gebhart/patrepeval huggingface dataset:
An integrated encyclopedia of DNA elements in the human genome (2020)

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription-factor association, chromatin structure and histone modification. In this overview, the Consortium guides the readers through the project itself, the data and their integrated analyses. Eighty per cent of the human genome now has at least one biochemical function assigned to it. In addition to expanding our understanding of how gene expression is regulated on a genome-wide scale, the newly identified functional elements should help researchers to interpret the results of genome-wide associated studies because many correspond to sites associated with human disease.
NEAT expression is associated with tumor recurrence and unfavorable prognosis in colorectal cancer (2015)

Long noncoding RNAs (lncRNAs) have recently been identified to be involved in various diseases including cancer. NEAT1 is a recently identified lncRNA with its function largely unknown in human malignancy. In the present study, we investigated NEAT1 expression in 239 cases of clinical colorectal cancer specimens and matched normal tissues. Statistical methods were utilized to analyze the association of NEAT1 with clinical features, disease-free and overall survival of patients. Results showed that NEAT1 expression in colorectal cancer was up-regulated in 72.0% (172/239) cases compared with corresponding normal counterparts, and related to tumor differentiation, invasion, metastasis and TNM stage. Kaplan-Meier analysis proved that NEAT1 was associated with both disease-free survival and overall survival of patients with colorectal cancer that patients with high NEAT1 expression tend to have unfavorable outcome. Moreover, cox's proportional hazards analysis showed that high NEAT1 expression was an independent prognostic marker of poor outcome. These results provided the first evidence that the expression of NEAT1 in colorectal cancer may play an oncogenic role in colorectal cancer differentiation, invasion and metastasis. It also proved that NEAT1 may serve as an indicator of tumor recurrence and prognosis of colorectal cancer.
Regulation of dendritic cell activation by microRNA let-7c and BLIMP1 (2013)

Mice with a DC-specific deletion of the transcriptional repressor B lymphocyte-induced maturation protein-1 (Blimp1) exhibit a lupus-like phenotype, secondary to enhanced DC production of IL-6. Here we explored further phenotypic changes in Blimp1-deficient DCs, the molecular mechanism underlying these changes, and their relevance to human disease. Blimp1-deficient DCs exhibited elevated expression of MHC II, and exposure to TLR agonists increased secretion of proinflammatory cytokines. This phenotype reflects enhanced expression of the microRNA let-7c, which is regulated by BLIMP1. Let-7c reciprocally inhibited Blimp1 and also blocked LPS-induced suppressor of cytokine signaling-1 (SOCS1) expression, contributing to the proinflammatory phenotype of Blimp1-deficient DCs. DCs from Blimp1 SLE-risk allele carriers exhibited analogous phenotypic changes, including decreased BLIMP1 expression, increased let-7c expression, and increased expression of proinflammatory cytokines. These results suggest that let-7c regulates DC phenotype and confirm the importance of BLIMP1 in maintaining tolerogenic DCs in both mice and humans.
Antiidiotype antibodies in cancer patients receiving monoclonal antibody to carcinoembryonic antigen. (1988)

The initial 10 patients of a Phase I clinical trial involving multiple injections of murine monoclonal anti-carcinoembryonic antigen (CEA) antibody, NP-2, were studied for the presence in their sera of antiidiotypic antibody. Most patients had advanced gastrointestinal adenocarcinoma and received 1 mg/m2 monoclonal antibody three times weekly, or once a week, resulting in five to 13 injections over 12 to 240 days. Antiidiotype antibody was detected with a blocking radioimmunoassay using [125I]NP-2-F(ab')2 binding to CEA-coated microwells and [125I]NP-4-F(ab')2 as a control antibody. Five out of 10 patients demonstrated 65-96% inhibition of NP-2 binding at 1/20 dilution of serum compared to NP-2 binding in the presence of pretreatment sera. The inhibitory activity was preserved after adsorption over a polyclonal mouse IgG immunoadsorbent whereas exposure to a NP-2 affinity column completely depleted the activity. Specificity testing, including the blocking effect of patient sera on the control antibody NP-4, and interference by the possible presence of circulating NP-2, circulating CEA, and human anti-CEA activity, confirmed that the inhibition observed was specific for NP-2 and was caused by an agent with CEA-like characteristics. Longitudinal studies demonstrated that elevated titers of antiidiotypic antibody appeared later in the course of immunization than did antibody against mouse immunoglobulin. These studies indicate that patients can be sensitized to the idiotype (anti-combining site and/or combining site-related) of monoclonal antibodies to CEA following multiple infusions.
68.2: Color and Flexible Electronic Paper Display using QR‐LPD® Technology (2006)

Abstract We have developed a color and flexible electronic paper display using electronic liquid powder. Novel types of color display either colored powder or color filter are discussed. We have also developed a flexible display with low cost substrate films with a high throughput roll‐to‐roll manufacturing system. These technologies enable QR‐LPD® to be used widely as an electronic paper display.
INHIBITION OF COMPLEMENT-MEDIATED ENDOTHELIAL CELL CYTOTOXICITY BY DECAY-ACCELERATING FACTOR (1991)

Complement plays a major role in hyperacute rejection of discordant xenografts. In immediately vascularized xenografts, such as porcine organs to humans, C activation contributes to triggering of endothelial cell activation and adhesion of leukocytes and platelets to the endothelial cells, which is followed by thrombosis and tissue necrosis. We investigated the potential utility of the membrane-associated inhibitor of C, decay accelerating factor (DAF), in the prevention of C-mediated tissue injury. We used an in vitro model of xenotransplantation consisting of porcine aortic endothelial cells incubated with human serum as the source of xenogeneic natural antibodies and C. Because C inhibitors such as DAF may be relatively species-specific, we tested whether human DAF would incorporate into porcine endothelial cells and function to inhibit cytotoxicity of such cells by human C. We found that purified radiolabeled human DAF incorporated into porcine endothelial cells in a dose-dependent manner and that human DAF very significantly protected the endothelial cells from the cytotoxic effect of human C.
Weak but Uniform Enrichment of the Histone Variant macroH2A1 along the Inactive X Chromosome (2008)

We studied the enrichment and distribution of the histone variant mH2A1 in the condensed inactive X (Xi) chromosome. By using highly specific antibodies against mH2A1 and stable HEK 293 cell lines expressing either green fluorescent protein (GFP)-mH2A1 or GFP-H2A, we found that the Xi chromosome contains approximately 1.5-fold more mH2A1 than the autosomes. To determine the in vivo distribution of mH2A1 along the X chromosome, we used a native chromatin immunoprecipitation-on-chip technique. DNA isolated from mH2A1-immunoprecipitated nucleosomes from either male or female mouse liver were hybridized to tiling microarrays covering 5 kb around most promoters or the entire X chromosome. The data show that mH2A1 is uniformly distributed across the entire Xi chromosome. Interestingly, a stronger mH2A1 enrichment along the pseudoautosomal X chromosome region was observed in both sexes. Our results indicate a potential role for macroH2A in large-scale chromosome structure and genome stability.
Butorphanol: Effects of a Prototypical Agonist-Antagonist Analgesic on κ-Opioid Receptors (2005)

The opioid analgesic, butorphanol (17-cyclobutylmethyl-3,14-dihydroxymorphinan) tartrate is a prototypical agonist-antagonist opioid analgesic agent whose potential for abuse has been the cause of litigation in the United States. With a published affinity for opioid receptors in vitro of 1:4:25 (mu:delta:kappa), the relative contribution of actions at each of these receptors to the in vivo actions of the drug are an issue of active investigation. A body of evidence has been developed which indicates that a substantial selective action of butorphanol on the kappa-opioid receptor mediates the development of tolerance to butorphanol and cross-tolerance to other opioid agonists; to the production of dependence upon butorphanol, particularly in the rodent; and to compensatory alterations in brain opioid receptor-effector systems. This perspective will identify the current state of understanding of the effects produced by butorphanol on brain opioid receptors, particularly on the kappa-opioid receptor subtype, and on the expression of phosphotyrosyl proteins following chronic treatment with butorphanol.
Ultra-high-power quasi-CW monolithic laser diode arrays with high power conversion efficiency (1987)

An optical power output of 134 W from one facet and power conversion efficiencies as high as 49% have been obtained from monolithic AlGaAs laser arrays with 1 cm emitting widths for 150^s pulse widths (quasi-CW operation). The arrays have etched grooves to prevent transverse lasing and amplified spontaneous emission.
Antibody to phosphatidylinositol 4,5-bisphosphate inhibits oncogene-induced mitogenesis. (1988)

The hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) has been shown to be enhanced in cells transformed by some types of oncogenes and tumor viruses, but it is still unknown whether the breakdown of PIP2 plays a role in oncogene-induced cell proliferation. For examination of this problem, monoclonal antibody specifically directed to PIP2 was injected into cells. This antibody bound to endogenous PIP2 and so inhibited its intracellular breakdown. Injection of this antibody into ras-transformed cells cultured in the presence of serum caused reversible and dose-dependent decrease in proliferation and reversion of the cell morphology to that of the normal phenotype. The antibody also inhibited the proliferation of src- and erbB-transformed cells but had no effect on the proliferation of untransformed or myc-transformed cells. These results show that the breakdown of PIP2 is involved in the signaling pathways for mitogenesis in cells transformed by oncogenes such as ras, src, and erbB.
Purinergic Receptor Expression and Cellular Responses to Purinergic Agonists in Human Prostate Cancer Cells (2017)

ATP and adenosine had an antiproliferative effect on PCa cells without affecting their motility, indicating their potential as a novel therapy for PCa.
Axially chiral P-N ligands for the copper catalyzed β-borylation of α,β-unsaturated esters (2009)

The synthesis and resolution of a new axially chiral Quinazolinap ligand are reported. The application of this and other related P-N ligands to the copper catalyzed beta-borylation of alpha,beta-unsaturated esters resulted in conversions of up to 100% and ee values of up to 79%. A diastereomerically pure palladacycle of the new ligand was characterised by X-ray crystallography.
A Neuro-behavioral Test and Algorithms for Quantification of Sleepiness and Characterization of Wake-Sleep Transitions (2005)

A neuro-behavioral test has been developed that quantifies sleepiness by means of a convenient and relatively short-duration (15 minute) protocol, and using a class of algorithms that track wake to sleep transitions. Utilizing an ambulatory EEG monitoring combined with an auditory-based vigilance test, this method acquires both behavioral response (i.e., reaction time) and EEG waveforms that are simultaneously analyzed to produce a time-varying EEG-based Drowsiness-Sleepiness Index (DSI). DSI index is computed from the time-varying power spectrum of EEG using an algorithm whose coefficients were determined based on an optimization procedure that maximized the correlation between the time profiles of DSI and those of the behavioral response. Sleepiness is quantified using an algorithm based on the consistency of the neuro-behavioral indices over the test period as well as the degree and profile of their degradation when the subject is incapable of maintaining alertness. This test was administered to 5 volunteers (separate from the subjects whose data were used for the above optimization of DSI) under the conditions of adequate prior night sleep and sleep restriction. Cross correlation analysis showed a close agreement between the time profiles of EEG-based DSI and behavioral response indices. Statistical analysis showed significant difference between the alert and sleepy conditions for the whole group as well as in each individual subject.
Quantum Algorithms for Some Hidden Shift Problems (2006)

Almost all of the most successful quantum algorithms discovered to date exploit the ability of the Fourier transform to recover subgroup structures of functions, especially periodicity. The fact that Fourier transforms can also be used to capture shift structure has received far less attention in the context of quantum computation. In this paper, we present three examples of “unknown shift” problems that can be solved efficiently on a quantum computer using the quantum Fourier transform. For one of these problems, the shifted Legendre symbol problem, we give evidence that the problem is hard to solve classically, by showing a reduction from breaking algebraically homomorphic cryptosystems. We also define the hidden coset problem, which generalizes the hidden shift problem and the hidden subgroup problem. This framework provides a unified way of viewing the ability of the Fourier transform to capture subgroup and shift structure.
FUNCTIONAL INTERCHANGEABILITY OF DNA REPLICATION GENES IN SALMONELLA TYPHIMURIUM AND ESCHERICHIA COLI DEMONSTRATED BY A GENERAL COMPLEMENTATION PROCEDURE (1984)

Twenty-four genes from Salmonella typhimurium that affect DNA replication were isolated from a lambda-Salmonella genomic library by lysogenic complementation of temperature-sensitive mutants of Salmonella or E. coli, using a new plaque complementation assay. The complementing lambda clones, which make red plaques in this assay, and noncomplementing mutant derivatives, which make uncolored plaques, were used to further characterize the temperature-sensitive Salmonella mutants and to establish the functional similarity of E. coli and Salmonella DNA replication genes. For 17 of 18 E. coli mutants representing distinct loci, a Salmonella gene that complemented the mutant was found. This result indicates that single Salmonella replication proteins are able to function in otherwise all E. coli replication complexes and suggests that the detailed properties of Salmonella and E. coli replication proteins are very similar. The other seven Salmonella genes that were cloned were unrelated functionally to any E. coli genes examined. --As an aid to the derivation of chromosomal mutations affecting some of the cloned genes, a general method was developed for placing a transposon in the Salmonella chromosome in a segment corresponding to cloned DNA. Chromosomal mutations were derived in Salmonella affecting a gene (dnaA) that was cloned by complementation of an E. coli mutant by using the transposon-encoded drug resistance as a selectable marker in local mutagenesis.
Peptide Nucleic Acids with a Conformationally Constrained Chiral Cyclohexyl‐Derived Backbone (1997)

Abstract Peptide nucleic acid (PNA) is an achiral nucleic acid mimic with a backbone consisting of partly flexible aminoethyl glycine units. By replacing the aminoethyl portion of the backbone by an amino cyclohexyl moiety, either in the ( S, S ) or the ( R, R ) configuration, we have synthesized conformationally constrained PNA residues. PNA oligomers containing ( S, S )‐cyclohexyl residues were able to form hybrid complexes with DNA or RNA, with little effect on the thermal stability ( T m = 1°C per ( S, S ) unit, depending on their number and the sequence). In contrast, incorporation of the ( R, R ) isomer resulted in a drastic decrease in the stability of the PNA‐DNA (or RNA) complex ( T m = −8°C per ( R, R ) unit). In PNA‐PNA duplexes, however, the ( R, R )‐ and ( S, S )‐cyclohexyl residues only exerted a minor effect on the stability, and the complexes formed with the two isomers are of opposite handedness, as evidenced from circular dichroism spectroscopy. In some cases the introduction of a single ( S, S ) residue in a PNA 15‐mer improves its sequence specificity for DNA or RNA. From the thermal stabilities and molecular modeling based on the solution structure of a PNA‐DNA duplex determined by NMR techniques, we conclude that the right‐handed helix can accommodate the ( S, S ) isomer more easily than the ( R, R ) isomer. Thermodynamic measurements of H and S upon PNA‐DNA duplex formation show that the introduction of an ( S, S )‐cyclohexyl unit in the PNA does indeed decrease the entropy loss, indicating a more conformationally constrained structure. However, the more favorable entropic contribution is balanced by a reduced enthalpic gain, indicating that the structure constrained by the cyclohexyl group is not so well suited for DNA hybridization.
Crosstalk-enhanced polymer digital optical switch based on a W-shape (2000)

A three branch digital optical switch in polymers with a crosstalk of -30 dB is presented. Its crosstalk is insensitive to increasing heat power, which is the main advantage to ordinary DOS.
Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions. (1992)

The RuvA, RuvB, and RuvC proteins of Escherichia coli are required for the recombinational repair of ultraviolet light- or chemical-induced DNA damage. In vitro, RuvC protein interacts with Holliday junctions in DNA and promotes their resolution by endonucleolytic cleavage. In this paper, we investigate the interaction of RuvA and RuvB proteins with model Holliday junctions. Using band-shift assays, we show that RuvA binds synthetic Holliday structures to form specific protein-DNA complexes. Moreover, in the presence of ATP, the RuvA and RuvB proteins act in concert to promote dissociation of the synthetic Holliday structures. The dissociation reaction requires both RuvA and RuvB and a nucleotide cofactor (ATP or dATP) and is rapid (40% of DNA molecules dissociate within 1 min). The reaction does not occur when ATP is replaced by either ADP or the nonhydrolyzable analog of ATP, adenosine 5'-[gamma-thio]triphosphate. We suggest that the RuvA and RuvB proteins play a specific role in the branch migration of Holliday junctions during postreplication repair of DNA damage in E. coli.
DRM renewability & interoperability (2004)

Current digital rights management systems employ proprietary methods to protect contents. Hence, they are incapable of interoperation with each other. This causes great inconvenience for users who want to subscribe to contents from different providers. We introduce a new, intellectual property management & protection method (IPMP extension), which enables users to enjoy content services delivered from different providers which are based on individual content protection mechanisms. The method is proposed to ISO/IEC JTC1/SC29/WG11 (MPEG) and the standardization is in the final stage. IPMP is also proposed to DVB-CPT (digital video broadcasting-copy protection technologies). TV Anytime Forum ISMA (Internet Streaming Media Alliance) have adopted IPMP in the ISMA1.0 Encryption & Authentication specification.
Needle insertion into soft tissue: A survey (2006)

Needle insertion in soft tissue has attracted considerable attention in recent years due to its application in minimally invasive percutaneous procedures such as biopsies and brachytherapy. This paper presents a survey of the current state of research on needle insertion in soft tissue. It examines the topic from several aspects, e.g. modeling needle insertion forces, modeling tissue deformation and needle deflection during insertion, robot-assisted needle insertion, and the effect of different trajectories on tissue deformation. All studies show that the axial force of a needle during insertion in soft tissue is the summation of different forces distributed along the needle shaft such as stiffness force, frictional force and cutting force. Some studies have modeled these forces. The force data in some procedures is used for identifying tissue layers as the needle is inserted or for path planning. Needle deflection and tissue deformation are major problems for accurate needle insertion and attempts have been made to model them. Using current models several insertion techniques have been developed which are briefly reviewed in this paper.
ExPASy: the proteomics server for in-depth protein knowledge and analysis (2003)

The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.
Cancer-Specific Synthetic Lethality between ATR and CHK1 Kinase Activities (2015)

ATR and CHK1 maintain cancer cell survival under replication stress and inhibitors of both kinases are currently undergoing clinical trials. As ATR activity is increased after CHK1 inhibition, we hypothesized that this may indicate an increased reliance on ATR for survival. Indeed, we observe that replication stress induced by the CHK1 inhibitor AZD7762 results in replication catastrophe and apoptosis, when combined with the ATR inhibitor VE-821 specifically in cancer cells. Combined treatment with ATR and CHK1 inhibitors leads to replication fork arrest, ssDNA accumulation, replication collapse, and synergistic cell death in cancer cells in vitro and in vivo. Inhibition of CDK reversed replication stress and synthetic lethality, demonstrating that regulation of origin firing by ATR and CHK1 explains the synthetic lethality. In conclusion, this study exemplifies cancer-specific synthetic lethality between two proteins in the same pathway and raises the prospect of combining ATR and CHK1 inhibitors as promising cancer therapy.