gebhart/patrepeval huggingface dataset:
Post-translational Addition of Chondroitin Sulfate Glycosaminoglycans (1989)

A melanoma proteoglycan model system has been used to examine the role of core protein asparagine-linked (N-linked) oligosaccharides in the transport and assembly of proteoglycan molecules. The use of agents which block discrete steps in the trimming and processing of core oligosaccharides (castanospermine, 1-deoxynojirimycin, N-methyldeoxynojirimycin, 1-deoxymannojirimycin, and swainsonine) demonstrates that removal of glucose residues from the N-linked oligosaccharides is required for the cell surface expression of a melanoma proteoglycan core protein and for the conversion of the core protein to a chondroitin sulfate proteoglycan. However, complete maturation of the oligosaccharides to a "complex" form is not required for these events. Treatment of M21 human melanoma cells with the glucosidase inhibitors castanospermine, 1-deoxynojirimycin, or N-methyldeoxynojirimycin results in a dose-dependent inhibition of glycosaminoglycan (GAG) addition to the melanoma antigen recognized by monoclonal antibody 9.2.27. In contrast, treatment with the mannosidase inhibitors 1-deoxymannojirimycin and swainsonine does not effect GAG addition. Identical results are obtained when the major histocompatibility complex class II antigen gamma chain proteoglycan is examined in inhibitor-treated melanoma and B-lymphoblastoid cells. These data, in conjunction with the known effects of the glucosidase and mannosidase inhibitors on the transport and secretion of other glycoproteins support the hypothesis that the addition, trimming, and processing of N-linked oligosaccharides is involved in the transport of certain proteoglycan core proteins to the site of GAG addition and to the cell surface.
Control of mucoidy in Pseudomonas aeruginosa: transcriptional regulation of algR and identification of the second regulatory gene, algQ (1989)

A new alginate regulatory gene, algQ, was identified in a chromosomal region which, when tandemly amplified, induces mucoidy in Pseudomonas aeruginosa. The algQ gene was found closely linked to the previously identified algR gene. Both algQ and algR were required for transcription of the key alginate biosynthetic gene, algD. In addition, expression of the algR gene was studied. The algR promoter was mapped by S1 nuclease and reverse transcription and found to be activated in mucoid cells. However, even in nonmucoid cells, transcription of algR was detectable at an approximately 50-fold-lower level, as opposed to the algD promoter, which was silent in the nonmucoid background. Transcription of both promoters was studied by using algR- and algD-specific oligonucleotides and total cellular RNA from fresh cystic fibrosis isolates of mucoid P. aeruginosa and their nonmucoid revertants. Identical patterns of activity were found in all strains: in mucoid cells, both algR and algD were activated. This finding indicated that common mechanisms were involved in the regulation of alginate gene expression. However, when the algR gene was cloned behind the tac promoter on a broad-host-range-controlled expression vector, induction of transcription with isopropropyl-beta-D-thiogalactopyranoside (IPTG) caused the appearance of a nonmucoid phenotype in previously mucoid cells. This effect was transient, since removal of the inducer (IPTG) made cells mucoid again. Since the algR gene product is homologous to transcriptional regulators from a class of environmentally responsive systems (known to have a second, sensory component), the algQ gene could be a candidate for the sensory component of the alginate system.
Acylcarnitines: drug absorption-enhancing agents in the gastrointestinal tract (1986)

Acylcarnitines were tested as potential absorption-enhancing agents for drugs that are poorly absorbed from the gastrointestinal tract. Urethan-anesthetized Sprague-Dawley rats and conscious Beagle dogs were used. Palmitoyl-DL-carnitine was the most effective acylcarnitine tested, although significant increases in drug absorption were observed with acylcarnitines containing C12 through C18 fatty acid chains. Palmitoyl-DL-carnitine afforded significant increases in the absorption of cefoxitin, gentamicin, cytarabine, somatostatin analogue, and alpha-methyldopa. The response to palmitoyl-DL-carnitine was concentration dependent and reversible within 60-120 min. Histological examination of the intestinal tissue revealed no apparent change in mucosal structural integrity at doses of palmitoyl-DL-carnitine that resulted in increased drug absorption. The acylcarnitines were effective in increasing drug absorption from the small intestine and the rectal compartment of both rats and dogs. The data also demonstrated effectiveness with aqueous and solid dosage forms (Witepsol H-15 suppositories). The data suggest that acylcarnitines may be effective and safe absorption-enhancing agents for a variety of drugs.
Characterization of Human and Murine T-Cell Immunoglobulin Mucin Domain 4 (TIM-4) IgV Domain Residues Critical for Ebola Virus Entry (2016)

With more than 28,000 cases and over 11,000 deaths during the largest and most recent Ebola virus (EBOV) outbreak, there has been increased emphasis on the development of therapeutics against filoviruses. Many therapies under investigation target EBOV cell entry. T-cell immunoglobulin mucin (TIM) domain proteins are cell surface factors important for the entry of many enveloped viruses, including EBOV. TIM family member TIM-4 is expressed on macrophages and dendritic cells, which are early cellular targets during EBOV infection. Here, we performed a mutagenesis screening of the IgV domain of murine and human TIM-4 to identify residues that are critical for EBOV entry. Surprisingly, we identified more human than murine TIM-4 IgV domain residues that are required for EBOV entry. Defining the TIM IgV residues needed for EBOV entry clarifies the virus-receptor interactions and paves the way for the development of novel therapeutics targeting virus binding to this cell surface receptor.
Quantifying the spread of botulinum toxin through muscle fascia (1991)

Botulinum toxin was recently approved for treating several head and neck dystonias. Paralysis of neighboring muscles is the major complication of its use. Spread of toxin from the injected muscle has been suggested as an etiology. This study examines how botulinum toxin crosses muscle fascia by a novel method of quantifying muscular paralysis. Botulinum toxin (0.2 to 10 U) was placed onto the fascia of rat tibialis anterior (TA) muscles (n = 6). Toxin was also placed on dose-matched muscles that had their fascia surgically removed (n = 6). Twenty-four hours later, the nerve to the tibialis anterior was electrically stimulated to deplete the muscle fibers of glycogen. Toxin-paralyzed fibers retained their glycogen and appeared purple on periodic acid-Schiff (PAS) stain. Botulinum toxin easily passed through muscle fascia even at subclinical doses. The presence of fascia reduced the spread of botulinum toxin by 23%. These results suggest that spread of botulinum toxin can be prevented only by delivering small doses to the center of a target muscle.
Focal application of neutralizing antibodies to soluble neurotrophic factors reduces collateral axonal branching after peripheral nerve lesion (2002)

A major reason for the insufficient recovery of function after motor nerve injury are the numerous axonal branches which often re-innervate muscles with completely different functions. We hypothesized that a neutralization of diffusable neurotrophic factors at the lesion site in rats could reduce the branching of transected axons. Following analysis of local protein expression by immunocytochemistry and by in situ hybridization, we transected the facial nerve trunk of adult rats and inserted both ends into a silicon tube containing (i) collagen gel with neutralizing concentrations of antibodies to NGF, BDNF, bFGF, IGF-I, CNTF and GDNF; (ii) five-fold higher concentrations of the antibodies and (iii) combination of antibodies. Two months later, retrograde labelling was used to estimate the portion of motoneurons the axons of which had branched and projected into three major branches of the facial trunk. After control entubulation in collagen gel containing non-immune mouse IgG 85% of all motoneurons projecting along the zygomatic branch sprouted and sent at least one twin axon to the buccal and/or marginal-mandibular branches of the facial nerve. Neutralizing concentrations of anti-NGF, anti-BDNF and anti-IGF-I significantly reduced sprouting. The most pronounced effect was achieved after application of anti-BDNF, which reduced the portion of branched neurons to 18%. All effects after a single application of antibodies were concentration-dependent and superior to those observed after combined treatment. This first report on improved quality of reinnervation by antibody-therapy implies that, in rats, the post-transectional collateral axonal branching can be reduced without obvious harmful effects on neuronal survival and axonal elongation.
Melatonin Secretion is Supersensitive to Light in Migraine (2004)

The present study examined the sensitivity to light of melatonin (MLT) secretion in familial migraine during a headache-free interval. Twelve female patients and 12 healthy controls were included in the trial. All subjects were studied twice. In each session, light exposure (300 lx) or placebo was randomly administered for 30 min between 00.30 and 01.00 h. Blood was sampled hourly between 20.00 and 24.00 h, and 02.00 and 04.00 h and every 15 min between 00.30 and 01.30 h. Plasma MLT levels were determined by radioimmunoassay. MLT suppression was more marked in the migraine group than in the control group [difference of area under curve (DeltaAUC)=-53.8 +/- 16.2 vs. 18.5 +/- 12.7 pg/h/ml, P<0.005; maximum of MLT suppression (Delta)=-35.7 +/- 10.2 vs. - 6.7 +/- 5.8 pg/ml, P<0.05]. These findings show a clear hypersensitivity to light in young female migraineurs during the headache-free period.
The immune-enhancing effects of dietary fibres and prebiotics (2002)

The gastrointestinal tract is subjected to enormous and continual foreign antigenic stimuli from food and microbes. This organ must integrate complex interactions among diet, external pathogens, and local immunological and non-immunological processes. It is critical that protective immune responses are made to potential pathogens, while hypersensitivity reactions to dietary antigens are minimised. There is increasing evidence that fermentable dietary fibres and the newly described prebiotics can modulate various properties of the immune system, including those of the gut-associated lymphoid tissues (GALT). This paper reviews evidence for the immune-enhancing effects of dietary fibres. Changes in the intestinal microflora that occur with the consumption of prebiotic fibres may potentially mediate immune changes via: the direct contact of lactic acid bacteria or bacterial products (cell wall or cytoplasmic components) with immune cells in the intestine; the production of short-chain fatty acids from fibre fermentation; or by changes in mucin production. Although further work is needed to better define the changes, mechanisms for immunomodulation, and the ultimate impact on immune health, there is convincing preliminary data to suggest that the consumption of prebiotics can modulate immune parameters in GALT, secondary lymphoid tissues and peripheral circulation. Future protocols on the physiological impact of consuming prebiotics should be designed to include assessments of the gut microflora, gut physiology and the function and composition of the various regions of GALT.
Nanoparticle Albumin-Bound Paclitaxel: A Novel Cremphor-EL ® -Free Formulation of Paclitaxel (2007)

Standard formulation paclitaxel requires the use of solvents, such as Cremphor-EL, which contribute to some of the toxicities commonly associated with paclitaxel-based therapy. Nanoparticle albumin-bound paclitaxel (nab-paclitaxel) is a novel solvent-free formulation of paclitaxel. The formulation is prepared by high-pressure homogenization of paclitaxel in the presence of serum albumin into a nanoparticle colloidal suspension. The human albumin-stabilized paclitaxel particles have an average size of 130 nm. Nab-paclitaxel has several practical advantages over Cremphor-EL-paclitaxel, including a shorter infusion time (30 min) and no need for premedications for hypersensitivity reactions. The nab-paclitaxel formulation eliminates the impact of Cremphor-EL on paclitaxel pharmacokinetics and utilizes the endogenous albumin transport mechanisms to concentrate nab-paclitaxel within the tumor. A recent Phase III trial compared nab- and Cremphor-EL-paclitaxel in patients with metastatic breast cancer. Patients treated with nab-paclitaxel experienced a higher response, longer time to tumor progression and, in patients receiving second-line or greater therapy, a longer median survival. Patients treated with nab-paclitaxel had a significantly lower rate of severe neutropenia and a higher rate of sensory neuropathy. The preclinical and clinical data indicate that the nab-paclitaxel formulation has significant advantages over Cremphor-EL-paclitaxel.
Probing pH-Tuned Morphological Changes in Core−Shell Nanoparticle Assembly Using Atomic Force Microscopy (2001)

This paper reports novel findings of an investigation of pH-tuned morphological changes in a core−shell gold nanoparticle assembly derived from hydrogen-bonding at the encapsulating shells. Our strategy couples the selective assembly of such hydrogen-bonding-linked nanoparticles at patterned substrates with the capability of atomic force microscopy to detect the nanostructural changes in the pH-tuned interfacial process. The selective assembly on a monolayer-patterned substrate provided an ideal imaging platform with an internal standard from the unassembled areas. The detection of significant and reversible changes of both friction and height in the nanoparticle-assembled areas provided new insights into understanding of ionic fluxes and solvation effect within the nanoporous structure, which have important implications to the design of nanoparticle-based interfaces for nanostructured catalysis and molecular recognition.
Palladium-Catalyzed Cross-Coupling of Organoboron Compounds with Iodonium Salts and Iodanes (1996)

The palladium-catalyzed cross-coupling reaction of iodinanes (iodonium salts and iodanes) with organoboron compounds to form carbon-carbon bonds was achieved at ambient temperature under aqueous conditions in the absence of base. Coupling of phenylboronic acid with diphenyliodonium tetrafluoroborate in the presence of Pd(PPh(3))(4) (0.2 mol %) or Pd(OAc)(2) (0.2 mol %) under aqueous conditions gave biphenyl in almost quantitative yield. Under the same conditions, substituted boronic acids, boronates, and trialkylboranes were readily coupled with diaryl-, alkenyl-, and alkynyliodonium salts. Finally, the iodanes ArI(OH)OTs underwent cross-coupling with boronic acids, boronates, and trialkylboranes to afford biphenyls and aryl-substituted alkenes.
Detection of Soluble Tumor-associated Antigens in Sera and Effusions Using Novel Monoclonal Antibodies, KL-3 and KL-6, against Lung Adenocarcinoma (1988)

Two novel monoclonal antibodies, KL-3 (IgM) and KL-6 (IgG1), which can detect soluble antigens in sera and effusions (molecular weights greater than 1,000 K) were produced against human pulmonary adenocarcinoma VMRC-LCR cells. KL-3 and KL-6 antibodies reacted with asialo- and sialo-carbohydrate antigenic determinants, respectively. Both carbohydrate epitopes appear, from competitive inhibition studies, to be different from Lex, Ley, sialyl Lea and sialyl Lexi which were recognized with FH2, AH6, NS19-9 and FH6 antibodies, respectively. Using an enzyme linked immunosorbent assay, elevated KL-6 antigen levels were frequently observed in the sera of patients with lung adenocarcinoma [52% (17/33)], pancreatic cancer [44% (4/9)] and breast cancer [40% (8/20)], but infrequently in the sera of patients with lung squamous cell carcinoma [18% (4/22)], lung small cell carcinoma [8% (1/13)], gastric cancer [0% (0/19)], colorectal cancer [0% (0/8)] and hepatocellular cancer [13% (1/8)]. The levels and positive rates of serum KL-6 antigen increased with the progression of clinical stage of lung adenocarcinoma. In pleural effusions, the prevalences of lung adenocarcinoma cases with elevated levels of KL-3 and KL-6 antigens were 76% (13/17) and 82% (14/17), respectively. These monoclonal antibodies can define novel soluble antigens in sera and effusions which could be useful in tumor diagnoses and for monitoring tumor progression.
Sinkhorn Distances: Lightspeed Computation of Optimal Transport (2013)

Abstract. Optimal transportation distances are a fundamental family of pa-rameterized distances for histograms. Despite their appealing theoretical prop-erties, excellent performance in retrieval tasks and intuitive formulation, their computation involves the resolution of a linear program whose cost is prohibi-tive whenever the histograms ’ dimension exceeds a few hundreds. We propose in this work a new family of optimal transportation distances that look at transportation problems from a maximum-entropy perspective. We smooth the classical optimal transportation problem with an entropic regularization term, and show that the resulting optimum is also a distance which can be com-puted through Sinkhorn-Knopp’s matrix scaling algorithm at a speed that is several orders of magnitude faster than that of transportation solvers. We also report improved performance over classical optimal transportation distances on the MNIST benchmark problem. 1.
Interactive shape modeling using a skeleton-mesh co-representation (2014)

We introduce the Polar-Annular Mesh representation (PAM). A PAM is a mesh-skeleton co-representation designed for the modeling of 3D organic, articulated shapes. A PAM represents a manifold mesh as a partition of polar (triangle fans) and annular (rings of quads) regions. The skeletal topology of a shape is uniquely embedded in the mesh connectivity of a PAM, enabling both surface and skeletal modeling operations, interchangeably and directly on the mesh itself. We develop an algorithm to convert arbitrary triangle meshes into PAMs as well as techniques to simplify PAMs and a method to convert a PAM to a quad-only mesh. We further present a PAM-based multi-touch sculpting application in order to demonstrate its utility as a shape representation for the interactive modeling of organic, articulated figures as well as for editing and posing of pre-existing models.
Fermentation of Fructooligosaccharides by Lactic Acid Bacteria and Bifidobacteria (2000)

Lactic acid bacteria and bifidobacteria were screened of their ability to ferment fructooligosaccharides (FOS) on MRS agar. Of 28 strains of lactic acid bacteria and bifidobacteria examined, 12 of 16 Lactobacillus strains and 7 of 8 Bifidobacterium strains fermented FOS. Only strains that gave a positive reaction by the agar method reached high cell densities in broth containing FOS.
Applications of confocal macroscope-microscope luminescence imaging to sediment cores (2006)

Abstract We demonstrate the successful application of a novel, confocal scanning laser macroscope-microscope (cslM/m) system for non-invasive imaging of samples taken from lake and ocean sediment cores. Advantages of the macroscope-microscope system over other macroscopic luminescence imaging techniques, such as scanning electron microscopy-based cathodoluminescence and scanning-stage laser imaging, are highlighted and the implications for new core analysis techniques are explored. The macroscope-microscope can image specimens ranging from 25 × 25 μm up to 7.5 × 7.5 cm in under 10 s using reflected light or photoluminescence as contrast mechanisms. Macroscope mode is used to rapidly survey the specimen and provide a photoluminescence ‘roadmap’. Microscope mode is used to provide ultra-high-resolution images of microfossils or areas of interest. Laser scanning is non-invasive and does not require any preparation of the specimen. Photoluminescence and fluorescence imaging results are shown for an entire core section recovered from Lake Huron by the Geological Survey of Canada (GSC). Photoluminescence images are shown for Ocean Drilling Program samples of a diatom mat and a radiolarian microfossil within the sample, a laminated interval of sediment from the Santa Barbara Basin (Site 893) and specimens from the Scotian Shelf (collected by the GSC).
Potential inhibitors of nucleotide biosynthesis. 2. Halomethyl ketone derivatives of pyrimidine nucleosides (1984)

Several halomethyl ketone derivatives of pyrimidine nucleosides have been prepared for evaluation as cytotoxic agents. The first series are 1-(8-halo-2,5,6,8- tetradeoxy -beta-D-erythro-oct-7 - ulofuranosyl )thymines (7-9), whereas the second type are halo derivatives of acetophenone (12-14 and 16). These compounds are cytotoxic, and one (13) showed activity against the P388 leukemia in vivo.
Fiber optical fluorosensor for determination of halothane and or oxygen (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFiber optical fluorosensor for determination of halothane and or oxygenOtto S. Wolfbeis, Hermann E. Posch, and Herbert W. KroneisCite this: Anal. Chem. 1985, 57, 13, 2556–2561Publication Date (Print):November 1, 1985Publication History Published online1 May 2002Published inissue 1 November 1985https://pubs.acs.org/doi/10.1021/ac00290a028https://doi.org/10.1021/ac00290a028research-articleACS PublicationsRequest reuse permissionsArticle Views273Altmetric-Citations100LEARN 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 Get e-Alerts
Two Tests for Detecting Nitriles and Amides (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTwo Tests for Detecting Nitriles and AmidesSwiatoslaw. Trofimenko and J. W. SeaseCite this: Anal. Chem. 1958, 30, 8, 1432–1434Publication Date (Print):August 1, 1958Publication History Published online1 May 2002Published inissue 1 August 1958https://pubs.acs.org/doi/10.1021/ac60140a043https://doi.org/10.1021/ac60140a043research-articleACS PublicationsRequest reuse permissionsArticle Views1570Altmetric-Citations10LEARN 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 Get e-Alerts