gebhart/patrepeval huggingface dataset:
Cross-talk between orientation-dependent recognition determinants of a complex control RNA element, the enterovirus oriR (2000)

The coxsackie B3 virus oriR is an element of viral RNA thought to promote the assembly of a ribonucleoprotein complex involved in the initiation of genome replication. The mutual orientation of its two helical domains X and Y is determined by a kissing interaction between the loops of these domains. Here, a genetic approach was worked out to identify spatial orientation-dependent recognition signals in these helices. Spatial orientation changes (due to linear and rotational shifts) were introduced by appropriate insertions/deletions of a single base pair into one or both of the domains, and phenotypic consequences caused by these mutations were studied. The insertion of a base pair into domain Y caused a defect in viral reproduction that could be suppressed by a base-pair insertion into domain X. Similarly, a defect in viral replication caused by a base-pair deletion from domain X could be suppressed by a base-pair deletion from domain Y. Thus, certain areas of the two domains should cross-talk to one another in the sense that a change of space position of one of them required an adequate reply (change of space position) from the other. Phenotypic effects of the local rotation of one or more base pairs (and of some other mutations) in either domain X or domain Y suggested that the two most distal base pairs of these domains served as orientation-dependent recognizable signals. The results were also consistent with the notion that the recognition of the distal base pair of domain Y involved a mechanism similar to the intercalation of an amino acid residue.
A cell-based platform to potentiate oncolytic virus: Potential approach for cancer therapies. (2020)

21 Background: Oncolytic virotherapy has been pursued by multiple companies and institutions with few candidates reaching the clinic and demonstrating limited efficacy. The therapeutic potential of oncolytic viruses can be severely restricted by innate and adaptive immune barriers. To overcome this obstacle, we load and protect tumor selective CAL1 oncolytic vaccinia virus into adipose-derived stem cells (AD-MSC) to generate a new therapeutic agent called SNV1(SuperNova1). Methods: SNV1s were generated by incubating AD-MSC with CAL1 virus. SNV1 was analyzed for its ability to kill cancer cell lines and protect virus in the presence of active neutralizing antibodies and complement. In animals, SNV1 was intratumorally injected in various xenograft and syngeneic models. Viral biodistribution was also evaluated by PCR. Immune infiltration were analyzed using flow cytometry. Results: Compared to the naked virus, SNV1 showed improved protection against the humoral barriers and efficient eradication of various human cancer cell lines in vitro. Intratumoral SNV1 treatment showed statistically significant and potentiated tumor growth inhibition compared to control or CAL1 naked virus treatment in all tested models (prostate, breast, melanoma, colon, and prostate cancers). Importantly, local administration of SNV1 induced systemic therapeutic effects. Five days after SNV1 administration, tumor infiltrating lymphocytes (TILs) from both treated and untreated tumors showed increased CD4 and CD8 T-cell populations. As well as decreased frequency of Tregs, and improved effector to Treg ratios, which was associated with inhibition of tumor growth at the treated tumor site and also at distant untreated sites. Ongoing and persistent virus infection could be detected in the treated tumor as late as 15 days after administration. Conclusions: This study demonstrates the ability of our cell-based platform to protect and potentiate oncolytic vaccinia virus by circumventing the innate and adaptive immune barriers, resulting in enhanced oncolytic virotherapy. These findings provide fundamental rationale for the development of cell-based platforms to maximize the therapeutic potential of various oncolytic viruses.
A Novel Function of Angiotensin II in Skin Wound Healing (2006)

The role of angiotensin II (Ang II) in the control of systemic blood pressure and volume homeostasis is well known and has been extensively studied. Recently, Ang II was suggested to also have a function in skin wound healing. In the present study, the in vivo function of Ang II in skin wound healing was investigated using Ang II type 1 receptor (AT1R) knock-out mice. Wound healing in these mice was found to be markedly delayed. Keratinocytes and fibroblasts play important roles in wound healing, and thus the effect of Ang II on the migration of these cells was examined. Ang II stimulated keratinocyte and fibroblast migration in a dose-dependent manner. It has been reported that G protein-coupled receptor (GPCR) activation induces epidermal growth factor (EGF) receptor (EGFR) transactivation through the shedding of heparin-binding EGF-like growth factor (HB-EGF). As AT1R is a GPCR, it was hypothesized that Ang II-induced keratinocyte and fibroblast migration is mediated by EGFR transactivation. Ang II induced EGFR phosphorylation, which was inhibited by an AT1R antagonist, HB-EGF neutralizing antibody, and an HB-EGF antagonist in both keratinocytes and in fibroblasts. Moreover, Ang II-induced migration of keratinocytes and fibroblasts was also prevented by these inhibitors. Taken together, these findings clearly demonstrate, for the first time, that Ang II plays an important role in skin wound healing and that it functions by accelerating keratinocyte and fibroblast migration in a process mediated by HB-EGF shedding.
Iron-Catalyzed Direct Arylation through an Aryl Radical Transfer Pathway (2010)

A general and efficient iron-catalyzed direct arylation of benzene and hetereoaryl derivatives using a cost-effective and environmentally benign catalyst is described. The reaction is performed under neat conditions and can proceed at room temperature.
A Procedure for the Rapid Preparation of<sup>14</sup>C-Aminoacyl-Transfer RNA and Its use in the Assay of Class I Ribonucleases and Ribonuclease Inhibitor (1981)

The presence of ribonuclease inhibitor and/or the activity of class I ribonucleases can conveniently be measured, at all stages of purification, by a highly sensitive assay based on the loss of radioactivity during the concomitant hydrolysis of tRNA and small amounts of 14C-labeled aminoacyl-tRNA. The rapid, economical assay, which is readily adaptable to homologous tRNA substrates, eliminates the necessity of filtration, centrifugation and ultraviolet spectroscopy measurements required by most other assays and is particularly suitable for multiple samples and kinetic measurements.
Articulated model based people tracking using motion models (2003)

This paper focuses on acquisition of human motion data such as joint angles and velocity for applications of virtual reality, using both an articulated body model and a motion model in the CONDENSATION framework. Firstly, we learn a motion model represented by Gaussian distributions, and explore motion constraints by considering the dependency of motion parameters and represent them as conditional distributions. Both are integrated into the dynamic model to concentrate factored sampling in the areas of state-space with most posterior information. To measure the observing density with accuracy and robustness, a PEF (pose evaluation function) modeled with a radial term is proposed. We also address the issue of automatic acquisition of initial model posture and recovery from severe failures. A large number of experiments on several persons demonstrate that our approach works well.
A Discourse-Level Named Entity Recognition and Relation Extraction Dataset for Chinese Literature Text (2017)

Named Entity Recognition and Relation Extraction for Chinese literature text is regarded as the highly difficult problem, partially because of the lack of tagging sets. In this paper, we build a discourse-level dataset from hundreds of Chinese literature articles for improving this task. To build a high quality dataset, we propose two tagging methods to solve the problem of data inconsistency, including a heuristic tagging method and a machine auxiliary tagging method. Based on this corpus, we also introduce several widely used models to conduct experiments. Experimental results not only show the usefulness of the proposed dataset, but also provide baselines for further research. The dataset is available at https://github.com/lancopku/Chinese-Literature-NER-RE-Dataset
Interleukin-1 Receptor-Associated Kinase-2 (IRAK2) Is a Critical Mediator of Endoplasmic Reticulum (ER) Stress Signaling (2013)

Endoplasmic reticulum (ER) stress occurs when unfolded proteins accumulate in the lumen of the organelle, triggering signal transduction events that contribute either to cellular adaptation and recovery or alternatively to cellular dysfunction and death. ER stress has been implicated in numerous diseases. To identify novel modulators of ER stress, we undertook a siRNA library screen of the kinome, revealing Interleukin-1 Receptor-Associated Kinase-2 (IRAK2) as a contributor to unfolded protein response (UPR) signaling and ER stress-induced cell death. Knocking down expression of IRAK2 (but not IRAK1) in cultured mammalian cells suppresses ER stress-induced expression of the pro-apoptotic transcription factor CHOP and activation of stress kinases. Similarly, RNAi-mediated silencing of the IRAK family member Tube (but not Pelle) suppresses activation of stress kinase signaling induced by ER stress in Drosophila cells. The action of IRAK2 maps to the IRE1 pathway, rather than the PERK or ATF6 components of the UPR. Interestingly, ER stress also induces IRAK2 gene expression in an IRE1/XBP1-dependent manner, suggesting a mutually supporting amplification loop involving IRAK2 and IRE1. In vivo, ER stress induces Irak2 expression in mice. Moreover, Irak2 gene knockout mice display defects in ER stress-induced CHOP expression and IRE1 pathway signaling. These findings demonstrate an unexpected linkage of the innate immunity machinery to UPR signaling, revealing IRAK2 as a novel amplifier of the IRE1 pathway.
Development of Carbon Blocks for Blast Furnace Hearths (2008)

Carbon blocks have been used as refractory for blast furnace hearths since 1951 in Nippon Steel. Besides excellent corrosion resistance, high thermal conductivity is required for the refractory for blast furnace hearths to help a protective layer form on the hot face by cooling. Nippon Steel has investigated the use of carbon blocks for blown-off blast furnaces, and based on the findings obtained, taken measures to suppress the infiltration of hot metal and improve the corrosion resistance and thermal conductivity of carbon blocks. The corrosion resistance of carbon blocks has been further improved lately by making a protective adhesion layer form at the iron/ carbon interface on the hot face.
Mixed-linker polymerase chain reaction: a new method for rapid fingerprinting of isolates of the Mycobacterium tuberculosis complex (1993)

Rapid recognition of multidrug-resistant strains of Mycobacterium tuberculosis is a desirable goal for treatment of patients and protection of health care workers. DNA fingerprints produced with the insertion sequence IS6110 generate restriction fragment length polymorphism (RFLP) patterns that reliably identify M. tuberculosis complex strains. This report describes a rapid technique for RFLP typing using the polymerase chain reaction. The method uses one primer specific for IS6110 and a second primer complementary to a linker ligated to the restricted genomic DNA. In one strand the linker contains uracil in place of thymidine, and specific amplification is obtained by elimination of this strand with uracil N-glycosylase. Mixed-linker fingerprinting clearly differentiated multidrug-resistant isolates from 12 outbreaks and unambiguously assigned them to 26 RFLP groups.
Towards a Theory of Codes for Iterative Decoding (2003)

Channel codes in combination with iterative decoding techniques are a both powerful and efficient method to protect data against disturbances in digital communication systems. This thesis deals with various code constructions for block-wise and continuous transmission that have the potential to achieve low bit error rates with iterative decoding, even when operating close to the Shannon limit. For a performance analysis of iterative decoding schemes with convolutional component codes it is of great value to understand and describe the exact behavior of a convolutional code. Analytic expressions for the bit error probabilities corresponding to maximum likelihood decoding of a rate one-half, memory two convolutional code are derived as a function of the crossover probability of the binary symmetric channel. Three different encoders for the same code are considered, and the Viterbi decoder is compared to the Max-Log-MAP decoder, which is often used in iterative decoding schemes as an alternative to an optimal a posteriori probability (APP) decoder. An ensemble of self-concatenated convolutional codes is introduced and the average weight spectrum of the codes is expressed by the solution to a system of recurrent equations. Based on this average weight spectrum a lower bound on the free distance and upper bounds on the burst error probability for maximum likelihood decoding are derived. A substantial part of the thesis is devoted to proving for various code families the existence of and deriving bounds on the iterative limit. This threshold determines when arbitrarily low error probabilities can asymptotically be achieved with iterative decoding. Braided block codes, a new code construction for continuous transmission based on block component codes, are introduced. For braided block codes with Hamming component codes as well as for the block and convolutional versions of low-density parity-check codes and turbo codes, bounds on the iterative limits are derived and compared to results of computer simulations. Furthermore, it is shown with a constructive permutor design procedure that there exist turbo codes for which the minimum distance grows logarithmically with the block length.
On the biochemical basis of HCN production in the millipede <i>Harpaphe haydeniana</i> (Xystodesmidae: Polydesmida) (1978)

Harpaphe haydeniana was shown to synthesize HCN and benzaldehyde in a manner similar to that of plants. By the injection of appropriate 14 C precursors it was possible to isolate small quantities of the radioactive intermediates, phenylacetaldoxime, phenylacetonitrile, a glycoside of mandelonitrile, and mandelonitrile. The millipede stores a large droplet of D-mandelonitrile ((R)-mandelonitrile) in the storage vestibule of each cyanogenic gland.Mandelonitrile dissociates in vivo to HCN and benzaldehyde. The HCN is incorporated into β-cyanoalanine and asparagine. and benzaldehyde is oxidized to P-hydroxybenzoic acid.Two enzymes, β-glucosidase and α-hydroxynitrile lyase, were detected in paranotal extracts of H. haydeniana. The α-hydroxynitrile lyase is restricted to the reaction chamber of the cyanogenic gland and functions to promote the immediate release of HCN. It was also detected in freshly excreted glandular fluid of Oxidus gracilis, Sigmoria nantahalae, Cherokia georgiana, and Cleptoria rileyi. The pH of the fluid in these reaction chambers was found to be about 4, which corresponds to the pH optimum of the lyase.
Kinetics of the in vivo interconversion of the carboxylate and lactone forms of irinotecan (CPT-11) and of its metabolite SN-38 in patients. (1994)

The kinetics of the in vivo interconversion of the carboxylate and lactone forms of the prodrug irinotecan, 7-ethyl-10-[4-(1-piperidino)-1- piperidino]carbonyloxycamptothecin (CPT-11), and its active metabolite SN-38 were studied in five patients using a HPLC method that allows the simultaneous determination of all four compounds and detects any hydrolysis of lactones due to inadequate sample handling and storage. The apparent conversion of CPT-11 lactone to the carboxylate in vivo was rapid with a mean half-life of 9.5 min; the carboxylate became the predominant form of plasma CPT-11 soon after the end of the infusion. The ratio of the area under the plasma concentration-time curves of the lactone to total CPT-11 was 36.8 +/- 3.5% (SD). In contrast, SN-38 was present predominantly as the lactone at all times and with little interpatient variability (lactone/total area under the plasma concentration-time curve ratio, 64.0 +/- 3.4%). This may explain in part the promising activity of CPT-11 because CPT derivatives are active against their target, topoisomerase I, only in their lactone form.
Clinicopathologic Study of Lacrimal Sac and Nasal Mucosa in 44 Patients with Complete Acquired Nasolacrimal Duct Obstruction (1992)

We studied 44 patients who had dacryocystorhinostomy for primary acquired complete nasolacrimal duct obstruction. The lacrimal sac and nasal mucosa adjacent to the osteotomy were examined histologically. The lacrimal sac had chronic inflammatory changes in 33 of 37 patients with varying degrees of fibrosis in 34 of 37. Focal ulceration of the lacrimal sac epithelium was present in 15 cases. Goblet cells, present in 11 specimens, were not identified in 26 specimens. Moderate or severe chronic inflammation was found in 14 of 44 nasal mucosal specimens and marked fibrosis in 22. The pathology of the lacrimal sac and nasal mucosa is similar to that of the nasolacrimal duct in complete nasolacrimal duct obstruction. The nasal inflammation may have resulted from dacryocystitis or alternatively contributed to the dacryocystitis.
Changing the glucose cut-off values that define hypoglycaemia has a major effect on reported frequencies of hypoglycaemia (2008)

The glucose cut-off point defining hypoglycaemia greatly affects the reported frequency of hypoglycaemia. When hypoglycaemia is to be defined by a predetermined glucose level, to have clinical relevance the cut-off should be set at a lower level than the threshold of 3.9 mmol/l proposed by the American Diabetes Association.
Rabbit Brain Glucose Transporter Responds to Insulin When Expressed in Insulin-sensitive Chinese Hamster Ovary Cells (1989)

Transfection of Chinese hamster ovary cells with the expression vector containing rabbit brain HepG2-type glucose transporter cDNA resulted in a dramatic over-expression (approximately 10-fold) of glucose transporter as assessed by either immunoblotting with antipeptide antibody against rabbit brain glucose transporter or photoaffinity labeling with [3H]cytochalasin B. 2-Deoxyglucose uptake was also increased 4-fold in the transfected cells, while no increase in transport activity or transporter amount was observed in cells that were transfected with the expression vector alone without glucose transporter cDNA. Significantly, insulin (10(-7) M) increased 2-deoxyglucose uptake in both control and transfected cells, but the increased amount of the transported 2-deoxyglucose by insulin in the transfected cells was 4.2-fold greater than that in control cells, indicating that the expressed rabbit brain HepG2-type glucose transporter responded to insulin. In addition, we have recently demonstrated that the HepG2-type glucose transporter exists in rat adipocytes and responds to insulin in a fashion similar to a majority of other types of glucose transporters (Oka, Y., Asano, T., Shibasaki, Y., Kasuga, M., Kanazawa, Y., and Takaku, F. (1988) J. Biol. Chem. 263, 13432-13439). In contrast, insulin did not stimulate glucose transport activity in HepG2 cells or IM-9 lymphocytes that have a significant amount of the HepG2-type glucose transporter. Thus, the results in this study further support the notion that insulin regulation of glucose transport activity depends on a tissue-specific signaling mechanism.
Vector-controlled induction motor drive with a self-commissioning scheme (1991)

Different vector-controlled structures are discussed, and their suitability for an economical and reliable industrial drive system is explored. From this, the design of a compact control hardware is derived, composed of an 80196 microcontroller and an ASIC (application-specific integrated circuit) for the generation of the pulsewidth modulation (PWM) signals. The drive system can be configured from a host computer or a hand-held servicing unit through a serial data link. Monitoring and diagnostic functions are included. A self-commissioning scheme permits the setting of the parameters for optimum dynamic performance of the induction motor. Various oscillograms demonstrate the behavior of the vector controller operating a 25-kVA PWM inverter.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reuse-aware modulo scheduling for stream processors (2010)

This paper presents reuse-aware modulo scheduling to maximizing stream reuse and improving concurrency for stream-level loops running on stream processors. The novelty lies in the development of a new representation for an unrolled and software-pipelined stream-level loop using a set of reuse equations, resulting in simultaneous optimization of two performance objectives for the loop, reuse and concurrency, in a unified framework. We have implemented this work in the compiler developed for our 64-bit FT64 stream processor. Our experimental results obtained on FT64 and by simulation using nine representative stream applications demonstrate the effectiveness of the proposed approach.
All‐Solid Actuator Consisting of Polyaniline Film and Solid Polymer Electrolyte (2003)

Abstract An all‐solid actuator, consisting of a polyaniline (PANI) film and a solid polymer electrolyte (SPE) of poly(ethylene oxide) derivative (STO288), clearly showed a reversible displacement in an atmosphere when a voltage was applied between the PANI film and the SPE layer. The displacement and the response rate are mainly dependent on the applied voltage and the employed supporting salt, but are influenced by the humidity and temperature of the environment. The results of the present experiments have revealed that the influences of the humidity and temperature on the performance of the actuator are predominantly through the ionic conductivity of the SPE. All‐solid actuator consisting of PANI and SPE. magnified image All‐solid actuator consisting of PANI and SPE.
[The cortical column, a new processing unit for cortex-like networks]. (1989)

We propose in this paper a new connectionnist model which is the result of a collaboration between computer science and neurobiology researchers. This model is based upon a cortical-like network close to cortical function simulation. We present its functional and architectural characteristics together with the very encouraging results obtained for the first simulations on the visual and auditory cortical functions in speech and character recognition.
Feasibility of Long-Term Closed-Loop Control: A Multicenter 6-Month Trial of 24/7 Automated Insulin Delivery (2016)

We conclude that CLC technology has matured and is safe for prolonged use in patients' natural environment. Based on these promising results, a large randomized trial is warranted to assess long-term CLC efficacy and safety.