gebhart/patrepeval huggingface dataset:
The Mammalian DNA Replication Elongation Checkpoint: Implication of Chk1 and Relationship with Origin Firing as Determined by Single DNA Molecule and Single Cell Analyses (2007)

The regulation of DNA replication initiation is well documented, for both unperturbed and damaged cells. The regulation of elongation, or fork velocity, however, has only recently been revealed with the advent of new techniques allowing us to view DNA replication at the single cell and single DNA molecule levels. Normally in S phase, the progression of replication forks and their stability are regulated by the ATR-Claspin-Chk1 pathway. We recently showed that replication fork velocity varies across the human genome in normal and cancer cells, but that the velocity of a given fork is positively correlated with the distance between origins on the same DNA fiber. (19) Accordingly, in DNA replication-deficient Bloom's syndrome cells, reduced fork velocity is associated with an increased density of replication origins. (21) Replication elongation is also regulated in response to DNA damage. In human colon carcinoma cells treated with the topoisomerase I inhibitor camptothecin, DNA replication is inhibited both at the level of initiation and at the level of elongation through a Chk1-dependent checkpoint mechanism. (10) Together, these new findings demonstrate that replication fork velocity (fork progression) is coordinated with inter-origin distance and that it can be actively slowed down by Chk1-dependent mechanisms in response to DNA damage. Thus, we propose that the intra-S phase checkpoint consist of at least three elements: (1) stabilization of damaged replication forks; (2) suppression of firing of late origins; and (3) arrests of normal ongoing forks to prevent further DNA lesions by replication of a damaged DNA template.
Reliability Criteria Evaluation for TDOA Estimates in a Variety of Real Environments (2006)

Time delay estimates in microphone pairs are commonly used for acoustic sound source localization. In real environments, the reliability of time delay estimates quickly degrades for increasing noise or room reverberation levels. The paper presents two computationally non-demanding criteria to determine the reliability of time delay estimates. The criteria are evaluated for real data in a variety of acoustic environments with different reverberation and noise levels. The results show the generality of the proposed reliability indicators in delivering information on the credibility of the current time delay estimate for many typical room environments.
MPEG-4 to H.264/AVC transcoding (2007)

In this paper, we consider the problem of MPEG-4 visual simple profile to H.264/AVC baseline profile (BP) transcoding. An efficient transcoding algorithm with fast mode selection and motion vector refinement is proposed. The proposed algorithm exploits the side information from the decoding stage to predict the coding modes and MVs of H.264/AVC BP coding. The proposed algorithm consists of two parts: INTRA macroblocks (MBs) transcoding and INTER MBs transcoding. By reusing the side information during the decoding stage, these techniques provide significant complexity reduction, when compared with the fully spatial domain approach.
Nuevas fuentes de información académica (2010)

Se describen las caracteristicas basicas de uso y consumo de la informacion cientifica, tecnica y medica (STM), y se presentan 3 recursos de informacion creados recientemente: DeepDyve; Science Research, de Deep Web Technologies; y WorldCat, de OCLC. Tambien se mencionan Q-Sensei, Base, Scitopia y Lumifi.
Genes in the ear: what have we learned over the last years? (2001)

In developed countries 50% of childhood hearing impairment is attributable to genetic causes. In a limited number of cases, the hearing impairment is part of a syndrome, and several genes for syndromic deafness have been identified over the last 10 years. In the majority of cases, the hearing impairment occurs without additional clinical abnormalities (non-syndromic). Progressive hearing loss is very frequent in adults. By the age of 80 approximately 50% of the population is affected by age-related hearing loss, which is due partly to genetic factors. Before 1994, little was known about the genes responsible for non-syndromic hearing impairment, although epidemiological studies have suggested that more than 100 genes might be involved. Over the last 6 years, extremely rapid progress was realized in the field of the molecular genetics of hearing and deafness. More than 70 genes for non-syndromic hearing impairment have been localized to the human genome, and 18 of these have been identified.
Towards Three And Four Dimensional Data Collection For Electrical Resistivity Data (2004)

Advances in hardware and software have made the collection of fully three-dimensional and four&lt;br&gt;dimensional resistivity data not only possible but practical. To fully utilize these new capabilities&lt;br&gt;requires new approaches to collecting data. This paper shows both theoretical and field comparisons of&lt;br&gt;data collection schemes comparing more traditional one- and two- dimensional data collection strategies&lt;br&gt;with fully three-dimensional strategies. These new approaches include array patterns, such as horizontal&lt;br&gt;subsurface dipoles, that were not possible in older schemes. Finding optimal arrays requires tradeoffs in&lt;br&gt;resolution, acquisition time, and signal levels. A new statistical based approach is shown that can be&lt;br&gt;used to determine optimal array types under various constraints. Tests of these new array types show&lt;br&gt;that they can provide substantial improvements in the resolution of subsurface resistivity and the change&lt;br&gt;in resistivity with time.
A strong tracking extended Kalman observer for nonlinear discrete-time systems (1999)

The authors show how the extended Kalman filter, used as an observer for nonlinear discrete-time systems or extended Kalman observer (EKO), becomes a useful state estimator when the arbitrary matrices, namely R/sub k/ and Q/sub k/, are adequately chosen. As a first step, we use the linearization technique given by Boutayed et al. (1997), which consists of introducing unknown diagonal matrices to take the approximation errors into account. It is shown that the decreasing Lyapunov function condition leads to a linear matrix inequality (LMI) problem, which points out the connection between a good convergence behavior of the EKO and the instrumental matrices R/sub k/ and Q/sub k/. In order to satisfy the obtained LMI, a particular design of Q/sub k/ is given. High performances of the proposed technique are shown through numerical examples under the worst conditions.
Synthetic Site-Selectively Mono-6-O-Sulfated Heparan Sulfate Dodecasaccharide Shows Anti-Angiogenic Properties In Vitro and Sensitizes Tumors to Cisplatin In Vivo (2016)

Heparan sulphate (HS), a ubiquitously expressed glycosaminoglycan (GAG), regulates multiple cellular functions by mediating interactions between numerous growth factors and their cell surface cognate receptors. However, the structural specificity of HS in these interactions remains largely undefined. Here, we used completely synthetic, structurally defined, alternating N-sulfated glucosamine (NS) and 2-O-sulfated iduronate (IS) residues to generate dodecasaccharides ([NSIS]6) that contained no, one or six glucosamine 6-O-sulfates (6S). The aim was to address how 6S contributes to the potential of defined HS dodecasaccharides to inhibit the angiogenic growth factors FGF2 and VEGF165, in vitro and in vivo. We show that the addition of a single 6S at the non-reducing end of [NSIS]6, i.e. [NSIS6S]-[NSIS]5, significantly augments the inhibition of FGF2-dependent endothelial cell proliferation, migration and sprouting in vitro when compared to the non-6S variant. In contrast, the fully 6-O-sulfated dodecasaccharide, [NSIS6S]6, is not a potent inhibitor of FGF2. Addition of a single 6S did not significantly improve inhibitory properties of [NSIS]6 when tested against VEGF165-dependent endothelial cell functions.In vivo, [NSIS6S]-[NSIS]5 blocked FGF2-dependent blood vessel formation without affecting tumor growth. Reduction of non-FGF2-dependent ovarian tumor growth occurred when [NSIS6S]-[NSIS]5 was combined with cisplatin. The degree of inhibition by [NSIS6S]-[NSIS]5 in combination with cisplatin in vivo equated with that induced by bevacizumab and sunitinib when administered with cisplatin. Evaluation of post-treatment vasculature revealed that [NSIS6S]-[NSIS]5 treatment had the greatest impact on tumor blood vessel size and lumen formation. Our data for the first time demonstrate that synthetic, structurally defined oligosaccharides have potential to be developed as active anti-angiogenic agents that sensitize tumors to chemotherapeutic agents.
Mutations that change the immunological subtype of hepatitis b virus surface antigen and distinguish between antigenic and immunogenic determination (1989)

The molecular basis of the d or y immunological subtype of hepatitis B virus (HBV) surface antigen (HBsAg) has been investigated by mutation of specific amino acid residues. When combined with substitution of serine 113 by threonine, replacement of arginine 122 by lysine or of tyrosine 134 by phenylalanine, or both of these changes, altered the antigenic subtype of HBsAg from y+d- to y+d+. These same mutations had a more dramatic effect on the subtype of antibodies induced by the antigens, a combination of all three mutations completely changing the subtype from y to d. Our study thus identifies residues in HBsAg that not only affect the subtype but discriminate between changes in antigenic and immunogenic behaviour. It also shows how the y and d subtypes may be manifest by the same molecule.
Low-temperature catalytic gasification of food processing wastes. 1995 topical report (1996)

The catalytic gasification system described in this report has undergone continuing development and refining work at Pacific Northwest National Laboratory (PNNL) for over 16 years. The original experiments, performed for the Gas Research Institute, were aimed at developing kinetics information for steam gasification of biomass in the presence of catalysts. From the fundamental research evolved the concept of a pressurized, catalytic gasification system for converting wet biomass feedstocks to fuel gas. Extensive batch reactor testing and limited continuous stirred-tank reactor tests provided useful design information for evaluating the preliminary economics of the process. This report is a follow-on to previous interim reports which reviewed the results of the studies conducted with batch and continuous-feed reactor systems from 1989 to 1994, including much work with food processing wastes. The discussion here provides details of experiments on food processing waste feedstock materials, exclusively, that were conducted in batch and continuous- flow reactors.
Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence (2018)

Molecular phylogenetics is often used to estimate the time since the divergence of modern gene sequences. For highly diverged sequences, such phylogenetic techniques sometimes estimate surprisingly recent divergence times. In the case of viruses, independent evidence indicates that the estimates of deep divergence times from molecular phylogenetics are sometimes too recent. This discrepancy is caused in part by inadequate models of purifying selection leading to branch-length underestimation. Here we examine the effect on branch-length estimation of using models that incorporate experimental measurements of purifying selection. We find that models informed by experimentally measured site-specific amino-acid preferences estimate longer deep branches on phylogenies of influenza virus hemagglutinin. This lengthening of branches is due to more realistic stationary states of the models, and is mostly independent of the branch-length-extension from modeling site-to-site variation in amino-acid substitution rate. The branch-length extension from experimentally informed site-specific models is similar to that achieved by other approaches that allow the stationary state to vary across sites. However, the improvements from all of these site-specific but time-homogeneous and site-independent models are limited by the fact that a protein's amino-acid preferences gradually shift as it evolves. Overall, our work underscores the importance of modeling site-specific amino-acid preferences when estimating deep divergence times---but also shows the inherent limitations of approaches that fail to account for how these preferences shift over time.
Bezier and B-spline Technology (2003)

Graphical curves and surfaces are hot topics in many di#erent areas of research and application, not least due to the rapid progression of computer aided design (CAD) and gaming technology. Two of the most popular representations for this field are the Bezier and B-spline curves and surfaces. This thesis will
Parenteral Glutathione Monoester Enhances Tissue Antioxidant Stores (1992)

Glutathione (GSH) is a potent endogenous antioxidant that protects major organs from oxidant injury. However, present nutrition regimens may inadequately support tissue stores of this tripeptide during critical illness. To determine whether GSH reserves can be enhanced in vivo with intravenous (IV) supplements, rats underwent central venous catheterization, were given chow and water ad libitum during a 2‐day recovery period, and were then randomized to receive one of three treatments as an IV bolus: (1) dextrose, (2) glutathione (GSH), or (3) glutathione monoethyl ester. GSH monoethyl ester is transported into cells more easily than is GSH. Tissue and plasma samples were analyzed for GSH at 2 and 4 hours after drug administration. Liver, renal, and ileal mucosal GSH were significantly increased in the GSH‐monoethyl ester rats compared with dextrose‐treated animals. In addition, plasma GSH was dramatically increased after monoester injection. In contrast, GSH administration depressed liver GSH stores and did not significantly affect GSH concentration in the other organs analyzed. Plasma GSH concentration was elevated 2 hours after GSH administration. We conclude that: (1) the monoethyl ester of glutathione can be used in vivo to enhance tissue and plasma GSH concentration and (2) IV GSH administration does not significantly increase tissue GSH levels and may paradoxically depress hepatic GSH in normal rats. Because the malnourished and critically ill are likely to have depleted GSH stores, nutrition strategies that include the provision of GSH monoester may lend additional support to those organs that are at risk for injury from oxygen free radicals during catabolic states. (Journal of Parenteral and Enteral Nutrition 16: 413–418, 1992)
Comparative Biochemistry of Four Polyester (PET) Hydrolases** (2020)

The potential of bioprocessing in a circular plastic economy has strongly stimulated research into the enzymatic degradation of different synthetic polymers. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic framework for comparisons of PET hydrolases (or other plastic-degrading enzymes) acting on the insoluble substrate has not been established. Herein, we propose such a framework, which we have tested against kinetic measurements for four PET hydrolases. The analysis provided values of k<sub>cat</sub> and K<sub>M</sub> , as well as an apparent specificity constant in the conventional units of M<sup>-1</sup> s<sup>-1</sup> . These parameters, together with experimental values for the number of enzyme attack sites on the PET surface, enabled comparative analyses. A variant of the PET hydrolase from Ideonella sakaiensis was the most efficient enzyme at ambient conditions; it relied on a high k<sub>cat</sub> rather than a low K<sub>M</sub> . Moreover, both soluble and insoluble PET fragments were consistently hydrolyzed much faster than intact PET. This suggests that interactions between polymer strands slow down PET degradation, whereas the chemical steps of catalysis and the low accessibility associated with solid substrate were less important for the overall rate. Finally, the investigated enzymes showed a remarkable substrate affinity, and reached half the saturation rate on PET when the concentration of attack sites in the suspension was only about 50 nM. We propose that this is linked to nonspecific adsorption, which promotes the nearness of enzyme and attack sites.
Role of soluble factors (gamones) and calcium ions in conjugation of the ciliate Euplotes patella syngen 2 (1985)

Abstract Conjugation between cells of mating type IV and V in Euplotes patella syngen 2 was studied with respect to mating inducing factors (gamones) and their effects on pair formation. Type IV cells excreted into the medium gamone(s) of type IV which induced selfing pairs in and enhanced the gamone's excretion by cells of type V. The same effects on type IV cells were induced by cells and gamone(s) of type V. The number of homotypic pairs (IV‐IV, V‐V) increased with an increase in the level of Ca 2+ in the medium. However, heterotypic pairs (IV‐V) were constantly formed even in the absence of Ca 2+ , and their formation was not influenced by the level of Ca 2+ . When cells of two types were mixed, heterotypic pairs were predominantly produced, although cells were capable of forming pairs between homotypic types. These results revealed that pair formation between heterotypic cells was different from that between homotypic cells in the requirement of Ca 2+ , and that the specificity of pair formation between heterotypic cells was more predominant than that of homotypic ones.
Co-integration of a quartz OCXO and Si MEMS inertial sensors for improved navigational accuracy (2016)

On-chip integration of quartz resonators with Si devices opens new opportunities for microsystem miniaturization and enhanced performance. In addition to integrating with electronics, the integration of piezoelectric quartz resonators with other sensors of different material composition is also possible. In this paper, we demonstrate that a VHF SC-cut quartz resonator can be integrated within a high-aspect-ratio Si disk gyro with on-chip heating for locally ovenizing both devices in the same wafer-level vacuum cavity. The SC-cut OCXO can be used to lock the frequency and temperature of the gyro to ≤ 2 ppb and ≤50 μK, respectively, for improved accuracy.
Code optimization as a side effect of instruction scheduling (2002)

An instruction scheduler utilizes code reordering techniques for generating schedules in which instructions can be issued without delays. In order to perform code reordering across branches, code motion is performed that hoists some instructions above branches and sinks others below branches. Following code reordering, compensation code must be introduced in order to preserve program semantics. In this paper, we demonstrate that several important code optimizations can be performed as a side-effect of generating compensation code. These optimizations include partial redundancy elimination, partial dead code elimination, elimination of redundant loads and elimination of dead stores. We demonstrate how existing data-flow frameworks for these optimizations can be extended for generating optimized compensation code.
Programmable Chessboard Mushroom-Type Metasurface with Memory (2021)

Here we propose and study a programmable metasurface (PMS) with analog memory that can be used for smart beamforming applications as well as for proactive control of the radio wave propagation environment. The operation of such PMS as a reconfigurable reflect-array is studied analytically and numerically. The PMS comprises a chess-board-like array of metallic patches placed over a dielectric slab with metallic vias connecting the patches to the controlling network. The network includes memory capacitors. The tunability is achieved with varactor loads placed at the corners of the patches. The proposed design has excellent angular stability of the resonant frequency for TE and TM polarizations. Analytical expressions are derived for the PMS surface impedance and reflection coefficient. The analytical results are verified with a number of numerical simulations.
Nanostructured Plasmonic Metal Surfaces as Optical Components for Infrared Imaging and Sensing (2021)

Thermal imaging and sensing technologies offer critical information about our thermally radiant world, and in recent years, have seen dramatic increases in usage for a range of applications. However, the cost and technical finesse of manufacturing infrared optical components remain a major barrier towards the democratization of these technologies. In this report, we present a solution processed plasmonic reflective filter or PRF as a scalable and inexpensive thermal infrared optic. The PRF selectively absorbs sunlight and specularly reflects thermal infrared TIR wavelengths with performance comparable to state-of-the-art TIR optics made of materials like Germanium. Unlike traditional infrared optical components, however, the PRF can be conveniently fabricated using inexpensive materials and a dip and dry chemical synthesis technique, and crucially, has manufacturing costs that are orders of magnitude lower. We experimentally demonstrate the core optical functionality of the PRF, as well as its integration into infrared imaging and sensing systems without compromising their thermographic or radiometric capabilities. From a practical standpoint, the inexpensive and convenient fabricability of the PRF represent a significant advance towards making the benefits of thermal imaging and sensing systems more affordable and accessible. Scientifically, our work demonstrates a previously unexplored optical functionality and a new direction for versatile chemical synthesis in designing optical components.
The Colletotrichum orbiculare species complex: Important pathogens of field crops and weeds (2013)

Colletotrichum orbiculare causes anthracnose of Cucurbitaceae and is phylogenetically closely related to pathogens of several other herbaceous hosts belonging to the Asteraceae, Fabaceae and Malvaceae. Most of them are known for their hemibiotrophic infection strategy and as destructive pathogens either of field crops or weeds. In order to study the phylogenetic relationships of these fungi, a multilocus analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2, GS) of 42 strains of C. orbiculare and related species was conducted. The analysis resulted in nine clades that confirmed the four species previously known as belonging to this species complex, C. lindemuthianum, C. malvarum, C. orbiculare and C. trifolii, and recognised four new species from weeds, namely C. bidentis, C. sidae, C. spinosum and C. tebeestii. The name C. orbiculare itself is widely used in plant pathology and science, but is invalid according to current nomenclatural rules. Therefore we described a new species with the same epithet and a type specimen that agrees with our current understanding of this species, and is linked to a living culture. Following the recent epitypification of C. lindemuthianum, we chose appropriate specimens with associated strains to serve as epitypes of C. malvarum and C. trifolii, and selected an authentic specimen of C. trifolii as lectotype.