gebhart/patrepeval huggingface dataset:
Alpha-synuclein oligomers activate NFAT proteins modulating synaptic homeostasis and apoptosis (2023)

Abstract Soluble oligomeric forms of alpha-synuclein (aSyn-O) are believed to be one of the main toxic species in Parkinson’s disease (PD) leading to degeneration. aSyn-O can induce Ca 2+ influx, over activating downstream pathways leading to PD phenotype. Calcineurin (CN), a phosphatase regulated by Ca 2+ levels, activates NFAT transcription factors that are involved in the regulation of neuronal plasticity, growth and survival. Here, we investigate NFAT’s role in neuronal degeneration induced by aSyn-O. aSyn-O are toxic to neurons leading to cell death, loss of neuron ramification and reduction of synaptic proteins which are reversed by CN inhibition with ciclosporin-A or VIVIT, a NFAT specific inhibitor. aSyn-O induce NFAT nuclear translocation and transactivation. We found that aSyn-O modulates the gene involved in the maintenance of synapses, synapsin 1 ( Syn 1 ). Syn1 mRNA and protein and synaptic puncta are drastically reduced in cells treated with aSyn-O which are reversed by NFAT inhibition. For the first time a direct role of NFAT in aSyn-O-induced toxicity and Syn1 gene regulation was demonstrated, enlarging our understanding of the pathways underpinnings synucleinopathies.
1,3‐Dipolar Cycloaddition as the Key Reaction in the Synthesis of Potent Renin Inhibitors (1991)

Substitued allylamines like 1 react with nitrones 2 by 1,3-dipolar cycloaddition to form isoxazolidines 3, which are separable by chromatography. Hydrogenolytic opening of the isoxazolidines yields 1,3-amino alcohols, which when built into the angiotensinogen sequence, lead to renin inhibitors of type 4.
Helicobacter nemestrinae ATCC 49396T is a strain of Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989, and Helicobacter nemestrinae Bronsdon et al. 1991 is therefore a junior heterotypic synonym of Helicobacter pylori. (2002)

Helicobacter nemestrinae Bronsdon et al. 1991, a gastric helicobacter species isolated from a pigtailed macaque, is thought to be the species most closely related to the important human pathogen Helicobacter pylori. The only available strain of this taxon is the type strain, ATCC 49396T. We sequenced seven housekeeping genes and two flagellin genes for H. nemestrinae ATCC 49396T. If ATCC 49396T were a separate species, these sequences should have been distinct from those of H. pylori. Instead, all sequences clustered together with sequences obtained previously for 20 or more H. pylori isolates from diverse geographical locations. The 16S rDNA sequence differed from that reported previously for this strain by 38 nucleotides and was most similar to that of H. pylori 85D08 (accession no. U00769), which was isolated from a rhesus macaque. It differed by less than 1% from 16S rDNA sequences of numerous other H. pylori strains, including the type strain, NCTC 11637T (= ATCC 43504T). These data indicate that the strain currently distributed as H. nemestrinae ATCC 49396T is really a strain of H. pylori and that H. nemestrinae Bronsdon et al. 1991 is a junior heterotypic synonym of Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989.
Event-related potentials and perception of signals in several types of background noise. (2011)

Many factors contribute to successful perception of auditory stimuli in noise, including neural encoding in the central auditory system. Physiological measures such as event-related potentials (ERPs) can provide a view of neural encoding that may inform our understanding of listeners’ abilities to perceive signals in the presence of background noise. We set out to determine the effect of stimulus type on neural encoding and perception of signals in noise. Nine young, normal-hearing adults participated. ERPs were recorded (the N1-P2 and P3), and a sentence-in-noise identification task was completed in quiet and in three noise conditions: (1) steady-state speech spectrum noise, (2) interrupted noise, and (3) four-talker babble. Stimuli were presented at a signal-to-noise ratio of −3 dB. Results demonstrated significant effects of noise type on both physiological and behavioral measures with the four-talker babble condition showing the largest decrements in ERP and behavioral measures relative to testing in quiet. In addition, significant correlations were found between ERPs and sentence-in-noise measures. Differential effects of noise type on N1 and P3 ERPs will be discussed and compared with behavioral results. Results suggest that ERPs may be a useful tool for measuring neurophysiological correlates of energetic and informational masking.
Ultrafast Spectroscopic and Matrix Isolation Studies of <i>p-</i>Biphenylyl, <i>o</i>-Biphenylyl, and 1-Naphthylnitrenium Cations (2007)

p-biphenylyl, o-biphenylyl, and 1-naphthyl azides were deposited in argon at low temperature in the presence and absence of HCl. In the absence of HCl, the known electronic and vibrational spectra of the corresponding triplet nitrenes, azirines, and didehydroazepines were observed, whereas in the presence of HCl, photolysis of these azides produces new electronic spectra assigned to the corresponding nitrenium cations. For p-biphenylyl azide the resulting spectrum of the nitrenium ion is very similar to the previously observed solution-phase spectrum of this species. The vibrational spectrum of this cation was recorded for the first time. Spectroscopic evidence for the previously unknown o-biphenylylnitrenium cation and 1-naphthylnitrenium cation are provided. The spectra of p- and o-biphenylylnitrenium cations and 1-naphthylnitrenium cation are well reproduced by CASSCF and CASPT2 calculations. The same nitrenium cations were detected in solution by femtosecond time-resolved laser flash photolysis of the appropriate azides in 88% formic acid. The transient spectra of the nitrenium cations recorded in solution are in good agreement with the spectra obtained in HCl matrices. The rates of formation of these cations equal the rates of decay of the singlet nitrenes in 88% formic acid and are as follows: p-biphenylyl (taugrowth = 11.5 ps), o-biphenylyl (taugrowth = 7.7 ps), and 1-naphthylnitrenium cations (taugrowth = 8.4 ps). The decay lifetimes of p- and o-biphenylylnitrenium cations are 50 and 27 ns, respectively. The decay lifetimes of 1-naphthylnitrenium cation is 860 ps in 88% formic acid.
Analysis of parallelism in logic programs. (volumes i and ii) (1984)

The research reported in this thesis characterizes and explores various aspects of parallelism in the framework of logic programming. Specifically, we analyze communication, process and resource control with respect to parallel execution of logic programs.
We introduce a computational model for AND/OR parallel execution of logic programs. The computational model is shown to support both old and new communication paradigms for the parallel interpretation of logic programs. The primitives that comprise the model are used to synthesize two parallel interpreters: Disjunctive System (DS) interpreters and Intelligent Channel Interpreters.
We show that the Intelligent Channel allows us to introduce parallelism to the execution of logic programs without the need for a separate binding environment for every active OR-branch.
Subsequently, we investigate several candidate control constructs for literal sequencing in terms of their efficiency, difficulty of implementation and closeness to the spirit of logic programming.
The investigated methods are: unification, control driven execution, data driven execution and event driven execution.
A simple event-based language is devised to control the execution of PRISM/Concurrent Prolog control structures. Based on this scheme several efficient implementations are presented.
A new control construct for sequencing atoms is proposed. We show that the new construct subsumes the notion of input/read-only variables. We demonstrate the utility of the construct to pass protected structures and to define interrupt-like execution in the framework of logic programs.
We introduce a simplified language called Controlled Logic Programs (CLP). The language is based on a two level language. The Logic Level is defined by the Horn-clause program, whereas the Control Level is provided by two simple primitives that allow the user to monitor the changing control state of the program.
The advantages of the language are: (1) It has a simple event based sequencing mechanism that allows user accessible control information. (2) The control exhibits a high degree of locality. (3) The control state and the logical state are syntactically distinguished.
Finally, we investigate parallelism in logic programs with respect to an efficient implementation on a multiprocessor.
Three methods for mapping the execution of a shared memory parallel interpreter to a multiprocessor are described and analyzed.
Since searching and intersecting (joining) are key components in many logic programming systems, optimal parallel algorithms for searching and intersection are developed.
Oxygen and nitrogen plasma hydrophilization and hydrophobic recovery of polymers (2012)

PLASMA HYDROPHILIZATION AND SUBSEQUENT HYDROPHOBIC RECOVERY ARE STUDIED FOR TEN DIFFERENT POLYMERS OF MICROFABRICATION INTEREST: polydimethylsiloxane (PDMS), polymethylmethacrylate, polycarbonate, polyethylene, polypropylene, polystyrene, epoxy polymer SU-8, hybrid polymer ORMOCOMP, polycaprolactone, and polycaprolactone/D,L-lactide (P(CL/DLLA)). All polymers are treated identically with oxygen and nitrogen plasmas, in order to make comparisons between polymers as easy as possible. The primary measured parameter is the contact angle, which was measured on all polymers for more than 100 days in order to determine the kinetics of the hydrophobic recovery for both dry stored and rewashed samples. Clear differences and trends are observed both between different polymers and between different plasma parameters.
Coexpression of FAS and FAS-Ligand in Chronic Pancreatitis: Correlation with Apoptosis (2000)

Activation of the Fas receptor by Fas-ligand (FasL) results in apoptosis, and dysregulation of this pathway may contribute to abnormal cell proliferation and cell death. The aim of this study was to compare the expression of Fas and FasL in the normal pancreas and chronic pancreatitis (CP). By Northern blotting, Fas messenger RNA (mRNA) levels were increased in CP in comparison to the normal pancreas. Immunostaining revealed that faint Fas and FasL immunoreactivity was present in ductal and islet cells of the normal pancreas. In CP, there was faint Fas and strong FasL immunoreactivity in the proliferating ductal cells. Additionally, many of these ductal cells in the CP samples exhibited an apoptotic signal, as determined by DNA 3'-OH end labeling. These findings suggest that activation of apoptosis through the Fas receptor may contribute to the pathobiology of CP.
Inhibition of Human Acetyl- and Butyrylcholinesterase by Novel Carbamates of (−)- and (+)-Tetrahydrofurobenzofuran and Methanobenzodioxepine (2006)

A new enantiomeric synthesis utilizing classical resolution provided two novel series of optically active inhibitors of cholinesterase: (-)- and (+)-O-carbamoyl phenols of tetrahydrofurobenzofuran and methanobenzodioxepine. An additional two series of (-)- and (+)-O-carbamoyl phenols of pyrroloindole and furoindole were obtained by known procedures, and their anticholinesterase actions were similarly quantified against freshly prepared human acetyl- (AChE) and butyrylcholinesterase (BChE). Both enantiomeric forms of each series demonstrated potent cholinesterase inhibitory activity (with IC(50) values as low as 10 nM for AChE and 3 nM for BChE), with the exception of the (+)-O-carbamoyl phenols of pyrroloindole, which lacked activity (IC(50) values >1 microM). Based on the biological data of these four series, a structure-activity relationship (SAR) analysis was provided by molecular volume calculations. In addition, a probable transition-state model was established according to the known X-ray structure of a transition-state complex of Torpedo californica AChE-m-(N,N,N-trimethylammonio)-2,2,2-trifluoroacetophenone (TcAChE-TMTFA). This model proved valuable in explaining the enantioselectivity and enzyme subtype selectivity of each series. These carbamates are more potent than, or similarly potent to, anticholinesterases in current clinical use, providing not only inhibitors of potential clinical relevance but also pharmacological tools to define drug-enzyme binding interactions within an enzyme crucial in the maintenance of cognition and numerous systemic physiological functions in health, aging, and disease.
Adding virtual plants leads to higher cognitive performance and psychological well-being in virtual reality (2023)

Previous research has shown the positive effects of exposure to real and virtual nature. To investigate how such benefits might generalize to ever-more-prevalent virtual workplaces, we examined the effects of the absence or presence of virtual plants in an office environment in Virtual Reality (VR) on users' cognitive performance and psychological well-being. The results of our user study with 39 participants show that in the presence of virtual plants, participants performed significantly better in both short-term memory and creativity tasks. Furthermore, they reported higher psychological well-being scores, including positive affect and attentive coping, whilst reporting lower feelings of anger and aggression after exposure to virtual plants in VR. The virtual office with plants was also perceived as more restorative and induced a higher sense of presence. Overall, these results highlight how the presence of virtual plants in VR can have positive influences on users, and therefore, constitute important design considerations when developing future working and learning spaces.
SHIME®: an advanced in vitro technology platform for studying the mode-of-action of probiotics in the gastrointestinal tract (2018)

The gastrointestinal microbiota plays a key role in human health. Over the past few decades, a lot of attention has been directed at improving health by modulating the gut microbial composition using probiotics. In vivo studies have limitations in providing mechanistic insights into the effect of probiotics and cannot be used to screen numerous test compounds. However, in vitro approaches can be used for mechanistic research under highly controlled environmental conditions. Here we describe how the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) can be used to produce data complementary to in vivo studies to help elucidate the mode-of-action of probiotics in the gastrointestinal tract.
<i>Trypanosoma brucei</i>ATG8: Structural insights into autophagic-like mechanisms in protozoa (2009)

Bioinformatic searches of genome databases revealed that the number of autophagy-related genes (ATG) is considerably lower in trypanosomes than in higher eukaryotes and even in yeast. This raises the question of whether autophagy in this protozoan parasite is more primitive and represents a rudimentary paradigm due to its early branching off the evolutionary tree. We here present the crystal structure of TbATG8B. This molecule (MW 13.7 kDa) belongs to the ubiquitin-like proteins showing the typical ubiquitin fold and strong sequence homology to LC3, the human homologue. Due to its characteristic folding, it should readily bind to TbATG4.1 for being processed. This presumption was tested by molecular modeling approaches, docking TbATG8B to a homology model of TbATG4.1. Although exchanges of several amino acids are evident from sequence comparisons, the overall structure seems very much alike and the necessary catalytic triad (C-D-H) is well conserved in TbATG4.1. Thus membrane formation during appearance of the autophagic bodies seems very similar in trypanosomes and their higher eukaryotic counterpart.
Frequency-temperature analysis of MEMS AT-cut quartz resonators (2004)

An analytical study of the frequency-temperature behavior of MEMS AT-cut quartz resonator structures was performed. The piezoelectric, Lagrangian equations for the frequency-temperature behavior of quartz were employed. Two types of resonator structures were studied: A 1 GHz rectangular plate with rectangular electrodes and a 1 GHz rectangular ring electrode mesa (REM) plate. For MEMS resonators, the REM design confers certain advantages in attaining higher resonant frequencies and lower electrode noise.
Standing together: the Muslim Association of Britain and the anti-war movement (2008)

One of the main groups involved in organising the mobilisation of millions of people in opposition to the Iraq war of 2003 was the Muslim Association of Britain (MAB). Much recent commentary has focused on the involvement of MAB (an offshoot of the Arab Muslim Brotherhood) in the coalition of organisations that led the anti-war movement. Less attention has been paid to how MAB activists themselves understood their working relationship with the other organised groups in the Stop the War coalition. Based mainly on interviews with MAB activists, this article examines their perspectives and experiences of working within a broad Left movement.
Maximizing Transmission Opportunities in Wireless Multihop Networks (2012)

Being readily available in most of 802.11 radios, multirate capability appears to be useful as WiFi networks are getting more prevalent and crowded. More specifically, it would be helpful in high-density scenarios because internode distance is short enough to employ high data rates. However, communication at high data rates mandates a large number of hops for a given node pair in a multihop network and thus, can easily be depreciated as per-hop overhead at several layers of network protocol is aggregated over the increased number of hops. This paper presents a novel multihop, multirate adaptation mechanism, called multihop transmission opportunity (MTOP), that allows a frame to be forwarded a number of hops consecutively to minimize the MAC-layer overhead between hops. This seemingly collision-prone nonstop forwarding is proved to be safe via analysis and USRP/GNU Radio-based experiment in this paper. The idea of MTOP is in clear contrast to the conventional opportunistic transmission mechanism, known as TXOP, where a node transmits multiple frames back-to-back when it gets an opportunity in a single-hop WLAN. We conducted an extensive simulation study via OPNET, demonstrating the performance advantage of MTOP under a wide range of network scenarios.
Investigation of surface and subsurface profile, techniques of measurement, and replication of the Chinese Magic Mirror (2013)

The Chinese magic mirror is an ancient convex bronze mirror, it reflects parallel light rays to form a unique image within the reflected patch of light by altering the reflected ray paths. Using Phase Measuring Reflectometry (PMR), surface irregularities of a micron range were found to be present on the mirror; these irregularities concentrate and disperse reflected light rays, giving rise to brighter and darker patches on the reflected image, forming a contrast, allowing the unique pattern to be observed. To ascertain location and nature of the surface defects that come in forms of indentations and raised platforms, other measurement techniques were employed. Reverse engineering then facilitated the exploration of reproduction of a very own original Chinese Magic Mirror with the use of optical principles behind the mirror.
In Planta Distribution of ‘<i>Candidatus</i> Liberibacter asiaticus’ as Revealed by Polymerase Chain Reaction (PCR) and Real-Time PCR (2008)

Huanglongbing (HLB) is one of the most devastating diseases of citrus worldwide, and is caused by a phloem-limited fastidious prokaryotic alpha-proteobacterium that is yet to be cultured. In this study, a combination of traditional polymerase chain reaction (PCR) and real-time PCR targeting the putative DNA polymerase and 16S rDNA sequence of 'Candidatus Liberibacter asiaticus,' respectively, were used to examine the distribution and movement of the HLB pathogen in the infected citrus tree. We found that 'Ca. Liberibacter asiaticus' was distributed in bark tissue, leaf midrib, roots, and different floral and fruit parts, but not in endosperm and embryo, of infected citrus trees. Quantification analysis of the HLB bacterium indicated that it was distributed unevenly in planta and ranged from 14 to 137,031 cells/mug of total DNA in different tissues. A relatively high concentration of 'Ca. Liberibacter asiaticus' was observed in fruit peduncles. Our data from greenhouse-infected plants also indicated that 'Ca. Liberibacter asiaticus' was transmitted systemically from infection site to different parts of the plant. Understanding the distribution and movement of the HLB bacterium inside an individual citrus tree is critical for discerning its virulence mechanism and to develop management strategies for HLB.
TAO1, a Representative of the Molybdenum Cofactor Containing Hydroxylases from Tomato (1997)

Aldehyde oxidase and xanthine dehydrogenase are a group of ubiquitous hydroxylases, containing a molybdenum cofactor (MoCo) and two iron-sulfur groups. Plant aldehyde oxidase and xanthine dehydrogenase activities are involved in nitrogen metabolism and hormone biosynthesis, and their corresponding genes have not yet been isolated. Here we describe a new gene from tomato, which shows the characteristics of a MoCo containing hydroxylase. It shares sequence homology with xanthine dehydrogenases and aldehyde oxidases from various organisms, and similarly contains binding sites for two iron-sulfur centers and a molybdenum-binding region. However, it does not contain the xanthine dehydrogenase conserved sequences thought to be involved in NAD binding and in substrate specificity, and is likely to encode an aldehyde oxidase-type activity. This gene was designated tomato aldehyde oxidase 1 (TAO1). TAO1 belongs to a multigene family, whose members are shown to map to clusters on chromosomes 1 and 11. MoCo hydroxylase activity is shown to be recognized by antibodies raised against recombinant TAO1 polypeptides. Immunoblots reveal that TAO1 cross-reacting material is ubiquitously expressed in various organisms, and in plants it is mostly abundant in fruits and rapidly dividing tissues.
Predicting molecular structures of surface metal oxide species on oxide supports under ambient conditions (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPredicting molecular structures of surface metal oxide species on oxide supports under ambient conditionsGoutam Deo and Israel E. WachsCite this: J. Phys. Chem. 1991, 95, 15, 5889–5895Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/j100168a033https://doi.org/10.1021/j100168a033research-articleACS PublicationsRequest reuse permissionsArticle Views1589Altmetric-Citations279LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts