gebhart/patrepeval huggingface dataset:
Site-Specific Recombination of Temperate <i>Myxococcus xanthus</i> Phage Mx8: Regulation of Integrase Activity by Reversible, Covalent Modification (1999)

Temperate Myxococcus xanthus phage Mx8 integrates into the attB locus of the M. xanthus genome. The phage attachment site, attP, is required in cis for integration and lies within the int (integrase) coding sequence. Site-specific integration of Mx8 alters the 3' end of int to generate the modified intX gene, which encodes a less active form of integrase with a different C terminus. The phage-encoded (Int) form of integrase promotes attP x attB recombination more efficiently than attR x attB, attL x attB, or attB x attB recombination. The attP and attB sites share a common core. Sequences flanking both sides of the attP core within the int gene are necessary for attP function. This information shows that the directionality of the integration reaction depends on arm sequences flanking both sides of the attP core. Expression of the uoi gene immediately upstream of int inhibits integrative (attP x attB) recombination, supporting the idea that uoi encodes the Mx8 excisionase. Integrase catalyzes a reaction that alters the primary sequence of its gene; the change in the primary amino acid sequence of Mx8 integrase resulting from the reaction that it catalyzes is a novel mechanism by which the reversible, covalent modification of an enzyme is used to regulate its specific activity. The lower specific activity of the prophage-encoded IntX integrase acts to limit excisive site-specific recombination in lysogens carrying a single Mx8 prophage, which are less immune to superinfection than lysogens carrying multiple, tandem prophages. Thus, this mechanism serves to regulate Mx8 site-specific recombination and superinfection immunity coordinately and thereby to preserve the integrity of the lysogenic state.
Some practical considerations in the design of steam injection wells (1968)

In general, heat loss causes an increase in casing temperature and in thermal casing stress. Although heat loss can be reduced in several ways, some methods for doing this may increase rather than decrease casing temperature. An attempt to protect the casing may inadvertently result in an increase in casing stress, which may lead to casing failure. Changes in steam pressure in the injection string, which are caused by friction, the weight of the steam column, and kinetic energy change, may have a significant effect on heat loss, on the properties of the steam reaching the formation, and on casing stress. Due to these effects, the fluid entering the formation may not have the desired properties. Heat-loss calculations which include the effects of pressure change may be used to design a well completion-steam injection program so steam will enter the formation at the desired pressure, temperature, and rate. Such calculations also allow conditions to be chosen so the casing will not be endangered and so heat loss will not be excessive. (11 refs.)
Zinc and Redox Signaling: Perturbations Associated with Cardiovascular Disease and Diabetes Mellitus (2010)

Cellular signal transduction pathways are influenced by the zinc and redox status of the cell. Numerous chronic diseases, including cardiovascular disease (CVD) and diabetes mellitus (DM), have been associated with impaired zinc utilization and increased oxidative stress. In humans, mutations in the MT-1A and ZnT8 genes, both of which are involved in the maintenance of zinc homeostasis, have been linked with DM development. Changes in levels of intracellular free zinc may exacerbate oxidative stress in CVD and DM by impacting glutathione homeostasis, nitric oxide signaling, and nuclear factor-kappa B-dependent cellular processes. Zinc ions have been shown to influence insulin and leptin signaling via the phosphoinositide 3′-kinase/Akt pathway, potentially linking an imbalance of zinc at the cellular level to insulin resistance and dyslipidemia. The oxidative modification of cysteine residues in zinc coordination sites in proteins has been implicated in cellular signaling and regulatory pathways. Despite the many interactions between zinc and cellular stress responses, studies investigating the potential therapeutic benefit of zinc supplementation in the prevention and treatment of oxidative stress-related chronic disease in humans are few and inconsistent. Further well-designed randomized controlled trials are needed to determine the effects of zinc supplementation in populations at various stages of CVD and DM progression.
Inhibition of Alzheimer’s amyloid toxicity with a tricyclic pyrone molecule <i>in vitro</i> and <i>in vivo</i> (2008)

Small beta-amyloid (Abeta) 1-42 aggregates are toxic to neurons and may be the primary toxic species in Alzheimer's disease (AD). Methods to reduce the level of Abeta, prevent Abeta aggregation, and eliminate existing Abeta aggregates have been proposed for treatment of AD. A tricyclic pyrone named CP2 is found to prevent cell death associated with Abeta oligomers. We studied the possible mechanisms of neuroprotection by CP2. Surface plasmon resonance spectroscopy shows a direct binding of CP2 with Abeta42 oligomer. Circular dichroism spectroscopy reveals monomeric Abeta42 peptide remains as a random coil/alpha-helix structure in the presence of CP2 over 48 h. Atomic force microscopy studies show CP2 exhibits similar ability to inhibit Abeta42 aggregation as that of Congo red and curcumin. Atomic force microscopy closed-fluid cell study demonstrates that CP2 disaggregates Abeta42 oligomers and protofibrils. CP2 also blocks Abeta fibrillations using a protein quantification method. Treatment of 5x familial Alzheimer's disease mice, a robust Abeta42-producing animal model of AD, with a 2-week course of CP2 resulted in 40% and 50% decreases in non-fibrillar and fibrillar Abeta species, respectively. Our results suggest that CP2 might be beneficial to AD patients by preventing Abeta aggregation and disaggregating existing Abeta oligomers and protofibrils.
Reduction of Tumorigenicity by α<sup>3</sup>Integrin in a Rhabdomyosarcoma Cell Line (1996)

International audience
Down-Modulation of L-Selectin by Lipopolysaccharide Is Not Required for Lipopolysaccharide-Induced Expression of CD14 in Mouse Bone Marrow Granulocytes (2001)

We established in previous studies that a constitutive lipopolysaccharide (LPS) receptor of low affinity is present on mouse bone marrow granulocytes (BMG). This yet-unidentified receptor is involved in the LPS-induced expression of a second LPS receptor, CD14. Because it has been claimed that L-selectin (CD62L) is a low-affinity LPS receptor in mature granulocytes (polymorphonuclear leukocytes), it may be asked whether this molecule could be the constitutive LPS receptor in BMG. We show in this study that L-selectin is constitutively present on BMG and is down-regulated after exposure of the cells to LPS. A phorbol ester induced a down-regulation of CD62L and blocked the LPS-induced expression of CD14. However, a metalloproteinase inhibitor (BB-3103) blocked the former but not the latter effect of PMA. We also observed an absence of cross-reactivity between LPS and a CD62L ligand (fucoidan) in binding studies with radiolabeled derivatives of the two agents. Furthermore, BMG from L-selectin-deficient mice expressed normal levels of CD14 in response to LPS. Taken together, these results demonstrate that in BMG, L-selectin is not the constitutive LPS receptor required for the LPS-induced expression of CD14.
Hip and shoulder rotations during the golf swing of sub-10 handicap players (1998)

The motion of the shoulders, arms and club during the golf swing has often been explained using the 'double pendulum' model. Despite subsequent explanations for the actions of the distal segments of the body, the coordination of more proximal segments during the swing is less well understood. To ascertain the pattern of centre of mass motion and hip and shoulder rotations that result in a high clubhead speed at impact, the swing used in driving from the tee of eight low-handicap golfers was videotaped and analysed using three-dimensional techniques. The shoulders rotated in excess of 90 degrees during the backswing and, in 75% of the golfers, continued rotating away from the flag as the hips began turning back towards it. This sequential pattern of hip and shoulder rotation indicated that they conformed to the 'summation of speed' principle, which is hypothesized to result in a greater torque being applied to the club before impact. The speed of the drive was also benefited by the centre of mass shifting exclusively in the intended direction of ball flight during impact.
FACTORS AFFECTING THE DURABILITY OF PRIMARY TOTAL KNEE PROSTHESES (2003)

Significant risk factors for failure of total knee arthroplasty were the type of implant, age and gender of the patient, diagnosis, type of fixation, and design of the patellar component. In the ideal situation-treatment of a woman over the age of seventy years who has inflammatory arthritis with a nonmodular, metal-backed tibial component, cement fixation, an all-polyethylene patellar component, and retention of the posterior cruciate ligament-the ten-year survivorship of the prosthesis was estimated to be 98% (95% confidence interval, 97% to 99%).
Oocyte aging underlies female reproductive aging: biological mechanisms and therapeutic strategies (2015)

In recent years, postponement of marriage and childbearing in women of reproductive age has led to an increase in the incidence of age-related infertility. The reproductive aging process in women is assumed to occur due to a decrease in both the quantity and quality of the oocytes, with the ultimate result being a decline in fecundity. This age-related decline in fecundity is strongly dependent on oocyte quality, which is critical for fertilization and subsequent embryo development. Aged oocytes display increased chromosomal abnormality and dysfunction of cellular organelles, both of which factor into oocyte quality. In particular, mitochondrial dysfunction has been suggested as a major contributor to the reduction in oocyte quality as well as to chromosomal abnormalities in aged oocytes and embryos. Participation of oxidative stress in the oocyte aging process has been proposed because oxidative stress has the capacity to induce mitochondrial dysfunction and directly damage many intracellular components of the oocytes such as lipids, protein, and DNA. In an attempt to improve mitochondrial function in aged oocytes, several therapeutic strategies have been investigated using both animal models and assisted reproductive technology. Here, we review the biological mechanisms and present status of therapeutic strategies in the female reproductive aging field and indicate possible future therapeutic strategies.
Piezoelectric polymer tactile sensor arrays for robotics (1989)

Six piezoelectric polymer tactile sensor arrays for robotics have been designed, fabricated, and evaluated for piezoelectric activity and tactile sensing. Two of the arrays were thermally poled. Each consisted of a planar 5*5 arrangement of identical (3 mm*3 mm) discrete sensors made of polyvinylidene fluoride with Al electrodes. PVDF provided a pressure sensing capability. The sensor's spatial configuration provides information for discerning an object's shape. The PVDF film was evaluated for two film thicknesses (25 and 40 mu m) and for two versions (unmetallized and vendor-metallized). Two electrode fabrication processes were developed to accommodate the inherent chemical and temperature limitations of the PVDF film. Four array configurations which performed significantly better than the others were square-pad designs that used the 40- mu m thick PVDF film. Two sensor-element spacings (500 and 750 mu m) and electrode-fabrication processes (evaporation and photolithographic) were represented equally in the fabrication of this set.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A dual-functional paramyxovirus F protein regulatory switch segment (2003)

Many viral fusion-mediating glycoproteins couple alpha-helical bundle formation to membrane merger, but have different methods for fusion activation. To study paramyxovirus-mediated fusion, we mutated the SV5 fusion (F) protein at conserved residues L447 and I449, which are adjacent to heptad repeat (HR) B and bind to a prominent cavity in the HRA trimeric coiled coil in the fusogenic six-helix bundle (6HB) structure. These analyses on residues L447 and I449, both in intact F protein and in 6HB, suggest a metamorphic region around these residues with dual structural roles. Mutation of L447 and I449 to aliphatic residues destabilizes the 6HB structure and attenuates fusion activity. Mutation of L447 and I449 to aromatic residues also destabilizes the 6HB structure despite promoting hyperactive fusion, indicating that 6HB stability alone does not dictate fusogenicity. Thus, residues L447 and I449 adjacent to HRB in paramyxovirus F have distinct roles in fusion activation and 6HB formation, suggesting this region is involved in a conformational switch.
FASD: A Fault-tolerant, Adaptive, Scalable, Distributed Search Engine (2002)

This paper introduces FASD, a fault-tolerant, adaptive, scalable, and distributed search layer designed to augment existing peer-to-peer applications. The FASD layer operates as a network of identical nodes that collectively pool their storage space to cache &quot;metadata keys&quot; and cooperatively route queries to the nodes most likely to satisfy them. A &quot;metadata key&quot; is a list of weighted terms that describe the information content of a document in the underlying network. Although completely decentralized, FASD&apos;s approach is able to e#ciently match the recall and precision of a centralized search engine. Simulation results indicate that latency and bandwidth consumption scale logarithmically with the size of a FASD network.
A Study on Encryption Algorithms and Modes for Disk Encryption (2009)

Data storage devices such as disk drives and personal storage devices (PSD) such as flash disks are now widely used in everyday appliances. Data breaches have grown rapidly in the recent years due to compromised confidential data from storage devices. These trends forced standardization of encryption methods to secure storage devices. This paper provides a comparison review of existing encryption algorithms and modes of operations that are suitable for securing storage devices, mainly disk drives. The recent IEEE approved standard for encryption mode of operation, XTS will be evaluated in term of performance with different algorithms (AES, Twofish, and RC6). The performance of XTS mode with other modes of operations (LRW and CBC) will be explored. This detailed review and performance analysis will provide guidelines for storage devices designers to implement disk encryption.
Social Components of Community Water Supply and Sanitation (1990)

The successful implementation of water supply and sanitation programs in developing countries depends not only on the provision of adequate funding and the selection of appropriate technologies but also the melding of social components at the community level. These factors include social, cultural and behavioral aspects of a society and their integration with technical and economic components. The paper reviews these various social components and explains the importance for consideration of these factors.
Phosphoryl exchange reaction catalyzed by enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Kinetic characterization. (1980)

Enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system catalyzes phosphoryl transfer from phosphoenolpyruvate to the heat-stable phosphoryl carrier protein, HPr.Enzyme I also catalyzes a rapid phosphoryl exchange reaction in which the phosphoryl moiety of phosphoenolpyruvate is transferred to pyruvate.Additionally, Enzyme I plus HPr catalyze the slow hydrolysis of phosphoenolpyruvate to pyruvate and inorganic phosphate.A simple and quantitative assay was developed for measuring these reactions."C-Labeled phosphoenolpyruvate or pyruvate was used, and the formation of ['4C]pyruvate or phosphoenolpyruvate was measured, respectively.The two radioactive products were separated by conversion of pyruvate to the dinitrophenylhydrazone derivative and extraction into ethyl acetate.Employing this assay, the Enzyme I-catalyzed phosphoryl exchange and sugar phosphorylation reactions showed sigmoidal kinetics when reaction rate was plotted versus Enzyme I concentration.The enzyme was activated by M g + , Mn2+, and Co2+ but not by other divalent cations tested.The pH optimum in the presence of Mg2' was 1.5.Kinetic binding constants were estimated as follows: P-enolpyruvate, 0.4 m ~; pyruvate, 2 m ~; Mg"', 2 mm; P-enolpyruvate (bound to phospho-Enzyme I), 2.5 m ~; and pyruvate (bound to free Enzyme I), 20 m ~.Low concentrations of bromopyruvate irreversibly inactivated the enzyme, while oxalate appeared to be a potent transition state inhibitor.Enzyme I catalyzed exchange reactions when a- ketobutyrate or fl-hydroxypyruvate replaced pyruvate, but higher homologues of pyruvate were essentially inactive.Bacterial extracts catalyzed the hydrolysis of phosphoenolpyruvate in the presence of low concentrations of Co2+.This activity was not attributable to a known enzyme constituent of the PTS.In their initial characterization of the bacterial phosphotransferase system, Kundig et al. (1) showed that the phosphorylation of sugars with phosphoenolpyruvate depended
Influence of annealing atmosphere on the performance of a β-Ga<sub>2</sub>O<sub>3</sub> thin film and photodetector (2018)

β-Ga2O3 epitaxial thin films were deposited by laser molecular beam epitaxy (LMBE) and annealed at 800°C for 30 minutes in air and oxygen atmospheres, respectively. Photodetectors were fabricated using as-grown and annealed Ga2O3 epilayers. The influence of the annealing atmosphere on the crystal structure and optical properties of Ga2O3 films was investigated. X-ray diffraction (XRD) measurements show that the in-plane compressive strain of Ga2O3 thin films could be relaxed after high temperature thermal annealing. Compared with the as-grown sample, the annealed samples exhibit a red shift of absorption edge in the transmittance spectra, indicating a reduced bandgap. According to the XPS measurement results, the atomic ratios of O to Ga also increased for the annealed samples. Moreover, the oxygen-annealed photodetector achieves a larger photocurrent, higher responsivity and better time-dependent photoresponse than the other two samples, which may be attributed to the decrease in the number of oxygen vacancies.
Proteome-wide analysis of head and neck squamous cell carcinomas using laser-capture microdissection and tandem mass spectrometry (2005)

Remarkable progress has been made to identify genes expressed in squamous cell carcinomas of the head and neck (HNSCC). However, limited information is available on their corresponding protein products, whose expression, post-translational modifications, and activity are ultimately responsible for the malignant behavior of this tumor type. We have combined laser-capture microdissection (LCM) with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify proteins expressed in histologically normal squamous epithelium and matching SCC. The protein fraction from approximately 10,000-15,000 normal and tumor cells was solubilized, digested with trypsin, and the resulting peptides were analyzed by LC-MS/MS. Database searching of the resulting sequence information identified 30-55 proteins per sample. Keratins were the most abundant proteins in both normal and tumor tissues. Among the proteins differentially expressed, keratin 13 was much lower in tumors, whereas heat-shock (Hsp) family members were highly expressed in neoplastic cells. Wnt-6 and Wnt-14 were identified in both normal and tumor tissues, respectively, and placental growth factor (PIGF) was detected only in tumors. Immunohistochemical analysis of HNSCC tissues revealed lack of keratin 13 in tumor tissues, and strong staining in normal epithelia, and high expression of Hsp90 in tumors. Our study, by combining LCM and proteomic technologies, underscores the advantages of this approach to investigate complex changes at the protein level in HNSCC, thus complementing existing and emerging genomic technologies. These efforts may likely result in the identification of new biomarkers for HNSCC that can be used to diagnose disease, predict susceptibility, and monitor progression in individual patients.
Radiation pressure and the photon momentum in dielectrics (2010)

Abstract We review the magnitudes of the photon momenta in free space, derived by Maxwell and Einstein, and those in homogeneous, dispersionless and lossless dielectrics, associated with Abraham and Minkowski. These momenta determine the forces exerted by light beams on material objects, as measured in radiation pressure experiments. It is shown that conservation conditions for components of the electromagnetic energy–momentum tensors derived by Abraham and Minkowski, also by Einstein and Laub, are equivalent relations simply derived from Maxwell's equations. The challenge for theory is the reliable interpretation of experimental momentum transfers from light to matter, which requires extensions of the basic theory to include material dispersion and surface effects. The main experiments are reviewed, together with details of a Lorentz-force theory that accounts for them. It is shown that the Abraham kinetic momentum is associated with the overall motion of a dielectric sample, while the Minkowski canonical momentum applies to the motion of bodies embedded in the dielectric. Keywords: Abraham momentumMinkowski momentumLorentz force theory Acknowledgements The authors thank Steve Barnett, Masud Mansuripur, Peter Milonni and Miles Padgett for considerable help in the writing of this Tutorial Review.
<i>syn</i>‐Selective and Enantioselective Direct Cross‐Aldol Reactions between Aldehydes Catalyzed by an Axially Chiral Amino Sulfonamide (2007)

Complementary to proline: An axially chiral amino sulfonamide (S)-1 was successfully applied as the catalyst to the direct cross-aldol reaction between two different aldehydes (see scheme; NMP=N-methylpyrrolidone). This catalyst has the advantage of giving mainly syn products, while proline shows the opposite anti selectivity.
Verification of a combinational loop based arbitration scheme in a system-on-chip integration architecture (2002)

We tackle the problem of verifying correctness properties on an HDL implementation of a system-on-chip bus-based integration architecture. The bus architecture is characterized by a 2-level arbitration scheme and the absence of a centralized controller. Checking correctness properties on an implementation can be hard because it is common for an implementation to contain constructs which are difficult to capture using a synchronous FSM model. The hard part in our case is that for performance reasons the second-level arbitration is based on a token-ring protocol implemented as a novel combinational loop. While the combinational loop is non-inverting, there is no acyclic implementation which can mimic its functionality. Our contribution has been to show how the combinational loop, and hence the arbitration scheme, can be modeled by means of mechanical transformations of the implementation model. We model check a 4-client base case implementation followed by an inductive argument for the correctness of an n-client implementation. Our approach including the combinational loop modeling and the inductive proof technique has general application to other similar protocols. Our verification methodology involved checking a Verilog implementation for desired properties using symbolic model checking in the VIS system from UC Berkeley. Checking properties on the base case required negligible amount of CPU resources. While there have been a number of formal verification case studies, we do not believe that any previous work has proposed a general purpose technique for modeling combinational loops.