gebhart/patrepeval huggingface dataset:
Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment (2005)

Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper 5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas marina lineage, but only in the top 1cm. Shift in community composition occurred earlier in the marine microcosms than in the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community of this functional group of bacteria may occur at different rates.
Schema Validation and Type Annotation for Encoded Trees (2004)

We argue that ecien t support for schema validation and type annotation in XQuery processors deserves as much attention as ecien t evaluation techniques for XPath queries have received in the past. To this end, we describe a validation procedure that operates on an encoding of trees that has already been succesfully used for XPath location step evaluation. The validation algorithm works without the construction of nite state automata and can exploit properties of the encoding to speed up the validation of already partially type-annotated trees. First experiments|carried out using the database back-end of the authors’ XQuery compiler|indicate that this approach can indeed lead to high-troughput validation support.
Cell-penetrating peptides as a promising tool for delivery of various molecules into the cells (2014)

Many biologically active compounds, including macromolecules that are used as various kinds of drugs, must be delivered to the interior of cell or organelles such as mitochondria or nuclei to achieve a therapeutic effect. However, very often, lipophilic cell membrane is impermeable for these molecules. A new method in the transport of macromolecules through the cell membrane is the one based on utilizing cell-penetrating peptides (CPPs). Invented 25 years ago, CPPs are currently the subject of intensive research in many laboratories all over the world. CPPs are short compounds comprising up to 30 amino acid residues, which penetrate the cell membrane but do not cause cell damage. Additionally, CPPs can transfer hydrophilic molecules (peptides, proteins, nucleic acids) which exceed their mass, and for which the cell membrane is generally impermeable. In this review, we concentrate on the cellular uptake mechanism of CPPs and a method of conjunction of CPPs to the transported molecules. We also highlight the potential of CPPs in delivering various kinds of macromolecules into cells, including compounds of therapeutic interest.
Addition of Methyl Thioglycolate and Benzylamine to (Z)-Ligustilide, a Bioactive Unsaturated Lactone Constituent of Several Herbal Medicines. An Improved Synthesis of (Z)-Ligustilide (1995)

(Z)-Ligustilide [1] is a dihydrophthalide purported to be the active ingredient of Ligusticum plant species widely used as herbal medicines in the Orient and in Native American and Hispanic cultures. It readily underwent 1,6-conjugate addition with methyl thioglycolate in the presence of triethylamine. The methyl thioglycolate reaction also yielded a product from addition to the C-6-C-7 double bond and a diadduct from both 1,6-addition and addition to the C-6-C-7 bond. Reaction of 1 with benzylamine did not afford a 1,6-adduct, but yielded instead an N-benzyllactam, presumably formed by rearrangement from initial 1,2-addition to the carbonyl. An improved total synthesis of 1 was developed. (Z)-Ligustilide had weak antiviral properties and weak antimicrobial activity against Gram-positive, Gram-negative, and yeast microorganisms. The broad biological activity of 1 and its electrophilic reactivity are consistent with the use of Ligusticum species in folk medicine.
Pyridoxine‐responsive hyper‐β‐alaninemia associated with Cohen's syndrome (1994)

We report intermittent seizures, lethargy, and Cohen's syndrome in a 4-year-old girl with hyper-beta-alaninemia and a partial deficiency of beta-alanyl-alpha-ketoglutarate transaminase (AKT). To examine the role of beta-alanine (beta ALA) in cellular metabolism, we cultured her skin fibroblasts in medium containing increasing amounts of beta ALA. At concentrations of 10 to 25 mM, beta ALA caused more than a 50% reduction in the growth of her cells compared with normal control skin fibroblasts. The addition of 0.1 mM of pyridoxine to the culture medium abolished these toxic effects and increased her skin fibroblast AKT enzyme activity more than twofold. During a 2-year period of clinical observation, there were no further episodes of seizures or somnolence in our patient while she received oral pyridoxine therapy.
Autonomous Error Recovery of Industrial Robots Using Hierarchical Planning System (2017)

In recent automated production lines, it is important for industrial robots to recover from unexpected errors autonomously without intervention by human operators. In this paper, a hierarchical planning system that realizes autonomous error recovery of robots is proposed and demonstrated, and its effectiveness in cooperative work is verified. In order to realize a variety of flexible error recovery functions, a partial order planning scheme as well as a re-planning capability utilizing semantic information on the production environment are proposed.
Diagnosis and treatment of heparin-induced thrombocytopenia (2003)

Heparin-induced thrombocytopenia (HIT) is a major side effect secondary to the administration of heparin. This syndrome is serious and potentially life threatening. This response is the result of antibodies formed against the platelet factor 4 (PF4)/heparin complex. The incidence of this immune-mediated syndrome has been estimated to be 1-3% of all patients receiving heparin therapy. The occurrence of HIT in patients requiring full anticoagulation for cardiopulmonary bypass (CPB), therefore, presents a serious challenge to the cardiac surgery team. The diagnosis of HIT should be based on both clinical and laboratory evidence. While functional assays, platelet aggregation tests, and the serotonin release assay can be used to support the diagnosis, the negative predictive value of these tests is generally less than 50%. In contrast, although non-functional antibody detection assays are more sensitive, they have a low specificity. HIT can be treated in several ways, including cessation of all heparin and giving an alternative thrombin inhibitor, platelet inhibition followed by heparin infusion, and the use of low molecular weight heparins. In this presentation, the pathology and current diagnostic tests, as well as the successful management of patients with HIT undergoing CPB at New York Presbyterian Hospital, are reviewed.
Identification of E-selectin as a Novel Target for the Regulation of Postnatal Neovascularization (2010)

SDF-1α-engineered cell-based therapy promotes diabetic wound healing in mice by specifically upregulating E-selectin expression in mature EC leading to increase EC-EPC adhesion, EPC homing, and increased wound neovascularization. These findings provide novel insight into the signals underlying the biological effect of SDF-1α on EPC homing and point to E-selectin as a new potential target for therapeutic manipulation of EPC trafficking in diabetic wound healing.
ChemInform Abstract: Novel 10‐Hydroxydocosapolyenoic Acids from Deep‐Water Scleractinian Corals. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Bidirectional Evolutionary Method for Stiffness Optimization (1999)

Evolutionary structural optimization (ESO) method was originally developed based on the idea that by systematically removing the inefficient material, the residual shape of the structure evolves toward an optimum. This paper presents an extension of the method called bidirectional ESO (BESO) for topology optimization subject to stiffness and displacement constraints. BESO allows for the material to be added as well as to be removed to modify the structural topology. Basic concepts of BESO including the sensitivity number and displacement extrapolation are proposed and optimization procedures are presented. Integrated with the finite element analysis technique, BESO is applied to several two-dimensional plane stress problems. Its effectiveness and efficiency are examined in comparison with the results obtained by ESO. It is found that BESO is more reliable and computationally more efficient than ESO in most cases. Its capability and limitation are discussed.
Advanced and authenticated marking schemes for IP traceback (2002)

Defending against distributed denial-of-service attacks is one of the hardest security problems on the Internet today. One difficulty to thwart these attacks is to trace the source of the attacks because they often use incorrect, or spoofed IP source addresses to disguise the true origin. In this paper, we present two new schemes, the advanced marking scheme and the authenticated marking scheme, which allow the victim to trace-back the approximate origin of spoofed IP packets. Our techniques feature low network and router overhead, and support incremental deployment. In contrast to previous work, our techniques have significantly higher precision (lower false positive rate) and fewer computation overhead for the victim to reconstruct the attack paths under large scale distributed denial-of-service attacks. Furthermore the authenticated marking scheme provides efficient authentication of routers' markings such that even a compromised router cannot forge or tamper markings from other uncompromised routers.
P36 Crohn??s ???cold??? collection detected by SPECT/CT (2007)

1Nuclear Medicine Department, Derby Hospitals Foundation NHS Trust, Derbyshire Royal Infirmary, London Road, Derby 2Nuclear Medicine Clinic, Department of Medical Physics, University of Nottingham, Nottingham, UK British Nuclear Medicine Society Oral and Poster Abstracts 2007
Dinuclear Oxidative Addition of N−H and S−H Bonds at Chromium. Reaction of •Cr(CO)3(C5Me5) with {o-(HA)C6H4S−Cr(CO)3(C5Me5)} (A = S, NH) Yielding [η2-o-(μ-A)C6H4S−Cr(C5Me5)]2 and H−Cr(CO)3(C5Me5) (2002)

Reaction of the 17-electron radical (*)Cr(CO)(3)Cp* (Cp* = C(5)Me(5)) with 0.5 equiv of 2-aminophenyl disulfide [(o-H(2)NC(6)H(4))(2)S(2)] results in rapid oxidative addition to form the initial product (o-H(2)N)C(6)H(4)S-Cr(CO)(3)Cp*. Addition of a second equivalent of (*)Cr(CO)(3)Cp* to this solution results in the formation of H-Cr(CO)(3)Cp* as well as (1)/(2)[[eta(2)-o-(mu-NH)C(6)H(4)S]CrCp*](2). Spectroscopic data show that (o-H(2)N)C(6)H(4)S-Cr(CO)(3)Cp* loses CO to form [eta(2)-(o-H(2)N)C(6)H(4)S]Cr(CO)(2)Cp*. Attack on the N-H bond of the coordinated amine by (*)Cr(CO)(3)Cp* provides a reasonable mechanism consistent with the observation that both chelate formation and oxidative addition of the N-H bond are faster under argon than under CO atmosphere. The N-H bonds of uncoordinated aniline do not react with (*)Cr(CO)(3)Cp*. Reaction of the 2 mol of (*)Cr(CO)(3)Cp* with 1,2-benzene dithiol [1,2-C(6)H(4)(SH)(2)] yields the initial product (o-HS)C(6)H(4)S-Cr(CO)(3)Cp and 1 mol of H-Cr(CO)(3)Cp*. Addition of 1 equiv more of (*)Cr(CO)(3)Cp to this solution also results in the formation of 1 equiv of H-Cr(CO)(3)Cp*, as well as the dimeric product (1)/(2)[[eta(2)-o-(mu-S)C(6)H(4)S]CrCp*](2). This reaction also occurs more rapidly under Ar than under CO, consistent with intramolecular coordination of the second thiol group prior to oxidative addition. The crystal structures of [[eta(2)-o-(mu-NH)C(6)H(4)S]CrCp*](2) and [[eta(2)-o-(mu-S)C(6)H(4)S]CrCp*](2) are reported.
Augmenting Transformers with KNN-Based Composite Memory for Dialog (2021)

Various machine learning tasks can benefit from access to external information of different modalities, such as text and images. Recent work has focused on learning architectures with large memories capable of storing this knowledge. We propose augmenting generative Transformer neural networks with KNN-based Information Fetching (KIF) modules. Each KIF module learns a read operation to access fixed external knowledge. We apply these modules to generative dialog modeling, a challenging task where information must be flexibly retrieved and incorporated to maintain the topic and flow of conversation. We demonstrate the effectiveness of our approach by identifying relevant knowledge required for knowledgeable but engaging dialog from Wikipedia, images, and human-written dialog utterances, and show that leveraging this retrieved information improves model performance, measured by automatic and human evaluation.
An on-chip 72&#x00D7;60 angle-sensitive single photon image sensor array for lens-less time-resolved 3-D fluorescence lifetime imaging (2014)

We present a 72×60, angle-sensitive single photon avalanche diode (A-SPAD) array, able to perform lens-less 3-D fluorescent lifetime imaging. A-SPAD pixels are comprised of (1) a SPAD to resolve precise timing information, reject high-powered UV stimulus, and map the lifetimes of different fluorescent sources and (2) integrated diffraction gratings over the SPAD to extract the incident angle of light, enabling 3-D localization at a micrometer scale. The chip integrates pixel-level counters and shared timing circuitry, and is implemented in unmodified 180nm CMOS.
Antiprotozoal Selectivity of Diimidazoline N-Phenylbenzamides (2015)

We discovered three diimidazolines with high antiplasmodial selectivity that had IC50 values of 1.9-28 nM against cultured Plasmodium falciparum. We also identified a gem-dimethyl diimidazoline with high antitrypanosomal selectivity that had an IC50 value of 26 nM against cultured Trypanosoma brucei rhodesiense. Two 2-imidazoline heterocycles in a para orientation on a N-phenylbenzamide or similar core structure were required for high antiprotozoal activity. Ring expansion of the imidazoline as well as heterocyclic variants with pKa values of <7 all decreased activity significantly.
Supplementary Figure 5 from Differential Effects of RUNX2 on the Androgen Receptor in Prostate Cancer: Synergistic Stimulation of a Gene Set Exemplified by SNAI2 and Subsequent Invasiveness (2023)

&lt;p&gt;PDF file - 53KB, SGK1 expression.&lt;/p&gt;
CHEETAH: A next generation thermochemical code (1994)

CHEETAH is an effort to bring the TIGER thermochemical code into the 1990s. A wide variety of improvements have been made in Version 1.0. We have improved the robustness and ease of use of TIGER. All of TIGER`s solvers have been replaced by new algorithms. We find that CHEETAH solves a wider variety of problems with no user intervention (e.g. no guesses for the C-J state) than TIGER did. CHEETAH has been made simpler to use than TIGER; typical use of the code occurs with the new standard run command. CHEETAH will make the use of thermochemical codes more attractive to practical explosive formulators. We have also made an extensive effort to improve over the results of TIGER. CHEETAH`s version of the BKW equation of state (BKWC) is able to accurately reproduce energies from cylinder tests; something that other BKW parameter sets have been unable to do. Calculations performed with BKWC execute very quickly; typical run times are under 10 seconds on a workstation. In the future we plan to improve the underlying science in CHEETAH. More accurate equations of state will be used in the gas and the condensed phase. A kinetics capability will be added to the code that will predict reaction zone thickness. Further ease of use features will eventually be added; an automatic formulator that adjusts concentrations to match desired properties is planned.
Dispersive-cohesive viscoelastic soft shell technique (1999)

Based on their physical properties, ophthalmic viscoelastic agents can be divided into 2 groups: higher-viscosity cohesive and lower-viscosity dispersive. Higher-viscosity cohesive agents are best at creating and preserving space, while lower-viscosity dispersive agents are retained better in the anterior chamber and are capable of partitioning spaces. The viscoelastic soft shell technique maximizes the advantages and minimizes the disadvantages of both groups by using dispersive and cohesive agents together in sequence based on the desired surgical goal.
Activation of the alternative complement pathway due to resistance of zymosan-bound. (1977)

The surface of zymosan (Zy), by affording a protected microenvironment for C3b and the amplification convertase stabilized by properdin, P,C3b,Bb, shifts the alternative complement pathway from slow fluid phase turnover to the amplification phase of its expression. This mode of activation is in contradistinction to that of the classical pathway, which follows conversion of a proenzyme, Cl, to its active form, C1. Under conditions in which the control proteins, C3b inactivator (C3bINA) and beta1H, completely, inactivated C3b on the sheep erythrocyte intermediate, EAC4b,3b, the activity of C3b bound to Zy,ZyC3b, was diminished by only one-third. Further, when ZyC3b was converted to ZyC3b,Bb,P there was an additional point of deregulation in that the convertase was resistant to beta1H-mediated decay-dissociation while P,C3b,Bb on the sheep erythrocyte exhibited the usual susceptibility to beta1H. That Zy alone could indeed promote rapid C3 cleavage by the alternative pathway through assembly and protection of the amplification convertase on its surface was demonstrated with a mixture of alternative pathway proteins, C3,B,D,P, C3bINA, and beta1H, that had each been purified to homogeneity. Interaction of these proteins at one-tenth their relative serum concentrations with Zy permitted low-grade inactivation of C3 and B to advance to the level of amplification after a 15 min lag period. Because the reaction of the purified proteins proceeded spontaneously when either regulatory protein was deleted, the effect of Zy was attributed to deregulation rather than to conversion of one of the proteins to a specific initiating state. The alternative pathway, through the normal presence of D, interacts with a microbial surface, such as Zy, to amplify deposition of C3b by circumvention of endogenous regulatory mechanisms, thereby augmenting host defense.
Hybrid DS/FH spread spectrum data transmission system for telemetry (2016)

In this paper a novel hybrid spread spectrum transmission system designed for transmitting telemetrie data from remote sites is presented. It can be used for low bit rates and long distance radio links. The system is based on Spreading-Code-Phase-Shift-Keying modulation and shows excellent immunity to narrowband and wideband interference. The implementation of the system in SDR technology is possible and multiple access is also straightforward.
Will the increase of paid coaches for youth sport travel teams or elite teams increase the pressure to win at all costs for the coach and the players? (1997)

(1997). Will the increase of paid coaches for youth sport travel teams or elite teams increase the pressure to win at all costs for the coach and the players? Journal of Physical Education, Recreation & Dance: Vol. 68, No. 4, pp. 10-11.
Wavelength Division Multiplexing of 194 Continuous Variable Quantum Key Distribution Channels (2020)

We demonstrate the first continuous variable quantum key distribution (CV-QKD) system with fully digital phase and polarization tracking, enabling the first wavelength division multiplexing experiment for CV-QKD. We transmit 194 × 0.5 GHz channels with 25 GHz channel spacing, demonstrating an aggregate estimated asymptotic secret key rate of 172.6 Mbit/s over 25 km.
Gene expression changes by amyloid β peptide-stimulated human postmortem brain microglia identify activation of multiple inflammatory processes (2005)

A central feature of the inflammatory pathology in Alzheimer's disease is activated microglia clustered around aggregated amyloid beta (Abeta) peptide-containing plaques. In vitro-cultured microglia can be activated to an inflammatory state by aggregated Abeta with the induction of a range of different neurotoxic factors and provide a model system for studying microglia Abeta interactions. Gene expression responses of human postmortem brain-derived microglia to aggregated Abeta were measured using whole genome microarrays to address the hypothesis that Abeta interactions with human microglia primarily induce proinflammatory genes and not activation of genes involved in Abeta phagocytosis and removal. The results demonstrated that Abeta activation of microglia induced a large alteration in gene transcription including activation of many proinflammatory cytokines and chemokines, most notably, interleukin (IL)-1beta, IL-8, and matrix metalloproteinases (MMP), including MMP1, MMP3, MMP9, MMP10, and MMP12. All of these genes could amplify ongoing inflammation, resulting in further neuronal loss. Changes in expression of receptors associated with Abeta phagocytosis did not match the changes in proinflammatory gene expression. Time-course gene expression profiling, along with real-time polymerase chain reaction validation of expression changes, demonstrated an acute phase of gene induction for many proinflammatory genes but also chronic activation for many other potentially toxic products. These chronically activated genes included indoleamine 2,3-dioxygenase and kynureninase, which are involved in formation of the neurotoxin quinolinic acid, and S100A8, a potential proinflammatory chemokine. These studies show that activation of microglia by Abeta induces multiple genes that could be involved in inflammatory responses contributing to neurodegenerative processes.
Communication scientifique : pour le meilleur et le PEER (2010)

Le projet PEER (Publishing and the Ecology of European Research), lance en 2007, vise a mieux connaitre les developpements actuels en matiere d'archives institutionnelles scientifiques alors que celles-ci proliferent. Il fait collaborer des editeurs scientifiques et des organismes de recherche et d'enseignement superieur. Il etudie en particulier les effets du depot systematique des travaux scientifiques sur la diffusion des publications, sur la viabilite des revues, sur la production de la recherche...