gebhart/patrepeval huggingface dataset:
Increased Adipogenesis and Myelopoiesis in the Bone Marrow of SAMP6, a Murine Model of Defective Osteoblastogenesis and Low Turnover Osteopenia (1997)

Bone formation and hematopoiesis are anatomically juxtaposed and share common regulatory mechanisms. However, little is known about the interrelationship between these two processes. We have previously shown that the senescence accelerated mouse-P6 (SAMP6) exhibits decreased osteoblastogenesis in the bone marrow that is temporally linked with a low rate of bone formation and decreased bone mineral density. Here we report that in contrast to decreased osteoblastogenesis, ex vivo bone marrow cultures from SAMP6 mice exhibited an increase in the number of colony-forming unit adipocytes, as well as an increase in the number of fully differentiated marrow adipocytes, compared with SAMR1 (nonosteopenic) controls. Further, long-term bone marrow cultures from SAMP6 produced an adherent stromal layer more rapidly, generated significantly more myeloid progenitors and produced more IL-6 and colony-stimulating activity. Consistent with this, the number of myeloid cells in freshly isolated marrow from SAMP6 mice was increased, as was the number of granulocytes in peripheral blood. The evidence that SAMP6 mice exhibit decreased osteoblastogenesis, and increased adipogenesis and myelopoiesis, strongly suggests that a switch in the differentiation program of multipotential mesenchymal progenitors may underlie the abnormal phenotype manifested in the skeleton and other tissues of these animals. Moreover, these observations support the contention for the existence of a reciprocal relationship between osteoblastogenesis and adipogenesis that may explain the association of decreased bone formation and the resulting osteopenia with the increased adiposity of the marrow seen with advancing age in animals and humans.
DNA Methylation, a Biomarker for Colorectal Cancer (2003)

Currently up to one-third of colorectal cancer patients present with locally advanced or metastatic disease that precludes a surgical cure. Performance limitations and low uptake of current screening tools have fueled research to develop minimally invasive approaches that can detect early-stage neoplasms. The observation that altered DNA can be amplified from the stool or circulation has stimulated research on its use as a biomarker of occult neoplasia. De novo methylation of CpG islands 5' to certain tumor suppressor genes has been associated with epigenetic silencing. At certain loci this phenomenon is specific for neoplastic populations, and it is frequently detected at early stages in colorectal tumorigenesis. Accordingly, hypermethylation events have been proposed by researchers as ideal targets for the basis of a screening panel to detect peripheral tumor DNA. This critique reviews research findings on the use of epigenetic biomarkers in screening for occult neoplasia. In addition, the authors consider the pathological utility of epigenetic testing in refining tumor staging and predicting disease recurrence.
Pluripotent stem cell lines (2008)

The derivation of human embryonic stem cells 10 years ago ignited an explosion of public interest in stem cells, yet this achievement depended on prior decades of research on mouse embryonic carcinoma cells and embryonic stem cells. In turn, the recent derivation of mouse and human induced pluripotent stem cells depended on the prior studies on mouse and human embryonic stem cells. Both human embryonic stem cells and induced pluripotent stem cells can self-renew indefinitely in vitro while maintaining the ability to differentiate into advanced derivatives of all three germ layers, features very useful for understanding the differentiation and function of human tissues, for drug screen and toxicity testing, and for cellular transplantation therapies. Here we review the family of pluripotent cell lines derived from early embryos and from germ cells, and compare them with the more recently described induced pluripotent stem cells.
An Introduction to Turbulent Flow (2000)

Most natural and industrial flows are turbulent. The atmosphere and oceans, automobile and aircraft engines, all provide examples of this ubiquitous phenomenon. In recent years, turbulence has become a very lively area of scientific research and application, attracting many newcomers who need a basic introduction to the subject. An Introduction to Turbulent Flow, first published in 2000, offers a solid grounding in the subject of turbulence, developing both physical insight and the mathematical framework needed to express the theory. It begins with a review of the physical nature of turbulence, statistical tools, and space and time scales of turbulence. Basic theory is presented next, illustrated by examples of simple turbulent flows and developed through classical models of jets, wakes, and boundary layers. A deeper understanding of turbulence dynamics is provided by spectral analysis and its applications. The final chapter introduces the numerical simulation of turbulent flows. This well-balanced text will interest graduate students in engineering, applied mathematics, and the physical sciences.
Preparation of Hepatocytes (2001)

This unit describes a process for isolation of intact, viable hepatocytes for use in integrated drug metabolism studies. Isolated hepatocytes are increasingly being used as a biological system for studying the in vitro metabolism of xenobiotics. The isolation of hepatocytes from laboratory animals and nontransplantable human livers donated for research activities involves a two-step enzymatic digestion of the liver tissue. Two methods for the perfusion of liver tissue are included: in situ perfusion and isolation of hepatocytes and perfusion of excised tissue. The basic protocol also includes suggestions for designing drug metabolism experiments using hepatocytes. The final protocol describes cryopreservation and long-term storage of isolated hepatocytes.
Texture analysis of optical coherence tomography images: feasibility for tissue classification (2003)

Optical coherence tomography (OCT) acquires cross-sectional images of tissue by measuring back-reflected light. Images from in vivo OCT systems typically have a resolution of 10 to 15 mm, and are thus best suited for visualizing structures in the range of tens to hundreds of microns, such as tissue layers or glands. Many normal and abnormal tissues lack visible structures in this size range, so it may appear that OCT is unsuitable for identification of these tissues. However, examination of structure-poor OCT images reveals that they frequently display a characteristic texture that is due to speckle. We evaluated the application of statistical and spectral texture analysis techniques for differentiating tissue types based on the structural and speckle content in OCT images. Excellent correct classification rates were obtained when images had slight visual differences (mouse skin and fat, correct classification rates of 98.5 and 97.3%, respectively), and reasonable rates were obtained with nearly identical-appearing images (normal versus abnormal mouse lung, correct classification rates of 64.0 and 88.6%, respectively). This study shows that texture analysis of OCT images may be capable of differentiating tissue types without reliance on visible structures.
Detection of nearest neighbors to specific fluorescently tagged ligands in rod outer segment and lymphocyte plasma membranes by photosensitization of 5-iodonaphthyl-1-azide (1989)

Lima bean agglutinin-fluorescein 5-isothiocyanate conjugate (FluNCS-lima bean lectin) interacts with specific receptor molecules on membranes both from the rod outer segment (ROS) of the frog retina and from S49 mouse lymphoma cells. When [125I]-5-iodonaphthyl 1-azide (125I-INA), which freely and randomly partitions into the lipid bilayer, is added to membranes and the suspension is irradiated at 480 nm, the FluNCS-conjugated lectin photosensitizes the [125I]INA but only at discrete sites. This results in the selective labeling of specific proteins: an 88-kDa protein on ROS membranes and a 56-kDa protein on S49 plasma membranes. Labeling is dependent upon the interaction of the FluNCS-lectin with glycosylated receptor sites, since N-acetylgalactosamine, but not methyl alpha-mannoside, blocked labeling of the 56-kDa protein on S49 membranes. In contrast, a random labeling pattern of membrane proteins was observed upon irradiation at 480 nm using other fluorescein conjugates, such as FluNCS-bovine serum albumin (FluNCS-BSA) or FluNCS-soybean trypsin inhibitor (FluNCS-STI), which interact with cell membranes in a nonselective manner, or with N-(fluorescein-5-thiocarbamoyl)-n-undecyclamine (FluNCS-NHC11), which is freely miscible in the membrane lipid. Random labeling was also obtained by direct photoexcitation of [125I]INA at 314 nm, with no distinct labeling of the 88- and 56-kDa proteins in the respective membranes. These results suggest that protein ligands can be used to guide sensitizers to discrete receptor sites and lead to their selective labeling by photosensitized activation of [125I]INA [Raviv, Y., Salomon, Y., Gitler, C., & Bercovici, T. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 6103-6107].(ABSTRACT TRUNCATED AT 250 WORDS)
Large-scale analysis of ion channel gene expression in the mouse heart during perinatal development (2006)

The immature and mature heart differ from each other in terms of excitability, action potential properties, contractility, and relaxation. This includes upregulation of repolarizing K(+) currents, an enhanced inward rectifier K(+) (Kir) current, and changes in Ca(2+), Na(+), and Cl(-) currents. At the molecular level, the developmental regulation of ion channels is scantily described. Using a large-scale real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assay, we performed a comprehensive analysis of ion channel transcript expression during perinatal development in the embryonic (embryonic day 17.5), neonatal (postnatal days 1-2), and adult Swiss-Webster mouse hearts. These data are compared with publicly available microarray data sets (Cardiogenomics project). Developmental mRNA expression for several transcripts was consistent with the published literature. For example, transcripts such as Kir2.1, Kir3.1, Nav1.5, Cav1.2, etc. were upregulated after birth, whereas others [e.g., Ca(2+)-activated K(+) (KCa)2.3 and minK] were downregulated. Cl(-) channel transcripts were expressed at higher levels in immature heart, particularly those that are activated by intracellular Ca(2+). Defining alterations in the ion channel transcriptome during perinatal development will lead to a much improved understanding of the electrophysiological alterations occurring in the heart after birth. Our study may have important repercussions in understanding the mechanisms and consequences of electrophysiological alterations in infants and may pave the way for better understanding of clinically relevant events such as congenital abnormalities, cardiomyopathies, heart failure, arrhythmias, cardiac drug therapy, and the sudden infant death syndrome.
Therapeutic photobiomodulation for methanol-induced retinal toxicity (2003)

Methanol intoxication produces toxic injury to the retina and optic nerve, resulting in blindness. The toxic metabolite in methanol intoxication is formic acid, a mitochondrial toxin known to inhibit the essential mitochondrial enzyme, cytochrome oxidase. Photobiomodulation by red to near-IR radiation has been demonstrated to enhance mitochondrial activity and promote cell survival in vitro by stimulation of cytochrome oxidase activity. The present studies were undertaken to test the hypothesis that exposure to monochromatic red radiation from light-emitting diode (LED) arrays would protect the retina against the toxic actions of methanol-derived formic acid in a rodent model of methanol toxicity. Using the electroretinogram as a sensitive indicator of retinal function, we demonstrated that three brief (2 min, 24 s) 670-nm LED treatments (4 J/cm(2)), delivered at 5, 25, and 50 h of methanol intoxication, attenuated the retinotoxic effects of methanol-derived formate. Our studies document a significant recovery of rod- and cone-mediated function in LED-treated, methanol-intoxicated rats. We further show that LED treatment protected the retina from the histopathologic changes induced by methanol-derived formate. These findings provide a link between the actions of monochromatic red to near-IR light on mitochondrial oxidative metabolism in vitro and retinoprotection in vivo. They also suggest that photobiomodulation may enhance recovery from retinal injury and other ocular diseases in which mitochondrial dysfunction is postulated to play a role.
Integrated-optics-based swept-source optical coherence tomography (2012)

We designed, fabricated, and characterized an integrated-optics-based swept-source optical coherence tomography (SS-OCT) system in TriPleX technology. An external 1300 nm swept source is coupled to the chip, which contains waveguide structures for interferometric depth ranging and balanced detection. The complete OCT chip has a footprint of 0.4 cm × 1.8 cm. Light from the chip is focused onto the sample using an aspheric lens; the lateral resolution is 21±1 μm. OCT measurements, performed with a moveable mirror, demonstrate a sensitivity of -80 dB and imaging up to the maximum depth of 5.09 mm. Corrected for dispersion, the measured OCT axial resolution of 12.7±0.5 μm is in good agreement with the bandwidth limited resolution. Finally, we demonstrate cross-sectional OCT imaging of a multilayered tissue phantom over the whole depth range with the integrated-optics-based SS-OCT system.
Development of a Subcutaneous Formulation for Trastuzumab - Nonclinical and Clinical Bridging Approach to the Approved Intravenous Dosing Regimen (2012)

A subcutaneous (SC) formulation has been developed for the humanized monoclonal antibody (mAb) trastuzumab as an alternative to established intravenous (IV) infusion. The ready-to-use liquid SC formulation is injected as a fixed dose in approximately 5 min, which is expected to increase patient's convenience, reduce pharmacy preparation time, and administration costs overall.The trastuzumab dose as well as the dose of recombinant human hyaluronidase (rHuPH20), an enzyme that enables SC administration of volumes larger than 2 mL, was selected based on nonclinical xenograft, pharmacology, and pharmacokinetics mouse and minipig studies.The basic assumption for bridging from the IV to the SC regimen was that comparable trastuzumab serum trough concentrations would result in comparable efficacy. This hypothesis is confirmed by the results from the Phase 3 study in the neo-adjuvant/adjuvant setting. The safety profiles of the trastuzumab SC and IV formulations are comparable and consistent with the known safety profile of trastuzumab.
Mining Argumentative Structure from Natural Language text using Automatically Generated Premise-Conclusion Topic Models (2017)

This paper presents a method of extracting argumentative structure from natural language text. The approach presented is based on the way in which we understand an argument being made, not just from the words said, but from existing contextual knowledge and understanding of the broader issues. We leverage highprecision, low-recall techniques in order to automatically build a large corpus of inferential statements related to the text's topic. These statements are then used to produce a matrix representing the inferential relationship between different aspects of the topic. From this matrix, we are able to determine connectedness and directionality of inference between statements in the original text. By following this approach, we obtain results that compare favourably to those of other similar techniques to classify premise-conclusion pairs (with results 22 points above baseline), but without the requirement of large volumes of annotated, domain specific data.
Assessing Impact of Weight on Quality of Life (1995)

This paper is a preliminary report on the development of a new instrument, the Impact of Weight on Quality of Life (IWQOL) questionnaire, that assesses the effects of weight on various areas of life. We conducted two studies utilizing subjects in treatment for obesity at Duke University Diet and Fitness Center. The first study describes item development, assesses reliability, and compares pre- and post-treatment scores on the IWQOL. In the second study we examined the effects of body mass index (BMI), gender, and age on subjects' perceptions of impact of weight on quality of life. Results indicate adequate psychometric properties with test-retest reliabilities averaging .75 for single items, and .89 for scales. Scale internal consistency averaged .87. Post-treatment scores differed significantly from pre-treatment scores on all scales, indicating that treatment produced positive changes in impact of weight on quality of life. The results of the second study indicate that the impact of weight generally worsened as the patients' size increased. However for women there was no association between BMI and impact of weight on Self-Esteem and Sexual Life. Even at the lowest BMI tertile studied, women reported that weight had a substantial impact in these areas. There were also significant gender differences, with women showing greater impact of weight on Self-Esteem and Sexual Life compared with men. The impact of age was a bit surprising, with some areas showing positive changes and others showing no change.
Long-term survival in metastatic pancreatic cancer. A case report and review of the literature. (2006)

This is the fifth case reported in the literature showing that long-term survival may be achieved even in advanced pancreatic cancer.
Two-Phase Modeling and Flooding Prediction of Polymer Electrolyte Fuel Cells (2005)

A newly developed theory of liquid water transport in hydrophobic gas diffusion layers is applied to simulate flooding in polymer electrolyte fuel cells (PEFCs) and its effects on performance. The numerical model accounts for simultaneous two-phase flow and transport of species and electrochemical kinetics, utilizing the well-established multiphase mixture formulation to efficiently model the two-phase transport processes. The two-phase model is developed in a single domain, yielding a single set of governing equations valid in all components of a PEFC. The model is used to explore the two-phase flow physics in the cathode gas diffusion layer. Multidimensional simulations reveal that flooding of the porous cathode reduces the rate of oxygen transport to the cathode catalyst layer and causes a substantial increase in cathode polarization. Furthermore, the humidification level and flow rate of reactant streams are key parameters controlling PEFC performance and two-phase flow and transport characteristics. It is also found that minimization of performance limitations such as membrane dry-out and electrode flooding depends not only on material characteristics but also on the optimization of these operating parameters. © 2005 The Electrochemical Society. All rights reserved.
Structure−Function Relationships in Aminoquinolines:  Effect of Amino and Chloro Groups on Quinoline−Hematin Complex Formation, Inhibition of β-Hematin Formation, and Antiplasmodial Activity (1999)

Comparison of 19 aminoquinolines supports the hypothesis that chloroquine and related antimalarials act by complexing ferriprotoporphyrin IX (Fe(III)PPIX), inhibiting its conversion to beta-hematin (hemozoin) and hence its detoxification. The study suggests that a basic amino side chain is also essential for antiplasmodial activity. 2- And 4-aminoquinolines are unique in their strong affinity for Fe(III)PPIX, and attachment of side chains to the amino group has relatively little influence on the strength of complex formation. Association with Fe(III)PPIX is necessary, but not sufficient, for inhibiting beta-hematin formation. Presence of a 7-chloro group in the 4-aminoquinoline ring is a requirement for beta-hematin inhibitory activity, and this is also unaffected by side chains attached to the amino group. In turn, beta-hematin inhibitory activity is necessary, but not sufficient, for antiplasmodial activity as the presence of an aminoalkyl group attached to the 4-amino-7-chloroquinoline template is essential for strong activity. We thus propose that the 4-aminoquinoline nucleus of chloroquine and related antimalarials is responsible for complexing Fe(III)PPIX, the 7-chloro group is required for inhibition of beta-hematin formation, and the basic amino side chain is required for drug accumulation in the food vacuole of the parasite.
Protein Adsorption Properties of Hydrothermally Prepared Hydroxyapatite (2007)

Micrometer-sized hydroxyapatite (HA) with rod-shape was prepared to investigate protein adsorption onto its crystal face, through hydrothermal processing. Adsorption of Bovine serum albumin (BSA) and Lysozyme from chicken egg white (LSZ) on rod-shaped HA crystals with approximately 50 μm in length and 1 μm thickness was examined in phosphate buffer solution. The amount of adsorbed BSA was decreased with increasing phosphate concentration in the examined solution. Adsorption of LSZ was increased with increasing phosphate concentration in the buffer solution up to 50 mmol/L (mM), while it was remarkably decreased when the phosphate concentration reached approximately 100 mM. These phenomena lead to understanding of chromatographic characters of HA for separation of acidic and basic proteins.
Evolutionary conservation of histone macroH2A subtypes and domains (1998)

Histone macroH2A is an unusual core histone that contains a large non-histone region, and a region that resembles a full length H2A. We examined theconservation of this novel structural arrangement by cloning chicken macroH2A cDNAs and comparing them to their rat counterparts. The amino acid sequences of the two known macroH2A subtypes are >95% identical between these species despite evolutionary separation of approximately 300 million years. The H2A region of macroH2A is completely conserved, and thus is even more conserved than conventional H2A in these species. The origin of the non-histone domain was examined by comparing its sequence to proteins found in bacteria and RNA viruses. These comparisons indicate that this domain is derived from a gene that originated prior to the appearance of eukaryotes, and suggest that the non-histone region has retained the basic function of its ancestral gene.