKay (1992a,b) can also be applied to classification problems. This framework successfully chooses the magnitude of weight decay terms, and ranks solutions found using different numbers of hidden units. Third, an information-based data selection criterion is derived and demonstrated within this framework.
Brain-based devices: intelligent systems based on principles of the nervous system (2004)

Our group has constructed a series of brain-based devices (BBDs); i.e. physical devices with simulated nervous systems that guide behavior, to serve as a heuristic for understanding brain function. Unlike conventional robots designed by engineering principles, BBDs are based on biological principles and alter their behavior to the environment through self-learning. The resulting systems autonomously generalize signals from the environment into perceptual categories and through adaptive behavior become increasingly successful in coping with the environment. Although the principal focus of developing BBDs has been to test theories of the nervous system, this approach may also provide a basis for robotic design and practical applications.
Micromachined three-dimensional microgratings for free-space integrated micro-optics (1995)

We report what we believe to be the first fabrication of a three-dimensional rotatable micrograting plate for free-space integrated micro-optics by surface micromachining. A free-space micro-optical system consisting of a micrograting, a micro-Fresnel lens, and a passively aligned diode laser was also demonstrated for the first time to our knowledge. Grating plays is important in many optical systems, such as tunable external-cavity lasers, microspectrometers, optical interconnects, and wavelength-division-multiplexed (WDM) systems. Conventional gratings lie on the surface of the substrate and are not suitable for monolithic integration for free-space optical systems. In this paper we report a novel three-dimensional grating, fabricated by surface micromachining, that is similar to the micro-Fresnel lens.1 The micrograting plate is supported by microhinges and microspring latches2 and is able to stand perpendicular to the silicon substrate. Micromachining permits the microgratings to be integrated with other micro-optical elements (lenses, mirrors, etc.) and active lasers on a silicon chip.
Restenosis in coronary bare metal stents. Importance of time to follow-up: A comparison of coronary angiograms 6 months and 4 years after implantation (2008)

Instent late lumen loss in bare metal stents decreases spontaneously over time. Maturation of early hyperplastic tissue reaction after stent implantation with subsequent thinning of fibrotic tissue might explain this phenomenon.
Growth promotion of <i>Bifidobacterium animalis </i>by bovine milk proteose-peptone (1994)

International audience
Destruction mechanism of multilayer ceramic actuators (2003)

The destruction mechanism in multilayer ceramic actuators under cyclic electric fields has been investigated. Crack propagation has been observed dynamically using CCD (charge-coupled device) microscopy, and the accompanying characteristics of the induced displacement and acoustic emission were measured simultaneously. The piezoelectric Pb(Ni/sub 1/3/Nb/sub 2/3/)O/sub 3/-PbTiO/sub 3/ and the phase-transition-related actuator material (antiferroelectric) PbZrO/sub 3/-PbSnO/sub 3/-PbTiO/sub 3/ exhibit a marked difference in the manner of destruction, probably due to the strain-induction mechanism. In the piezoelectrics, the crack initiated near the edge of the internal electrode and propagated basically in three directions: two cracks moved toward the outside electrostrictively inactive region, forming an angle of 100 degrees with each other, while the third moved along the ceramic-electrode interface. In antiferroelectrics, the crack began slightly inside the edge of the internal electrode and propagated along the center area between the pair electrodes. Later crack branches were generated around the electrode edge. A very smart actuator system containing a safety feedback function, which can stop an actuator drive safely without causing any serious damage to the work, e.g., in a precision lathe machine, is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Application of the Suzuki biphenyl synthesis to the natural products biphenomycin and vancomycin (1992)

The synthesis of the unsymmetrical biphenyls 10 and 25 has been carried out by the palladium(0) catalysed coupling of the aryl boronic acid derivatives 5 and 20 with the aryl bromides 9 and 23 derived from (R)-4-hydroxyphenylglycine and (S)-tyrosine. In the former case unsuccessful attempts were made to bring about cyclization to compound 4 which is an analogue of the biphenyl ring system found in vancomycin. In the latter case, a variety of cyclization methods were used to give the cyclic products 34 and 35 which are analogues of the biphenomycin antibiotics.
Infrared Devices And Techniques (Revision) (2014)

Abstract The main objective of this paper is to produce an applications-oriented review covering infrared techniques and devices. At the beginning infrared systems fundamentals are presented with emphasis on thermal emission, scene radiation and contrast, cooling techniques, and optics. Special attention is focused on night vision and thermal imaging concepts. Next section concentrates shortly on selected infrared systems and is arranged in order to increase complexity; from image intensifier systems, thermal imaging systems, to space-based systems. In this section are also described active and passive smart weapon seekers. Finally, other important infrared techniques and devices are shortly described, among them being: non-contact thermometers, radiometers, LIDAR, and infrared gas sensors.
Antibodies that neutralize cellular uptake of elosulfase alfa are not associated with reduced efficacy or pharmacodynamic effect in individuals with Morquio A syndrome (2016)

Many enzyme replacement therapies (ERTs) for lysosomal storage disorders use the cell-surface cation-independent mannose-6 phosphate receptor (CI-M6PR) to deliver ERTs to the lysosome. However, neutralizing antibodies (NAb) may interfere with this process. We previously reported that most individuals with Morquio A who received elosulfase alfa in the phase 3 MOR-004 trial tested positive for NAbs capable of interfering with binding to CI-M6PR ectodomain in an ELISA-based assay. However, no correlation was detected between NAb occurrence and clinical efficacy or pharmacodynamics. To quantify and better characterize the impact of NAbs, we developed a functional cell-based flow cytometry assay with a titer step that detects antibodies capable of interfering with elosulfase alfa uptake. Serum samples collected during the MOR-004 trial were tested and titers were determined. Consistent with earlier findings on NAb positivity, no correlations were observed between NAb titers and the clinical outcomes of elosulfase alfa-treated individuals with Morquio A.
New substrate for determination of serum lecithin:cholesterol acyltransferase (1987)

Serum lecithin:cholesterol acyltransferase (LCAT) was estimated by enzymatically measuring the decrease in unesterified cholesterol after incubation of serum with liposomes. A high-performance liquid chromatography (HPLC) study showed the uptake of the lipids of liposomes by serum high density lipoprotein. Of all the examined liposomes prepared from cholesterol and various synthetic phosphatidylcholines, liposomes with dimyristoylphosphatidylcholine (DMPC) were found to be the most reactive in the LCAT reaction. When serum was used as an enzyme source, addition of purified apolipoprotein A-I, which is known to be an endogenous activator of LCAT, to the assay mixture resulted in a slight decrease in enzyme activity. Using DMPC-cholesterol liposomes as the substrate, the LCAT activities in 120 human sera showed a mean value of 485.4 +/- 64.6 nmol/hr per ml (mean +/- SD), which is 4.4- to 5.4-fold higher than the values obtained by self-substrate methods. LCAT activity was a linear function of the serum sample volume up to 670 nmol/hr per ml and coefficients of variation (CV) less than 4% were obtained under the standardized conditions. Moreover, when partially purified LCAT was added to various heat-inactivated sera, the activity was efficiently recovered. These results suggest that this method is sensitive, reproducible, and not greatly influenced by serum components.
Correction of the DNA repair defect in xeroderma pigmentosum group E by injection of a DNA damage-binding protein. (1994)

Cells from a subset of patients with the DNA-repair-defective disease xeroderma pigmentosum complementation group E (XP-E) are known to lack a DNA damage-binding (DDB) activity. Purified human DDB protein was injected into XP-E cells to test whether the DNA-repair defect in these cells is caused by a defect in DDB activity. Injected DDB protein stimulated DNA repair to normal levels in those strains that lack the DDB activity but did not stimulate repair in cells from other xeroderma pigmentosum groups or in XP-E cells that contain the activity. These results provide direct evidence that defective DDB activity causes the repair defect in a subset of XP-E patients, which in turn establishes a role for this activity in nucleotide-excision repair in vivo.
Reviews of Books (1904)

Reviews of Books Get access C. L. S. C. L. S. Search for other works by this author on: Oxford Academic Google Scholar The English Historical Review, Volume XIX, Issue LXXVI, October 1904, Pages 816-a–816, https://doi.org/10.1093/ehr/XIX.LXXVI.816-a Published: 01 October 1904
DNA methylation as an intermediate biomarker in colorectal cancer (1994)

Several studies have suggested that DNA hypomethylation is an early step in colorectal carcinogenesis. However, it is not clear at which stage in carcinogenesis this hypomethylation occurs, what promotes it, the extent to which it can be reversed and the consequences of such reversal in affecting tumour development. In an attempt to address some of these questions, we studied three groups of subjects with similar age and gender distributions: a group of 12 patients with colorectal carcinomas; a group of 12 patients with colorectal adenomas; and a group of eight healthy control subjects. Two experimental protocols were employed. In the first protocol, intrinsic DNA methylation was evaluated in neoplastic and in normal-appearing rectal mucosa of patients with colonic carcinomas or adenomas, compared with a group of healthy controls. In the second protocol, we examined, in a prospective and controlled fashion, the effect of folic acid supplementation (10 mg/day) on the degree of DNA methylation of rectal mucosa from those same patients after removal of the neoplasms. The degree of intrinsic DNA methylation was assessed on the basis of the capacity of the DNA isolates to serve as methyl acceptors in in vitro incubations that contained DNA methylase and [3H-methyl] S-adenosylmethionine. Intrinsic DNA methylation was significantly lower in carcinomas than in adenomas (P < 0.005). In addition, normal-appearing rectal mucosa from patients with carcinomas was significantly less methylated than in healthy controls (P < 0.005); the mean value found in the latter was also greater than the value observed in patients with adenomas, but not significantly so (P > 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)
Reovirus-Induced Apoptosis Is Preceded by Increased Cellular Calpain Activity and Is Blocked by Calpain Inhibitors (1999)

The cellular pathways of apoptosis have not been fully characterized; however, calpain, a cytosolic calcium-activated cysteine protease, has been implicated in several forms of programmed cell death. Reoviruses induce apoptosis both in vitro and in vivo and serve as a model for studying virus-induced cell death. We investigated the potential role of calpain in reovirus-induced apoptosis in vitro by measuring calpain activity as well as evaluating the effects of calpain inhibitors. L929 cells were infected with reovirus type 3 Abney (T3A), and calpain activity, measured as cleavage of the fluorogenic calpain substrate Suc-Leu-Leu-Val-Tyr-AMC, was monitored. There was a 1.6-fold increase in calpain activity in T3A-infected cells compared to mock-infected cells; this increase was completely inhibited by preincubation with calpain inhibitor I (N-acetyl-leucyl-leucyl-norleucinal [aLLN]), an active-site inhibitor. Both aLLN and PD150606, a specific calpain inhibitor that interacts with the calcium-binding site, inhibited reovirus-induced apoptosis in L929 cells by 54 to 93%. Apoptosis induced by UV-inactivated reovirus was also reduced 65 to 69% by aLLN, indicating that inhibition of apoptosis by calpain inhibitors is independent of effects on viral replication. We conclude that calpain activation is a component of the regulatory cascade in reovirus-induced apoptosis.
Expanding Role of Delta-Like 4 Mediated Notch Signaling in Cardiovascular and Metabolic Diseases (2013)

Cardiometabolic disease, a global health threat, has been linked to chronic inflammation, in which activated macrophages play a key role. Macrophages are highly heterogeneous hematopoietic cells found in nearly every tissue in the body. Various stimuli recruit monocytes into the cardiovascular system and metabolic organs, where they differentiate to macrophages, and activate these pro-inflammatory phagocytes, leading to the initiation and development of inflammation in these organs. Key regulators of macrophage activation therefore may serve as therapeutic targets for cardiometabolic disease. The Notch signaling pathway, involving 5 ligands and 4 receptors, regulates the differentiation of various cell types during development, and also contributes to the disease processes in adults. We found that the Notch ligand delta-like 4 (Dll4) activates macrophages in vitro as determined by the induction of genes and pathways associated with cardiovascular and metabolic disorders. Our recent study demonstrated in vivo that blockade of Dll4 by a neutralizing antibody attenuates key features typical of cardiovascular and metabolic diseases, such as accumulation of activated macrophages in arteries and fat; chronic atherosclerosis; arterial and valvular calcification; insulin resistance; and fatty liver. These results suggest that Dll4-mediated Notch signaling participates in the shared disease mechanisms for cardiovascular and metabolic disorders. This review summarizes the role of macrophages and Dll4/Notch signaling in the development of inflammation in both the cardiovascular system and metabolic organs.
Interactions among Subunits of the Oligosaccharyltransferase Complex (1997)

The mammalian oligosaccharyltransferase (OST) is an oligomeric complex composed of three membrane proteins of the endoplasmic reticulum: ribophorin I (RI), ribophorin II (RII), and OST48. In addition, sequence homology between the Ost2 subunit of the yeast OST complex and Dad1 (defender against apoptotic death) suggests that Dad1 may represent a fourth subunit of the mammalian OST complex. In attempts to elucidate the structural organization of this complex, we have studied the interactions among its subunits. Using the yeast two-hybrid system, we have shown that the luminal domains of RI and RII (RIL and RIIL, respectively) interacted with the luminal domain of OST48 (OST48L), but no direct interaction was observed between RIL and RIIL. These results were confirmed by biochemical assays. Deletion analyses using the yeast two-hybrid system showed that subdomain of RIL or RIIL adjacent to the respective transmembrane domains interacted with OST48L. Of the three equal length subdomains of OST48L, the one at the N terminus and the one next to the transmembrane domain interacted with RIL. None of these three subdomains of OST48L interacted with RIIL. The yeast two-hybrid assay also revealed affinity between the cytoplasmically located N-terminal region of Dad1 and the short cytoplasmic tail of OST48, thus placing Dad1 firmly into the OST complex. In addition, we found a homotypic interaction between the cytoplasmic domains of RI, which may play a role in the formation of the oligomeric array formed by components of the translocation machinery.
Functionalized thia-crown ethers. Synthesis, structure, and properties (1990)

A caesium promoted synthesis of this-crown ethers containing isobutenyl units in the periphery is described, including structural data and a method involving diborane for functionalization of the methylene group.