gebhart/patrepeval huggingface dataset:
Autologous Schwann Cells Drive Regeneration through a 6-cm Autogenous Venous Nerve Conduit (2001)

Peripheral nerve regeneration is a complex series of events, involving bi-directional interactions between regenerating axons and Schwann cells. These authors have demonstrated in their laboratory that nerves will regenerate through a 3-cm autogenous venous nerve conduit (AVNC) in an animal model and, with Dr. David Chiu, a similar distance in the human. They have shown that the upper limit of nerve regeneration in an empty AVNC was 3 cm, with no evidence of nerve growth at the 6-cm mark (no-growth model). Most recently, they have demonstrated rapid growth at 1 month in a 3-cm AVNC filled with Schwann cells, compared to poor-to-no-regrowth at 1 month in controls. While, in theory, Schwann-cell-derived growth factor should be sufficient to supplant the requirement for Schwann cells, in practice, therapies with growth factors have failed in clinical trials, with some resulting in severe morbidity and mortality for the subjects. The present study showed excellent nerve regeneration through a 6-cm AVNC with the addition of autologous Schwann cells, breaking the barrier in the previous no-growth model. In the first stage, autologous Schwann cells were harvested from the contralateral peroneal nerve of the rabbit and expanded in culture. The Schwann cells were purified to >99 percent homogeneity using differential adhesion and antibody-compliment-mediated cytolysis. In the second stage, 6 cm of gluteal vein were harvested and used as a conduit that was filled with either Matrigel or a slurry of Matrigel and 10(6)/ml autologous Schwann cells (n=6 control and 6 experimental animals). The non-donor side peroneal was exposed and transected, leaving a gap of 6 cm. The filled gluteal vein graft (AVNC) was then anastomosed to the proximal and distal peroneal nerve stumps, and the rabbits were allowed to recover. Four months postoperatively, the animals were subjected to transcardiac perfusion with EM grade fixative. The grafts were analyzed at the light and electronmicroscopic levels, and showed excellent growth of nerve at 6 cm, the distal end of the AVNC.
Covalently Bonded Adducts of Deoxyribonucleic Acid (DNA) Oligonucleotides with Single-Wall Carbon Nanotubes:  Synthesis and Hybridization (2002)

We have developed a multistep route to the formation of covalently linked adducts of single-wall carbon nanotubes (SWNT) and deoxyribonucleic acid (DNA) oligonucleotides. X-ray photoelectron spectroscopy was used to characterize the initial chemical modification to form amine-terminated SWNTs, which were then covalently linked to DNA. The resulting DNA−SWNT adducts hybridize selectively with complementary sequences, with only minimal interaction with noncomplementary sequences.
Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction (1992)

The polymerase chain reaction (PCR) was used to amplify an Escherichia coli 16S ribosomal gene fragment from sediments with high contents of humic substances. Total DNA was extracted from 1 g of E. coli seeded or unseeded samples by a rapid freeze-and-thaw method. Several approaches (use of Bio-Gel P-6 and P-30 and Sephadex G-50 and G-200 columns, as well as use of the Stoffel fragment) were used to reduce interference with the PCR. The best results were obtained when crude DNA extracts containing humic substances were purified by using Sephadex G-200 spun columns saturated with Tris-EDTA buffer (pH 8.0). Eluted fractions were collected for PCR analyses. The amplified DNA fragment was obtained from seeded sediments containing fewer than 70 E. coli cells per g. Because only 1/100 of the eluted fractions containing DNA extracts from 70 cells per g was used for the PCR, the sensitivity of detection was determined to be less than 1 E. coli cell. Thus, DNA direct extraction coupled with this technique to remove interference by humic substances and followed by the PCR can be a powerful tool to detect low numbers of bacterial cells in environmental samples containing humic substances.
Nonlinear Techniques for Predicting 305-Day Lactation Production of Holsteins and Jerseys (1977)

Abstract A technique of nonlinear model to predict the 305-day milk and fat yields of Canadian Holstein and Jersey cattle is described. The parameters of this model were estimated from Canadian Record of Performance test-day records collected from 1966 to 1970. By multiplicative factors and regression coefficients derived from the same data, three methods of extending records in progress to 305 days were compared. The method of nonlinear model was at least as accurate as either the multiplicative or regression methods, required less computer storage for parameter estimates than for multiplicative factors, and could be implemented easily into a milk recording program.
Activation of Epstein‐Barr virus promoters by a growth‐factor and a glucocorticoid (1991)

Transforming growth factor-beta (TGF-beta) and a glucocorticosteroid, Dexamethasone (DXM), both cause transcriptional induction of Epstein-Barr virus (EBV) early antigens (EA) in Daudi lymphoma cells. The viral induction occurs through the viral promoter DR overlapping an origin of replication which is active during the lytic cycle. Each hormone requires specific regions on the DR promoter. Since these regions also mediate the action of two viral transcription factors, EB1 and R, it may be emphasized that EB1 and/or R are involved in the EA induction process by TGF-beta and by DXM.
Involvement of the N Terminus of Ribosomal Protein L11 in Regulation of the RelA Protein of Escherichia coli (2001)

Amino acid-deprived rplK (previously known as relC) mutants of Escherichia coli cannot activate (p)ppGpp synthetase I (RelA) and consequently exhibit relaxed phenotypes. The rplK gene encodes ribosomal protein L11, suggesting that L11 is involved in regulating the activity of RelA. To investigate the role of L11 in the stringent response, a derivative of rplK encoding L11 lacking the N-terminal 36 amino acids (designated 'L11) was constructed. Bacteria overexpressing 'L11 exhibited a relaxed phenotype, and this was associated with an inhibition of RelA-dependent (p)ppGpp synthesis during amino acid deprivation. In contrast, bacteria overexpressing normal L11 exhibited a typical stringent response. The overexpressed 'L11 was incorporated into ribosomes and had no effect on the ribosome-binding activity of RelA. By several methods (yeast two-hybrid, affinity blotting, and copurification), no direct interaction was observed between the C-terminal ribosome-binding domain of RelA and L11. To determine whether the proline-rich helix of L11 was involved in RelA regulation, the Pro-22 residue was replaced with Leu by site-directed mutagenesis. The overexpression of the Leu-22 mutant derivative of L11 resulted in a relaxed phenotype. These results indicate that the proline-rich helix in the N terminus of L11 is involved in regulating the activity of RelA.
Induction of cytotoxic T-cell responses against immunoglobulin V region–derived peptides modified at human leukocyte antigen–A2 binding residues (2001)

Cytotoxic T-lymphocyte (CTL) responses can be generated against peptides derived from the immunoglobulin (Ig) V region in some but not all patients. The main reason for this appears to be the low peptide-binding affinity of Ig-derived peptides to major histocompatibility complex (MHC) class I molecules and their resulting low immunogenicity. This might be improved by conservative amino acid modifications at the MHC-binding residues of the peptides (heteroclitic peptides). In this study, it was found that in 18 Ig-derived peptides, that heteroclitic peptides from the Ig gene with improved binding to human leukocyte antigen (HLA)-A*0201 can be used to improve CTL responses. Amino acid substitution substantially increased predicted binding affinity, and there was a strong correlation between predicted and actual binding to HLA-A*0201. CTLs generated against the heteroclitic peptide had not only enhanced cytotoxicity against the heteroclitic peptide but also increased killing of antigen-presenting cells pulsed with the native peptide. Surprisingly, no difference was observed in the frequency of T cells detected by MHC class I peptide tetramers after stimulation with the heteroclitic peptide compared with the native peptide. CTLs generated against heteroclitic peptides could kill patients' tumor cells, showing that Ig-derived peptides can be presented by the tumor cell and that the failure to mount an immune response (among other reasons) likely results from the low immunogenicity of the native Ig-derived peptide. These results suggest that heteroclitic Ig-derived peptides can enhance immunogenicity, thereby eliciting immune responses, and that they might be useful tools for enhancing immunotherapy approaches to treating B-cell malignant diseases.
Evaluation of Registration of PET Images With CT Images (1988)

We describe the evaluation of the registration of Positron Emission Tomography (PET) scans with X-ray Computed Tomography (CT) scans of the human brain. A CT scan and a PET scan of the same person were obtained with fiducial markers placed on the person's head. The CT scan and the PET scan were then registered, first by using the fiducial markers, and next by applying the registration method currently under question, completely ignoring fiducial markers. In both cases, the positions of fiducial markers in PET scan and the positions of corresponding fiducial markers in CT scan were compared. The results based on aligning only one patient scans are encouraging, and in the future we hope to obtain more PET and CT scan pairs to validate the registration method.
3D active appearance model for aligning faces in 2D images (2008)

Perceiving human faces is one of the most important functions for human robot interaction. The active appearance model (AAM) is a statistical approach that models the shape and texture of a target object. According to a number of the existing works, AAM has a great success in modeling human faces. Unfortunately, the traditional AAM framework could fail when the face pose changes as only 2D information is used to model a 3D object. To overcome this limitation, we propose a 3D AAM framework in which a 3D shape model and an appearance model are used to model human faces. Instead of choosing a proper weighting constant to balance the contributions from appearance similarity and the constraint on consistent 2D shape with 3D shape in the existing work, our approach directly matches 2D visual faces with the 3D shape model. No balancing weighting between 2D shape and 3D shape is needed. In addition, only frontal faces are needed for training and non-frontal faces can be aligned successfully. The experimental results with 20 subjects demonstrate the effectiveness of the proposed approach.
Synthesis and application of highly ordered arrays of TiO2 nanotubes (2007)

Highly ordered, vertically oriented TiO2 nanotube arrays fabricated by potentiostatic anodization of titanium constitute a material architecture that offers a large internal surface area without a concomitant decrease in geometric and structural order. The precisely oriented nature of the crystalline (after annealing) nanotube arrays makes them excellent electron percolation pathways for vectorial charge transfer between interfaces. Herein are briefly considered their fabrication, as well as their initial application to hydrogen gas sensing, solar generation of hydrogen by water photoelectrolysis, and in heterojunction solar cells.
Understanding C-H Bond Oxidations: H⋅ and H - Transfer in the Oxidation of Toluene by Permanganate (1995)

The oxidation of toluene by permanganate has been studied as a model for the oxidation of C-H bonds by metal reagents, metalloenzymes, and metal oxide surfaces. In water, the reaction proceeds by hydride (H-) transfer from toluene to a permanganate oxygen, whereas in toluene solution, permanganate abstracts a hydrogen atom (H.). The ability of permanganate to abstract a hydrogen atom is rationalized on the basis of the strong O-H bond formed on H. addition to permanganate. This approach allows understanding and prediction of the rates of hydrogen atom transfer from substrates to metal active sites.
Gene Therapy and Animal Models for Retinal Disease (2003)

Those plagued by retinal diseases are often robbed of their vision, as often, effective treatments do not exist. Knowledge of the pathophysiology of retinal diseases stems from research on available animal models. Gene therapy may be useful for both genetic and acquired retinal diseases. This review will focus on retinal diseases for which gene therapy has demonstrated promise. The diseases are presented in order of the age at which they are generally first symptomatic and include retinopathy of prematurity, Leber congenital amaurosis, mucopolysaccharidoses, retinoblastoma, retinitis pigmentosa, diabetic retinopathy, glaucoma and age-related macular degeneration. We will describe the animal models used to study these disorders and emphasize the progress that has been made in using gene therapy for the treatment of retinal disease.
Better OPM/L Text Compression (1986)

An OPM/L data compression scheme suggested by Ziv and Lempel, LZ77, is applied to text compression. A slightly modified version suggested by Storer and Szymanski, LZSS, is found to achieve compression ratios as good as most existing schemes for a wide range of texts. LZSS decoding is very fast, and comparatively little memory is required for encoding and decoding. Although the time complexity of LZ77 and LZSS encoding is <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O(M)</tex> for a text of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</tex> characters, straightforward implementations are very slow. The time consuming step of these algorithms is a search for the longest string match. Here a binary search tree is used to find the longest string match, and experiments show that this results in a dramatic increase in encoding speed. The binary tree algorithm can be used to speed up other OPM/L schemes, and other applications where a longest string match is required. Although the LZSS scheme imposes a limit on the length of a match, the binary tree algorithm will work without any limit.
Effects of Pre-exercise Listening to Slow and Fast Rhythm Music on Supramaximal Cycle Performance and Selected Metabolic Variables (2003)

We examined the effect of listening to two different types of music (with slow and fast rhythm), prior to supramaximal cycle exercise, on performance, heart rate, the concentration of lactate and ammonia in blood, and the concentration of catecholamines in plasma. Six male students participated in this study. After listening to slow rhythm or fast rhythm music for 20 min, the subjects performed supramaximal exercise for 45 s using a cycle ergometer. Listening to slow and fast rhythm music prior to supramaximal exercise did not significantly affect the mean power output. The plasma norepinephrine concentration immediately before the end of listening to slow rhythm music was significantly lower than before listening (p < 0.05). The plasma epinephrine concentration immediately before the end of listening to fast rhythm music was significantly higher than before listening (p < 0.05). The type of music had no effect on blood lactate and ammonia levels or on plasma catecholamine levels following exercise. In conclusion, listening to slow rhythm music decreases the plasma norepinephrine level, and listening to fast rhythm music increases the plasma epinephrine level. The type of music has no impact on power output during exercise.
Production of Pseudotype‐Retroviral Vectors (1997)

Abstract Retrovirus pseudotype is defined as the genome of one retrovirus encapsidated by the envelope protein of a second virus. The host range of the pseudotype is that of the virus donating the envelope protein. Two procedures that use 293GP cells, which are derived from human kidney 293 cells, are described here. The first is based on the high transient transfection efficiency of 293 cells. The retroviral construct and an expression plasmid for VSV‐G are co‐transfected into 293GP cells that stably express MLV gag and pol proteins. Transiently generated virus is then harvested during consecutive days following DNA transfection. The second procedure involves stable 293GP cell lines containing the VSV‐G gene under the control of a promoter whose activity is regulated by tetracycline. Cell lines containing the retroviral vector of interest are established under noninduced conditions. Infectious virus can be harvested following the induction of VSV‐G expression in these cell lines.Retrovirus pseudotype is defined as the genome of one retrovirus encapsidated by the envelope protein of a second virus.
Synthesis of Chiral 2-(4-Phenoxyphenylsulfonylmethyl)thiiranes as Selective Gelatinase Inhibitors (2005)

[reactions: see text] Compound 1, 2-(4-phenoxyphenylsulfonylmethyl)thiirane, is a selective inhibitor of gelatinases, which is showing high promise in studies of animal models for cancer metastasis and stroke. The (R)-1 and (S)-1 enantiomers of compound 1 were each synthesized in this study and were shown to be equally active in inhibition of gelatinases.
Trichloroethylene degradation by two independent aromatic-degrading pathways in Alcaligenes eutrophus JMP134 (1990)

The bacterium Alcaligenes eutrophus JMP134(pJP4) degrades trichloroethylene (TCE) by a chromosomal phenol-dependent pathway and by the plasmid-encoded 2,4-dichlorophenoxyacetic acid pathway. The two pathways were independent and exhibited different rates of removal and capacities for quantity of TCE removed. The phenol-dependent pathway was more rapid (0.2 versus 0.06 nmol of TCE removed per min per mg of protein) and consumed all detectable TCE. The 2,4-dichlorophenoxyacetic acid-dependent pathway removed 40 to 60% of detectable TCE.
Versatility of Adipose Tissue as a Source of Stem Cells. (2003)

The stem cells are promising for future cell-based therapy such as tissue engineering or regenerative medicine. Although Embryonic Stem Cells (ESCs) are theoretically highly beneficial, there are various limitations on their use posed by cell regulations and ethical considerations. Therefore, adult stem cells are considered to be highly available with neither ethical nor immunoreactive considerations as long as they are of autologous tissue origin. Much of work has focused on the Mesenchymal Stem Cells (MSCs) isolated from bone marrow stroma, which have been shown to possess adipogenic, osteogenic, chondrogenic, myogenic and neurogenic potential in vitro. However bone marrow procurement is severely painful for patients and the harvested cells yields low number. Our preliminary studies have identified a putative stem cell population isolated from human adipose tissue. This cell population, termed Processed Lipoaspirate Cells (PLA Cells), is found to differentiate into adipogenic, osteogenic, chondrogenic and myogenic lineage in vitro in lineage-specific culture media. In addition to these findings, our recent data shows that PLA cells can be induced to differentiate into neural precursors, which are of an ectodermal origin. Furthermore, PLA cells express multiple CD marker antigens similar to those observed on MSCs. Finally, some of PLA clonal cells have capabilities of differentiate into adipogenic, osteogenic and chondrogenic lineage. These findings suggest that human PLA have a mesodermal stem cell population. Since human adipose tissue is ubiquitous, easily obtainable in large quantity under local anesthesia with little patient discomfort, it may be an alternative stem cell source for mesenchymal tissue regeneration and engineering.
Merging visible and invisible: two Camera-Augmented Mobile C-arm (CAMC) applications (1999)

This paper presents the basic concept of CAMC and some of its applications. A CCD camera is attached to a mobile C-arm fluoroscopy X-ray system. Both optical and X-ray imaging systems are calibrated in the same coordinate system in an off-line process. The new system is able to provide X-ray and optical images simultaneously. The CAMC framework has great potential for medical augmented reality. We briefly introduce two new CAMC applications to the augmented reality research community. The first application aims at merging video images with a pre-computed tomographic reconstruction of the 3D volume of interest. This is a logical continuation of our work on 3D reconstruction using a CAMC (1999). The second approach is a totally new CAMC design where using a double mirror system and an appropriate calibration procedure the X-ray and optical images are merged in real-time. This new system enables the user to see an optical image, an X-ray image, or an augmented image where both visible and invisible are combined in real-time. The paper is organized in two independent sections describing each of the above. Experimental results are provided at the same time as the methods and apparatus are described for each section.
MMAE Delivery Using the Bicycle Toxin Conjugate BT5528 (2020)

The EphA2 receptor is found at high levels in tumors and low levels in normal tissue and high EphA2 expression in biopsies is a predictor of poor outcome in patients. Drug discovery groups have therefore sought to develop EphA2-based therapies using small molecule, peptide, and nanoparticle-based approaches (1-3). However, until now only EphA2-targeting antibody-drug conjugates (ADC) have entered clinical development. For example, MEDI-547 is an EphA2-targeting ADC that displayed encouraging antitumor activity in preclinical models and progressed to phase I clinical testing in man. Here we describe the development of BT5528, a bicyclic peptide ("<i>Bicycle</i>") conjugated to the auristatin derivative maleimidocaproyl-monomethyl auristatin E to generate the <i>Bicycle</i> toxin conjugate BT5528. The report compares and contrasts the Pharmacokinetics (PK) characteristics of antibody and <i>Bicycle</i>-based targeting systems and discusses how the PK and payload characteristics of different delivery systems impact the efficacy-toxicity trade off which is key to the development of successful cancer therapies. We show that BT5528 gives rise to rapid update into tumors and fast renal elimination followed by persistent toxin levels in tumors without prolonged exposure of parent drug in the vasculature. This fast in, fast out kinetics gave rise to more favorable toxicology findings in rats and monkeys than were observed with MEDI-547 in preclinical and clinical studies.<b>Graphical Abstract:</b> http://mct.aacrjournals.org/content/molcanther/19/7/1385/F1.large.jpg.