gebhart/patrepeval huggingface dataset:
Consensus transcriptome signature of perineural invasion in pancreatic carcinoma (2009)

Perineural invasion, the growth of tumor cells along nerves, is a key feature of pancreatic cancer. The cardinal symptom of pancreatic cancer, abdominal pain often radiating to the back, as well as the high frequency of local tumor recurrence following resection are both attributed to the unique ability of pancreatic tumor cells to invade the neuronal system. The molecular mechanisms underlying the neuroaffinity of pancreatic tumors are not completely understood. In this study, we developed a novel method to monitor ex vivo perineural invasion into surgically resected rat vagal nerves by different human pancreatic tumor cell lines. Genome-wide transcriptional analyses were employed to identify the consensus set of genes differentially regulated in all highly nerve-invasive (nerve invasion passage 3) versus less invasive (nerve invasion passage 0) pancreatic tumor cells. The critical involvement of kinesin family member 14 (KIF14) and Rho-GDP dissociation inhibitor beta (ARHGDIbeta) in perineural invasion was confirmed on RNA and protein levels in human pancreatic tumor specimens. We found significant up-regulation of KIF14 and ARHGDIbeta mRNA levels in patients with pancreatic cancer, and both proteins were differentially expressed in tumor cells invading the perineural niche of pancreatic cancer patients as detected by immunohistochemistry. Moreover, functional knockdown of KIF14 and ARHGDIbeta using small interfering RNA resulted in altered basal and/or perineural invasion of pancreatic tumor cells. Our work provides novel insights into the molecular determinants of perineural invasion in pancreatic cancer. The established nerve invasion model and the consensus signature of perineural invasion could be instrumental in the identification of novel therapeutic targets of pancreatic cancer as exemplified by KIF14 and ARHGDIbeta.
Hardware-Accelerated High-Quality Reconstruction on PC Hardware (2001)

We describe a method for exploiting commodity 3D graphics hard-ware in order to achieve hardware-accelerated high-quality filtering with arbitrary filter kernels. Our approach is based on reordering the evaluation of the filter convolution sum to accommodate the way the hardware works. We exploit multiple rendering passes to-gether with the capability of current graphics hardware to index into several textures at the same time (multi-texturing). The method we present is applicable in one, two, and three di-mensions. The cases we are most interested in up to now are two-dimensional reconstruction of object-aligned slices through volu-metric data, and three-dimensional reconstruction of arbitrarily ori-ented slices. As a fundamental building block, the basic algorithm can be used in order to directly render an entire volume by blend-ing a stack of slices reconstructed with high quality on top of each other. We have used bicubic and tricubic B-splines and Catmull-Rom splines, as well as windowed sinc filters, as reconstruction kernels. However, it is important to emphasize that our approach has no fundamental restrictions with regard to the filters that can be used.
Fiber-optic communication in the wavelength-division multiplex mode (1983)

Abstract The new wavelength-division multiplex technique applied to fiber-optic communication systems frequently allows more efficient utilization of the large transmission capacity of glass fibers. The physical design, operating principle, and properties of the various microoptical wavelength-division multiplex and demultiplex couplers are surveyed, and the criteria on which their practical application depend are defined.
A new family of genes coding for an antigen recognized by autologous cytolytic T lymphocytes on a human melanoma. (1995)

Human melanoma MZ2-MEL expresses several distinct antigens that are recognized by autologous cytolytic T lymphocytes (CTL). Some of these antigens are encoded by genes MAGE-1, MAGE-3, and BAGE, which are expressed in a large fraction of tumors of various histological types but are silent in normal adult tissues with the exception of testis. We report here the identification of the gene coding for MZ2-F, another antigen recognized by autologous CTL on MZ2-MEL cells. This gene, which was named GAGE-1, is not related to any presently known gene. It belongs to a family of genes that are expressed in a variety of tumors but not in normal tissues, except for the testis. Antigenic peptide YRPRPRRY, which is encoded by GAGE-1, is recognized by anti-MZ2-F CTL on class I molecule HLA-Cw6. The two genes of the GAGE family that code for this peptide, namely GAGE-1 and GAGE-2, are expressed in a significant proportion of melanomas (24%), sarcomas (25%), non-small cell lung cancers (19%), head and neck tumors (19%), and bladder tumors (12%). About 50% of melanoma patients carry on their tumor at least one of the presently defined antigens encoded by the MAGE, BAGE, and GAGE genes.
Optimizing Cancer Treatments to Induce an Acute Immune Response: Radiation Abscopal Effects, PAMPs, and DAMPs (2012)

Clinical results indicate improved survival in poorly differentiated prostate cancer patients following a treatment schedule that maximizes hormone therapy prior to radiation. This may be because of a systemic immune response, called an abscopal effect. A literature review showed an association between acute infection and abscopal cancer remission. This led to the theory that, in the presence of endogenous cancer-specific antigens exposed by cancer necrosis, an innate immune response can adapt to respond to those antigens via a cross-talk mechanism. This theory was validated in an animal model. An acute innate immune T-cell response was stimulated using cluster vaccination with Poly(I:C). In the presence of exogenous cancer-specific antigens, this immune response became adaptive, creating an abscopal effect that resulted in cancer resolution. These concepts may be of clinical value, improving outcomes by inducing systemic abscopal effects.
Atmospheric‐pressure Penning ionization of aliphatic hydrocarbons (2006)

A study has been made of the atmospheric-pressure Penning ionization (APPeI) of aliphatic hydrocarbons (pentane, hexane, heptane, and octane) with long-lived rare gas atoms (Rg*). The metastable rare gas atoms (He*, Ne*, Ar* and Kr*) were generated by the negative-mode corona discharge of atmospheric-pressure rare gases. In the Rg*APPeI mass spectra for aliphatic hyrocarbons, the relative abundances of fragment ions were found to increase in the order of He* --> Ne* --> Ar* --> Kr*. The order is in the opposite direction to the internal energies of the Rg*. The less fragmentation observed for He* may be because the nascent molecular ions [M(+.)]* formed by Penning ionization have lifetimes long enough for them to be collisionally deactivated in the atmospheric-pressure ion source. It was found that the relative abundances of fragment ions in Ar*APPeI increased when the sample pressure in the ion source was reduced. This is attributed to the collision of Ar* with molecular ions followed by fragmentation.
Neurite Outgrowth on Nanofiber Scaffolds with Different Orders, Structures, and Surface Properties (2009)

Electrospun nanofibers can be readily assembled into various types of scaffolds for applications in neural tissue engineering. The objective of this study is to examine and understand the unique patterns of neurite outgrowth from primary dorsal root ganglia (DRG) cultured on scaffolds of electrospun nanofibers having different orders, structures, and surface properties. We found that the neurites extended radially outward from the DRG main body without specific directionality when cultured on a nonwoven mat of randomly oriented nanofibers. In contrast, the neurites preferentially extended along the long axis of fiber when cultured on a parallel array of aligned nanofibers. When seeded at the border between regions of aligned and random nanofibers, the same DRG simultaneously expressed aligned and random neurite fields in response to the underlying nanofibers. When cultured on a double-layered scaffold where the nanofibers in each layer were aligned along a different direction, the neurites were found to be dependent on the fiber density in both layers. This biaxial pattern clearly demonstrates that neurite outgrowth can be influenced by nanofibers in different layers of a scaffold, rather than the topmost layer only. Taken together, these results will provide valuable information pertaining to the design of nanofiber scaffolds for neuroregenerative applications, as well as the effects of topology on neurite outgrowth, growth cone guidance, and axonal regeneration.
Inhibition of Nuclear Factor Kappa B (NF-B):: An Emerging Theme in Anti-Inflammatory Therapies (2002)

The application of anti-inflammatory therapies began thousands of years ago with the use of readily available natural resources. It is only recently, however, that the cellular and molecular mechanisms of inflammation have been appreciated sufficiently to design anti-inflammatory strategies with limited side effects. For example, salicylates and glucocorticoids, two widely used anti-inflammatory drug classes, are now known to inhibit the activation of NF-kappa B, a transcription factor that regulates the inducible expression of a wide range of proinflammatory mediators. New generations of NF-kappa B-targeting anti-inflammatory agents that are specific, efficacious, and cost-effective may therefore complement or replace current therapies. In this review, we describe various classes of NF-kappa B inhibitors and discuss important unresolved issues regarding their use.
FOUR GENERATIONS OF PROBABLE PERSON-TO-PERSON TRANSMISSION OF HUMAN MONKEYPOX (1986)

This paper examines an outbreak of five cases of human monkeypox which occurred in children belonging to two families living in the West Kasai region of Zaire during May-July 1983. Epidemiologic investigations suggest that the first case was infected from an animal source, possibly a monkey, and that each of the other four cases was infected from a previous human case. Three of these cases of presumed person-to-person transmission occurred in close household contacts. The other case infection occurred either by casual contact within the hospital compound, or possibly because of infection due to use of the same syringe for injections. Human monkeypox is the most important orthopoxvirus infection in the post-smallpox eradication period. The disease is a zoonosis and person-to-person transmission is rather difficult. Thus, this episode is a rare event and special analysis of the circumstances is discussed. However, it supports the necessity to carry out surveillance and research on this disease as recently reported by Arita et al.
Polymer electroluminescent devices processed by inkjet printing: I. Polymer light-emitting logo (1998)

Inkjet printing (IJP) technology is a popular technology for desktop publishing. Since some of the conducting (or conjugated) polymers are solution processable, IJP technology becomes an ideal method for printing polymer light-emitting diodes with high resolution. Unfortunately, the polymer film printed from an inkjet printer usually consists of pin-holes, and this intrinsic character makes it unsuitable for fabricating high quality polymer electronic devices, particularly for devices in the sandwich structure. In this letter, we submit a hybrid structure, which consists of an inkjet printed layer in conjunction with another uniform spin coated polymer layer, as an alternative to the regular inkjet printed structure. The uniform layer serves as a buffer layer to seal the pin-holes and the IJP layer is the layer consisting of the desired pattern, for example the red–green–blue dots for a multicolor display. To demonstrate, we applied this hybrid technology to fabricate efficient and large area polymer light-emitting logos. The use of this concept represents a whole new technology of fabricating polymer electronic devices with lateral patterning capability.
Mutational Analysis of Hepatitis C Virus Nonstructural Protein 5A: Potential Role of Differential Phosphorylation in RNA Replication and Identification of a Genetically Flexible Domain (2005)

Nonstructural protein 5A of the hepatitis C virus (HCV) is a highly phosphorylated molecule implicated in multiple interactions with the host cell and most likely involved in RNA replication. Two phosphorylated variants of NS5A have been described, designated according to their apparent molecular masses (in kilodaltons) as p56 and p58, which correspond to the basal and hyperphosphorylated forms, respectively. With the aim of identifying a possible role of NS5A phosphorylation for RNA replication, we performed an extensive mutation analysis of three serine clusters that are involved in phosphorylation and hyperphosphorylation of NS5A. In most cases, alanine substitutions for serine residues in the central cluster 1 that enhanced RNA replication to the highest levels led to a reduction of NS5A hyperphosphorylation. Likewise, several highly adaptive mutations in NS4B, which is also part of the replication complex, resulted in a reduction of NS5A hyperphosphorylation too, arguing that alterations of the NS5A phosphorylation pattern play an important role for RNA replication. On the other hand, a deletion encompassing all highly conserved serine residues in the C-terminal region of NS5A that are involved in basal phosphorylation did not significantly affect RNA replication but reduced formation of p56. This region was found to tolerate even large insertions with only a moderate effect on replication. Based on these results, we propose a model of the role of NS5A phosphorylation in the viral life cycle.
Metabolites of Lactose Synthesis in Milk from Diabetic and Nondiabetic Women During Lactogenesis II (1994)

Summary The concentrations of lactose, glucose, glucose 6-phosphate (G6P), glucose 1-phosphate (G1P), UDPglucose (UDPglc), UDPgalactose (UDPgal), and inorganic phosphate (Pi) (metabolites in the lactose synthesis pathway) were measured in mammary secretion from nondiabetic (ND) and insulin-dependent diabetic (IDD) mothers during the first 10 days postpartum to determine their relationship with the amount of lactose synthesized and their association with the delay in lactose synthesis in IDD mothers. For all mothers the concentrations of all metabolites were low initially, and in ND mothers the first increases occurred as follows: lactose day 2; glucose, G6P and Pi—day 3; G1P and UDPglc—day 4; and UDPgal—day 6. The first increases for IDD mothers occurred 1–4 days later than for ND mothers. The concentrations of glucose, G6P, G1P, UDPglc, and Pi were related to the amount of lactose synthesized. Since the rate of lactose synthesis and concentrations of other metabolites were less than half-maximal while the concentration of glucose was low, and since there was a delay in the increase in mammary gland concentrations of glucose in IDD mothers, it is concluded that glucose availability has the potential to play a role in the regulation of the rate of lactose synthesis at lactogenesis II.
The tumor immunosuppressive microenvironment impairs the therapy of anti-HER2/neu antibody (2012)

It has been well established that immune surveillance plays critical roles in preventing the occurrence and progression of tumor. More and more evidence in recent years showed the host anti-tumor immune responses also play important roles in the chemotherapy and radiotherapy of cancers. Our previous study found that tumor- targeting therapy of anti-HER2/neu mAb is mediated by CD8(+) T cell responses. However, we found here that enhancement of CD8(+) T cell responses by combination therapy with IL-15R/IL-15 fusion protein or anti-CD40, which are strong stimultors for T cell responses, failed to promote the tumor therapeutic effects of anti-HER2/neu mAb. Analysis of tumor microenviornment showed that tumor tissues were heavily infiltrated with the immunosuppressive macrophages and most tumor infiltrating T cells, especially CD8(+) T cells, expressed high level of inhibitory co-signaling receptor PD-1. These data suggest that tumor microenvironment is dominated by the immunosuppressive strategies, which thwart anti-tumor immune responses. Therefore, the successful tumor therapy should be the removal of inhibitory signals in the tumor microenvironment in combination with other therapeutic strategies.
Über Digitanolglykoside, 15. Synthese von 12α.20R‐Epoxy‐5α.14β.17βH‐pregnanen (1967)

Abstract Ausgehend von Hecogeninacetat wurden auf zwei verschiedenen Wegen erstmals synthetisch 5α.14β.17βH‐Pregnane ( 9, 19 ) mit einem 12α.20 R ‐Oxidring hergestellt, wie er im Diginigenin, dort allerdings in der 20 S ‐Konfiguration, vorkommen soll.
An Approach to Scientific Array Processing: The Architectural Design of the AP-120B/FPS-164 Family (1981)

Architecture, not hardware, gives the FPS array processor family its computational speed. Here is an inside look at the trade-offs and ideas that went into its design.
Perfusion and function at rest and treadmill exercise using technetium-99m-sestamibi: comparison of one- and two-day protocols in normal volunteers. (1990)

The purpose of this study was to explore the feasibility of performing rest and exercise technetium-99m-sestamibi (99mTc-sestamibi) studies on the same day. We prospectively studied 34 asymptomatic volunteers using two different protocols (17 patients studied using one-day protocol and 17 patients studied using two-day protocol). For the one-day protocol, the rest study was performed first. For the two-day protocol, the exercise study was performed first followed by a second-day rest study. Left and right ventricular ejection fractions, myocardium/lung, myocardium/liver, myocardium/spleen, and myocardium/gallbladder count ratios were similar for the one- and two-day groups. No significant difference was observed in any variable measured. These data suggest that 99mTc-sestamibi can be used for rest and treadmill exercise studies performed on the same day to provide assessment of ventricular function and perfusion similar to studies performed on separate days.
Implementing a Dynamic Compressed Trie. (1998)

We present an order-preserving general purpose data structure for binary data, the LPC-trie. The structure is a highly compressed trie, using both level and path compression. The memory usage is similar to that of a balanced binary search tree, but the expected average depth is smaller. The LPC-trie is well suited to modern language environments with efficient memory allocation and garbage collection. We present an implementation in the Java programming language and show that the structure compares favorably to a balanced binary search tree. 1. Introduction We describe a dynamic main memory data structure for binary data, the level and path compressed trie or LPC-trie. The structure is a dynamic variant of a static level compressed trie or LC-trie [2]. The trie is a simple order preserving data structure supporting fast retrieval of elements and efficient nearest neighbor and range searches. There are several implementations of dynamic trie structures in the literature [5, 6, 8,...
A tyrosine-phosphorylated carboxy-terminal peptide of the fibroblast growth factor receptor (Flg) is a binding site for the SH2 domain of phospholipase C-gamma 1. (1991)

Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR; encoded by the flg gene) and other receptors with tyrosine kinase activity. It has been demonstrated that the src homology region 2 (SH2 domain) of PLC-gamma and of other signalling molecules such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85 direct their binding toward tyrosine-autophosphorylated regions of the epidermal growth factor or platelet-derived growth factor receptor. In this report, we describe the identification of Tyr-766 as an autophosphorylation site of flg-encoded FGFR by direct sequencing of a tyrosine-phosphorylated tryptic peptide isolated from the cytoplasmic domain of FGFR expressed in Escherichia coli. The same phosphopeptide was found in wild-type FGFR phosphorylated either in vitro or in living cells. Like other growth factor receptors, tyrosine-phosphorylated wild-type FGFR or its cytoplasmic domain becomes associated with intact PLC-gamma or with a fusion protein containing the SH2 domain of PLC-gamma. To delineate the site of association, we have examined the capacity of a 28-amino-acid tryptic peptide containing phosphorylated Tyr-766 to bind to various constructs containing SH2 and other domains of PLC-gamma. It is demonstrated that the tyrosine-phosphorylated peptide binds specifically to the SH2 domain but not to the SH3 domain or other regions of PLC-gamma. Hence, Tyr-766 and its flanking sequences represent a major binding site in FGFR for PLC-gamma. Alignment of the amino acid sequences surrounding Tyr-766 with corresponding regions of other FGFRs revealed conserved tyrosine residues in all known members of the FGFR family. We propose that homologous tyrosine-phosphorylated regions in other FGFRs also function as binding sites for PLC-gamma and therefore are involved in coupling to phosphatidylinositol breakdown.
Healos/Recombinant Human Growth and Differentiation Factor-5 Induces Posterolateral Lumbar Fusion in a New Zealand White Rabbit Model (2006)

In this rabbit fusion model, Healos/rhGDF-5 induced fusion in 100% of the rabbits studied. This rate was significantly higher than the fusion rate induced by autograft (38%). Overall, these results support continued research of Healos/rhGDF-5 as a potential bone graft alternative.
New gout treatment approved (2009)

Journal Article New gout treatment approved Get access Kate Traynor Kate Traynor Search for other works by this author on: Oxford Academic Google Scholar American Journal of Health-System Pharmacy, Volume 66, Issue 7, 1 April 2009, Page 606, https://doi.org/10.2146/news090028 Published: 01 April 2009
Characterization of lipopolysaccharide heterogeneity in Salmonella enteritidis by an improved gel electrophoresis method (1995)

Salmonella enteritidis field isolates of different phage types and pathogenicities were assessed for changes in lipopolysaccharide (LPS) structure, using an improved method of polyacrylamide gel electrophoresis (PAGE) that revealed the same degree of structural detail as mass spectroscopy. The method allowed characterization of an LPS chemotype that may be associated, regardless of phage type, with increased virulence of S. enteritidis. The virulent variant SE6-E21, which efficiently contaminates eggs and yields high numbers of organisms from chick spleens, had an O-antigen/core ratio of 2.8, as determined from gels by densitometry, and 1.67 micrograms of mannose per microgram of 2-keto-3-deoxy-octulosonic acid (KDO), while the avirulent variant SE6-E5 had O-antigen/core ratios of 1.2 and 1.00. The association between O antigen and virulence was also seen on analysis of five new field isolates. One of the new field isolates generated a mixed population of smooth and semismooth variants in agreement with its mixed virulence in chicks. When LPS was purified from large-volume cultures, only the most virulent isolate yielded high amounts of O antigen (1.6 micrograms of mannose per microgram of KDO), while the other isolates had ratios characteristic of semismooth variants (< or = 1.0 microgram of mannose per microgram of KDO), including the isolate of mixed virulence. These results indicate that the improved PAGE method might provide a rapid, sensitive, in vitro assessment of field isolate virulence prior to the performance of definitive infectivity trials.