gebhart/patrepeval huggingface dataset:
Oral mucositis (2006)

Mucositis and xerostomia are the most common oral complications of the non-surgical therapy of cancer. Mucositis, a common sequel of radio- (DXR), chemo-(CXR) and radiochemo-therapy in patients with cancer, or patients requiring haemopoietic stem cell transplants (HSCT), has a direct and significant impact on the quality of life and cost of care, and also affects survival--because of the risk of infection. Apart from dose reduction, preventive and treatment options for mucositis are scarce, although multiple agents have been tested. Evidence suggests that cryotherapy, topical benzydamine and amifostine might provide some benefit in specific situations. The recombinant human keratinocyte growth factor Palifermin (Kepivance) was recently approved as a mucositis intervention in patients receiving conditioning regimens before HSCT for the treatment of haematological malignancies. A number of mechanistically based interventions are in various stages of development. Unfortunately, many other approaches have not been rigorously tested. This paper reviews the clinical features, prevalence, diagnosis, complications, pathogenesis, prophylaxis and management of mucositis.
Synthesis of Functional Human Hemoglobin in Transgenic Mice (1989)

Human alpha- and beta-globin genes were separately fused downstream of two erythroid-specific deoxyribonuclease (DNase) I super-hypersensitive sites that are normally located 50 kilobases upstream of the human beta-globin gene. These two constructs were coinjected into fertilized mouse eggs, and expression was analyzed in transgenic animals that developed. Mice that had intact copies of the transgenes expressed high levels of correctly initiated human alpha- and beta-globin messenger RNA specifically in erythroid tissue. An authentic human hemoglobin was formed in adult erythrocytes that when purified had an oxygen equilibrium curve identical to the curve of native human hemoglobin A (Hb A). Thus, functional human hemoglobin can be synthesized in transgenic mice. This provides a foundation for production of mouse models of human hemoglobinopathies such as sickle cell disease.
Interfacing Materials Science and Biology for Drug Carrier Design (2015)

Over the last ten years, there has been considerable research interest in the development of polymeric carriers for biomedicine. Such delivery systems have the potential to significantly reduce side effects and increase the bioavailability of poorly soluble therapeutics. The design of carriers has relied on harnessing specific variations in biological conditions, such as pH or redox potential, and more recently, by incorporating specific peptide cleavage sites for enzymatic hydrolysis. Although much progress has been made in this field, the specificity of polymeric carriers is still limited when compared with their biological counterparts. To synthesize the next generation of carriers, it is important to consider the biological rationale for materials design. This requires a detailed understanding of the cellular microenvironments and how these can be harnessed for specific applications. In this review, several important physiological cues in the cellular microenvironments are outlined, with a focus on changes in pH, redox potential, and the types of enzymes present in specific regions. Furthermore, recent studies that use such biologically inspired triggers to design polymeric carriers are highlighted, focusing on applications in the field of therapeutic delivery.
Defining Differences among Perivascular Cells Derived from Human Pluripotent Stem Cells (2014)

Distinguishing between perivascular cell types remains a hurdle in vascular biology due to overlapping marker expressions and similar functionalities. Clarifying and defining heterogeneities in vitro among perivascular cells could lead to improved cell-based tissue regeneration strategies and a better understanding of human developmental processes. We studied contractile vascular smooth muscle cells (vSMCs), synthetic vSMCs, and pericytes derived from a common human pluripotent stem cell source. Using in vitro cultures, we show unique cell morphology, subcellular organelle organization (namely endoplasmic reticulum, mitochondria, and stress fibers), and expression of smooth muscle myosin heavy chain and elastin for each cell type. While differences in extracellular matrix deposition and remodeling were less pronounced, the multipotency, in vivo, migratory, invasion, and contractile functionalities are distinctive for each cell type. Overall, we define a repertoire of functional phenotypes in vitro specific for each of the human perivascular cell types, enabling their study and use in basic and translational research.
Structural Analysis of the Gene Encoding the Murine Interleukin-11 Receptor α-Chain and a Related Locus (1996)

In this study the gene for the murine interleukin-11 receptor alpha chain (IL-11Ralpha) has been characterized. The gene spans 9 kilobase pairs of DNA, and the organization of its 14 exons conforms to the pattern observed for other members of the hematopoietin receptor family. Analysis of the 5' end of the cDNA using 5' RACE showed that the first two exons, designated exons 1a and 1b, are spliced to form alternate transcripts. Transcripts initiating from exon 1b were not found in adult tissues but were present in embryonic stem cells. S1 nuclease and 5' rapid amplification of cDNA ends assays demonstrated multiple major and minor sites of transcription initiation for each exon. The putative promoter regions of both exons lacked TATA boxes, although potential recognition sites for several transcription factors including Sp1, AP1, and AP2 were present. A comparison of the murine and human IL-11Ralpha revealed that the 5' sequence upstream of the major site of transcription initiation site for exon 1b is highly conserved. Northern analysis showed that IL-11Ralpha is expressed in many adult murine tissues. A second IL-11Ralpha-like locus containing a sequence homologous to exons 2-13 was also identified.
RNA editing-like phenomenon in paramyxovirus V gene mRNA observed in insect cells infected with a recombinant baculovirus. (1999)

The V gene of the paramyxovirus human parainfluenza virus type 2 (hPIV2) is transcribed into both V and P mRNA. The V mRNA is a faithful transcript of the V gene; however, the P mRNA is transcribed by an RNA-editing mechanism in hPIV2-infected mammalian cells. Recombinant baculoviruses (rBV) were constructed containing the wild-type V gene, which has seven G residues at its editing site, and a manipulated V gene with ten G residues at its editing site. A small amount of the P protein was synthesized, in addition to the V protein, when the wild-type V gene was expressed in rBV-infected insect cells. Furthermore, synthesis of the P protein increased when rBV containing the manipulated V gene was used to infect insect cells. Both the P and V proteins were detected after in vitro translation of mRNA from rBV-infected cells. Moreover, G-residue insertions and a deletion were detected in mRNA. Since the P protein was not detected after in vitro translation of V RNA that had been transcribed in vitro by T7 RNA polymerase, these results suggest that the non-encoded G residues were inserted and deleted during transcription in insect cells. This RNA editing-like phenomenon and the implications of the length of the G cluster are discussed.
Thickness‐Gradient Films for High Gauge Factor Stretchable Strain Sensors (2015)

High-gauge-factor stretchable strain sensors are developed by utilizing a new strategy of thickness-gradient films with high durability, and high uniaxial/isotropic stretchability based on the self-pinning effect of SWCNTs. The monitoring of detailed damping vibration modes driven by weak sound based on such sensors is demonstrated, making a solid step toward real applications.
Surgical robotics: Impact of motion scaling on task performance (2004)

Motion scaling, rather than tremor filtration, plays the major role in the enhanced accuracy seen in robotic surgical systems. Robotic assistance with MS significantly improved accuracy above laparoscopic instruments alone and robotic assistance with tremor filtration alone. MS also creates ambidexterity in an otherwise unidextrous population, optimizing the surgeon's ability to undertake tasks requiring microsurgical accuracy.
Ondansetron Plus Metopimazine Compared With Ondansetron Plus Metopimazine Plus Prednisolone as Antiemetic Prophylaxis in Patients Receiving Multiple Cycles of Moderately Emetogenic Chemotherapy (2001)

Ondansetron plus metopimazine plus prednisolone is highly effective and superior to ondansetron plus metopimazine during nine cycles of moderately emetogenic chemotherapy.
Time critical lumigraph rendering (1997)

It was illustrated in 1996 that the light leaving the convex hull of an object (or entering a convex region of empty space) Cm be my characterized by a 4D function over the space" of rays crowing a surface surrounding the object (or surrounding the empty apace) [10, 8]. Methods to repre sent this function and quickly render individual images from this representation given an arbitrary cameras were also described. This paper extends the work outlined by Gortler et al [8] by demonstrating a taxonomy of methods to accelerate the rendering process by trading off quality for time. Given the speciiic limitation of a given hardware configuration, we discuss methods to tailor a critical time rendering strategy using these methods.
Human von Willebrand factor gene sequences target expression to a subpopulation of endothelial cells in transgenic mice. (1995)

The present study was undertaken to define the 5' and 3' regulatory sequences of human von Willebrand factor gene that confer tissue-specific expression in vivo. Transgenic mice were generated bearing a chimeric construct that included 487 bp of 5' flanking sequence and the first exon fused in-frame to the Escherichia coli lacZ gene. In situ histochemical analyses in independent lines demonstrated that the von Willebrand factor promoter targeted expression of LacZ to a subpopulation of endothelial cells in the yolk sac and adult brain. LacZ activity was absent in the vascular beds of the spleen, lung, liver, kidney, testes, heart, and aorta, as well as in megakaryocytes. In contrast, in mice containing the lacZ gene targeted to the thrombomodulin locus, the 5-bromo-4-chloro-3-indolyl beta-D-galactopyranoside reaction product was detected throughout the vascular tree. These data highlight the existence of regional differences in endothelial cell gene regulation and suggest that the 733-bp von Willebrand factor promoter may be useful as a molecular marker to investigate endothelial cell diversity.
A rapid purification method for calf thymus casein kinase II (1988)

We report here the rapid purification to homogeneity of a cyclic nucleotide-independent protein kinase sensitive to 5'6-dichloro-1-beta-D-ribofuranozylbenzimidazole (DRB), identical to the previously described casein kinase II, from lyophilized calf thymus by chromatography on phosphocellulose and Mono-Q FPLC columns.
Silicon dioxide chemical vapor deposition using silane and hydrogen peroxide (1996)

SiH4 and H2O2 have been successfully used for the deposition of silicon dioxide for shallow trench isolation. With this chemistry, it is possible to fill up trenches without voids up to an aspect ratio 2.3:1. The very good gap filling is due to the presence of SiOH groups in the oxide film. To obtain a density close to that of thermal oxide, the film must be annealed at high temperature. The electrical characteristics are equivalent to those obtained using thermal silicon dioxide.
Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood (2011)

Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here, we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1169 case and control individuals revealed an excess of differentially methylated sites in genomic regions that were previously associated with T2DM through genetic studies. Next, in-depth analyses were performed at selected top-ranking regions. A CpG site in the first intron of the FTO gene showed small (3.35%) but significant (P = 0.000021) hypomethylation of cases relative to controls. The effect was independent of the sequence polymorphism in the region and persists among individuals carrying the sequence-risk alleles. The odds of belonging to the T2DM group increased by 6.1% for every 1% decrease in methylation (OR = 1.061, 95% CI: 1.032-1.090), the odds ratio for decrease of 1 standard deviation of methylation (adjusted to gender) was 1.5856 (95% CI: 1.2824-1.9606) and the sensitivity (area under the curve = 0.638, 95% CI: 0.586-0.690; males = 0.675, females = 0.609) was better than that of the strongest known sequence variant. Furthermore, a prospective study in an independent population cohort revealed significant hypomethylation of young individuals that later progressed to T2DM, relative to the individuals who stayed healthy. Further genomic analysis revealed co-localization with gene enhancers and with binding sites for methylation-sensitive transcriptional regulators. The data showed that low methylation level at the analyzed sites is an early marker of T2DM and suggests a novel mechanism by which early-onset, inter-individual methylation variation at isolated non-promoter genomic sites predisposes to T2DM.
Microporous Structure and Drug Release Kinetics of Polymeric Nanoparticles (2007)

The aim of the present study was to characterize pegylated nanoparticles (NPs) for their microporosity and study the effect of microporosity on drug release kinetics. Blank and drug-loaded NPs were prepared from three different pegylated polymers, namely, poly(ethylene glycol)1%-graft-poly(D,L)-lactide, poly(ethylene glycol)5%-graft-poly(D,L)-lactide, and the multiblock copolymer (poly(D,L)-lactide-block-poly(ethylene glycol)-block-poly(D,L)-lactide)n. These NPs were characterized for their microporosity using nitrogen adsorption isotherms. NPs of the multiblock copolymer showed the least microporosity and Brunauer-Emmett-Teller (BET) surface area, and that of PEG1%-g-PLA showed the maximum. Based on these results, the structural organization of poly(D,L)-lactide (PLA) and poly(ethylene glycol) (PEG) chains inside the NPs was proposed and was validated with differential scanning calorimetry (DSC) and X-ray photoelectron spectroscopy (XPS) surface analysis. An in vitro drug release study revealed that PEG1%-g-PLA NPs exhibited slower release despite their higher surface area and microporosity. This was attributed to the presence of increased microporosity forming tortuous internal structures, thereby hindering drug diffusion from the matrix. Thus, it was concluded that the microporous structure of NPs, which is affected by the molecular architecture of polymers, determines the release rate of the encapsulated drug.
Probabilistic visual learning for object representation (1997)

We present an unsupervised technique for visual learning, which is based on density estimation in high-dimensional spaces using an eigenspace decomposition. Two types of density estimates are derived for modeling the training data: a multivariate Gaussian (for unimodal distributions) and a mixture-of-Gaussians model (for multimodal distributions). Those probability densities are then used to formulate a maximum-likelihood estimation framework for visual search and target detection for automatic object recognition and coding. Our learning technique is applied to the probabilistic visual modeling, detection, recognition, and coding of human faces and nonrigid objects, such as hands.
The cleavage preference of the proteasome governs the yield of antigenic peptides. (1995)

Proteasomes degrade endogenous proteins in the cytosol. The potential contribution of the proteasome to the effect of flanking sequences on the presentation of an antigenic epitope presented by the major histocompatibility complex class I allele Ld was studied. Peptides generated in cells from minigenes coding for peptides of 17- and 19-amino acid length were compared with the in vitro 20S proteasome degradation products of the respective synthetic peptides. The quality of generated peptides was independent of ubiquitination. In vivo and in vitro processing products were indistinguishable with respect to peptide size and abundance. Altering the neighboring sequence substantially improved the yield of the final antigenic nonapeptide by 20S proteasome cleavage. These results suggest that, in addition to the presence of major histocompatibility complex class I allelic motifs, the cleavage preference of the proteasome can define the antigenic potential of a protein.
Growth of GexSi1−x alloys on Si(110) surfaces (1991)

We have studied the growth of GexSi1−x alloys on Si(110) surfaces. For this growth normal, there are only two inclined {111} glide planes intersecting the interfacial plane. Both intersections are along the same in-plane [11̄0] direction, thus classic a/2〈110〉{111} glide misfit dislocations can form along only one interfacial direction. This produces an orthorhombic unit cell following strain relaxation by misfit dislocations. At sufficiently high stresses, previously unobserved misfit dislocation structures are activated. The critical thickness for misfit dislocation introduction is found to be shifted to lower Ge compositions with respect to growth on the (100) surface, consistent with a higher angular factor resolving the interfacial component of the dislocation Burgers vector in the (110) system.
Manganese uptake and distribution in the central nervous system (CNS). (1999)

Information about the nature of manganese (Mn)-binding ligands in plasma and serum, and its transport mechanism across the blood-brain barrier (BBB) is sparse. Most studies to date have focused on distribution, excretion, and accumulation of intravenous and intraperitoneal solutions of soluble divalent salts of Mn. Mn is transported in the blood primarily in the divalent oxidation state (Mn2+) and crosses the BBB via specific carriers at a rate far slower than in other tissues. Mn transport across the BBB occurs both in the 2+ and 3+ oxidation state. Within the CNS, Mn accumulates primarily within astrocytes, presumably because the astrocyte-specific enzyme, glutamine synthetase (GS), represents an important regulatory target of Mn. Compared to Mn2+, Mn3+ has a slower elimination rate and therefore, may have a greater tendency to accumulate in tissues. Furthermore, in view of the dependence of Mn accumulation within the CNS on iron (Fe) homeostasis, the oxidation state of Mn may represent a key determinant in the differential distribution, accumulation and secretion profiles of Mn, a fact that has received little attention in experimental biology toxicology. Accordingly, the distribution and membrane transport of Mn emphasizes the importance of: 1) the oxidation state of Mn, as it governs the affinity of Mn to endogenous ligands, and 2) the reaction of Mn3+ with transferrin, the plasma iron-carrying protein. This review will focus on transport kinetics of Mn across the BBB (both in the 2+ and 3+ oxidation state), the putative role of transferrin in the transport of Mn across the BBB, the transport of Mn by astrocytes, as well as the physiological significance of Mn to the function GS.
Rise of the Graphics Processor (2008)

The modern graphics processing unit (GPU) is the result of 40 years of evolution of hardware to accelerate graphics processing operations. It represents the convergence of support for multiple market segments: computer-aided design, medical imaging, digital content creation, document and presentation applications, and entertainment applications. The exceptional performance characteristics of the GPU make it an attractive target for other application domains. We examine some of this evolution, look at the structure of a modern GPU, and discuss how graphics processing exploits this structure and how nongraphical applications can take advantage of this capability. We discuss some of the technical and market issues around broader adoption of this technology.
CpG Oligodeoxynucleotides Act as Adjuvants that Switch on T Helper 1 (Th1) Immunity (1997)

Synthetic oligodeoxynucleotides (ODN) that contain unmethylated CpG motifs (CpG ODN) induce macrophages to secrete IL-12, which induces interferon (IFN)-gamma secretion by natural killer (NK) cells. Since these cytokines can induce T helper 1 (Th1) differentiation, we examined the effects of coadministered CpG ODN on the differentiation of Th responses to hen egg lysozyme (HEL). In both BALB/c (Th2-biased) and B10.D2 (Th1-biased) mice, immunization with HEL in incomplete Freund's adjuvant (IFA) resulted in Th2-dominated immune responses characterized by HEL-specific secretion of IL-5 but not IFN-gamma. In contrast, immunization with IFA-HEL plus CpG ODN switched the immune response to a Th1-dominated cytokine pattern, with high levels of HEL-specific IFN-gamma secretion and decreased HEL-specific IL-5 production. IFA-HEL plus CpG ODN also induced anti-HEL IgG2a (a Th1-associated isotype), which was not induced by IFA-HEL alone. Control non-CpG ODN did not induce IFN-gamma or IgG2a, excepting lesser increases in B10.D2 (Th1-biased) mice. Thus, CpG ODN provide a signal to switch on Th1-dominated responses to coadministered antigen and are potential adjuvants for human vaccines to elicit protective Th1 immunity.
Physical−Chemical Aspects of Protein Corona: Relevance toin Vitroandin VivoBiological Impacts of Nanoparticles (2011)

It is now clearly emerging that besides size and shape, the other primary defining element of nanoscale objects in biological media is their long-lived protein ("hard") corona. This corona may be expressed as a durable, stabilizing coating of the bare surface of nanoparticle (NP) monomers, or it may be reflected in different subpopulations of particle assemblies, each presenting a durable protein coating. Using the approach and concepts of physical chemistry, we relate studies on the composition of the protein corona at different plasma concentrations with structural data on the complexes both in situ and free from excess plasma. This enables a high degree of confidence in the meaning of the hard protein corona in a biological context. Here, we present the protein adsorption for two compositionally different NPs, namely sulfonated polystyrene and silica NPs. NP-protein complexes are characterized by differential centrifugal sedimentation, dynamic light scattering, and zeta-potential both in situ and once isolated from plasma as a function of the protein/NP surface area ratio. We then introduce a semiquantitative determination of their hard corona composition using one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrospray liquid chromatography mass spectrometry, which allows us to follow the total binding isotherms for the particles, identifying simultaneously the nature and amount of the most relevant proteins as a function of the plasma concentration. We find that the hard corona can evolve quite significantly as one passes from protein concentrations appropriate to in vitro cell studies to those present in in vivo studies, which has deep implications for in vitro-in vivo extrapolations and will require some consideration in the future.