gebhart/patrepeval huggingface dataset:
New multivalent cationic lipids reveal bell curve for transfection efficiency versus membrane charge density: lipid–DNA complexes for gene delivery (2005)

Abstract Background Gene carriers based on lipids or polymers—rather than on engineered viruses—constitute the latest technique for delivering genes into cells for gene therapy. Cationic liposome–DNA (CL‐DNA) complexes have emerged as leading nonviral vectors in worldwide gene therapy clinical trials. To arrive at therapeutic dosages, however, their efficiency requires substantial further improvement. Methods Newly synthesized multivalent lipids (MVLs) enable control of headgroup charge and size. Complexes comprised of MVLs and DNA have been characterized by X‐ray diffraction and ethidium bromide displacement assays. Their transfection efficiency (TE) in L‐cells was measured with a luciferase assay. Results Plots of TE versus the membrane charge density (σ M , average charge/unit area of membrane) for the MVLs and monovalent 2,3‐dioleyloxypropyltrimethylammonium chloride (DOTAP) merge onto a universal, bell‐shaped curve. This bell curve leads to the identification of three distinct regimes, related to interactions between complexes and cells: at low σ M , TE increases with increasing σ M ; at intermediate σ M , TE exhibits saturated behavior; and unexpectedly, at high σ M , TE decreases with increasing σ M . Conclusions Complexes with low σ M remain trapped in the endosome. In the high σ M regime, accessible for the first time with the new MVLs, complexes escape by overcoming a kinetic barrier to fusion with the endosomal membrane (activated fusion), yet they exhibit a reduced level of efficiency, presumably due to the inability of the DNA to dissociate from the highly charged membranes in the cytosol. The intermediate, optimal regime reflects a compromise between the opposing demands on σ M for endosomal escape and dissociation in the cytosol. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Non-fouling properties of polysaccharide-coated surfaces (1999)

Hyaluronic acid and alginic acid, examples of hydrophilic polysaccharides whose biological and technological properties are deeply related to strong interaction with water, have been coupled to substrate surfaces. These coatings can prevent mammalian cells adhesion and greatly reduce bacterial cells adhesion in vitro and in several in vivo applications. The anti-adhesive properties of these surfaces are discussed in terms of the surface fractional coverage by the polysaccharide, as evaluated by XPS analysis and water contact angle. The implications of chemical-molecular considerations to the properties of these coatings are discussed from an analytical and mechanistic point of view.
Mode of delivery is not associated with asthma or atopy in childhood (2004)

Delivery by caesarean section was not associated with the subsequent development of asthma, wheezing or atopy in later childhood in this population.
Helix Dipole Movement and Conformational Variability Contribute to Allosteric GDP Release in GαiSubunits, (2009)

Heterotrimeric G proteins (Galphabetagamma) transmit signals from activated G protein-coupled receptors (GPCRs) to downstream effectors through a guanine nucleotide signaling cycle. Numerous studies indicate that the carboxy-terminal alpha5 helix of Galpha subunits participates in Galpha-receptor binding, and previous EPR studies suggest this receptor-mediated interaction induces a rotation and translation of the alpha5 helix of the Galpha subunit [Oldham, W. M., et al. (2006) Nat. Struct. Mol. Biol. 13, 772-777]. On the basis of this result, an engineered disulfide bond was designed to constrain the alpha5 helix of Galpha(i1) into its EPR-measured receptor-associated conformation through the introduction of cysteines at position 56 in the alpha1 helix and position 333 in the alpha5 helix (I56C/Q333C Galpha(i1)). A functional mimetic of the EPR-measured alpha5 helix dipole movement upon receptor association was additionally created by introduction of a positive charge at the amino terminus of this helix, D328R Galpha(i1). Both proteins exhibit a dramatically elevated level of basal nucleotide exchange. The 2.9 A resolution crystal structure of I56C/Q333C Galpha(i1) in complex with GDP-AlF(4)(-) reveals the shift of the alpha5 helix toward the guanine nucleotide binding site that is anticipated by EPR measurements. The structure of the I56C/Q333C Galpha(i1) subunit further revealed altered positions for the switch regions and throughout the Galpha(i1) subunit, accompanied by significantly elevated crystallographic temperature factors. Combined with previous evidence in the literature, the structural analysis supports the critical role of electrostatics of the alpha5 helix dipole and overall conformational variability during nucleotide release.
Identification of important residues within the putative nucleoside binding site of HSV-1 thymidine kinase by random sequence selection: Analysis of selected mutants in vitro (1993)

Random sequence mutagenesis in conjunction with genetic complementation was used to map the function of amino acid residues within the putative nucleoside binding site of the herpes simplex virus type 1 (HSV-1) thymidine kinase (TK). Six codons of the putative nucleoside binding site of the HSV-1 tk were substituted by a duplex of extended oligonucleotides containing 20% random sequences. Approximately 260 mutants were screened for the ability to genetically complement a TK-deficient Escherichia coli. Of those screened, 32% conferred TK activity. Approximately 60% of the TK positive clones contained single amino acid changes, 23% contained double changes, and 13.4% encoded the wild-type TK amino acid sequence. A small percentage of clones, 2.4% and 1.2%, contained triple or quadruple alterations, respectively. Three residues (D162, H163, and R164) appeared to be highly conserved especially with regard to the type of residues able to substitute. Secondary screening results indicated that several of the mutants had higher affinities for acyclovir and/or 3'-azido-3'-deoxythymidine than thymidine in complementation assays. In addition, a number of clones were unable to form colonies on selection medium at elevated temperatures (42 degrees C). Eight selected mutants were subcloned into an in vitro transcription vector and the derived transcripts used to program a rabbit reticulocyte lysate cell-free translation system. Biologically active translation products were then analyzed in vitro for thymidine kinase activity, for thermal stability, and for the ability to phosphorylate selected nucleoside analogues. Two of the eight mutants had an elevated thymidine kinase activity, two were significantly thermolabile, and three exhibited enhanced efficiency in phosphorylation of nucleoside analogues.
Role of the Insulin-like Growth Factor System in Adrenocortical Growth Control and Carcinogenesis (2004)

Clinically silent adrenocortical adenomas are the most frequent abnormalities in the adrenal gland. In contrast, adrenocortical carcinoma is a rare tumor with an extremely poor prognosis. The factors responsible for the frequent occurrence of benign adrenocortical tumors on one hand and the rare malignant transformation on the other are not known. Several genetic alterations such as loss of imprinting or loss of heterozygosity of the 11p15 gene locus causing a strong IGF-II overexpression have been demonstrated in the majority of adrenocortical carcinomas. In addition to IGF-II overexpression, increased levels of the IGF-I-receptor and IGFBP-2 have been found in advanced human adrenocortical carcinomas, suggesting an important role for the IGF-system in adrenocortical carcinogenesis. IGFs are potent mitogens regulating growth and apoptosis through interaction with the IGF-I-receptor, and overexpression of the human IGF-I-receptor promotes ligand-dependent neoplastic transformation in a variety of different cell systems. It is evident, therefore, that high levels of IGF-II in combination with overexpression of the IGF-I-receptor can provide a significant growth advantage for adrenocortical carcinoma cells and thus contribute to the highly malignant phenotype of this rare type of cancer. Additionally, it has been shown that overexpression of IGFBP-2 can promote malignant transformation of Y1 mouse adrenocortical tumor cells through unknown IGF-independent mechanisms. As one possible mechanism, we have recently found altered expression of catalase in IGFBP-2-overexpressing tumor cells, thus implicating IGFBP-2 in influencing intracellular peroxide levels. However, since transgenic mice with IGF-II or IGFBP-2 overexpression in the adrenal gland do not show an increased frequency of adrenal tumors, IGF-II or IGFBP-2 may act as progression factors but not as initiation factors in adrenocortical tumorigenesis.
Insights into the aetiology and pathogenesis of multiple sclerosis (1998)

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system, and the most common neurological disease affecting young adults. Multiple sclerosis is a clinically heterogeneous disorder. It is believed to be an autoimmune disease, with cell-mediated and humoral responses directed against myelin proteins. This hypothesis largely comes from pathological parallels with an animal model, experimental autoimmune encephalomyelitis (EAE). Autoimmunity to myelin proteins in humans may be inadvertently triggered by microbes which have structural homologies with myelin antigens (molecular mimicry). As with other autoimmune diseases, susceptibility to MS is associated with certain MHC genes/haplotypes. Full genomic screening of mutiplex families has underscored the role for MHC genes as exerting moderate but the most significant effects in susceptibility. The primary target autoantigen in MS has yet to be definitively identified, but as well as the major myelin proteins, it is now clear that minor myelin components, such as myelin oligodendrocyte glycoprotein (MOG) may play a primary role in disease initiation. This review examines the current knowledge about the aetiology and pathogenesis of MS, and the important similarities with EAE. A better understanding of the molecular mechanisms of autoimmune pathology will provide the basis for more rational immunotherapies to treat MS.
Effects of heterologous hematopoietic cytokines on in vitro differentiation of cultured porcine inner cell masses (1996)

An exogenous supply of hematopoietic cytokines is essential for maintaining murine embryonic stem (ES) cells in a proliferative yet undifferentiated state. Recently, it was demonstrated that hematopoietic cytokines utilize the gp130 signal transduction pathway to maintain this phenotype, although their involvement toward maintaining porcine ES cell pluripotency has not been established. Therefore, the objective of this study was to determine the effectiveness of several heterologous hematopoietic cytokines at maintaining the isolated porcine inner cell masses (pICM) in an undifferentiated state. pICMs (day 7) were isolated by immunosurgery and cultured 4 days in one of six treatments: control medium, human leukemia inhibitory factor (hLIF; 1,000 mu/ml), human interleukin-6 (hIL-6; 100 ng/ml), hIL-6 + hIL-6 soluble receptor (hIL6 + sR; 100 ng/ml + 2.5 micrograms/ml), human oncostatin M (hOSM; 100 ng/ml), or rat ciliary neurotrophic factor (rCNTF; 100 ng/ml). All cytokines were prepared in Dulbecco's Modified Eagle's Medium/Ham's F-10 (1:1)-based medium. Morphology of pICMs was evaluated on a scale of 1 (fully undifferentiated) to 5 (fully differentiated) at 24-h intervals. Differentiation was significantly lower on day 2 for rCNTF vs. hLIF cultured pICMs (2.07 +/- 0.15 vs. 2.70 +/- 0.16; P < 0.05). Furthermore, addition of rCNTF gave the lowest overall mean differentiation score (2.53 +/- 0.15). However, none of the cytokines significantly delayed differentiation over controls for the 4-day culture period (P > 0.05). Since these heterologous cytokines were unable to inhibit differentiation, it is unlikely they will be beneficial towards isolating porcine ES cell lines under current conditions. Future work with homologous cytokines and dose effects may prove more beneficial.
High-density Hapten Labeling and HRP Conjugation of Oligonucleotides for Use as In Situ Hybridization Probes to Detect mRNA Targets in Cells and Tissues (2000)

Oligonucleotides that carry a detectable label can be used to probe for mRNA targets in in situ hybridization experiments. Oligonucleotide probes (OPs) have several advantages over cDNA probes and riboprobes. These include the easy synthesis of large quantities of probe, superior penetration of probe into cells and tissues, and the ability to design gene- or allele-specific probes. One significant disadvantage of OPs is poor sensitivity, in part due to the constraints of adding and subsequently detecting multiple labels per oligonucleotide. In this study, we compared OPs labeled with multiple detectable haptens (such as biotin, digoxigenin, or fluorescein) to those directly conjugated with horseradish peroxidase (HRP). We used branching phosphoramidites to add from two to 64 haptens per OP and show that in cells, 16-32 haptens per OP give the best detection sensitivity for mRNA targets. OPs were also made by directly conjugating the same oligonucleotide sequences to HRP. In general, the HRP-conjugated OPs were more sensitive than the multihapten versions of the same sequence. Both probe designs work well both on cells and on formaldehyde-fixed, paraffin-embedded tissues. We also show that a cocktail of OPs further increases sensitivity and that OPs can be designed to detect specific members of a gene family. This work demonstrates that multihapten-labeled and HRP-conjugated OPs are sensitive and specific and can make superior in situ hybridization probes for both research and diagnostic applications.
Arthroscopic bankart repair in a high demand patient population (1997)

In this prospective study, 40 consecutive patients identified as high risk for recurrent instability were managed by an arthroscopic Bankart repair using nonabsorbable sutures and anchors. The technique employed is an arthroscopic modification of the capsulolabral repair described by Jobe. One-and-one-half to 3 years postoperatively (average 30 months), 37 of the 40 patients (93%) remained stable. The average Bankart score was 90. Thirty-seven of the 40 patients returned to normal activities, including sports, by 6 months postoperatively. Twenty-nine of the 32 patients involved in athletic activities returned to their respective sports at the same or higher level. Three patients had discontinued sporting activities due to graduation but felt as though they could resume their activities at the same level. Three patients developed recurrent instability, all of whom required surgical restabilization. Arthroscopic Bankart Repair using suture anchor technique in a high demand population provided results superior to those previously reported with the suture punch technique in our patient population. The results may be equivalent to open reconstruction in this high-risk patient population.
ABCs of Natriuretic Peptides: Growth (2007)

&lt;i&gt;Background:&lt;/i&gt; Although they are better known for their cardiovascular and antiproliferative effects, natriuretic peptides also have been found to produce skeletal overgrowth in transgenic rodents. This finding has unmasked a novel paracrine role in endochondral bone growth for this family of hormones. Genetic studies in which key components in the C-type natriuretic peptide (CNP) signaling pathway are disrupted or overexpressed and spontaneous mutations in the CNP receptor in humans indicate that CNP plays a crucial role in determining postnatal skeletal elongation. CNP appears to promote expansion within several areas of the growth plate, but its effects are most obvious in the hypertrophic zone. Since its actions are largely paracrine in nature, new approaches are needed to study CNP’s role in vivo. CNP itself degrades rapidly, but amino-terminal pro-CNP (NT pro-CNP) escapes rapid degradation and can be readily detected in plasma. &lt;i&gt;Methodology:&lt;/i&gt; Studies have been made of changes in CNP synthesis in humans and sheep by measuring NT pro-CNP levels. Plasma NT pro-CNP levels are markedly elevated in newborns, but fall progressively as growth velocity declines in both children and lambs. In keeping with these growth-related changes, CNP levels are inhibited by glucocorticoids and malnutrition in lambs and are stimulated by growth hormone and testosterone in adolescent boys. Further, levels fall abruptly in children receiving growth-suppressing chemotherapy regimens. &lt;i&gt;Conclusions:&lt;/i&gt; Plasma NT pro-CNP levels may be an indicator of CNP synthesis within skeletal tissues and provide a much needed biomarker of linear growth, with applications for diagnosis and management of growth disorders.
ROAD WEATHER INFORMATION SYSTEM ENVIRONMENTAL SENSOR STATION SITING GUIDELINES (2005)

A Road Weather Information System (RWIS) consists of the hardware, software, and communications interfaces necessary to collect and transfer road weather observations from or near the roadway to a display device at the user's location. While the original purpose of RWIS was to address winter weather conditions, applications have been developed to detect and monitor a variety of road weather conditions impacting road operations and maintenance. Most RWISs now consist of several meteorological and pavement condition monitoring stations strategically located near highways to help transportation managers make more informed operational decisions. An Environmental Sensor Station (ESS) is considered the collection component of an RWIS and consists of the equipment and sensors installed within or along a roadway. This document provides guidelines for siting an RWIS ESS and its associated environmental and pavement sensors. These guidelines are intended to help establish uniformity in siting ESSs and to improve the usefulness of road weather information derived from ESS observations. The document provides siting criteria that satisfy as many road weather monitoring, detection, and prediction requirements as possible. The siting criteria are based on an analysis of published documents on the siting of weather and pavement sensors, and the results of interviews with nearly two dozen road weather experts representing state departments of transportation, equipment suppliers, and consultants. The recommendations encourage uniformity in ESS siting and in the application of the road weather observations. Many of the recommended criteria include a range of values. These values reflect both the complexity of the roadway environment and the need for additional research. The guidelines recommend that siting decisions be made by a team of transportation operations, road maintenance, and weather experts. The siting guidelines contained in this document do not represent standards for agencies or vendors to follow, but rather a set of recommendations to consider.
Clonal expansion of melan a-specific cytotoxic T lymphocytes in a melanoma patient responding to continued immunization with melanoma-associated peptides (2000)

Peptides derived from human tumor antigens have been used in a number of clinical trials to induce specific immune responses against autologous tumors in cancer patients. Although favorable clinical results were observed in single patients, immune responses correlating with tumor regression were either not detected or in case of responses, the T-cell specificity was difficult to demonstrate. In this study, we analyzed antigen-specific T-cell responses induced in the skin and in peripheral blood lymphocytes (PBL) in an HLA-A2-positive melanoma patient. The patient showed major regression of metastatic melanoma under continued immunization with peptides derived from the melanocyte differentiation antigens Melan A/MART-1, tyrosinase and gp100/Pmel17. Based on the identification of different T-cell receptor (TCR) families reactive with Melan A/MART-1, we have demonstrated that i.d. immunization with peptides alone leads to oligoclonal expansion of Melan A/MART-1-specific cytotoxic T lymphocytes (CTL), detectable in local delayed-type hypersensitivity (DTH) reactions and PBL. A monoclonal expansion of a Melan A/MART-1-specific TCR VB 16 CTL was reproducibly observed after in vitro stimulation with Melan A/MART-1 peptides. The same TCR VB 16 CTL clone was detected in skin biopsies taken from vitiligo areas. Our findings provide strong evidence for the effective induction of specific T-cell responses to Melan A/MART-1 by i.d. immunization with peptide alone, which accounts for dermal depigmentation, specific cytotoxicity against Melan A/MART-1-expressing melanoma cells and clinical tumor regression.
Tracheal Climate in Laryngectomees after Use of a Heat and Moisture Exchanger (2005)

The results indicate that short-term use of the HME Prim-Air system rapidly changes the tracheal climate. The significant increase in tracheal temperature and humidity may have beneficial effects on tracheal dryness in laryngectomized patients.
Ultra‐compact silicon nanophotonic modulator with broadband response (2012)

Abstract Electro‐optic modulators have been identified as the key drivers for optical communication and signal processing. With an ongoing miniaturization of photonic circuitries, an outstanding aim is to demonstrate an on‐chip, ultra‐compact, electro‐optic modulator without sacrificing bandwidth and modulation strength. While silicon‐based electro‐optic modulators have been demonstrated, they require large device footprints of the order of millimeters as a result of weak non‐linear electro‐optical properties. The modulation strength can be increased by deploying a high‐Q resonator, however with the trade‐off of significantly sacrificing bandwidth. Furthermore, design challenges and temperature tuning limit the deployment of such resonance‐based modulators. Recently, novel materials like graphene have been investigated for electro‐optic modulation applications with a 0.1 dB per micrometer modulation strength, while showing an improvement over pure silicon devices, this design still requires device lengths of tens of micrometers due to the inefficient overlap between the thin graphene layer, and the optical mode of the silicon waveguide. Here we experimentally demonstrate an ultra‐compact, silicon‐based, electro‐optic modulator with a record‐high 1 dB per micrometer extinction ratio over a wide bandwidth range of 1 μm in ambient conditions. The device is based on a plasmonic metal‐oxide‐semiconductor (MOS) waveguide, which efficiently concentrates the optical modes’ electric field into a nanometer thin region comprised of an absorption coefficient‐tuneable indium‐tin‐oxide (ITO) layer. The modulation mechanism originates from electrically changing the free carrier concentration of the ITO layer which dramatically increases the loss of this MOS mode. The seamless integration of such a strong optical beam modulation into an existing silicon‐on‐insulator platform bears significant potential towards broadband, compact and efficient communication links and circuits.