gebhart/patrepeval huggingface dataset:
Negative Interaction between the RelA(p65) Subunit of NF-κB and the Progesterone Receptor (1996)

Interactions between transcription factors are an important means of regulating gene transcription. The present study describes the mutual repression of two transcription factors, the RelA(p65) subunit of NF-kappaB and the progesterone receptor (PR). This trans-repression is shown to occur independent of PR isoform, reporter construct, or cell type used. Together with the demonstration of an interaction between PR and RelA in vitro, these findings suggest that the mutual repression is due to a direct interaction between these proteins. Furthermore, activation of NF-kappaB by tumor necrosis factor-alpha also results in repression of PR, while PR is able to repress tumor necrosis factor-alpha-induced NF-kappaB activity. Since NF-KB-regulating cytokine receptors are expressed in progesterone target tissues, like breast and endometrium, the mutual repression of PR and RelA could play an important role in a wide variety of physiological processes in these tissues, including maintenance of pregnancy, immunosuppression, and tumorigenesis.
Early death after feline infectious peritonitis virus challenge due to recombinant vaccinia virus immunization (1990)

The gene encoding the fusogenic spike protein of the coronavirus causing feline infectious peritonitis was recombined into the genome of vaccinia virus. The recombinant induced spike-protein-specific, in vitro neutralizing antibodies in mice. When kittens were immunized with the recombinant, low titers of neutralizing antibodies were obtained. After challenge with feline infectious peritonitis virus, these animals succumbed earlier than did the control group immunized with wild-type vaccinia virus (early death syndrome).
Angels on the Lawn (2011)

The introductory chapter explains how mushrooms develop. The complex fungal life cycle involves the germination of spores, the expansion of feeding colonies, and mating processes that can involve tens of thousands of sexes in a single mushroom species. The study of these mechanisms began with the Florentine genius, Anton Micheli in the eighteenth century, and, later, engaged fascinating personalities including children's author Beatrix Potter, Worthington Smith (who got most of his facts spectacularly wrong), and Elsie Wakefield (who got her facts right). The modern study of mushroom development is a challenge for the field of molecular genetics and computer simulations have provided useful insights. Recent changes in seasonal patterns of mushroom fruiting may relate to global climate change.
Tool for Thought (2005)

But if the modern word processor has become a near-universal tool for today's writers, its impact has been less revolutionary than you might think. Word processors let us create sentences without the unwieldy cross-outs and erasures of paper, and despite the occasional catastrophic failure, our hard drives are better suited for storing and retrieving documents than file cabinets. But writers don't normally rely on the computer for the more subtle arts of inspiration and association. We use the computer to process words, but the ideas that animate those words originate somewhere else, away from the screen. The word processor has changed the way we write, but it hasn't yet changed the way we think.
Alternative splicing of follicle-stimulating hormone receptor pre-mRNA: cloning and characterization of two alternatively spliced mRNA transcripts (1998)

Glycoprotein hormone receptors contain a large extracellular domain that is encoded by multiple exons, facilitating the possibility of expressing alternatively spliced transcripts. We have cloned two new splice variants of the rat follicle-stimulating hormone (FSH) receptor gene: FSH-R1 and FSH-R2. The splice variant FSH-R1 differs from the full-length FSH receptor mRNA by the inclusion of a small extra exon between exons 9 and 10. FSH-R2 lacks the first three base pairs of exon 4, contains an extra exon between exons 4 and 5, and has an extended 3'-untranslated region. According to the predicted open reading frames, both mRNAs encode truncated FSH receptor proteins, consisting of the entire extracellular domain (FSH-R1) or the amino-terminal half of the extracellular domain (FSH-R2), and are expressed at a low level in testes and ovaries. The levels of expression of the FSH-R1 and FSH-R2 mRNAs in the gonads show a constant ratio to the expression level of the full-length FSH receptor mRNA. Furthermore, in vitro co-expression of either one of the truncated proteins with the full-length FSH receptor in COS1 cells did not affect signal transduction through the full-length FSH receptor. The absence of a function of the truncated FSH receptors in FSH signal transduction in vitro, and the lack of differential regulation of the alternative transcripts, indicate that there is no clear function for alternative splicing of the FSH receptor pre-mRNA in the postnatal testis and the cycling adult ovary.
Paullones are potent inhibitors of glycogen synthase kinase‐3β and cyclin‐dependent kinase 5/p25 (2000)

Paullones constitute a new family of benzazepinones with promising antitumoral properties. They were recently described as potent, ATP-competitive, inhibitors of the cell cycle regulating cyclin-dependent kinases (CDKs). We here report that paullones also act as very potent inhibitors of glycogen synthase kinase-3beta (GSK-3beta) (IC50: 4-80 nM) and the neuronal CDK5/p25 (IC50: 20-200 nM). These two enzymes are responsible for most of the hyperphosphorylation of the microtubule-binding protein tau, a feature observed in the brains of patients with Alzheimer's disease and other neurodegenerative 'taupathies'. Alsterpaullone, the most active paullone, was demonstrated to act by competing with ATP for binding to GSK-3beta. Alsterpaullone inhibits the phosphorylation of tau in vivo at sites which are typically phosphorylated by GSK-3beta in Alzheimer's disease. Alsterpaullone also inhibits the CDK5/p25-dependent phosphorylation of DARPP-32 in mouse striatum slices in vitro. This dual specificity of paullones may turn these compounds into very useful tools for the study and possibly treatment of neurodegenerative and proliferative disorders.
N-[N-[(S)-1,3-Dicarboxypropyl]Carbamoyl]-4-[18F]Fluorobenzyl-l-Cysteine, [18F]DCFBC: A New Imaging Probe for Prostate Cancer (2008)

[18F]DCFBC localizes to PSMA+-expressing tumors in mice, permitting imaging by small-animal PET. This new radiopharmaceutical is an attractive candidate for further studies of PET imaging of prostate cancer.
CYTOMEGALOVIRUS SEROLOGIC STATUS AND POSTOPERATIVE INFECTION CORRELATED WITH RISK OF DEVELOPING CHRONIC REJECTION AFTER PULMONARY TRANSPLANTATION (1991)

Twenty-seven patients received pulmonary transplants during the period since we began routine use of cytomegalovirus-seronegative blood products for CMV-seronegative recipients. Preoperative serologic status of the recipient and the occurrence of cytomegalovirus infection in the postoperative period were correlated with development of obliterative bronchiolitis (OB) as diagnosed by transbronchial biopsy (TBB). Patients included 20 heart-lung and 7 double-lung recipients. OB occurred in 18 of 27 patients. All 3 CMV seronegative recipients receiving lungs from a seropositive donor and 9 of 10 CMV recipients seropositive at the time of transplantation developed OB compared with only 6 of 14 CMV seronegative patients receiving seronegative grafts (P = 0.018). CMV infection occurred in 10/27 patients, of whom 5 were asymptomatic; 90% of these patients developed OB. Donor-specific alloreactivity, based on primed lymphocyte testing (PLT) of bronchoalveolar lavage cells was found at the time of diagnosis of OB in 23 of 27 patients. A positive PLT was significantly associated with the presence of OB (P = 0.017). We conclude that preoperative seropositive status for CMV, grafting of organs from seropositive donors, and postoperative CMV infection are significant risk factors for developing OB. That OB is, in part, an immunologically mediated form of injury and represents chronic rejection is supported by the presence of donor-specific alloreactivity in BAL lymphocytes from all recipients with OB.
Back-propagation neural network for nonlinear self-tuning adaptive control (2003)

A backpropagation neural network is applied to a nonlinear self-tuning tracking problem. Traditional self-tuning adaptive control techniques can only deal with linear systems or some special nonlinear systems. The emerging backpropagation neural networks have the capability to learn arbitrary nonlinearity and show great potential for adaptive control applications. A scheme for combining backpropagation neural networks with self-tuning adaptive control techniques is proposed. The control mechanism is analyzed. Simulation results show that the new self-tuning scheme can deal with a large unknown nonlinearity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene conversion of immunoglobulin variable regions in mutagenesis cassettes by replacement PCR mutagenesis. (1992)

A technique, Replacement PCR Mutagenesis, was developed to replace one immunoglobulin variable region (V) in a M13 phage cassette with a different, homologous V. This allows the use of the same mutagenesis and subsequent expression vectors for many V regions or V segments. The method combines PCR of V fragments and in vitro mutagenesis. Primers homologous to 3' and 5' ends of both V regions initiate PCR synthesis of the V DNA fragment (donor) that will replace the V region (recipient) in M13. Donor V PCR DNA may originate from mRNA, cloned V genes or genomic templates. The donor V PCR DNA is denatured and annealed to the M13 cassette containing the recipient V to be supplanted. The second strand is synthesized, transfected into bacteria and mutant plaques selected by hybridization. Since restriction sites in primers are not required, altered primer-encoded amino acids are avoided. Further, the PCR donor piece can be of any length if it shares homology with the recipient gene. This allows construction and expression of complete gene replacements and chimeras. This method is also applicable to V "humanization" and studying sets of homologous genes containing polymorphic or evolutionary disparities. The potential uses of the technique are discussed.
Autocrine/paracrine cytokine stimulation of leukemic cell proliferation in smoldering and chronic adult T-cell leukemia (2010)

Adult T-cell leukemia (ATL), a heterogeneous disease, can be divided into smoldering, chronic, lymphoma, and acute types clinically. In addition to different clinical manifestations, different stages of ATL have different molecular signatures. Here, we demonstrated that smoldering/chronic ATL peripheral blood mononuclear cells spontaneously proliferated ex vivo in a cytokine (interleukin-12 [IL-12]/IL-9/IL-15)-dependent manner, while acute-type ATL peripheral blood mononuclear cells did not proliferate or proliferated independent of cytokines. Smoldering/chronic ATL cells produced IL-2 and IL-9 in 6-day ex vivo cultures. Interestingly, the addition of an anti-IL-2R-α monoclonal antibody profoundly inhibited IL-9 expression, suggesting optimal expression of IL-9 was dependent on IL-2 signaling in these patients. To determine whether there would be autonomous proliferation of ATL leukemic cells, we purified leukemic cells from patients with smoldering/chronic ATL. Purified leukemic cells cultured alone produced IL-2/IL-9, and the downstream Janus kinase/signal transducer and activator of transcription pathway was activated. However, the leukemic cells did not proliferate independently, but required coculture with autologous monocytes to induce proliferation. Moreover, interaction between leukemic cells and monocytes was contact dependent, and major histocompatibility complex class II expression may have contributed to this interaction. In conclusion, our data provide evidence that there is autocrine/paracrine cytokine stimulation of leukemic cell proliferation in patients with smoldering/chronic ATL that could be targeted for treatment.
Antiviral activities of individual murine IFN-alpha subtypes in vivo: intramuscular injection of IFN expression constructs reduces cytomegalovirus replication. (1998)

The IFN-alpha cytokines belong to a multigene family. However, the in vivo biological functions of each of the IFN-alpha subtypes is unknown. Recently, we developed an experimental model in which the tibialis anterior muscles of mice were transfected in situ with naked DNA plasmids encoding an IFN transgene. Here we use this model to investigate the in vivo effect of the expression of three murine IFN-alpha subtypes (A1, A4, and A9) on murine CMV replication in C57BL/6, BALB/c, and A/J mice. CMV was shown to replicate in the tibialis anterior muscles of mice for at least 6 days and induced an inflammatory infiltrate. However, mice expressing the IFN-alpha transgenes showed a marked reduction in the peak titers of virus replication, with less severe inflammation in the muscles compared with control mice that were inoculated with blank vectors. Moreover, mice expressing the IFN-alpha1 transgene had significantly lower CMV titers in the inoculated muscle than mice expressing either the IFN-alpha4 or the IFN-alpha9 transgenes. Furthermore, IFN-alpha/beta receptor knockout mice had markedly higher levels of CMV replication in the tibialis anterior muscles than the wild-type parental strain (129/Sv/Ev) following IFN-alpha1 transgene inoculation, suggesting that the protection observed is due to host cell-mediated IFN signaling. These data provide the first evidence indicating that there are in vivo differences in the antiviral efficacy of the IFN-alpha subtypes.
MAGNET: Columbia's Integrated Network Testbed (1985)

Fundamental issues arising in the design and implementation of architectures and protocols for integrated local area networks (ILAN's) supporting video, voice, graphics, data, and facsimile, are addressed, and open questions are identified. To characterize the performance of ILAN's, a set of performance evaluation guidelines is established. A class of conceptual solutions for ILAN's is proposed, and its expected performance is obtained by means of simulation. The class includes priority assignment schemes, parametrized sequential and simultaneous scheduling algorithms, and centralized and decentralized access control mechanisms. Our analysis, based upon simulations, shows that the bandwidth freed up by the video and voice calls during periods of little movement in the images and silence periods in the speech signals can be efficiently utilized for graphics and data transmission. The optimal priority mechanism among the different user classes depends on the traffic mix. Finally, it is argued that additional experimentation providing empirical data is imperative for understanding the real-time behavior of ILAN's. Consequently, a network testbed (NTB) called MAGNET is proposed for evaluating the performance of the proposed theoretical systems. It consists of an adaptive ILAN whose mediaaccess protocol is controlled by an Expert System.
Oral melphalan, prednisone and thalidomide for newly diagnosed myeloma patients (2004)

6549 Background: Thalidomide (T) alone or in combination has been tested and proved effective in multiple myeloma. No data are available on the association of T with oral Melphalan and Prednisone (MP) in newly diagnosed patients. Here, we evaluated the potential additive and synergistic effect of the combination Melphalan, Prednisone and Thalidomide (MPT) Methods: Between June 2002 and June 2003, 42 patients (median age 72, range 61–80) with newly diagnosed symptomatic multiple myeloma received 6 courses of MP (melphalan 4 mg/sqm and prednisone 40 mg/sqm for 7 days every month) plus T 100 mg/day continuously until any sign of disease progression or relapse. The dose of T was reduced to 50% when grade 2 WHO toxicity occurred, and suspended for any grade 3. All patients have completed the 6 assigned MP courses and were evaluated for both toxicity and response rate. Results: T increased the hematologic toxicity induced by MP: grade 3–4 WHO neutropenia was observed in 14% of patients. Constipation occurred in 28% of patients. Neurological toxicity was recorded in 38% of patients. The major acute adverse events were infections (26%) and deep-vein thrombosis (19%). One patient died for septicemia, and one for pulmonary thromboembolism. T discontinuation was required in 36% of patients (thromboembolic event, infection, costipation, hematologic toxicity). After treatment, partial responses (myeloma protein reduction >50%) were observed in 93% of patients, no responses (myeloma protein reduction <50%) in 7%. Complete remissions (disappearance of monoclonal protein and negative immunofixation) were 26%, near complete remissions (disappearance of monoclonal protein and positive immunofixation) were 19%, responses with myeloma protein reduction 90–99% were 12%. Time required to obtain the maximum response was 4 months in 88% of patients. Conclusions: The incidence of infections and deep-vein thrombosis was high, suggesting the need for antibiotic and anticoagulant prophylaxis. MPT induced a response rate significantly higher in comparison with any other conventional chemotherapy program. The CR rate was similar to those observed after transplant. No significant financial relationships to disclose.
Interactions of Mitochondrial and Nuclear Genes That Affect Male Gametophyte Development (2004)

Apart from their agronomic importance in hybrid seed production, mutations that encode cytoplasmic male sterility (CMS) provide a means to probe the role of the mitochondrion in reproductive development. Fertility restorers are examples of nuclear genes that affect cytoplasmic gene expression, and
Error Correction Codes (2015)

An error correction code is an essential part of wireless communication systems. This chapter designs the turbo encoder/decoder, turbo product encoder/decoder, and low-density parity check (LDPC) encoder/decoder. It looks into design criteria, describes the algorithms, and discusses hardware implementation issues. The turbo codes achieved very low error probability which is close to the Shannon limit. The idea of the revolutionary error correction codes originates from concatenated encoding, randomness, and iterative decoding. The turbo decoder based on an iterative scheme is composed of two Soft Input Soft Output (SISO) component decoders. The SISO decoder is based on the Maximum a Posteriori (MAP) algorithm (also known as Bahl-Cocke- Jelinek-Raviv (BCJR) algorithm). The chapter also discusses the hardware design issues of MAP decoder, turbo product encoding process, and LDPC codes. It ends with a brief discussion on the belief propagation algorithm and log domain sum product algorithm.
Quantum Simulations of Classical Annealing Processes (2008)

We describe a quantum algorithm that solves combinatorial optimization problems by quantum simulation of a classical simulated annealing process. Our algorithm exploits quantum walks and the quantum Zeno effect induced by evolution randomization. It requires order 1/sqrt delta steps to find an optimal solution with bounded error probability, where delta is the minimum spectral gap of the stochastic matrices used in the classical annealing process. This is a quadratic improvement over the order 1/delta steps required by the latter.
INRECA - A Seamless Integration of Induction and Case-Based Reasoning for Decision Support Tasks (1995)

We propose an integrated approach to decision support and diagnostic problems based on topdown induction of decision trees (TDIDT) and case-based reasoning (CBR). This approach has been implemented within the INRECA 1 Esprit project. While different ways of integration (Auriol, Manago et al., 1994) and evaluation (Althoff, Auriol et al., 1995; Althoff, 1995a;
A Saccharomyces cerevisiae Gene Required for Heterologous Fatty Acid Elongase Activity Encodes a Microsomal β-Keto-reductase (2002)

A number of Saccharomyces cerevisiae membrane-bound oxidoreductases were examined for potential roles in microsomal fatty acid elongation, by assaying heterologous elongating activities in individual deletion mutants. One yeast gene, YBR159w, was identified as being required for activity of both the Caenorhabditis elegans elongase PEA1 (F56H11.4) and the Arabidopsis thaliana elongase FAE1. Ybr159p shows some limited homology to human steroid dehydrogenases and is a member of the short-chain alcohol dehydrogenase superfamily. Disruption of YBR159w is not lethal, in contrast to previous reports, although the mutants are slow growing and display high temperature sensitivity. Both Ybr159p and an Arabidopsis homologue were shown to restore heterologous elongase activities when expressed in ybr159Delta mutants. Biochemical characterization of microsomal preparations from ybr159Delta cells revealed a primary perturbation in beta-ketoacyl reduction, confirming the assignment of YBR159w as encoding a component of the microsomal elongase.
Boosted gate MOS (BGMOS): device/circuit cooperation scheme to achieve leakage-free giga-scale integration (2002)

This paper proposes a new device and circuit scheme that drastically suppresses the stand-by leakage current for the deep sub-0.1 /spl mu/m era while maintaining the circuit speed. Applying boosted gate voltage on the low leakage switches with higher V/sub th/ and thicker T/sub ox/, extremely low stand-by power for battery type application is achieved, while degradation of circuit performance and an increase of area overhead are sufficiently suppressed. The combination with a negative gate voltage scheme and the application of the boosted voltage scheme to SRAMs are also discussed.
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons (2005)

The V(D)J recombination reaction in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Yet no transposase sequence similar to RAG1 or RAG2 has been found. Here we show that the approximately 600-amino acid "core" region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes. Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust. We demonstrate that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon. Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs. We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%-30% identical to the RAG1 N-terminal domain and the RAG1 core. Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons. We propose that only the RAG1 core was derived from the Transib transposase, whereas the N-terminal domain was assembled from separate proteins of unknown function that may still be active in sea urchin, lancelet, hydra, and starlet sea anemone. We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction.