gebhart/patrepeval huggingface dataset:
GDNF and NGF released by synthetic guidance channels support sciatic nerve regeneration across a long gap (2002)

The present work was performed to determine the ability of neurotrophic factors to allow axonal regeneration across a 15-mm-long gap in the rat sciatic nerve. Synthetic nerve guidance channels slowly releasing NGF and GDNF were fabricated and sutured to the cut ends of the nerve to bridge the gap. After 7 weeks, nerve cables had formed in nine out of ten channels in both the NGF and GDNF groups, while no neuronal cables were present in the control group. The average number of myelinated axons at the midpoint of the regenerated nerves was significantly greater in the presence of GDNF than NGF (4942 +/-1627 vs. 1199 +/-431, P < or = 0.04). A significantly greater number of neuronal cells in the GDNF group, when compared to the NGF group, retrogradely transported FluoroGold injected distal to the injury site before explantation. The total number of labelled motoneurons observed in the ventral horn of the spinal cord was 98.1 +/-23.4 vs. 20.0 +/-8.5 (P < or = 0.001) in the presence of GDNF and NGF, respectively. In the dorsal root ganglia, 22.7% +/- 4.9% vs. 3.2% +/-1.9% (P +/-0.005) of sensory neurons were labelled retrogradely in the GDNF and NGF treatment groups, respectively. The present study demonstrates that, sustained delivery of GDNF and NGF to the injury site, by synthetic nerve guidance channels, allows regeneration of both sensory and motor axons over long gaps; GDNF leads to better overall regeneration in the sciatic nerve.
Polysaccharides of the Genus Bacillus Cross-Reactive with the Capsular Polysaccharides of Diplococcus pneumoniae Type III, Haemophilus influenzae Type b, and Neisseria meningitidis Group A (1973)

We studied 174 strains of the genus Bacillus for cross-reacting antigens to the capsular polysaccharides of groups A and C meningococcus, types I and III pneumococcus, and Haemophilus influenzae type b. Cross-reactions were detected by immunodiffusion in agarose gel by using type-specific antisera and confirmed by absorption and inhibition experiments. Of 20 Bacillus pumilis strains, six had an antigen cross-reacting with group A meningococcal polysaccharide. Other cross-reactions included one strain of B. pumilis with H. influenzae type b, one of B. cereus var. mycoides with pneumococcus type III, and one of B. alvei with both type b and SIII polysaccharides. These cross-reacting antigens are polysaccharides of vegetative cells and may be extracellular in location. Because these bacilli have antigens cross-reacting with the virulence factors of pyogenic bacteria, they may, as normal flora, be an antigenic stimulus for "natural" serum anti-capsular antibodies to the type b Haemophilus and group A meningococcus polysaccharides.
Investigating Mobility, Technology, And Space In Homes, Starting With “Great Rooms” (2005)

Certain American-style homes include large multifunctional spaces, often with vaulted or otherwise high ceilings, that incorporate living, dining, and kitchen areas. As an American cultural phenomenon, these “great rooms” symbolize and instantiate a particular vision of the good life or ideal home, including for example concepts such as openness and togetherness, or in less favorable interpretations, wastefulness and lack of privacy. As such, we see great rooms as complex and contradictory symptoms of unresolved tensions in the politics of everyday life. We describe our approach of starting with a provocative and problematic topic within a larger domain of interest and examining it from a number of perspectives. We argue that sites that are contentious are particularly interesting candidates for technological innovation, in which technology is not limited to assimilating to well-established and understood processes, but rather can participate in an ongoing process, responding to and challenging concerns.
The reverse DNA sequencing using Bst DNA polymerase. (1992)

The reverse DNA sequencing (RDS) [1] is a rapid method used to check the DNA sequences by sequencing them from the opposite orientation. Because the RDS is basically a double stranded sequencing, the quality of the sequence patterns so obtained generally is not as good as those obtained by the single stranded sequencing, and extra bands and higher background are produced more frequently. This paper shows that the RDS could now generate as good sequence patterns as those obtained by sequencing on the single stranded DNA template if Bst DNA polymerase instead of the conventional enzymes, such as the Klenow enzyme, was used in the RDS. Bst DNA polymerase is heat stable (optimum reaction temperature 65 degrees C) and has recently been successfully used in the conventional DNA sequencing. The RDS has recently been further simplified to meet the need of large DNA sequencing projects such as the human genome project. The combination of the simplified RDS and the use of Bst polymerase should be expected to facilitate greatly the work on sequence confirmation and correction.
Development of an Annotated Library of Neutral Human Milk Oligosaccharides (2010)

Human milk oligosaccharides (HMOs) perform a number of functions including serving as prebiotics to stimulate the growth of beneficial intestinal bacteria, as receptor analogues to inhibit binding of pathogens, and as substances that promote postnatal brain development. There is further evidence that HMOs participate in modulating the human immune system. Because the absorption, catabolism, and biological function of oligosaccharides (OS) have strong correlations with their structures, structure elucidation is key to advancing this research. Oligosaccharides are produced by competing enzymes that provide the large structural diversity and heterogeneity that characterizes this class of compounds. Unlike the proteome, there is no template for oligosaccharides, making it difficult to rapidly identify oligosaccharide structures. In this research, annotation of the neutral free oligosaccharides in milk is performed to develop a database for the rapid identification of oligosaccharide structures. Our strategy incorporates high performance nanoflow liquid chromatography and mass spectrometry for characterizing HMO structures. HPLC-Chip/TOF MS provides a sensitive and quantitative method for sample profiling. The reproducible retention time and accurate mass can be used to rapidly identify the OS structures in HMO samples. A library with 45 neutral OS structures has been constructed. The structures include information regarding the epitopes such as Lewis type, as well as information regarding the secretor status.
Characterization and Optimization of Selective, Nonpeptidic Inhibitors of Cathepsin S with an Unprecedented Binding Mode (2007)

The substrate activity screening (SAS) method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain a novel (2-arylphenoxy)acetaldehyde inhibitor, 2, with a 0.49 microM Ki value (Wood, W. J. L.; Patterson, A. W.; Tsuruoka, H.; Jain, R. K.; Ellman, J. A. J. Am. Chem. Soc. 2005, 127, 15521-15527). In this paper we disclose the X-ray structure of a complex between cathepsin S and inhibitor 2 which reveals an unprecedented binding mode. On the basis of this structure, additional 2-biaryloxy substrates with greatly increased cleavage efficiency were designed. Conversion of the optimized substrates to the corresponding aldehyde inhibitors yielded a low molecular weight (304 Daltons) and potent (9.6 nM) cathepsin S inhibitor that showed from 100- to >1000-fold selectivity relative to cathepsins B, L, and K.
HER3 Is a Determinant for Poor Prognosis in Melanoma (2008)

Our results provide novel insights into the role of HER3 in melanoma and point out new possibilities for therapeutic intervention.
GALECTIN‐3 AND LAMININ EXPRESSION IN NEOPLASTIC AND NON‐NEOPLASTIC THYROID TISSUE (1997)

Galectin-3 is a 31 kD β-galactoside-binding lectin which is expressed by several types of non-neoplastic and neoplastic cells and which may be involved in cell–extracellular matrix interactions. An immunohistochemical study has been made of the expression of galectin-3, as well as its ligand, laminin, in a spectrum of benign and malignant thyroid neoplasms and in some non-neoplastic conditions. Immunohistochemistry with anti-human recombinant galectin-3 antibody showed consistent, intense positivity in the neoplastic cells of 18 cases of papillary carcinoma and less intense staining in the five anaplastic carcinomas studied. In addition, two out of three poorly differentiated carcinomas, three out of six medullary carcinomas, and four out of eight follicular carcinomas had less intense or focal positivity. One case of Hürthle cell carcinoma showed scattered strongly positive cells. Eight follicular adenomas, three hyperplastic nodules, five nodular goitres, and normal thyroid tissue were negative. Galectin-3 mRNA expression was also evaluated in three of the papillary carcinomas, two follicular adenomas, and one hyperplastic nodule with matched normal tissue. Northern blot analysis demonstrated mRNA overexpression in the three cases of papillary carcinomas, whereas normal and benign tissues were negative. Laminin distribution in neoplastic and non-neoplastic tissue varied with architectural patterns but did not correlate with galectin-3 immunohistochemical expression. We conclude that expression of galectin-3 is limited to inflammatory foci in normal and benign thyroid tissue and is a phenotypic feature of malignant thyroid neoplasms, especially papillary carcinomas. © 1997 by John Wiley & Sons, Ltd.
Cystatin C--a paradigm of evidence based laboratory medicine. (2008)

Cystatin C is a 13-kDa protein, of the cysteine proteinase inhibitor superfamily, produced by all nucleated cells. Its production rate is constant throughout the ages of 1 to 50 years. It is freely filtered at the glomerulus and then resorbed and fully catabolised by proximal renal tubules, making it an ideal marker of glomerular filtration rate (GFR). Serum creatinine, the most established marker of renal function, is affected by age, gender, muscle mass, nutritional status and analytical interference. The abbreviated Modification of Diet in Renal Diseases (MDRD) equation has recently been introduced in an attempt to overcome these shortcomings, but still has many limitations. Cystatin C is not affected by gender, muscle mass, malignancy, its production rate is usually constant and its plasma concentration therefore is dependent only on GFR. Cystatin C has been demonstrated to be more accurate than serum creatinine in the detection of early renal impairment and in specific populations may allow for early detection of renal disease. Cystatin C has also been found to be a strong predictor of long-term clinical outcomes in patients with cardiovascular diseases. Although cystatin C may have advantages in detection of early renal impairment there is a paucity of evidence that it significantly improves clinical decision making over creatinine. This coupled with assay cost may be the reason why cystatin C, although well recognised, has not been introduced into routine operational use, although that may eventuate with emerging evidence.
Rat multiple organ blocks: Microsurgical technique of removal for ex vivo aerobic organ preservation using a fluorocarbon emulsion (2000)

A multiple organ block (MOB) is composed of en bloc removed organs (heart, lungs, liver, pancreas, kidneys, and bowel), connected by the vascular system, of which blood circulation is maintained by the heart and oxygenation by the lungs under artificial ventilation. The aim of this study is the description of a surgical technique of MOB removal in the rat. Ninety-five MOBs were removed from Wistar rats. The rats were anesthetized, a tracheotomy was performed, and the cannula was connected to a pressure-regulated respirator. A colectomy was performed. Ureters, vena cava inferior, aorta, and bile duct were cannulated using an operative microscope. The vessels that joined the MOB to the carcass were tied or coagulated to make removal of the MOBs possible. Once removed, the MOBs were placed in a vaseline oil bath at 37 degrees C and the aorta and vena cava were connected to an accessory vascular circuit to stabilize arterious pressure. Success rate (ex vivo survival of more than 10 min) after the 30th attempt was 90% and after the 60th attempt was 95% (global success rate 82%). Ex vivo survival of MOBs at 37 degrees C ranged from 1 to 450 min. Rat MOBs allows us to study the normothermic preservation of all the organs susceptible of being transplanted in one single series of experiments. We showed that removal of rat MOBs is feasible. This microsurgical technique is codified. Rat MOBs are suitable if perfusion liquids are difficult to obtain or if a great number of experiments are required. As MOBs are composed of synergically functioning organs in the absence of striated muscle, bone, and nervous system, they also could be useful for physiologic and pharmacologic studies.
Cys-diabody Quantum Dot Conjugates (ImmunoQdots) for Cancer Marker Detection (2009)

The present work demonstrates the use of small bivalent engineered antibody fragments, cys-diabodies, for biological modification of nanoscale particles such as quantum dots (Qdots) for detection of target antigens. Novel bioconjugated quantum dots known as immunoQdots (iQdots) were developed by thiol-specific oriented coupling of tumor specific cys-diabodies, at a position away from the antigen binding site to amino PEG CdSe/ZnS Qdots. Initially, amino PEG Qdot 655 were coupled with reduced anti-HER2 cys-diabody by amine-sulfhydryl-reactive linker [N-ε-maleimidocaproyloxy] succinimide ester (EMCS) to produce anti-HER2 iQdot 655. Spectral characterization of the conjugate revealed that the spectrum was symmetrical and essentially identical to unconjugated Qdot. Specific receptor binding activity of anti-HER2 iQdot 655 was confirmed by flow cytometry on HER2 positive and negative cells. Immunofluorescence results showed homogeneous surface labeling of the cell membrane with Qdot 655 conjugate. In addition, cys-diabodies specific for HER2, as well as prostate stem cell antigen (PSCA), were conjugated successfully with amino PEG Qdot 800. All of these iQdots retain the photoluminescence properties of the unconjugated Qdot 800 as well as the antigen binding specificity of the cys-diabody as demonstrated by flow cytometry. Simultaneous detection of two tumor antigens on LNCaP/PSCA prostate cancer cells (which express PSCA and HER2) in culture was possible using two iQdots, anti-HER2 iQdot 655 and anti-PSCA iQdot 800. Thus, these iQdots are potentially useful as optical probes for sensitive, multiplexed detection of surface markers on tumor cells. The present thiol-specific conjugation method demonstrates a general approach for site-specific oriented coupling of cys-diabodies to a wide variety of nanoparticles without disturbing the antigen binding site and maintaining small size compared to intact antibody.
Virus inactivation in red cell concentrates by photosensitization with phthalocyanines: protection of red cells but not of vesicular stomatitis virus with a water‐soluble analogue of vitamin E (1995)

These findings indicate that Trolox protects RBCs from phthalocyanine-photosensitized damage without affecting virus kill. The addition of Trolox would be beneficial for improving the quality of RBCs subjected to photodynamic treatment.
Glucosyl- and Acetyltransferases Involved in the Biosynthesis of Glycolipids from Candida bogoriensis (1972)

Abstract 1. Crude extracts prepared by sonicating Candida bogoriensis cells contained glucosyltransferases catalyzing the transfer of glucose from UDP-[14C]glucose to 13-hydroxydocosanoic acid (HDA) (transferase 1) and methyl 13-glucopyranosyloxydocosanoate (methyl GlcHDA) (transferase 2) when these lipids were added as acceptors. The enzymatic products were characterized by thin layer chromatographic and gas-liquid chromatographic comparison to derivatives of GlcHDA and 13-glucopyranosylglucopyranosyloxydocosanoate (Glc2HDA) prepared from cultures of C. bogoriensis. 2. The transferases were purified 20- and 30-fold, respectively, with no separation of the two activities and with a constant ratio of the two activities obtained in successive peak fractions from a DEAE-Sephadex column, a hydroxyl-apatite column, a gel filtration column, and a disc gel electrophoresis fractionation. 3. Both transferases were specific for UDP-glucose, showing apparent Km values of 104 and 88 µm, respectively, for this compound. 4. Glucosyltransferase 1 showed 4- to 5-fold greater activity with HDA than with its methyl ester. A series of hydroxystearate isomers also showed acceptor activity. The activity with 9-hydroxystearate was 60% of that with HDA, whereas the acceptor activity decreased as the hydroxyl group was moved toward either the methyl or carboxyl end of the fatty acid chain. 5. Glucosyltransferase 2 exhibited severe substrate inhibition with GlcHDA as acceptor and a much higher reaction velocity when the methyl ester of GlcHDA was utilized as acceptor. 6. Crude extracts of C. bogoriensis also contained acetyltransferase(s) catalyzing incorporation of [14C]acetate from [14C]acetyl coenzyme A into Ac2Glc2HDA (the diacetate of Glc2HDA) characterized by thin layer chromatographic comparison with the glycolipid isolated from C. bogoriensis cultures. 7. Acetone extraction of the lyophilized extracts, followed by DEAE-Sephadex chromatography, freed the acetyl-transferase(s) of endogenous acceptor, making activity dependent upon added methyl Glc2HDA or its monoacetate as acceptor. Methyl GlcHDA was a poor acceptor for the acetyl groups. 8. In fermentor cultures the peak of glucosyltransferase 1 and 2 activities was reached in 1½ days and the peak of acetyltransferase activity was reached in 3 days. This time course is consistent with involvement of these enzymes in the biosynthesis of extracellular Ac2Glc2HDA, and with the tentative conclusion that extracellular AcGlc2HDA and Glc2HDA were formed by deacetylation of Ac2Glc2HDA.
Dose-Dependent Kinetics of Probenecid in Rhesus Monkeys &ndash; Infusion Studies (1984)

14 infusion studies to steady state with probenecid were carried out in 2 monkeys. Plasma clearance decreased with increasing rate of infusion. The urinary excretion data showed a decrease in the fraction of the dose excreted as probenecid conjugate, an increase in the total N-depropyl metabolites, and no change in the 2-hydroxy metabolites with increasing probenecid dose. Pooled Michaelis-Menten constants for probenecid metabolism were estimated from a plot of the linearized Michaelis-Menten equation using infusion rates of probenecid versus the plasma clearances of the drug.
Henry Adams Meets Robert Louis Stevenson: Ambiguous Perceptions of the South Seas (1992)

There is little scribal literature in nineteenth-century Polynesia, since those societies were 'oral'. There were only a few literary travellers from the West to this part of the world, and few who attempted to record the literature. Virtually all that is 'literate' about the South Seas of that time are the visions by Europeans expressing their own ambiguous approaches to an Otherness which challenged Western life. This paper is a short study of two literary travellers who did observe the societies of the South Seas and recorded some of the literatures, but at the same time persisted in making these observations merely a reflection of their own interests.
635. Systemic Oncolytic and Immunologic Therapy for Cancer with JX-594, a Targeted Poxvirus Expressing GM-CSF (2006)

Targeted oncolytic viruses and immunostimulatory therapeutics are being developed as novel cancer treatment platforms. These two treatment approaches can be combined through the expression of immunostimulatory cytokines from targeted oncolytic viruses as has been reported for adenoviruses and herpes viruses. Although intratumoral injection of such viruses has been associated with systemic tumor growth inhibition, eradication of distant visceral metastases was not reported. The major limitations for this approach to date have been 1) inefficient intravenous virus delivery to tumors, and 2) the lack of predictive, immunocompetent preclinical models to optimize this approach. In order to overcome these hurdles, we used 1) a targeted, thymidine kinase(-) vaccinia virus expressing human GM-CSF (hGM-CSF) for intravenous (i.v.) delivery (JX-594), and 2) we identified and extensively characterized two immunocompetent, orthotopic, replication-permissive and hGM- CSF-sensitive tumor models: a carcinogen-induced rat liver cancer model and a rabbit liver tumor model with reproducible, time- dependent metastases to the lungs. Intravenous JX-594 was well- tolerated and had highly significant efficacy, including complete responses, against orthotopic liver tumors in both models. In addition, lung metastases progressed in 100% of control rabbits (mean number 15+/−8 per animal), whereas none of the treated animals had detectable lung metastases. Tumor-specific virus replication and gene expression, systemically-detectable levels of hGM-CSF and tumor- infiltrating CTLs were also demonstrated. JX-594 holds promise as an intravenously delivered, targeted virotherapeutic. These two tumor models hold promise for the optimization of this approach. Authors are shareholders in Jennerex Biotherapeutics, Inc.
Self-calibrating photometric stereo (2010)

We present a self-calibrating photometric stereo method. From a set of images taken from a fixed viewpoint under different and unknown lighting conditions, our method automatically determines a radiometric response function and resolves the generalized bas-relief ambiguity for estimating accurate surface normals and albedos. We show that color and intensity profiles, which are obtained from registered pixels across images, serve as effective cues for addressing these two calibration problems. As a result, we develop a complete auto-calibration method for photometric stereo. The proposed method is useful in many practical scenarios where calibrations are difficult. Experimental results validate the accuracy of the proposed method using various real-world scenes.
Focused ultrasound neuromodulation of cortical and subcortical brain structures using 1.9 MHz (2016)

The motor movements and pupillary dilation observed in this study demonstrate the capability of FUS to modulate cortical and subcortical brain structures without inducing any damage. The variety of responses observed here demonstrates the capability of FUS to perform functional brain mapping.
Cloning a synthetic gene for human stefin B and its expression in E. coli (1988)

A gene coding for human stefin B was synthesized by the solid-phase phosphite method and cloned in the pUC8 cloning vector. The insert with the verified DNA sequence was subcloned into two expression vectors and expressed in E. coli as a fusion protein with beta-galactosidase and as a native protein. The CNBr cleaved fusion protein and the native recombinant stefin B were inhibitory to papain and reacted with antibodies against human stefin B.