gebhart/patrepeval huggingface dataset:
Activation of LPS-inducible genes by the antitumor agent 5,6-dimethylxanthenone-4-acetic acid in primary murine macrophages. Dissection of signaling pathways leading to gene induction and tyrosine phosphorylation. (1994)

The synthetic flavone analogue 5,6-dimethylxanthenone-4-acetic acid (5,6-MeXAA) has shown promise as an antitumor agent and is currently a candidate for clinical trials. Because 5,6-MeXAA has been shown in a murine macrophage and a human myelomonocytic cell line to induce TNF-alpha mRNA and to activate macrophages to become tumoricidal, actions that are shared with bacterial LPS, we sought to determine the level of LPS mimetic activity exhibited by this low m.w. macrophage-activating agent. To elucidate its mechanisms of action, the capacity to induce a panel of LPS-inducible genes was assessed. 5,6-MeXAA was found to induce a subset of LPS-inducible genes within the panel in both Lpsn and Lpsd primary murine macrophages. Of the six LPS-inducible genes examined, there was marked induction of IP-10, D8, and D3; low induction of TNF-alpha gene expression; and insignificant induction of TNFR-2 and IL-1 beta genes. 5,6-MeXAA was also found to be a potent inducer of IFNs in macrophages of both strains, and of increased expression of the genes that encode the IFN regulatory factors IRF-1, IRF-2, and ICSBP. In contrast with LPS, 5,6-MeXAA failed to induce significantly any of the 40- to 45-kDa tyrosine phosphoproteins induced by LPS. These data suggest that 5,6-MeXAA shares with LPS certain biochemical pathways that lead to gene induction and allow for the additional dissection of the relationship of tyrosine phosphorylation and the expression of specific genes.
Lineage Commitment and Maturation in Hematopoietic Cells: The Case for Extrinsic Regulation (1998)

THE TWO SPECIFIC QUESTIONS at issue in the present discussion are (1) whether extrinsic signaling by hematopoietic regulators can influence the occurrence or nature of the differentiation commitment decisions a cell makes and (2) whether these regulators can initiate or influence maturation events
Cloning, Characterization, and Phylogenetic Analysis of Siglec-9, a New Member of the CD33-related Group of Siglecs (2000)

The Siglecs are a subfamily of I-type lectins (immunoglobulin superfamily proteins that bind sugars) that specifically recognize sialic acids. We report the cloning and characterization of human Siglec-9. The cDNA encodes a type 1 transmembrane protein with three extracellular immunoglobulin-like domains and a cytosolic tail containing two tyrosines, one within a typical immunoreceptor tyrosine-based inhibitory motif (ITIM). The N-terminal V-set Ig domain has most amino acid residues typical of Siglecs. Siglec-9 is expressed on granulocytes and monocytes. Expression of the full-length cDNA in COS cells induces sialic-acid dependent erythrocyte binding. A recombinant soluble form of the extracellular domain binds to alpha2-3 and alpha2-6-linked sialic acids. Typical of Siglecs, the carboxyl group and side chain of sialic acid are essential for recognition, and mutation of a critical arginine residue in domain 1 abrogates binding. The underlying glycan structure also affects binding, with Galbeta1-4Glc[NAc] being preferred. Siglec-9 shows closest homology to Siglec-7 and both belong to a Siglec-3/CD33-related subset of Siglecs (with Siglecs-5, -6, and -8). The Siglec-9 gene is on chromosome 19q13.3-13.4, in a cluster with all Siglec-3/CD33-related Siglec genes, suggesting their origin by gene duplications. A homology search of the Drosophila melanogaster and Caenorhabditis elegans genomes suggests that Siglec expression may be limited to animals of deuterostome lineage, coincident with the appearance of the genes of the sialic acid biosynthetic pathway.
Dual Device User Interface Design for Ubiquitous Language Learning: Mobile Phone and Interactive Television (iTV) (2006)

In this paper we describe the design and development of a system that facilitates language learning from a combination of two devices, interactive television (iTV) and mobile phone. We present a number of requirements for technologies to support informal language learning based on theories of language learning, theories of formal and informal learning, our own studies of adult language learners and the affordances of iTV as a medium to support learning. We describe TAMALLE (television and mobile phone assisted language learning environment), a prototype system based on these requirements and discuss some of the user interface design issues that arise in the context of cross platform dual device systems for ubiquitous learning.
Serum FSH, LH, and testosterone concentrations in presumably fertile men: effect of age. (1993)

Apparently, a rise in FSH and reduction in testosterone precede a rise in LH concentration.
PI3K-Akt Signaling and Viral Infection (2008)

PI3K-Akt pathway is an important mechanism through which viral infection influences various cell functions. Activating PI3K-Akt signaling is a strategy employed by viruses to slow down apoptosis and prolong viral replication in both acute and persistent infection. It is also probable that prevention of cell death facilitates virus-induced carcinogenesis. Accumulating evidence suggests that the activity of PI3K or Akt is critical for survival of a few viruses. Adenovirus relies on PI3K-mediated organization of actin filament for active internalization. Non-segmented negative-sense RNA viruses require Akt to enhance synthesis of viral RNAs. On the other hand, PI3K-Akt signaling is associated with up-regulating interferon response. Higher PI3K-Akt activity might impede viral propagation due to activation of cellular defenses. Influenza A virus is an interesting case which requires active PI3K for penetration despite the negative effects of inducing immune response. Unlike most viruses, it was reported that VP1 protein of foot-and-mouth disease virus inhibits Akt to promote cell death. These reports confirm the multiple roles of PI3K-Akt pathway in viral infection. Here, more new information on the interaction between PI3K-Akt signaling and viral infection is discussed.
Expression, Localization, and Functional Activity of TL1A, a Novel Th1-Polarizing Cytokine in Inflammatory Bowel Disease (2003)

TL1A is a novel TNF-like factor that acts as a costimulator of IFN-gamma secretion through binding to the death domain-containing receptor, DR3. The aim of this study was to test the hypothesis that TL1A may play an important role in inflammatory bowel disease (IBD) by functioning as a Th1-polarizing cytokine. The expression, cellular localization, and functional activity of TL1A and DR3 were studied in intestinal tissue specimens as well as isolated lamina propria mononuclear cells from IBD patients and controls. TL1A mRNA and protein expression was up-regulated in IBD, particularly in involved areas of Crohn's disease (CD; p < 0.03 vs control). TL1A production was localized to the intestinal lamina propria in macrophages and CD4(+) and CD8(+) lymphocytes from CD patients as well as in plasma cells from ulcerative colitis patients. The amount of TL1A protein and the number of TL1A-positive cells correlated with the severity of inflammation, most significantly in CD. Increased numbers of immunoreactive DR3-positive T lymphocytes were detected in the intestinal lamina propria from IBD patients. Addition of recombinant human TL1A to cultures of PHA-stimulated lamina propria mononuclear from CD patients significantly augmented IFN-gamma production by 4-fold, whereas a minimal effect was observed in control patients. Our study provides evidence for the first time that the novel cytokine TL1A may play an important role in a Th1-mediated disease such as CD.
Automatic Semantic Parsing of CT Scans via Multiple Randomized Decision Trees (2009)

We introduce a new, efficient algorithm for the automatic detection and localization of anatomical structures within 3D CT images. Our algorithm builds upon recent randomized decision tree classifiers and produces accurate posterior probabilities for each of the classes (e.g. organ labels) in the training set. Accurate results are obtained by exploiting the high level of generalization offered by the classifier. Furthermore, its massive parallelism yields high computational efficiency.
Proneurotrophin-3 Is a Neuronal Apoptotic Ligand: Evidence for Retrograde-Directed Cell Killing (2009)

Although mature neurotrophins are well described trophic factors that elicit retrograde survival signaling, the precursor forms of neurotrophins (i.e., proneurotrophins) can function as high-affinity apoptotic ligands for selected neural populations. An outstanding question is whether target-derived proneurotrophins might affect neuronal survival/death decisions through a retrograde transport mechanism. Since neurotrophin-3 (NT-3) is highly expressed in non-neural tissues that receive peripheral innervation, we investigated the localized actions of its precursor (proNT-3) on sympathetic neurons in the present study. Pharmacological inhibition of intracellular furin proteinase activity in 293T cells resulted in proNT-3 release instead of mature NT-3, whereas membrane depolarization in cerebellar granule neurons stimulated endogenous proNT-3 secretion, suggesting that proNT-3 is an inducible bona fide ligand in the nervous system. Our data also indicate that recombinant proNT-3 induced sympathetic neuron death that is p75(NTR)- and sortilin-dependent, with hallmark features of apoptosis including JNK (c-Jun N-terminal kinase) activation and nuclear fragmentation. Using compartmentalized culture systems that segregate neuronal cell bodies from axons, proNT-3, acting within the distal axon compartment, elicited sympathetic neuron death and overrode the survival-promoting actions of NGF. Together, these results raise the intriguing possibility that dysregulation of proneurotrophin processing/release by innervated targets can be deleterious to the neurons projecting to these sites.
Biologic attachment, growth, and differentiation of cultured human epidermal keratinocytes on a graftable collagen and chondroitin-6-sulfate substrate. (1988)

Repair of full-thickness burns requires replacement of both the dermal and the epidermal components of the skin. Use of tissue culture methods allows very large expansions of surface area to be covered by cultured normal human epidermal keratinocytes (HK). Porous and resorbable materials, such as collagen and chondroitin-6-sulfate membranes, may be expected to adhere to wounds and promote fibrovascular ingrowth better than grafts of cultured epidermal keratinocytes alone. This article demonstrates the in vitro formation of biologic attachments between HK and a collagen and chondroitin-6-sulfate dermal skin replacement. Dermal membranes are prepared as generic acellular sheets and stored in the dry state for extended periods. Subconfluent HK cultures in logarithmic phase growth can attach quickly to dermal membranes in vitro, form a confluent epithelial sheet on the surface of each membrane, and exhibit mitotic cells for at least 1 week in vitro. Transmission electron microscopy demonstrates the formation of hemidesmosomes, extracellular matrix, and banded collagen at the interface of the epidermal cells and the dermal membrane. By comparison, HK cultures as confluent sheets released enzymatically with Dispase do not attach to the dermal membranes in vitro, under the conditions tested, although complete coverage of the membrane by the cell sheets is obtained. Growth assays show that subconfluent HK cells retain sufficient growth potential to maintain logarithmic phase growth, but that HK cells disaggregated from confluent sheets become growth arrested in comparison. The composite material has discrete dermal and epidermal compartments, has total thickness comparable to split-thickness skin graft, and can be applied to full-thickness skin defects in a single procedure.
Can We Learn To Distinguish between “Drug-like” and “Nondrug-like” Molecules? (1998)

We have used a Bayesian neural network to distinguish between drugs and nondrugs. For this purpose, the CMC acts as a surrogate for drug-like molecules while the ACD is a surrogate for nondrug-like molecules. This task is performed by using two different set of 1D and 2D parameters. The 1D parameters contain information about the entire molecule like the molecular weight and the the 2D parameters contain information about specific functional groups within the molecule. Our best results predict correctly on over 90% of the compounds in the CMC while classifying about 10% of the molecules in the ACD as drug-like. Excellent generalization ability is shown by the models in that roughly 80% of the molecules in the MDDR are classified as drug-like. We propose to use the models to design combinatorial libraries. In a computer experiment on generating a drug-like library of size 100 from a set of 10 000 molecules we obtain at least a 3 or 4 order of magnitude improvement over random methods. The neighborhoods defined by our models are not similar to the ones generated by standard Tanimoto similarity calculations. Therefore, new and different information is being generated by our models, and so it can supplement standard diversity approaches to library design.
Cloning and Expression of the Gene for the Na + -Coupled Serine Transporter from Escherichia coli and Characteristics of the Transporter (1998)

We cloned a gene (sstT) for the Na+/serine symporter from the chromosome of Escherichia coli by using a low-copy-number vector and sequenced it. According to the deduced amino acid sequence, the transporter (SstT) consists of 414 amino acid residues. Hydropathy analysis suggested that the SstT protein possesses 9, instead of 12, hydrophobic domains.
Exitatory Amino Acids in Health and Disease (1995)

Pharmacological manipulation of the excitatory amino acid receptors is likely to be of benefit in important and common diseases of the nervous system. Only a few of the currently available drugs that modify excitatory neurotransmission, such as remacemide, lamotrigine, and tizanidine, have an acceptable therapeutic index. The identification of numerous receptor subtypes, topographic variabilities of distribution, and multiple modulatory sites will provide a true challenge to the neuropharmacologist.
Distance metric learning under covariate shift (2011)

Learning distance metrics is a fundamental problem in machine learning. Previous distance-metric learning research assumes that the training and test data are drawn from the same distribution, which may be violated in practical applications. When the distributions differ, a situation referred to as covariate shift, the metric learned from training data may not work well on the test data. In this case the metric is said to be inconsistent. In this paper, we address this problem by proposing a novel metric learning framework known as consistent distance metric learning (CDML), which solves the problem under covariate shift situations. We theoretically analyze the conditions when the metrics learned under covariate shift are consistent. Based on the analysis, a convex optimization problem is proposed to deal with the CDML problem. An importance sampling method is proposed for metric learning and two importance weighting strategies are proposed and compared in this work. Experiments are carried out on synthetic and real world datasets to show the effectiveness of the proposed method.
Teletext Systems: Considering the Prospective User (1980)

An overview of teletext systems is given, stressing in particular the viewpoint of the potential user. The expected reaction of the North American consumer to teletext is analyzed. Such a forecast is important because a consumer teletext system has not yet been implemented in North America. Although teletext has many potential categories of users and can be implemented in many different ways, this paper concentrates on broadcast teletext as an ancillary service for consumers. The analysis is based on considerations of technical feasibility and the constraints imposed by consumer behavior. The results of this analysis have important implications on system design.
Electrodeposition of nickel nanowires and nanotubes using various templates (2008)

Nickel nanotubes and nanowires are grown by galvanostatic electrodeposition in the pores of 1000, 100, and 15 nm polycarbonate as well as in anodised alumina membranes at a current density of 10 mA cm-2. The effects of pore size, porosity, electrodeposition time, effective current density, and pore aspect ratio are investigated. Nickel nanotube structures are obtained with 1000 nm pore size polycarbonate membrane without any prior treatment method. At the early stages of electrodeposition hollow nickel nanotubes are produced and nanotubes turn into nanowires at longer depositon times. As effective current density accounting for the membrane porosity decreases, the axial growth direction is favoured yielding nanowires rather than nanotubes. However, for smaller pore size polycarbonate membranes, nanowires are obtained even though effective current densities were higher. We believe that when the pore diameter is below a critical size, nanowires grow regardless of current density since narrow pores promote layer by layer growth of nanorods due to smaller surface area of the pore bottom compared to pore walls. Pore size has a dominant effect over effective current density in determining the structure of the fibres produced for small pores. Nickel nanowires are also obtained in the small pores of anodised alumina, which has higher aspect ratios. High aspect ratio membranes favour the fabrication of nanowires regardless of current density.
Mitomycin C (MMC) combined with paclitaxel (PCTX)-a clinical and pharmacokinetic study (1999)

Clinical Pharmacology & Therapeutics (1999) 65, 198–198; doi:
Impact of Aortic Stiffness Attenuation on Survival of Patients in End-Stage Renal Failure (2001)

Background —Aortic pulse wave velocity (PWV) is a predictor of mortality in patients with end-stage renal failure (ESRF). The PWV is partly dependent on blood pressure (BP), and a decrease in BP can attenuate the stiffness. Whether the changes in PWV in response to decreases in BP can predict mortality in ESRF patients has never been investigated. Methods and Results —One hundred fifty ESRF patients (aged 52±16 years) were monitored for 51±38 months. From entry until the end of follow-up, the changes of PWV in response to decreased BP were measured ultrasonographically. BP was controlled by adjustment of “dry weight” and, when necessary, with ACE inhibitors, calcium antagonists, and/or β-blockers, in combination if necessary. Fifty-nine deaths occurred, including 40 cardiovascular and 19 noncardiovascular events. Cox analyses demonstrated that independent of BP changes, the predictors of all-cause and cardiovascular mortality were as follows: absence of PWV decrease in response to BP decrease, increased left ventricular mass, age, and preexisting cardiovascular disease. Survival was positively associated with ACE inhibitor use. After adjustment for all confounding factors, the risk ratio for the absence of PWV decrease was 2.59 (95% CI 1.51 to 4.43) for all-cause mortality and 2.35 (95% CI 1.23 to 4.41) for cardiovascular mortality. The risk ratio for ACE inhibitor use was 0.19 (95% CI 0.14 to 0.43) for all-cause mortality and 0.18 (95% CI 0.06 to 0.55) for cardiovascular mortality. Conclusions —These results indicate that in ESRF patients, the insensitivity of PWV to decreased BP is an independent predictor of mortality and that use of ACE inhibitors has a favorable effect on survival that is independent of BP changes.
Effect of monoclonal antibodies on limited proteolysis of native glycoprotein gD of herpes simplex virus type 1 (1982)

We examined the properties of 17 monoclonal antibodies to glycoprotein gD of herpes simplex type 1 (HSV-1) (gD-1) and HSV-2 (gD-2). The antibodies recognized eight separate determinants of gD, based on differences in radioimmuno-precipitation and neutralization assays. The determinants were distributed as follows: three were gD-1 specific, one was gD-2 specific, and four were type common. Several type-specific and type-common determinants appeared to be involved in neutralization. We developed a procedure for examining the effect that binding of monoclonal antibody has on proteolysis of native gD-1 by Staphylococcus aureus protease V8. We showed that several different patterns of protease V8 cleavage were obtained, depending on the monoclonal antibody used. The proteolysis patterns were generally consistent with the immunological groupings. With four groups of antibodies, we found that fragments of gD-1 remained bound to antibody after V8 treatment. A 38,000-dalton fragment remained bound to antibodies in three different groups of monoclonal antibodies. This fragment appeared to contain one type-common and two type-specific determinants. A 12,000-dalton fragment remained bound to antibodies belonging to one type-common group of monoclonal antibodies. Tryptic peptide analysis revealed that the 12,000-dalton fragment represented a portion of the 38,000-dalton fragment and was enriched in a type-common arginine tryptic peptide.
Specific Detection of Chikungunya Virus Using a RT‐PCR/Nested PCR Combination (2002)

Chikungunya (CHIK) virus is enzootic in many countries in Asia and throughout tropical Africa. In Asia the virus is transmitted from primates to humans almost exclusively by Aedes aegypti, while various aedine mosquito species are responsible for human infections in Africa. The clinical picture is characterized by a sudden onset of fever, rash and severe pain in the joints which may persist in a small proportion of cases. Although not listed as a haemorrhagic fever virus, illness caused by CHIK virus can be confused with diseases such as dengue or yellow fever, based on the similarity of the symptoms. Thus, laboratory confirmation of suspected cases is required to launch control measures during an epidemic. CHIK virus diagnosis based on virus isolation is very sensitive, yet requires at least a week in conjunction with virus identification using monovalent sera. We developed a reverse transcription-polymerase chain reaction (RT-PCR) assay which amplifies a 427-bp fragment of the E2 gene. Specificity was confirmed by testing representative strains of all known alphavirus species. To verify further the viral origin of the amplicon and to enhance sensitivity, a nested PCR was performed subsequently. This RT-PCR/nested PCR combination was able to amplify a CHIK virus-specific 172-bp amplicon from a sample containing as few as 10 genome equivalents. This assay was successfully applied to four CHIK virus isolates from Asia and Africa as well as to a vaccine strain developed by USAMRIID. Our method can be completed in less than two working days and may serve as a sensitive alternative in CHIK virus diagnosis.
Cellular Protein WDR11 Interacts with Specific Herpes Simplex Virus Proteins at thetrans-Golgi Network To Promote Virus Replication (2015)

While the TGN has been proposed to be the major site of HSV-1 secondary envelopment, this process is incompletely understood, and in particular, the role of cellular TGN components in this pathway is unknown. Additionally, little is known about the cellular functions of WDR11, although the disruption of this protein has been implicated in multiple human diseases. Therefore, our finding that WDR11 is a TGN-resident protein that interacts with specific viral proteins to enhance viral yields improves both our understanding of basic cellular biology as well as how this protein is co-opted by HSV.
Non-planar shorted double C-patch antennas for portable communication equipment (2002)

Rectangular, circular and ring microstrip antennas on cylindrical, spherical or conical surfaces have been studied by many authors. However, in these studies, only open circuit, half-wavelength, conventional microstrip antenna geometries have been considered. In this paper, non-planar shorted and partially shorted double C-patch antennas [Sanad, 1995] with and without parasitic elements have been studied experimentally.