gebhart/patrepeval huggingface dataset:
The interaction of yeast hexokinase with Procion Green H-4G (1981)

1. A number of reactive triazine dyes specifically and irreversibly inactive yeast hexokinase at pH 8.5 and 33 degrees C. Under these conditions, the enzyme is readily inactivated by 100 microM-Procion Green H-4G, Blue H-B, Turquoise H-7G and Turquoise H-A, is less readily inactivated by Procion Brown H-2G. Green HE-4BD, Red HE-3B and Yellow H-5G and is not inactivated at all by Procion Yellow H-A. 2. The inactivation of hexokinase by Procion Green H-4G is competitively inhibited by the adenine nucleotides ATP and ADP and the sugar substrates D-glucose, D-mannose and D-fructose but not by nonsubstrates such as D-arabinose and D-galactose. 3. Quantitatively inhibited hexokinase contains approx. 1 mol of dye per mol of monomer of mol.wt. 51000. The inhibition is irreversible and activity cannot be recovered on incubation with high concentration (20 mM) of ATP or D-glucose. 4. Mg2+ protects the enzyme against inactivation by Procion Green H-4G but enhances the rate of inactivation by all the other Procion dyes tested. In the presence of 10 mM-Mg2+ the apparent dissociation constant between enzyme and dye is reduced from 199.0 microM to 41.6 microM. Binding of the dye to hexokinase is accompanied by characteristic spectral changes in the range 560-700 nm. 5. Mg2+ promotes binding of yeast hexokinase to agarose-immobilized Procion Green H-4G but not to the other dyes tested. Elution could be effected by omission of Mg2+ from the column irrigants or by inclusion of MgATP or D-glucose, but not by D-galactose. These effects can be exploited to purify hexokinase from crude yeast extracts. 6. The specific active-site-directed binding of triazine dyes to yeast hexokinase is interpreted in terms of the crystallographic structure of the hexokinase monomer.
Autocrine regulation of asthmatic airway inflammation: role of airway smooth muscle (2001)

Chronic airway inflammation is one of the main features of asthma. Release of mediators from infiltrating inflammatory cells in the airway mucosa has been proposed to contribute directly or indirectly to changes in airway structure and function. The airway smooth muscle, which has been regarded as a contractile component of the airways responding to various mediators and neurotransmitters, has recently been recognised as a rich source of pro-inflammatory cytokines, chemokines and growth factors. In this review, we discuss the role of airway smooth muscle cells in the regulation and perpetuation of airway inflammation that contribute to the pathogenesis of asthma.
FLIP: a flexible protocol for efficient communication between heterogeneous devices (2002)

Interconnecting heterogeneous devices, that is, devices with varying capabilities, has raised new challenges in the design of network protocols. This paper describes the design of the Flexible Interconnecting Protocol, or FLIP, whose goal is to interconnect heterogeneous devices. FLIP is a flexible protocol that addresses the needs of heterogeneous networks: it incurs little overhead when run by simple devices, while still providing a range of functions that can be performed by more sophisticated devices. We describe a simplified implementation of FLIP under Linux. We also conducted a preliminary evaluation of FLIP's overhead and functionality in the context of IP (IPv4 and IPv6) and sensor network environments. FLIP incurs reasonably low overhead when providing IPv4 and IPv6 functionality (1 and 3 bytes respectively), yet it does particularly well in the case of small payloads. When compared to a sensor-specific protocol, FLIP incurs a small overhead increase while still providing full protocol functionality.
Exendin-3, a novel peptide from Heloderma horridum venom, interacts with vasoactive intestinal peptide receptors and a newly described receptor on dispersed acini from guinea pig pancreas. Description of exendin-3(9-39) amide, a specific exendin receptor antagonist. (1991)

Exendin-3 increased cellular cAMP levels and amylase release from dispersed acini from guinea pig pancreas. Low concentrations (0.1-3 nM) caused a 12-fold increase in cAMP, whereas higher concentrations (0.3-3 microM) caused an additional 24-fold increase in cAMP. Maximal cAMP with the highest concentration tested was the same as the maximal response with secretin, vasoactive intestinal peptide (VIP), peptide histidine isoleucine, helodermin, or helospectin-I. In terms of amylase release, exendin-3 had the same efficacy but was the least potent of these peptides. Exendin-3-induced increases in amylase release were inhibited by VIP receptor antagonists and the new peptide (greater than 0.1 microM) competed with radiolabeled VIP for binding sites on dispersed acini. Increasing concentrations of an exendin-3 fragment, exendin-3(9-39) amide, did not increase cAMP or amylase release but inhibited the increase in cAMP observed with 0.1-3 nM exendin-3. The fragment did not alter the effects of other peptides that are known to increase acinar cAMP. We conclude that exendin-3 interacts with at least two receptors on guinea pig pancreatic acini; at high concentrations (greater than 100 nM) the peptide interacts with VIP receptors, thereby causing a large increase in cAMP and stimulating amylase release; at lower concentrations (0.1-3 nM) the peptide interacts with a putative exendin receptor, thereby causing a smaller increase in cAMP of undetermined function. Exendin-3(9-39) amide is a specific exendin receptor antagonist.
Reciprocal Regulation of Myocardial microRNAs and Messenger RNA in Human Cardiomyopathy and Reversal of the microRNA Signature by Biomechanical Support (2009)

These results show that miRs are more sensitive than mRNAs to the acute functional status of end-stage heart failure, consistent with important functions for regulated miRs in the myocardial response to stress. Combined miR and mRNA profiling may have superior potential as a diagnostic and prognostic test in end-stage cardiomyopathy.
Solving ptychography with a convex relaxation (2014)

Ptychography is a powerful computational imaging technique that transforms a collection of low-resolution images into a high-resolution sample reconstruction. Unfortunately, algorithms that are currently used to solve this reconstruction problem lack stability, robustness, and theoretical guarantees. Recently, convex optimization algorithms have improved the accuracy and reliability of several related reconstruction efforts. This paper proposes a convex formulation of the ptychography problem. This formulation has no local minima, it can be solved using a wide range of algorithms, it can incorporate appropriate noise models, and it can include multiple a priori constraints. The paper considers a specific algorithm, based on low-rank factorization, whose runtime and memory usage are near-linear in the size of the output image. Experiments demonstrate that this approach offers a 25% lower background variance on average than alternating projections, the current standard algorithm for ptychographic reconstruction.
Transforming Growth Factor-β Blockade Down-Regulates the Renin-Angiotensin System and Modifies Cardiac Remodeling after Myocardial Infarction (2008)

After myocardial infarction (MI), the heart may undergo progressive ventricular remodeling, resulting in a deterioration of cardiac function. TGF-beta is a key cytokine that both initiates and terminates tissue repair, and its sustained production underlies the development of tissue fibrosis, particularly after MI. We investigated the effects of a novel orally active specific inhibitor of the TGF-beta receptor 1 (SD-208) in an experimental model of MI. Mice underwent ligation of the left coronary artery to induce MI and were subsequently treated for 30 d after infarction with either SD-208 or a vehicle control. Blockade of TGF-beta signaling reduced mean arterial pressure in all groups. SD-208 treatment after MI resulted in a trend for reduced ventricular and renal gene expression of TGF-beta-activated kinase-1 (a downstream modulator of TGF-beta signaling) and a significant decrease in collagen 1, in association with a marked decrease in cardiac mass. Post-MI SD-208 treatment significantly reduced circulating levels of plasma renin activity as well as down-regulating the components of the cardiac and renal renin-angiotensin system (angiotensinogen, angiotensin converting enzyme, and angiotensin II type I receptor). Our findings indicate that blockade of the TGF-beta signaling pathway results in significant amelioration of deleterious cardiac remodeling after infarction.
Transcriptomic analysis of the venom gland of the red-headed krait (Bungarus flaviceps) using expressed sequence tags (2010)

The 3FTxs were found to be the major component of the venom (39%). We found eight groups of unique 3FTxs and most of them were different from the well-characterized 3FTxs. We found three groups of Kunitz-type serine protease inhibitors (SPIs); one group was comparable to the classical SPIs and the other two groups to chain B of beta-bungarotoxins (with or without the extra cysteine) based on sequence identity. The latter group may be functional equivalents of dendrotoxins in Bungarus venoms. The natriuretic peptide (NP) found is the first NP for any Asian elapid, and distantly related to Australian elapid NPs. Our study identifies several unique toxins in B. flaviceps venom, which may help in understanding the evolution of venom toxins and the pathophysiological symptoms induced after envenomation.
Parallel scheduling for cyber-physical systems (2013)

As the complexity of software for Cyber-Physical Systems (CPS) rapidly increases, multi-core processors and parallel programming models such as OpenMP become appealing to CPS developers for guaranteeing timeliness. Hence, a parallel task on multi-core processors is expected to become a vital component in CPS such as a self-driving car, where tasks must be scheduled in real-time.
A non-blocking transaction data flow graph based approach for replicated data (1993)

Regplicated data management systems adopt the 1-copy serializability criteria for processing transactions. In order to achieve this goal, many approaches, rely on obtaining votes from other sites, for processing update requests. In this paper, a technique for generation of precedence graphs for each transaction execution is proposed. The transaction data flow graph approach is a fully distributed approach. The proposed technique, is free from deadlocks, and avoids resubmission of transactions.
Chondromalacia Patellae (1979)

Degeneration of the cartilage on the under surface of the patella is shown to be the most frequent cause of "internal derangement of the knee" (63%). The axial view of the patellofemoral joint in 4 angles of flexion constitutes the procedure of choice for diagnostic exploration of patellar cartilage with, perhaps, the restriction for the medial compartment where arthroscopy is probably preferrable. The information obtained from single contrast arthrography of the patellofemoral joint has contributed greatly to the understanding of the sometimes confusing problem of chondromalacia of the patella. It has given an anatomic basis to the patellar syndrome and has served as a basis for a precise typographic system of classification. From this, we have been able to correlate localization and etiology which has then allowed logical solutions to be proposed for each group, based upon biomechanical considerations in both the frontal and saggital planes of the knee.
Modular organization of related Archaeal plasmids encoding different restriction-modification systems inMethanobacterium thermoformicicum (1992)

Nucleotide sequence comparison of the related 13513-bp plasmid pFV1 and the 11014-bp plasmid pFZ1 from the thermophilic archaeon Methanobacterium thermoformicicum THF and Z-245, respectively, revealed a homologous, approximately 8.2 kb backbone structure that is interrupted by plasmid-specific elements. Various highly conserved palindromic structures and an ORF that could code for a NTP-binding protein were identified within the backbone structure and may be involved in plasmid maintenance and replication. Each plasmid contains at comparable locations a module which specifies components of different restriction-modification (R/M) systems. The R/M module of pFV1 contained, in addition to the genes of the GGCC-recognizing R/M system MthTI, an ORF which may be involved in repair of G-T mismatches generated by deamination of m5C at high temperatures.
Reactions of CH‐Acids with α,β‐Unsaturated Aldehydes in Ionic Liquids. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Construction of an adenovirus type 7a E1A- vector (1997)

A strategy for constructing replication-defective adenovirus vectors from non-subgroup C viruses has been successfully demonstrated with adenovirus type 7 strain a (Ad7a) as the prototype. An E1A-deleted Ad7a reporter virus expressing the chloramphenicol acetyltransferase (CAT) gene from the cytomegalovirus promoter enhancer was constructed with DNA fragments isolated from Ad7a, an Ad7a recombination reporter plasmid, and the 293 cell line. The Ad7a-CAT virus particle transduces A549 cells as efficiently as Ad5-based vectors. Intravenous infections in a murine model indicate that the Ad7a-CAT virus infects a variety of tissues, with maximal levels of CAT gene expression found in the liver. The duration of Ad7a-CAT transgene expression in the liver was maximally maintained 2 weeks postinfection, with a decline to baseline activity by the week 4 postinfection. Ad7a-CAT represents the first example of a non-subgroup C E1A- adenovirus gene transfer vector.
Ultrasonic sensor for photoresist process monitoring (1999)

An ultrasonic sensor has been developed to monitor photoresist processing in situ, during semiconductor manufacturing. Photoresist development, pre-exposure bake, and post-exposure bake were monitored for the Shipley 1800 series I-line resists, and the pre-exposure bake of Shipley APEX-E deep-uv (DUV) resist was monitored as well. Development monitoring was achieved by measuring thickness changes in the resist as it was removed. Data regarding dependence of development rate on exposure dose was obtained for the I-line resist with exposure doses varying from 20 to 68 mJ/cm/sup 2/. Measurements showed an increase in average development rate from 0.04 to 0.155 /spl mu/m/s, with the rate leveling off at around 55 mJ/cm/sup 2/. Pre-exposure bake monitoring results demonstrated the ability of the sensor to measure the glass transition temperature of the resist film during prebake as well as the ability to invert out the elastic constants of the film using reflection theory. The glass transition temperature (T/sub g/) is an important parameter in both the pre- and post-exposure bakes and therefore could be useful in monitoring these processes. Results of pre-exposure bake T/sub g/ measurements are presented for both-I-line and DUV resists. The glass transition temperature during prebake was found to be higher for the DUV resist than for the I-line series. The I-line resist post-exposure bake measurement of glass transition temperature confirmed the reported T/sub g/ of 118/spl deg/C for the I-line novolac resin. The multiple uses of this sensor make it suitable for integration into a manufacturing setting.
The CB2 Cannabinoid Receptor Controls Myeloid Progenitor Trafficking (2008)

Cannabinoids are potential agents for the development of therapeutic strategies against multiple sclerosis. Here we analyzed the role of the peripheral CB(2) cannabinoid receptor in the control of myeloid progenitor cell trafficking toward the inflamed spinal cord and their contribution to microglial activation in an animal model of multiple sclerosis (experimental autoimmune encephalomyelitis, EAE). CB(2) receptor knock-out mice showed an exacerbated clinical score of the disease when compared with their wild-type littermates, and this occurred in concert with extended axonal loss, T-lymphocyte (CD4(+)) infiltration, and microglial (CD11b(+)) activation. Immature bone marrow-derived CD34(+) myeloid progenitor cells, which play a role in neuroinflammatory pathologies, were shown to express CB(2) receptors and to be abundantly recruited toward the spinal cords of CB(2) knock-out EAE mice. Bone marrow-derived cell transfer experiments further evidenced the increased contribution of these cells to microglial replenishment in the spinal cords of CB(2)-deficient animals. In line with these observations, selective pharmacological CB(2) activation markedly reduced EAE symptoms, axonal loss, and microglial activation. CB(2) receptor manipulation altered the expression pattern of different chemokines (CCL2, CCL3, CCL5) and their receptors (CCR1, CCR2), thus providing a mechanistic explanation for its role in myeloid progenitor recruitment during neuroinflammation. These findings demonstrate the protective role of CB(2) receptors in EAE pathology; provide evidence for a new site of CB(2) receptor action, namely the targeting of myeloid progenitor trafficking and its contribution to microglial activation; and support the potential use of non-psychoactive CB(2) agonists in therapeutic strategies for multiple sclerosis and other neuroinflammatory disorders.
Mechanisms of Inhibition of in Vitro Dimerization of HIV Type I RNA by Sense and Antisense Oligonucleotides (1996)

Retroviruses display a strong selective pressure to maintain the dimeric nature of their genomic RNAs, suggesting that dimerization is essential for viral replication. Recently, we identified the cis-element required for initiation of human immunodeficiency virus type I (HIV-I) RNA dimerization in vitro. The dimerization initiation site (DIS) is a hairpin structure containing a self-complementary sequence in the loop. We proposed that dimerization is initiated by a loop-loop kissing interaction involving the self-complementary sequence present in each monomer. We tested the ability of sense and antisense oligonucleotides targeted against the DIS to interfere with a preformed viral RNA dimer. Self-dimerization and inhibition properties of the tested oligonucleotides are dictated by the nature of the loop. An RNA loop is absolutely required in the case of sense oligonucleotides, whereas the nature and the sequence of the stem is not important. They form reversible loop-loop interactions and act as competitive inhibitors. Antisense oligonucleotides are less efficient in self-dimerization and are more potent inhibitors than sense oligonucleotides. They are less sensitive to the nature of the loop than the antisense oligonucleotides. Antisense hairpins with either RNA or DNA stems are able to form highly stable and irreversible complexes with viral RNA, resulting from complete extension of base pairing initiated by loop-loop interaction.
Long‐term analysis of the palliative benefit of 2‐chlorodeoxyadenosine for myelofibrosis with myeloid metaplasia (2005)

This study confirmed relevant and frequently durable palliation of symptoms in about half the patients. 2-CdA is a reasonable palliative option in postsplenectomy patients with MMM who have problematic myeloproliferation.
Gamete intra-fallopian transfer (GIFT): a new treatment for infertility. (1985)

Cet article rapporte l'experience des auteurs au sujet d'une serie de quatre patientes ayant subi la technique de transfert de gamete intra-tubaire qui consiste a placer les deux gametes, spermatozoide et ovocyte, a l'interieur de la trompe de Fallope, site normal de fecondation chez l'homme, par l'intermediaire d'un laparoscope ou d'une minilaparotomie. Les resultats de cette etude montrent que cette technique est efficace pour provoquer une grossesse chez des couples au long passe de sterilite
A RANK/TRAF6-dependent Signal Transduction Pathway Is Essential for Osteoclast Cytoskeletal Organization and Resorptive Function (2002)

Signaling through receptor activator of nuclear factor-kappaB (RANK) is essential for the differentiation and activation of osteoclasts, the cell principally responsible for bone resorption. Animals genetically deficient in RANK or the cognate RANK ligand are profoundly osteopetrotic because of the lack of bone resorption and remodeling. RANK provokes biochemical signaling via the recruitment of intracellular tumor necrosis factor receptor-associated factors (TRAFs) after ligand binding and receptor oligomerization. To understand the RANK-mediated signal transduction mechanism in osteoclastogenesis, we have designed a system to recapitulate osteoclast differentiation and activation in vitro by transfer of the RANK cDNA into hematopoietic precursors genetically deficient in RANK. Gene transfer of RANK constructs that are selectively incapable of binding different TRAF proteins revealed that TRAF pathways downstream of RANK that affect osteoclast differentiation are functionally redundant. In contrast, the interaction of RANK with TRAF6 is absolutely required for the proper formation of cytoskeletal structures and functional resorptive activity of osteoclasts. Moreover, signaling via the interleukin-1 receptor, which also utilizes TRAF6, rescues the osteoclast activation defects observed in the absence of RANK/TRAF6 interactions. These studies are the first to define the functional domains of the RANK cytoplasmic tail that control specific differentiation and activation pathways in osteoclasts.
Surgical Treatment for the Painful Motion Segment (2005)

Posterior fusion techniques have been and will continue to be among the most commonly performed procedures in lumbar spine surgery. The different methods of fusion are well defined, as are the possible complications and outcomes. They are effective techniques when performed on appropriately selected patients by a surgeon knowledgeable in the techniques and indications. Further studies are needed regarding promising but relatively unproven developments such as minimally invasive surgery and the use of osteoinductive agents.
Telomere Inhibition and Telomere Disruption as Processes for Drug Targeting (2003)

The components and cofactors of the holoenzyme telomerase and its substrate telomeric DNA are attractive targets for anticancer agents that act by inhibiting the activity of telomerase. This review outlines recent advances in telomerase inhibition that have been achieved using antisense oligonucleotides and ribozymes that target the telomerase mRNA or its hTR RNA template. Although these are potent catalytic inhibitors of telomerase, they are challenging to implement in the clinic due to their delayed effectiveness. Drugs that directly bind to the telomeres, the complex structures that are associated at the telomeric ends, and stabilize secondary DNA structures such as G-quadruplexes are also potent inhibitors of telomerase. Special focus is given here to the telomeres, the biological machinery that works in tandem with telomerase to elongate telomeres, the causes of telomere disruption or dysfunction, and the consequences of disruption/dysfunction on the activity and design of anticancer agents.
Epidermal Stem Cells as Targets for Gene Transfer (2000)

One of the characteristics of the epidermis that makes it an attractive tissue for gene therapy is that it is renewed through proliferation of stem cells. If the stem cells can be transduced with the gene of interest then expression of that gene should continue throughout adult life. This article discusses current research on epidermal stem cells, highlighting progress in their identification and in discovering the mechanisms that regulate exit from the stem cell compartment.