gebhart/patrepeval huggingface dataset:
Truncations in CCND1 mRNA 3′ UTR Alters microRNA Regulation in Mantle Cell Lymphoma. (2007)

Abstract Mantle Cell Lymphoma (MCL) represents only 5–10% of all non-Hodgkins lymphomas, making it an uncommon but difficult form of lymphoma to treat. It has a poor prognosis among the B cell lymphomas with median survival of three years. The genetic hallmark of MCL is the t(11,14) translocation causing amplification of cyclin D1 (CCND1), a known cell cycle regulator which is overexpressed in many other cancers. MicroRNAs (miRNA) are a new class of abundant small RNAs that play important regulatory roles at the post transcriptional level. They act by binding to the 3′ untranslated region (UTR) of mRNAs and block either their translation or initiate their degradation. Recent reports have shown truncations in the CCND1 3′ UTR occur in MCL and indicate a worse prognosis. We hypothesized that truncations in 3′ UTR of CCND1 alter it’s regulation by microRNAs. Based on bioinformatics, we identified microRNA 16 with putative docking sites in the 3′UTR of CCND1. Mir-16 has been implicated as a cell cycle regulator. We identified 2 cell lines (Jeko-1 and Z138) with truncations in CCND1 3′ UTR and demonstrated increased CCND1 mRNA expression by qRT-PCR, increased protein expression by western blot, and higher proliferative potential by cell cycle. We prepared a reporter construct by ligating the full length 3′ UTR of CCND1 to GFP. We then co-transfected this construct with mimics of mir-16 into a cancer cell line and demonstrated downregulation of CCND1 protein expression by flow cytometry. In the MCL cell line Granta-519 with non-truncated CCND1, transfection with mimics of mir-16 deminstrated decreased expression of CCND1 mRNA. These studies suggest that the overexpression of CCDN1 In MCL may result from altered regulation of gene expression from loss of a miRNA regulatory site and may give new clues into the patho-biology of this disease and insights into possible new therapies.
Protein immobilization techniques for microfluidic assays (2013)

Microfluidic systems have shown unequivocal performance improvements over conventional bench-top assays across a range of performance metrics. For example, specific advances have been made in reagent consumption, throughput, integration of multiple assay steps, assay automation, and multiplexing capability. For heterogeneous systems, controlled immobilization of reactants is essential for reliable, sensitive detection of analytes. In most cases, protein immobilization densities are maximized, while native activity and conformation are maintained. Immobilization methods and chemistries vary significantly depending on immobilization surface, protein properties, and specific assay goals. In this review, we present trade-offs considerations for common immobilization surface materials. We overview immobilization methods and chemistries, and discuss studies exemplar of key approaches-here with a specific emphasis on immunoassays and enzymatic reactors. Recent "smart immobilization" methods including the use of light, electrochemical, thermal, and chemical stimuli to attach and detach proteins on demand with precise spatial control are highlighted. Spatially encoded protein immobilization using DNA hybridization for multiplexed assays and reversible protein immobilization surfaces for repeatable assay are introduced as immobilization methods. We also describe multifunctional surface coatings that can perform tasks that were, until recently, relegated to multiple functional coatings. We consider the microfluidics literature from 1997 to present and close with a perspective on future approaches to protein immobilization.
Service Fading of Disperse Dyestuffs by Chemical Agents Other than the Oxides of Nitrogen (1955)

An extensive trial of acetate drapery fabrics dyed with new "gas-fast" blues has shown that active agents in the atmosphere, in addition to the oxides of nitrogen, can cause fading in service. This fading is oxidative in nature. It has been reproduced by an accelerated laboratory test in which fabrics have been exposed to concentrations of ozone somewhat higher than those ordinarily found in the atmosphere. This type of fading has been designated as "O-fading." All of the disperse blue dyes and some of the reds and yellows have been found to be subject to O-fading. However, the major problem is with the blues. Anthraquinone blues are bleached by O-fading without the reddening associated with gas fading. The O-fading can be inhibited by antioxidants such as the gas-fading inhibitor diphenyl ethylene diamine and the nongas-fading inhibitor p-octyl phenol. For optimum re sistance to both forms of atmospheric fading, acetate fabrics dyed with disperse blues, including gas-fast blues, should be processed with inhibitors. Laboratory tests have shown that O-fading takes place on Dacron 1 as well as on acetate and Arnel. 2 With Arnel and Dacron, a marked increase in resistance to O-fading is obtained on heat treatment. The penetration of the dye into the fiber is a factor in O-fading behavior, as evidenced by the increase in resistance to O-fading of Dacron fabrics dyed with carrier and by the effect of heat treatment. Optimum resistance to atmospheric fading of Arnel is obtained by the use of inhibitor plus heat treatment.
Slc7a9-deficient mice develop cystinuria non-I and cystine urolithiasis (2003)

Cystinuria is a common recessive disorder of renal reabsorption of cystine and dibasic amino acids that results in urolithiasis of cystine. Cystinuria is caused by defects in the amino acid transport system b0,+ (i.e. the rBAT/b0,+AT heteromeric complex). Mutations in SLC3A1, encoding rBAT, cause cystinuria type A, characterized by a silent phenotype in heterozygotes (phenotype I). Mutations in SLC7A9, encoding b0,+AT, cause cystinuria type B, in which heterozygotes in most cases hyperexcrete cystine and dibasic amino acids (phenotype non-I). To facilitate in vivo investigation of b0,+AT in cystinuria, Slc7a9 knockout mice have been generated. Expression of b0,+AT protein is completely abolished in the kidney of Slc7a9-/- mice ('Stones'). In contrast, Stones expressed significant amounts of rBAT protein, which is covalently linked to unidentified light subunit(s). Stones mice present a dramatic hyperexcretion of cystine and dibasic amino acids, while Slc7a9+/- mice show moderate but significant hyperexcretion of these amino acids (phenotype non-I). Forty-two per cent of Stones mice develop cystine calculi in the urinary system. Calculi develop during the first month of life and grow throughout the life span of the animals. Histopathology in kidney reveals typical changes for urolithiasis (tubular and pelvic dilatation, tubular necrosis, tubular hyaline droplets and chronic interstitial nephritis). The fact that some Stones mice, generated in a mixed genetic background, develop cystine calculi from an early age, while others do not develop them in their first year of life, suggests the involvement of modifier genes in the lithiasis phenotype. Thus, Stones provide a valid model of cystinuria which can be used in the study of genetic, pharmacological and environmental factors involved in cystine urolithiasis.
Planar Impedance Standards and Accuracy Considerations in Vector Network Analysis (1986)

An equation is given for theoretical errors in oneport corrected vector S-parameter measurements (in any transmission media). The error analysis is used to investigate parasitics peculiar to planar impedance standards. Experimental results verify the error analysis, and show that parasitics as small as 5 pH are repeatably measurable. Application to GaAsFET measurements through 26 GHz is discussed.
Acoustofluidics 20: Applications in acoustic trapping (2012)

This part of the Acoustofluidics tutorial series reviews applications in acoustic trapping of micron-sized particles and cells in microfluidic systems. Acoustic trapping enables non-invasive and non-contact immobilisation of cells and particles in microfluidic systems. Acoustic trapping has been used for reducing the time needed to create 3D cell clusters, enhance particle-based bioassays and facilitated interaction studies of both cells and particles. An area that is increasingly interesting is the use of acoustic trapping for enriching low concentration samples and the washing or fractioning of cell populations prior to sensitive detection methods (MALDI-MS, PCR etc.) The main focus of the review is systems where particles can be retained against a flow while applications in which particles are positioned in a stationary fluid will be addressed in part 21 of the Acoustofluidics tutorial series (M. Wiklund, S. Radel and J. J. Hawkes, Lab Chip, 2012, 12, DOI: 10.1039/c2lc41073g).
The renal cell carcinoma-associated antigen G250 encodes a human leukocyte antigen (HLA)-A2.1-restricted epitope recognized by cytotoxic T lymphocytes. (1999)

Evidence has accumulated that the immune system can play a significant role in the defense against tumors in humans. Especially melanoma and renal cell carcinoma (RCC) are considered immunogenic tumors. In contrast to melanoma, hardly any RCC-associated antigens have been identified as targets for RCC-reactive T cells. Here, we report the identification of a human leukocyte antigen (HLA)-A2.1-restricted T-cell epitope within the G250 antigen. This antigen is expressed in 85% of RCCs but not by neighboring normal kidney tissue and has recently been molecularly defined and shown to be identical to MN/CA IX. Computer-aided motif prediction revealed the presence of 60 potential HLA-A2.1-binding peptides within the G250 antigen. Subsequent binding analysis showed that 13 of these peptides bound to HLA-A2.1 with high-to-intermediate affinity. Analysis of their immunogenicity in HLA-A2.1Kb transgenic mice indicated that 4 of the 13 peptides gave rise to cytotoxic T lymphocytes (CTLs) capable of lysing peptide-loaded target cells. However, only the G250 peptide 254-262 induced CTLs that recognized target cells that endogenously expressed the G250 antigen. Similarly, we were also able to raise human CTLs against the G250 peptide 254-262, which lysed target cells that endogenously expressed the G250 antigen. These findings and the high prevalence of this antigen in RCC patients makes G250 a potential target for anti-RCC immunotherapy.
Absorption, distribution, metabolism, and excretion of macitentan, a dual endothelin receptor antagonist, in humans (2012)

Macitentan is a tissue-targeting, dual endothelin receptor antagonist, currently under phase 3 investigation in pulmonary arterial hypertension. In this study the disposition and metabolism of macitentan were investigated following administration of a single oral 10 mg dose of (14)C-macitentan to six healthy male subjects. The total radioactivity in matrices was determined using liquid scintillation counting. The proposed structure of metabolites was based on mass spectrometry characteristics and, when available, confirmed by comparison with reference compounds. Mean (± SD) cumulative recovery of radioactivity from faeces and urine was 73.6% (± 6.2%) of the administered radioactive dose, with 49.7% (± 3.9%) cumulative recovery from urine, and 23.9% (± 4.8%) from faeces. In plasma, in addition to parent macitentan, ACT-132577, a pharmacologically active metabolite elicited by oxidative depropylation and the carboxylic acid metabolite ACT-373898 were identified. In urine, four entities were identified, with the hydrolysis product of ACT-373898 as the most abundant one. In faeces, five entities were identified, with the hydrolysis product of macitentan and ACT-132577 as the most abundant one. Concentrations of total radioactivity in whole blood were lower compared to plasma, which indicates that macitentan and its metabolites poorly bind to or penetrate into erythrocytes.
[Rituximab]. (2003)

CHOP has been the standard chemotherapy for aggressive non-Hodgkin's lymphoma (NHL). However, indolent NHL remains largely an incurable diseases, with nearly static overall survival, and only 40% of patients with aggressive NHL are cured by CHOP. Monoclonal antibodies are an exciting advance in the treatment of lymphoma. Rituximab is a mouse/human chimeric monoclonal antibody that targets the CD20 antigen found on the surface of malignant and normal cells of the B-cell lineage, but not on primitive stem cells or mature plasma cells. Rituximab is safe and well-tolerated, and exhibit little cross-resistance with conventional chemotherapeutic agents. Clinical trials with rituximab indicate that the drug has broad application to NHL, although further clarification is needed to determine its optimal use in many of these clinical settings. In indolent NHL, rituximab has shown useful response rates, both as first-line therapy in relapsed disease. In aggressive lymphomas, diffuse large B-cell lymphoma is the most common form, the addition of rituximab to CHOP chemotherapy significantly lengthens disease-free and overall survival compared to CHOP alone as first line therapy, at least in elderly patients. These included combination with chemotherapy, prolonged or increased dosing regimens, and maintenance therapy, in which rituximab is administered to patients in remission to eliminate minimal residual disease and reduce the risk of relapse. Rituximab in vivo purging and maintenance is also being evaluated in autologous transplantation setting. Newer agents, including radiolabelled antibodies, Immunotoxin-linked antibodies and antibodies against novel target antigens are being tested in on-going clinical trial.
Synthesis, Properties, and Design Principles of Donor–Acceptor Nanohoops (2015)

We have synthesized a series of aza[8]cycloparaphenylenes containing one, two, and three nitrogens to probe the impact of nitrogen doping on optoelectronic properties and solid state packing. Alkylation of these azananohoops afforded the first donor-acceptor nanohoops where the phenylene backbone acts as the donor and the pyridinium units act as the acceptor. The impact on the optoelectronic properties was then studied experimentally and computationally to provide new insight into the effect of functionalization on nanohoops properties.
Therapeutic approaches for prion and Alzheimer's diseases (2007)

Alzheimer's and prion diseases belong to a category of conformational neurodegenerative disorders [Prusiner SB (2001) N Eng J Med344, 1516-1526; Sadowski M & Wisniewski T (2007) Curr Pharm Des 13, 1943-1954; Beekes M (2007) FEBS J 274, 575]. Treatments capable of arresting or at least effectively modifying the course of disease do not yet exist for either one of these diseases. Alzheimer's disease is the major cause of dementia in the elderly and has become an ever greater problem with the aging of Western societies. Unlike Alzheimer's disease, prion diseases are relatively rare. Each year only approximately 300 people in the USA and approximately 100 people in the UK succumb to various forms of prion diseases [Beekes M (2007) FEBS J 274, 575; Sigurdsson EM & Wisniewski T (2005) Exp Rev Vaccines 4, 607-610]. Nevertheless, these disorders have received great scientific and public interest due to the fact that they can be transmissible among humans and in certain conditions from animals to humans. The emergence of variant Creutzfeld-Jakob disease demonstrated the transmissibility of the bovine spongiform encephalopathy to humans [Beekes M (2007) FEBS J 274, 575]. Therefore, the spread of bovine spongiform encephalopathy across Europe and the recently identified cases in North America have put a large human population at risk of prion infection. It is estimated that at least several thousand Britons are asymptomatic carriers of prion infections and may develop variant Creutzfeld-Jakob disease in the future [Hilton DA (2006) J Pathol 208, 134-141]. This delayed emergence of human cases following the near elimination of bovine spongiform encephalopathy in the UK may occur because prion disease have a very prolonged incubation period, ranging from months to decades, which depends on the amount of inoculum, the route of infection and the genetic predisposition of the infected subject [Hilton DA (2006) J Pathol 208, 134-141]. Therefore, there is a great need for effective therapies for both Alzheimer's disease and prion diseases.
The Three Human Syntrophin Genes Are Expressed in Diverse Tissues, Have Distinct Chromosomal Locations, and Each Bind to Dystrophin and Its Relatives (1996)

The syntrophins are a biochemically heterogeneous group of 58-kDa intracellular membrane-associated dystrophin-binding proteins. We have cloned and characterized human acidic (alpha 1-) syntrophin and a second isoform of human basic (beta 2-) syntrophin. Comparison of the deduced amino acid structure of the three human isoforms of syntrophin (together with the previously reported human beta 1-syntrophin) demonstrates their overall similarity. The deduced amino acid sequences of human alpha 1- and beta 2-syntrophin are nearly identical to their homologues in mouse, suggesting a strong functional conservation among the individual isoforms, Much like beta 1-syntrophin, human beta 2-syntrophin has multiple transcript classes and is expressed widely, although in a distinct pattern of relative abundance. In contrast, human alpha 1-syntrophin is most abundant in heart and skeletal muscle, and less so in other tissues. Somatic cell hybrids and fluorescent in situ hybridization were both used to determine their chromosomal locations: beta 2-syntrophin to chromosome 16q22-23 and alpha 1-syntrophin to chromosome 20q11.2. Finally, we used in vitro translated proteins in an immunoprecipitation assay to show that, like beta 1-syntrophin, both beta 2- and alpha 1-syntrophin interact with peptides encoding the syntrophin-binding region of dystrophin, utrophin/dystrophin related protein, and the Torpedo 87K protein.
Stretchable, Large‐area Organic Electronics (2010)

Stretchability will significantly expand the application scope of electronics, particularly large-area electronics-displays, sensors, and actuators. If arbitrary surfaces and movable parts could be covered with stretchable electronics, which is impossible with conventional electronics, new classes of applications are expected to emerge. A large hurdle is manufacturing electrical wiring with high conductivity, high stretchability, and large-area compatibility. This Review describes stretchable, large-area electronics based on organic field-effect transistors for applications to sensors and displays. First, novel net-shaped organic transistors are employed to realize stretchable, large-area sensor networks that detect distributions of pressure and temperature simultaneously. The whole system is functional even when it is stretched by 25%. In order to further improve stretchability, printable elastic conductors are developed by dispersing single-walled carbon nanotubes (SWNTs) as dopants uniformly in rubbers. Further, we describe integration of printable elastic conductors with organic transistors to construct a rubber-like stretchable active matrix for large-area sensor and display applications. Finally, we will discuss the future prospects of stretchable, large-area electronics with delineating a picture of the next-generation human/machine interfaces from the aspect of materials science and electronic engineering.
CTL recognition of west Nile virus-infected fibroblasts is cell cycle dependent and is associated with virus-induced increases in class I MHC antigen expression. (1994)

Confluent and non-confluent mouse embryo fibroblast (CMEF and NCMEF) monolayers were infected with West Nile virus (WNV) for 24 hr, and class I major histocompatibility complex antigen (MHC-I) concentrations measured by flow cytometry (FCM). Concentrations on CMEF increased significantly more than on NCMEF. This was not owing to differences in interferon-beta (IFN-beta)-mediated MHC induction, as the IFN-beta quantity secreted by each infected fibroblast was similar in each culture, and IFN-beta-mediated MHC-I induction on NCMEF was greater than on CMEF. Furthermore, despite neutralization of WNV-induced supernatant IFN-beta, CMEF increased MHC-I expression significantly more than NCMEF. Functionally, WNV-infected CMEF were lysed 10-fold better by WNV-specific and allospecific cytotoxic T cells, than infected NCMEF. FCM demonstrated 76% CMEF and 68% NCMEF distributed in G0/G1. This represented G0 in CMEF, and G1 in NCMEF, confirmed by ribonucleotide reductase M1 subunit labelling, where only 20% CMEF was labelled, compared to 84% NCMEF. The possible implications for antiviral immune responses are discussed.
Everest: scaling down peak loads through I/O off-loading (2008)

Bursts in data center workloads are a real problem for storage subsystems. Data volumes can experience peak I/O request rates that are over an order of magnitude higher than average load. This requires significant overprovisioning, and often still results in significant I/O request latency during peaks.In order to address this problem we propose Everest, which allows data written to an overloaded volume to be temporarily off-loaded into a short-term virtual store. Everest creates the short-term store by opportunistically pooling underutilized storage resources either on a server or across servers within the data center. Writes are temporarily off-loaded from overloaded volumes to lightly loaded volumes, thereby reducing the I/O load on the former. Everest is transparent to and usable by unmodified applications, and does not change the persistence or consistency of the storage system. We evaluate Everest using traces from a production Exchange mail server as well as other benchmarks: our results show a 1.4-70 times reduction in mean response times during peaks.
A new pyridine-based 12-membered macrocycle functionalised with different fluorescent subunits; coordination chemistry towards CuII, ZnII, CdII, HgII, and PbII (2004)

The coordination chemistry of the new pyridine-based, N2S2-donating 12-membered macrocycle 2,8-dithia-5-aza-2,6-pyridinophane (L1) towards Cu(II), Zn(II), Cd(II), Hg(II), and Pb(II) has been investigated both in aqueous solution and in the solid state. The protonation constants for L1 and stability constants with the aforementioned metal ions have been determined potentiometrically and compared with those of ligand L2, which contains a N-aminopropyl side arm. The measured values show that Hg(II) in water has the highest affinity for both ligands followed by Cu(II), Cd(II), Pb(II), and Zn(II). For each metal ion considered, 1:1 complexes with L1 have also been isolated in the solid state, those of Cu(II) and Zn(II) having also been characterised by X-ray crystallography. In both complexes L1 adopts a folded conformation and the coordination environments around the two metal centres are very similar: four positions of a distorted octahedral coordination sphere are occupied by the donor atoms of the macrocyclic ligand, and the two mutually cis-positions unoccupied by L1 accommodate monodentate NO3- ligands. The macrocycle L1 has then been functionalised with different fluorogenic subunits. In particular, the N-dansylamidopropyl (L3), N-(9-anthracenyl)methyl (L4), and N-(8-hydroxy-2-quinolinyl)methyl (L5) pendant arm derivatives of L1 have been synthesised and their optical response to the above mentioned metal ions investigated in MeCN/H2O (4:1 v/v) solutions.