gebhart/patrepeval huggingface dataset:
Signal Recovery by Proximal Forward-Backward Splitting (2005)

We show that various inverse problems in signal recovery can be formulated as the generic problem of minimizing the sum of two convex functions with certain regularity properties. This formulation makes it possible to derive existence, uniqueness, characterization, and stability results in a unified and standardized fashion for a large class of apparently disparate problems. Recent results on monotone operator splitting methods are applied to establish the convergence of a forward-backward algorithm to solve the generic problem. In turn, we recover, extend, and provide a simplified analysis for a variety of existing iterative methods. Applications to geometry/texture image decomposition schemes are also discussed. A novelty of our framework is to use extensively the notion of a proximity operator, which was introduced by Moreau in the 1960s.
Confinement Spectroscopy: Probing Single DNA Molecules with Tapered Nanochannels (2009)

We demonstrate a confinement spectroscopy technique capable of probing small conformational changes of unanchored single DNA molecules in a manner analogous to force spectroscopy, in the regime corresponding to femtonewton forces. In contrast to force spectroscopy, various structural forms of DNA can easily be probed, as indicated by experiments on linear and circular DNA. The extension of circular DNA is found to scale according to the de Gennes exponent, unlike for linear DNA.
Magnetoresistance of symmetric spin valve structures (1994)

A spin valve configuration is presented in which an unpinned ferromagnetic film is separated from exchange-pinned ferromagnetic films on either side by two nonmagnetic spacers, thereby creating a symmetric spin valve structure. The symmetric spin valve is shown to increase the magnetoresistance by 50% over the values of individual spin valves. The increase is attributed to a reduction of spin-independent outer boundary scattering and doubling the number of spin-dependent scattering interfaces. The magnetoresistance and coupling fields of the spin valves that comprise the symmetric structure have been measured as a function of Cu spacer thickness. Oscillatory antiferromagnetic to ferromagnetic coupling was observed in standard spin valves, which had /spl Delta/R/R as high as 13%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prognostic value of p53, glutathione S-transferase pi, and thymidylate synthase for neoadjuvant cisplatin-based chemotherapy in head and neck cancer. (1999)

Neoadjuvant cisplatin-based chemotherapy has been widely used in the last decade for organ preservation or unresectable disease in advanced stage head and neck cancer. We examined the expression of a series of tumor markers that have been associated with chemotherapy resistance in pretreatment biopsies from 68 patients who received cisplatin-based neoadjuvant chemotherapy at either of two institutions. Patients received either cisplatin/5-fluorouracil (n = 49) or cisplatin/paclitaxel (n = 19). Expression of p53, glutathione S-transferase pi (GSTpi), thymidylate synthase (TS), c-erbB2, and multidrug resistance-associated protein was examined by immunohistochemistry. Expression of glutathione synthetase mRNA was measured by in situ hybridization. The overall response rate for cisplatin-based neoadjuvant treatment was 79%. The expression of several of the tumor markers was associated with resistance to neoadjuvant treatment, but none reached statistical significance. Overall survival (OS) was strongly correlated with the absence of p53 expression. The OS at 3 years was 81% in the p53-negative group, whereas it was 30% in the p53-positive group for patients treated with neoadjuvant chemotherapy (P < 0.0001). Expression of GST pi and TS was also significantly correlated with decreased OS after neoadjuvant treatment. At 3 years, the OS rate was 82% in the low GSTpi score group, compared to 46% in the high GSTpi score group (P = 0.0018). In the TS-negative group, the 3-year OS rate was 71% compared with 40% in the TS-positive group (P = 0.0071). We conclude that p53, GSTpi, and TS may be clinically important predictors of survival in patients receiving neoadjuvant chemotherapy for head and neck cancer.
Trichorhinophalangeal syndrome type I (1998)

A 32-year-old short statured woman with alopecia, typical facies, shortened angulated fingers and toes with Trichorhinophalangeal syndrome type I (TRPS I) is reported. The absence of exostosis and mental retardation rule out TRPS II. The absence of generalized shortness of all phalanges, metacarpals and metatarsals distinguish it from TRPS III. Possibly the various types of Trichorhinophalangeal syndrome are genetically identical but have a varied clinical spectrum.
Vaspin Serum Concentration in Patients with Type 2 Diabetes and Carotid Plaque (2012)

A significant inverse association was found, in patients with T2DM within 3 years of diagnosis, between serum vaspin concentration and the presence of carotid plaque.
A Novel Detection and Identification Technique for Plant Viruses: Rapid Immunofilter Paper Assay (RIPA) (1992)

A rapid immunofilter paper assay (RIPA) for cucumber mosaic virus (CMV) or tobacco mosaic virus (TMV) was developed using latex beads coated with antibodies to either virus. White latex-coated antibody was immobilized as a solid in a line on the surface near the bottom of a filter paper strip. The bottom end of this paper strip was dipped for 3 min into a mixture of leaf extract from an infected plant and dyed-latex coated with the virus antibody. A colored band appeared on the line where the white latex had been immobilized. With RIPA, as little as 5 ng/ml of purified TMV or 50 ng/ml of purified CMV could be detected with the naked eye(.)
Severe idiopathic gastroparesis due to neuronal and interstitial cells of Cajal degeneration: pathological findings and management (2003)

Delayed gastric emptying can be due to muscular, neural, or humoral abnormalities. In the absence of an identified cause, gastroparesis is labelled as idiopathic. We present the case of a patient with severe idiopathic gastroparesis. Pharmacological approaches failed, as well as reduction in gastric emptying resistance with pyloric injection of botulinum toxin and pyloroplasty. Therefore, subtotal gastrectomy was performed. Histological and immunohistochemical study of the resected specimen showed hypoganglionosis, neuronal dysplasia, and a marked reduction in both myenteric and intramuscular interstitial cells of Cajal. To our knowledge, this is the first time these rare histological findings have been described in a patient with idiopathic gastroparesis.
In vivo particle-mediated cytokine gene transfer into canine oral mucosa and epidermis. (1996)

Cytokines can stimulate immune effector cells present within the oral mucosa and epidermis to respond to vaccination or to combat cancer. However, intravenous cytokine delivery is often inefficient and frequently accompanied by systemic toxicity. The goal of this study was to evaluate dogs as a large animal model for gene therapy of cancer because they develop spontaneous oral and epidermal tumors. In this report, we demonstrate that particle-mediated gene transfer of beta-galactosidase, luciferase, interleukin-2, interleukin-6, and granulocyte-macrophage colony stimulating factor (GM-CSF) complementary DNA (cDNA) into the oral mucosa and epidermis of healthy dogs resulted in effective, localized, transgenic protein expression. Additionally, the epidermal sites transfected with GM-CSF developed a profound inflammatory reaction characterized by neutrophilic infiltration. Clinical pathology analyses were unremarkable. These results demonstrate that in vivo particle-mediated gene transfer of canine oral mucosa and epidermis with cytokine cDNA can result in production of biologically active transgenic cytokines with minimal toxicity. These findings have applications to cancer immunotherapy using a gene gun approach.
One-Step Formation of Morphologically Controlled Nanoparticles with Projection Coronas (2003)

Nanoparticles with projection coronas were prepared by the one-step dispersion terpolymerization of styrene, acrylonitrile, and poly(ethylene glycol) monomethacrylate in ethanol−water solution, and their morphologies were controlled. When the mole composition of acrylonitrile to the total monomers CAN was 0.49−0.66, electron microscopy showed that the nanoparticles were spherical and had a number of projections on the surface. A CAN of more than 0.66 yielded no nanospheres, and a CAN smaller than 0.49 yielded projection-free nanospheres. The morphology of the nanospheres could be controlled by changing the reaction conditions, and some conditions yielded a regular arrangement of uniform projections on the surface similar to that seen in some coronaviruses. X-ray and spectroscopic studies suggested that the projections might be formed as a result of the nonequilibrated swelling of acrylonitrile and poly(ethylene glycol) domains on the surface.
The genetics of pain and pain inhibition. (1996)

The present review summarizes the current state of knowledge about the genetics of pain-related phenomena and illustrates the scope and power of genetic approaches to the study of pain. We focus on work performed in our laboratories in Jastrzebiec, Poland; Portland, OR; and Los Angeles, which we feel demonstrates the continuing usefulness of classical genetic approaches, especially when used in combination with newly available molecular genetic techniques.
Rational Design of a Minimal and Highly Enriched CYP102A1 Mutant Library with Improved Regio‐, Stereo‐ and Chemoselectivity (2009)

A minimal CYP102A1 mutant library of only 24 variants plus wild type was constructed by combining five hydrophobic amino acids (alanine, valine, phenylalanine, leucine and isoleucine) in two positions. Both positions are located close to the centre of the haem group. The first, position 87, has been shown to mediate substrate specificity and regioselectivity in CYP102A1. The second hotspot, position 328, was predicted to interact with all substrates during oxidation and has previously been identified by systematic analysis of 31 crystal structures and 6300 sequences of cytochrome P450 monooxygenases. By systematically altering the size of the side chains, a broad range of binding site shapes was generated. All variants were functionally expressed in E. coli. The library was screened with four terpene substrates geranylacetone, nerylacetone, (4R)-limonene and (+)-valencene. Only three variants showed no activity towards all four terpenes, while eleven variants demonstrated either a strong shift or improved regio- or stereoselectivity during oxidation of at least one substrate as compared to CYP102A1 wild type.
Stabilization and Delivery Approaches for Protein and Peptide Pharmaceuticals: An Extensive Review of Patents (2013)

Proteins and peptides are the building blocks of human body and act as the arsenal to combat against the invading pathogenic organisms for treatment and management of diseases. Majority of such biomacromolecules are synthesized by the human body itself. However, entry of disease causing pathogens causes misleading in the synthesis of desired proteins for antibody formation. In such alarming situations, the delivery of requisite protein and peptide from external source helps in augmenting the body's immunity. The major drawbacks underlying poor biopharmaceutical performance of high molecular weight protein and peptide drugs are due to poor oral absorption, formulation stability, degradation in the gastric milieu, susceptible to presystemic metabolism. Numerous literature recounts the application of myriad drug delivery strategies for the effective delivery of protein and peptides viz. parentral, oral, transdermal, nasal, pulmonary, rectal, buccal and ocular drug delivery systems. There are many reviews on various delivery strategies for protein and peptide pharmaceuticals, but the present review article provides a bird's eye view on various novel drug delivery systems used for enhanced delivery of protein and peptide pharmaceuticals in the light of patent literature. Apart from this, the present manuscript endeavor provides idea on possible causes and major degradation pathways responsible for poor stability of protein and peptide drugs along with recent market instances on them utilizing novel drug delivery systems.
PERP, an apoptosis-associated target of p53, is a novel member of the PMP-22/gas3 family (2000)

The p53 tumor suppressor activates either cell cycle arrest or apoptosis in response to cellular stress. Mouse embryo fibroblasts (MEFs) provide a powerful primary cell system to study both p53-dependent pathways. Specifically, in response to DNA damage, MEFs undergo p53-dependent G(1) arrest, whereas MEFs expressing the adenovirus E1A oncoprotein undergo p53-dependent apoptosis. As the p53-dependent apoptosis pathway is not well understood, we sought to identify apoptosis-specific p53 target genes using a subtractive cloning strategy. Here, we describe the characterization of a gene identified in this screen, PERP, which is expressed in a p53-dependent manner and at high levels in apoptotic cells compared with G(1)-arrested cells. PERP induction is linked to p53-dependent apoptosis, including in response to E2F-1-driven hyperproliferation. Furthermore, analysis of the PERP promoter suggests that PERP is directly activated by p53. PERP shows sequence similarity to the PMP-22/gas3 tetraspan membrane protein implicated in hereditary human neuropathies such as Charcot-Marie-Tooth. Like PMP-22/gas3, PERP is a plasma membrane protein, and importantly, its expression causes cell death in fibroblasts. Taken together, these data suggest that PERP is a novel effector of p53-dependent apoptosis.
Molecular mimicry of carbohydrate and protein structures by hybridoma antibodies (1987)

Abstract A large proportion of tumour‐associated antigens seem to be determined by carbohydrate structures. Advances in the study of the antigenicity of cell‐surface carbohydrates have been hampered by the absence of advanced monoclonal hybridoma technology comparable to that available for the study of protein antigens. Monoclonal antibodies have been raised against a carbohydrate epitope (43–9F) that is associated with the proliferative features of squamous lung carcinomas. These were used in turn to generate anti‐idiotype antibodies with homology to 43–9F. The method and its possible applications are described, together with a procedure to detect rare cell membrane variants within large populations.
The Arusha Project: A Framework for Collaborative UNIX System Administration (2001)

The Arusha Project is an independent open-source project centered on the premise that the best hope for Unix system administration at modest-sized sites is through large-scale Internet-wide collaboration. We present a simple object model as a thinking tool, and an XML-based configuration language as a concrete notation for expressing system-administrative facts. We show how this framework allows a gentle evolution from current practices, but gets us quickly to very powerful ways of working.
Isolation and functional analysis of histidine‐tagged elongation factor Tu (1992)

The study of the structure/function relationships of the Escherichia coli elongation factor Tu (EF-Tu) via mutagenesis has been hampered by difficulties encountered in separating the mutated factor from other proteins, in particular native EF-Tu. Here we describe a novel system for the purification of EF-Tu mutant species, based on metal-ion affinity chromatography. To facilitate rapid and efficient purification we designed a recombinant EF-Tu with an additional C-terminal sequence of one serine and six histidine residues. A cell extract containing the His-tagged EF-Tu (EF-TuHis) is applied to a Ni(2+)-nitrilotriacetic acid column. EF-TuHis can be selectively eluted with an imidazole containing buffer, yielding a preparation of more than 95% purity, free of wild-type EF-Tu. In-vitro and in-vivo functional analyses show that EF-TuHis resembles the wild-type EF-Tu, which makes this one-step isolation procedure a promising tool for the study of the interactions of mutant EF-Tu with the various components of the elongation cycle. The new isolation procedure was successfully applied for the purification of a mutant EF-TuHis with a Glu substitution for Lys237, a residue possibly involved in the binding of aminoacyl-tRNA.
Experimental Myocardial Cryoinjury: Local Electromechanical Changes, Arrhythmogenicity, and Methods for Determining Depth of Injury (1987)

To characterize the electromechanical effects of acute and 2-week-old cryoinjury, programmed stimulation and epicardial M-mode echo mapping (7.5 mHz) were performed prior to, at 15 minutes and 15 +/- 2 days after cryoinjury in 10 dogs. Epicardial and intramural bipolar and unipolar electrograms were recorded in five of the dogs. Cryoinjury was produced with a 5 mm in diameter flat cryoprobe at -60 degrees C applied to the left ventricular epicardium for 10 minutes at each of six contiguous sites. Cryoinjury, acutely and at 2 weeks, was characterized by a loss of normal intramural systolic thickening and a decrease in echo density. The maximum depth of cryoinjury determined by echo ranged from .55 to .85 cm acutely, and .50 to .80 cm chronically and it correlated acutely and chronically (r = .80; r = .85) with pathologically documented depth of cryoinjury at 2 weeks. Acutely, the presence of either an abnormal intramural unipolar or bipolar electrogram also defined the depth of cryoinjury within .16 cm. In contrast, epicardial electrograms were not useful for judging depth of cryoinjury. A QS complex on the epicardial unipolar electrogram was recorded over the cryoinjury acutely and at 2 weeks in four of five dogs despite preserved subendocardial systolic wall thickening and normal histology extending 40 to 65% of the wall thickness. Epicardial bipolar electrograms uniformly showed a marked decrease in amplitude and slope of the intrinsic deflection, a small but insignificant increase in width and no multicomponent activity. Ventricular fibrillation was reproducibly initiated with three ventricular extrastimuli in five of 10 dogs at 2 weeks. No ventricular tachycardia was initiated.(ABSTRACT TRUNCATED AT 250 WORDS)
A comparison of the heme binding pocket in globins and cytochrome b5. (1975)

Of the 85 three-dimensionally characterized residues of cytochrome b5, 51 are found to be structurally and topologically equivalent to the globin fold. When these proteins have been superimposed, the heme irons are found to be less than 1.4 A separated and the heme normals are inclined by less than 9.5 degrees. The proximal histidine of the globins and two adjacent helices are equivalent to the sixth iron ligand and adjacent helices of cytochrome b5. Larger differences in structure are observed on the distal side of the heme, coincident with the most changeable part of the globin structures. The heme itself is rotated by 53 degrees about its normal but such a change is energetically minimal and conservative as the heme side groups are not directly involved in the function of the molecules. The beta-sheet of cytochrome b5 is inserted into a corresponding cavity of the globins forming an additional lining to the heme pocket. The roughly 50 residues missing at the carboxy end of the known cytochrome b5 fragment could correspond in part to the H helix in the globins. While it would seem probable that these similarities represent divergent evolution from a primordial heme-binding protein, the possibility of structural convergence to a functionally satisfactory protein cannot be excluded.
Screening and Enrichment of Metal Nanoparticles with Novel Optical Properties (1998)

A rapid screening and enrichment method is reported for exploring the size and shape diversities (libraries) of nanometer-scale colloidal particles. With the use of surface-enhanced Raman scattering, a new class of metal nanoparticles has been identified from heterogeneous silver colloids. These particles are relatively large, faceted nanocrystals that are able to enhance the efficiencies of surface optical processes by as much as 14−15 orders of magnitude. The population of these novel nanoparticles is only about 0.1−1% in standard colloid preparations but can be enriched to about 10−15% by size-selective fractionation. This new class of nanoparticles could find potential uses in optoelectronic devices, ultrasensitive chemical sensors, and single-molecule detection.
Three-dimensional shape analysis using moments and Fourier descriptors (1988)

A procedure for using moment-based feature vectors to identify a three-dimensional object from a two-dimensional image recorded at an arbitrary viewing angle and range is presented. A moment form called standard moments, rather than the usual moment invariants, is considered. A standard six-airplane experiment was used to compare different techniques. Fourier descriptors and moment invariants were both compared to the present scheme for normalized moments. Various experiments were conducted using mixtures of silhouette and boundary moments and different normalization techniques. Standard moments gave slightly better results than Fourier descriptors for this experiment; both of these techniques were much better than moment invariants.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heptacoordinate Heteroleptic Salan (ONNO) and Thiosalan (OSSO) Titanium(IV) Complexes: Investigation of Stability and Cytotoxicity (2015)

Seven heptacoordinate titanium(IV) complexes were synthesized based on the concept of hetero-bis-chelate stabilization of salan (ONNO) and thiosalan (OSSO) titanium(IV)alkoxides with 2,6-pyridinedicarboxylic acid (dipic) and derivatives thereof. The resulting compounds were investigated in a solid by X-ray diffraction and in solution by NMR spectroscopy. A thiosalan (OSSO) titanium(IV) complex could be isolated and its conformational stabilization by dipic was shown by (1)H NMR spectroscopy to lead to nonfluxional behavior even at room temperature. The stability of selected complexes was assessed at pH 1.9, 6.8, and 12.1 by an UV-vis monitored hydrolysis study with >5 Mio. equivalents of water. Even at pH 12.1 [L(1)Ti(dipic)(1)] showed t1/2 of more than 2 days. The cytotoxicity of all compounds was investigated in two human carcinoma cell lines. IC50-values in the range of cisplatin were achieved by all tested compounds except for [L(4)Ti(dipic)(1)], which was proven to be nontoxic. The functionalization of dipic was thus well tolerated and did neither interfere with the stability nor the cytotoxicity of the heteroleptic complexes.
Active transposition in zebrafish. (1996)

We have identified a new family of Tc1-like transposons in the zebrafish, Danio rerio. The sequence of a candidate active transposon, deduced from sample Tzf elements, shows limited resemblance to the previously described Tdr1 elements of zebrafish. Both the Tzf and the Tdr elements are extremely abundant in zebrafish. We describe here a general strategy for detecting transposition events in a complex genome and demonstrate its utility by selectively monitoring hundreds of potentially active Tzf copies in the zebrafish genome against a background of other related elements. We have followed members of a zebrafish pedigree, using this two-dimensional transposon display strategy, to identify the first examples of active transposition of such elements in vertebrates.
The five-minute rule 20 years later (and how flash memory changes the rules) (2009)

Revisiting Gray and Putzolu's famous rule in the age of Flash.