gebhart/patrepeval huggingface dataset:
Immune Properties of Human Umbilical Cord Wharton's Jelly-Derived Cells (2008)

Cells isolated from Wharton's jelly, referred to as umbilical cord matrix stromal (UCMS) cells, adhere to a tissue-culture plastic substrate, express mesenchymal stromal cell (MSC) surface markers, self-renew, and are multipotent (differentiate into bone, fat, cartilage, etc.) in vitro. These properties support the notion that UCMS cells are a member of the MSC family. Here, the immune properties of UCMS cells are characterized in vitro. The overall hypothesis is that UCMS cells possess immune properties that would be permissive to allogeneic transplantation. For example, UCMS cells will suppress of the proliferation of "stimulated" lymphocytes (immune suppression) and have reduced immunogenicity (e.g., would be poor stimulators of allogeneic lymphocyte proliferation). Hypothesis testing was as follows: first, the effect on proliferation of coculture of mitotically inactivated human UCMS cells with concanavalin-A-stimulated rat splenocytes was assessed in three different assays. Second, the effect of human UCMS cells on one-way and two-way mixed lymphocyte reaction (MLR) assays was determined. Third, the expression of human leukocyte antigen (HLA)-G was examined in human UCMS cells using reverse transcription-polymerase chain reaction, since HLA-G expression conveys immune regulatory properties at the maternal-fetal interface. Fourth, the expression of CD40, CD80, and CD86 was determined by flow cytometry. Fifth, the cytokine expression of UCMS cells was evaluated by focused gene array. The results indicate that human UCMS cells inhibit splenocyte proliferation response to concanavalin A stimulation, that they do not stimulate T-cell proliferation in a one-way MLR, and that they inhibit the proliferation of stimulated T cells in a two-way MLR. Human UCMS cells do not inhibit nonstimulated splenocyte proliferation, suggesting specificity of the response. UCMS cells express mRNA for pan-HLA-G. UCMS cells do not express the costimulatory surface antigens CD40, CD80, and CD86. UCMS cells express vascular endothelial growth factor and interleukin-6, molecules previously implicated in the immune modulation observed in MSCs. In addition, the array data indicate that UCMS cells make a cytokine and other factors that may support hematopoiesis. Together, these results support previous observations made following xenotransplantation; for example, there was no evidence of frank immune rejection of undifferentiated UCMS cells. The results suggest that human UCMS will be tolerated in allogeneic transplantation. Disclosure of potential conflicts of interest is found at the end of this article.
An Anti-Wnt-2 Monoclonal Antibody Induces Apoptosis in Malignant Melanoma Cells and Inhibits Tumor Growth (2004)

Activation of the Wnt/beta-catenin signaling pathway has been associated with human cancers. To test whether Wnt-2 signal is a survival factor in human melanoma cells and thus represents a potential therapeutic target, we investigated the effects of inhibition of Wnt-2 signaling in human melanoma cell lines. We have developed a novel monoclonal antibody against the NH(2) terminus of the human Wnt-2 ligand that induces apoptosis in human melanoma cells overexpressing Wnt-2. Whereas incubation of this antibody with normal cells lacking Wnt-2 expression does not induce apoptosis, Wnt-2 signaling blockade by the ligand-binding antibody is confirmed by down-regulation of Dishevelled and beta-catenin. Wnt-2 small interfering RNA treatment in these cells yielded similar apoptotic effects and downstream changes. Down-regulation of an inhibitor of apoptosis family protein, survivin, was observed in both the Wnt-2 antibody-treated and small interfering RNA-treated melanoma cell lines, suggesting that the antibody induces apoptosis by inactivating survivin. In an in vivo study, this monoclonal anti-Wnt-2 antibody suppresses tumor growth in a xenograft model. These findings suggest that the anti-Wnt-2 monoclonal antibody may be useful for the treatment of patients with malignant melanoma.
Toll-like receptors. (2002)

The ability of a host to sense invasion by pathogenic organisms and to respond appropriately to control infection is paramount to survival. In the case of sepsis and septic shock, however, an exaggerated systemic response may, in fact, contribute to the morbidity and mortality associated with overwhelming infections. The innate immune system has evolved as the first line of defense against invading microorganisms. The Toll-like receptors (TLRs) are a part of this innate immune defense, recognizing conserved patterns on microorganisms. These TLRs and their signaling pathways are represented in such diverse creatures as mammals, fruit flies, and plants. Ten members of the TLR family have been identified in humans, and several of them appear to recognize specific microbial products, including lipopolysaccharide, bacterial lipoproteins, peptidoglycan, and bacterial DNA. Signals initiated by the interaction of TLRs with specific microbial patterns direct the subsequent inflammatory response. Thus, TLR signaling represents a key component of the innate immune response to microbial infection.
An efficient method for the rescue and analysis of functional HIV-1 env genes (1996)

Objective To establish a robust procedure for the isolation and characterization of full-length expression-competent HIV-1 env genes directly from patient samples. Design HIV exists as a quasispecies which can be disturbed by in vitro culture, in which numerous members of the population are likely to be defective due to the high error rate of the viral reverse transcriptase. Defective viruses are unlikely to play a dominant role in disease progression. Since env gene translation products play major roles in the initiation and spread of infection we need to study genes with open reading frames. Methods A nested polymerase chain reaction (PCR) approach has been used to rescue intact (2.6kb) env genes, which are cloned into a T7-promoter-containing vector. Expression of gp160 in CV-1 cells is detected by Western blot. Expression-competent clones are sequenced and resulting sequences used for phylogenetic studies. Translation products are analysed in relation to the known immunogenic structure of gp160. Results From random patient samples collected in London clinics, only HIV-1 subtype B was found. Two of the samples contained viruses with an additional pair of cysteine residues in their V1 regions. For samples collected in Uganda, HIV-1 subtypes A, D and an A/D recombinant were recovered. Conclusion An effective procedure is described for the isolation of HIV-1 env genes directly from patient samples, which has worked for A, B and D subtypes to date. The PCR primers can be utilized with other subtypes with the possible exception of subtype O viruses. Phyiogenetic analyses revealed the potential importance of a G/C-rich region near the tat/rev splice site as a site of recombination. The sequences and translation products generated may be more relevant to disease progression in vivo and vaccine formulations than those obtained from viruses selected in long-term culture.
Immune epitope database analysis resource (IEDB-AR) (2008)

We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune epitopes. New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope prediction tools, four T-cell epitope prediction tools and two analysis tools.
Chronic resistance training in women potentiates growth hormone in vivo bioactivity: characterization of molecular mass variants (2006)

This investigation determined the influence of acute and chronic resistance exercise on responses of growth hormone (GH) molecular variants in women. Seventy-four healthy young women (23 +/- 3 yr, 167 +/- 7 cm, 63.8 +/- 9.3 kg, 26.3 +/- 4.0% body fat) performed an acute bout of resistance exercise (6 sets of 10 repetition maximum squat). Blood samples were obtained pre- and postexercise. Resulting plasma was fractionated by molecular mass (fraction A, >60 kDa; fraction B, 30-60 kDa; and fraction C, <30 kDa) using chromatography. Fractionated and unfractionated (UF) plasma was then assayed for GH using three different detection systems (monoclonal immunoassay, polyclonal immunoassay, and rat tibial line in vivo bioassay). Subjects were then matched and randomly placed into one of four resistance exercise training groups or a control group for 24 wk. All experimental procedures were repeated on completion of the 24-wk resistance training programs. After acute exercise, immunoassays showed consistent increases in UF GH samples and fractions B and C; increases in fraction A using immunoassay were seen only in the monoclonal assay. No consistent changes in bioactive GH were found following acute exercise. Conversely, chronic exercise induced no consistent changes in immunoassayable GH of various molecular masses, whereas, in general, bioassayable GH increased. In summary, although acute exercise increased only immunoactive GH, chronic physical training increased the biological activity of circulating GH molecular variants. Increased bioactive GH was observed across all fractions and training regimens, suggesting that chronic resistance exercise increased a spectrum of GH molecules that may be necessary for the multitude of somatogenic and metabolic actions of GH.
A retinoic acid-enhanced, multicellular human blood-brain barrier model derived from stem cell sources (2014)

Blood-brain barrier (BBB) models are often used to investigate BBB function and screen brain-penetrating therapeutics, but it has been difficult to construct a human model that possesses an optimal BBB phenotype and is readily scalable. To address this challenge, we developed a human in vitro BBB model comprising brain microvascular endothelial cells (BMECs), pericytes, astrocytes and neurons derived from renewable cell sources. First, retinoic acid (RA) was used to substantially enhance BBB phenotypes in human pluripotent stem cell (hPSC)-derived BMECs, particularly through adherens junction, tight junction, and multidrug resistance protein regulation. RA-treated hPSC-derived BMECs were subsequently co-cultured with primary human brain pericytes and human astrocytes and neurons derived from human neural progenitor cells (NPCs) to yield a fully human BBB model that possessed significant tightness as measured by transendothelial electrical resistance (~5,000 Ωxcm(2)). Overall, this scalable human BBB model may enable a wide range of neuroscience studies.
GOK: a gene at 11p15 involved in rhabdomyosarcoma and rhabdoid tumor development. (1997)

The expression of GOK, a gene recently identified at 11p15.5, was studied in breast cancer, rhabdomyosarcoma, and rhabdoid tumor cell lines. In these neoplasms, deletions at 11p15 and suppression of tumorigenicity induced by a normal human chromosome 11 were previously demonstrated. Whereas breast cancer cell lines express readily detectable levels of GOK mRNA, expression is absent in rhabdomyosarcoma and rhabdoid tumor cell lines. This is in contrast with the high expression of GOK in skeletal muscle, the normal tissue of origin of rhabdomyosarcomas, suggesting that down-regulation of GOK expression could be involved in tumor development. In agreement with this hypothesis, transfection of GOK cDNA into G401 derived from a rhabdoid tumor and RD cells derived from a rhabdomyosarcoma that do not express detectable levels of GOK mRNA, induced cell death. Because GOK expression is not compatible with growth of these tumor cells, these results support the hypothesis that loss of GOK expression plays a role in tumor establishment or progression and suggest that GOK may act as a recessive tumor suppressor gene in rhabdomyosarcomas and rhabdoid tumors. On the contrary, transfection of GOK cDNA into the breast cancer cell line HBL100 produced no detectable effects, indicating that the growth-suppressive effect of GOK in RD and G401 cells was specific. Because rhabdomyosarcomas have been observed in cases of Beckwith-Wiedemann syndrome, a genetic disorder linked to 11p15, a role of GOK in this disease cannot be excluded.
120 Gbit/s Over 500-km Using Single-Band Polarization-Multiplexed Self-Coherent Optical OFDM (2009)

In this paper, we experimentally demonstrate a single-band self-coherent polarization-multiplexed optical orthogonal frequency-division multiplex system with a raw data rate of 120 Gbit/s. The transmitter uses a novel RF structure that eliminates the need for RF mixers and optical filters. The receiver uses a novel architecture where the optical carrier is filtered and amplified for self-coherent detection. The receiver is polarization diverse and allows for the usual frequency guard band between the carrier and the sideband to be reduced in width, thus increasing spectral efficiency. Using two commercial 20 GS/s arbitrary-waveform generators to generate a single information-carrying band per polarization, we achieve a raw data rate of 120 Gbit/s over 500 km of standard single-mode fiber.
Adaptive multi-robot wide-area exploration and mapping (2008)

The exploration problem is a central issue in mobile robotics. A complete terrain coverage is not practical if the environment is large with only a few small hotspots. This paper presents an adaptive multi-robot exploration strategy that is novel in performing both wide-area coverage and hotspot sampling using non-myopic path planning. As a result, the environmental phenomena can be accurately mapped. It is based on a dynamic programming formulation, which we call the Multi-robot Adaptive Sampling Problem (MASP). A key feature of MASP is in covering the entire adaptivity spectrum, thus allowing strategies of varying adaptivity to be formed and theoretically analyzed in their performance; a more adaptive strategy improves mapping accuracy. We apply MASP to sampling the Gaussian and log-Gaussian processes, and analyze if the resulting strategies are adaptive and maximize wide-area coverage and hotspot sampling. Solving MASP is non-trivial as it comprises continuous state components. So, it is reformulated for convex analysis, which allows discrete-state monotone-bounding approximation to be developed. We provide a theoretical guarantee on the policy quality of the approximate MASP (aMASP) for using in MASP. Although aMASP can be solved exactly, its state size grows exponentially with the number of stages. To alleviate this computational difficulty, anytime algorithms are proposed based on aMASP, one of which can guarantee its policy quality for MASP in real time.
TNF-Related Ligands and Their Receptors (1998)

Multicellular organisms have the challenging task of coordinating the activities of many distinct cell types. This coordination is accomplished largely by cell-associated and soluble signalling molecules that act locally or distantly to alter target-cell physiology. The tumour necrosis factor family of cytokines are type II transmembrane proteins that are important regulators of homeostasis and have been implicated as mediators of disease. These molecules serve as ligands for a family of cell-surface receptors termed the tumour necrosis factor/nerve growth factor (TNF/NGF) receptor family. The receptors are type I transmembrane proteins capable of mediating a wide range of responses in vitro and in vivo. Signal transduction is mediated by several newly discovered cytoplasmic proteins that couple these receptors to downstream signalling events. The elucidation and use of spontaneously occurring mutants in TNF-related ligands and receptors in addition to gene-targeting experiments have begun to clarify the diverse biological effects mediated by this superfamily of cytokines.
SIGNALING AT THE GROWTH CONE: Ligand-Receptor Complexes and the Control of Axon Growth and Guidance (2003)

The guidance of axons during the establishment of the nervous system is mediated by a variety of extracellular cues that govern cytoskeletal dynamics in axonal growth cones. A large number of these guidance cues and their cell-surface receptors have now been identified, and the intracellular signaling pathways by which these cues induce cytoskeletal rearrangements are becoming defined. This review summarizes our current understanding of the major families of axon guidance cues and their receptors, with a particular emphasis on receptor signaling mechanisms. We also discuss recent advances in understanding receptor cross talk and how the activities of guidance cues and their receptors are modulated during neural development.
In Vivo Molecular Photoacoustic Tomography of Melanomas Targeted by Bioconjugated Gold Nanocages (2010)

Early diagnosis, accurate staging, and image-guided resection of melanomas remain crucial clinical objectives for improving patient survival and treatment outcomes. Conventional techniques cannot meet this demand because of the low sensitivity, low specificity, poor spatial resolution, shallow penetration, and/or ionizing radiation. Here we overcome such limitations by combining high-resolution photoacoustic tomography (PAT) with extraordinarily optical absorbing gold nanocages (AuNCs). When bioconjugated with [Nle(4),D-Phe(7)]-alpha-melanocyte-stimulating hormone, the AuNCs can serve as a novel contrast agent for in vivo molecular PAT of melanomas with both exquisite sensitivity and high specificity. The bioconjugated AuNCs enhanced contrast approximately 300% more than the control, PEGylated AuNCs. The in vivo PAT quantification of the amount of AuNCs accumulated in melanomas was further validated with inductively coupled plasma mass spectrometry (ICP-MS).
Mammalian keratin gene families: organisation of genes coding for the B2 high-sulphur proteins of sheep wool (1983)

We have isolated two genomic clones containing three B2 high-sulphur keratin genes from a sheep genomic library constructed in Charon 4A. These genes do not contain intervening sequences. Two genes, encoding the B2A and B2D proteins are closely linked in the genome, being separated by 1.9 kb, and are transcribed in the same direction. Although there is extensive sequence conservation in the 5' non-coding and coding regions, the 3' non-coding regions diverge both in length and sequence. Within the 5' non-coding region adjacent to the initiating AUG there is a highly conserved 18 bp sequence which is also present in another gene coding for a member of a different, unrelated high-sulphur keratin family. In the B2A-B2D intergene region, tightly linked to the B2D gene, there is a putative, divergently transcribed gene.
Real-Time Impedance Assay to Follow the Invasive Activities of Metastatic Cells in Culture (2002)

Here we present research detecting the invasive activities of metastatic cells in vitro using electric cell-substrate impedance sensing (ECIS). The assay is based on previous microscopic observations, where metastatic cells added over established endothelial cell layers were observed to attach to and invade the cell layer. Human umbilical vein endothelial cells (HUVECs) werefirst grown to confluence on small gold electrodes. The impedance of these electrodes was followed after the addition of suspensions of different sublines of the Dunning murine prostatic adenocarcinoma series (G, AT1, AT2, AT3, ML, and MLL). For highly metastatic sublines, within an hour after being challenged, the impedance of the confluent HUVEC layer was substantially reduced. The effect of the weakly metastatic sublines was less pronounced, and the extent and the rate of this drop in impedance could be correlated with the metastatic potential of each of six sublines tested. The real-time assay is effective in both normal and low (1%) serum concentrations, and the detected activity requires the presence of viable transformed cells. In addition to the murine cell lines, similar behavior was observed using four established human prostatic cancer lines (DU145, PC3, TSU, and PPC1). These results suggest that this ECIS-based assay might be used with primary human cultures to establish the metastatic abilities of cells isolated from biopsies.
Inhibition of Platelet-Collagen Interaction by Propolypeptide of von Willebrand Factor (1989)

A collagen-binding glycoprotein was isolated from human platelets using affinity chromatography of immobilized collagen. Based upon characterizations of this protein we confirmed that it was identical to the propolypeptide of von Willebrand factor (pp-vWF), which is also called von Willebrand antigen II. The characteristics we have investigated are molecular weight, existence of carbohydrate chains, and the NH2-terminal amino acid sequence. pp-vWF has strong affinity to collagen and inhibits collagen-induced aggregation of human platelets at a concentration as low as 2 micrograms/ml even in the presence of plasma. This inhibitory effect is specific for collagen-induced aggregation since it does not inhibit aggregation of platelets induced by other agonists such as ADP, arachidonic acid, platelet-activating factor, ionophore A23187, and ristocetin. As pp-vWF is quickly released from platelets upon activation by various agonists, it is possible that pp-vWF functions as a repressor for excess platelet aggregation induced by collagen and constitutes a negative feed-back mechanism. Considering the fact that mature vWF supports platelet adhesion to subendothelium, present observations suggest that the propeptide portion and the mature protein could have opposing effects on hemostasis.
A Systematic Review of Studies That Aim to Determine Which Outcomes to Measure in Clinical Trials in Children (2008)

Very few studies address the appropriate choice of outcomes for clinical research with children, and in most paediatric specialties no research has been undertaken. Among the studies we did assess, very few involved parents or children in selecting outcomes that should be measured, and none directly involved children. Research should be undertaken to identify the best way to involve parents and children in assessing which outcomes should be measured in clinical trials.
Incorporation of adenovirus into a ligand-based DNA carrier system results in retention of original receptor specificity and enhances targeted gene expression (1994)

Adenovirus type 5 was modified by coupling an asialoglycoprotein-polylysine conjugate to the virus by reactions that activate carbohydrate residues. Wild-type virus modified in this manner had greatly decreased infectivity toward normally susceptible HeLa S3 (asialoglycoprotein receptor (-)) and SK Hep1 (asialoglycoprotein receptor (-)) cells leaving 91 and 86% viable, respectively, after 48 h. However, with Huh 7 (asialoglycoprotein receptor (+)) cells, modified virus retained its infectivity leaving only 19% of cells viable under identical conditions. Modified virus was complexed to DNA in the form of a plasmid, pSVHBV surf, containing the gene for hepatitis B surface antigen as a marker of gene expression. Huh 7, receptor (+), cells treated with modified wild type, and modified replication-defective d1312 virus complexed to DNA raised antigen levels by approximately 13- and 30-fold, respectively, compared with asialoglycoprotein-polylysine DNA complex alone. Competition with a large excess of an asialoglycoprotein blocked the enhancement by more than 95%. Using a beta-galactosidase marker gene, the number of cells transfected by modified virus was found to be 200-fold higher than complex alone. Yet, specificity was retained exclusively for asialoglycoprotein receptor-bearing cells. These data indicate that adenovirus can be chemically modified by coupling ligands resulting in targeted gene expression dictated specifically by receptor recognition of the attached ligand.