gebhart/patrepeval huggingface dataset:
Multiprocessor System-on-Chip (MPSoC) Technology (2008)

The multiprocessor system-on-chip (MPSoC) uses multiple CPUs along with other hardware subsystems to implement a system. A wide range of MPSoC architectures have been developed over the past decade. This paper surveys the history of MPSoCs to argue that they represent an important and distinct category of computer architecture. We consider some of the technological trends that have driven the design of MPSoCs. We also survey computer-aided design problems relevant to the design of MPSoCs.
Sorption of linear alkylbenzene sulfonate to soil components and effects on microbial iron reduction (2003)

When sewage sludge is applied to arable land, linear alkylbenzene sulfonate (LAS) is released into the environment. In soils, LAS has been shown to impede microbial processes, such as bacterial iron reduction. The aim of the present study was to quantify LAS adsorption and desorption to agricultural soils and iron oxides and relate this to the inhibition of microbial iron reduction. Two agricultural soils were used, namely, Askov (coarse sandy loam soil) and Lundgaard (coarse sandy soil). In both soils, LAS inhibited microbial iron reduction even at low LAS concentrations with 10% effect concentrations of 6 to 7 and 26 to 32 mg LAS/kg dry-weight soil for Lundgaard and Askov soil, respectively. The sorption isotherms showed that sorption of LAS to iron oxides was 10 to 100 times stronger than sorption to the agricultural soils. Also, it appeared that at low LAS concentrations (< 10 mg/kg dry-wt soil), Lundgaard soil adsorbed approximately 10 times more LAS than Askov soil. Thus, the inhibitory effect of LAS on microbial iron reduction was highest in the Lundgaard soil, which exhibited both the strongest sorption and the lowest desorption of the two soils. A possible hypothesis to explain this correlation was that LAS toxicity toward bacterial iron reduction was, at least partly, caused by LAS adsorbed to iron oxides, which could interfere with transfer of electrons between the bacteria and their respiratory electron acceptor.
Homodimerization of LDB1 is necessary for activation of the mouse β‐globin gene in vivo (2011)

A multiprotein complex that includes LDB1, TAL1, GATA‐1 and LMO2 proteins participates in long‐distant interaction in the β‐globin locus. The complex occupies the locus control region and the β‐globin promoter and mediates their proximity. Reduction of LDB1 using RNAi disrupts long‐distant interaction and blocks expression of the β‐globin gene. LDB1 protein has two defined domains that may participate in this process. The C‐terminal LIM‐interaction domain (LID) of LDB1 interacts with LMO2 which provides association of LDB1 with chromatin through DNA‐binding partners GATA‐1 and TAL1. It is known that the N‐terminal dimerisation domain (DD) of LDB1 participates in homodimerisation of the protein in vitro. We proposed that the DD domain of LDB1 plays a key role in long‐distant interaction between the LCR and β‐major gene promoter in vivo. Several deletions of LDB1 and a fusion protein that contains LMO2 and the DD domain of LDB1 were expressed in the background of endogenous LDB1 knock down MEL cells. These experiments demonstrated an important role for the LDB1 DD domain in β‐globin gene activation and LDB1 protein stability. Co‐immunoprecipitation of a truncated LDB1 protein consisting of only the DD domain with endogenous LDB1 confirms that homodimerisation of LDB1 in vivo occurs by interaction between DD domains. These results confirm the necessity of homodimerisation of LDB1 in the gene regulation processes.
Imaging Multimodalities for Dissecting Alzheimer's Disease: Advanced Technologies of Positron Emission Tomography and Fluorescence Imaging (2015)

The rapid progress in advanced imaging technologies has expanded our toolbox for monitoring a variety of biological aspects in living subjects including human. In vivo radiological imaging using small chemical tracers, such as with positron emission tomography, represents an especially vital breakthrough in the efforts to improve our understanding of the complicated cascade of neurodegenerative disorders including Alzheimer's disease (AD), and it has provided the most reliable visible biomarkers for enabling clinical diagnosis. At the same time, in combination with genetically modified animal model systems, the most recent innovation of fluorescence imaging is helping establish diverse applications in basic neuroscience research, from single-molecule analysis to animal behavior manipulation, suggesting the potential utility of fluorescence technology for dissecting the detailed molecular-based consequence of AD pathophysiology. In this review, our primary focus is on a current update of PET radiotracers and fluorescence indicators beneficial for understanding the AD cascade, and discussion of the utility and pitfalls of those imaging modalities for future translational research applications. We will also highlight current cutting-edge genetic approaches and discuss how to integrate individual technologies for further potential innovations.
Behaviour of niobium during early Earth’s differentiation: insights from its local structure and oxidation state in silicate melts at high pressure (2018)

Niobium (Nb) is one of the key trace elements used to understand Earth's formation and differentiation, and is remarkable for its deficiency relative to tantalum in terrestrial rocks compared to the building chondritic blocks. In this context, the local environment of Nb in silica-rich melts and glasses is studied by in situ x-ray absorption spectroscopy (XAS) at high pressure (P) up to 9.3 GPa and 1350 K using resistive-heating diamond-anvil cells. Nb is slightly less oxidized in the melt (intermediate valence between +4 and +5) than in the glass (+5), an effect evidenced from the shift of the Nb-edge towards lower energies. Changes in the pre-edge features are also observed between melt and glass states, consistently with the observed changes in oxidation state although likely enhanced by temperature (T) effects. The oxidation state of Nb is not affected by pressure neither in the molten nor glassy states, and remains constant in the investigated P-range. The Nb-O coordination number is constant and equal to [Formula: see text] below 5 GPa, and only progressively increases up to [Formula: see text] at 9.3 GPa, the maximum P investigated. If these findings were to similarly apply to basaltic melts, that would rule out the hypothesis of Nb/Ta fractionation during early silicate Earth's differentiation, thus reinforcing the alternative hypothesis of fractionation during core formation on reduced pre-planetary bodies.
Measurements of trabecular bone structure in man (for radionuclide dosimetry (1976)

A quantitative analysis of trabecular bone structure is presented, based on omnidirectional distributions of paths across (a) trabeculation and (b) marrow cavities. The omnidirectional distributions, which take into account structural anisotropy, are generated from measured distributions of paths. Representative examples are given, together with values of two commonly quoted structural parameters, the ratio of endosteal surface to bone volume and percentage bone volume. Data on the biological and age variations in the third lumbar vertebra are also presented and an index of trabecular anisotropy suggested. Finally, the results are compared with those of other workers and estimates of useful skeletal parameters given.
Epigenetic mechanisms in senescence, immortalisation and cancer (2010)

Cancer is controlled not only by genetic events but also by epigenetic events. The active acquisition of epigenetic changes is a poorly understood but very important process in mammalian development, differentiation, and disease. It is well established that epigenetic events are controlled by a specific subgroup of proteins, such as DNA methyltransferases, histone acetylases histone lysine methyltransferases or histone deacetylases, that influence methylation or acetylation patterns to modulate gene expression. We and others have identified S-adenosylhomocysteine hydrolase in a high-throughput genetic screen focused on discovering novel genes whose inhibition induces immortalisation of primary cells. Herein, we address the importance of genes involved in epigenetic mechanisms during senescence and how their effects might determine senescence bypass and immortalisation. The ways in which genes that regulate epigenetic mechanisms might modulate senescence/immortalisation and how these pathways could influence cancer development are explored. Overall, epigenetic modifications seem to play a major role in cancer, influencing tumour outcome by interfering with key senescence pathways.
HotpotQA: A Dataset for Diverse, Explainable Multi-hop Question Answering (2018)

Zhilin Yang, Peng Qi, Saizheng Zhang, Yoshua Bengio, William Cohen, Ruslan Salakhutdinov, Christopher D. Manning. Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing. 2018.
The robustness of controllability and observability for discrete linear time-varying systems with norm-bounded uncertainty (2005)

Controllability and observability of discrete linear time-varying systems with norm-bounded parameter uncertainties are analyzed in this note. Like in the continuous case, we propose the sufficient conditions, which ensure controllability and observability of the uncertain system. The proposed conditions allow the evaluation of controllability and observability of the uncertain system without knowledge of specific values of uncertainties.
Application of efficient linear FM matched filtering algorithms to synthetic aperture radar processing (1985)

The applicability of two relatively new linear FM matched filtering algorithms to the processing of synthetic-aperture radar (SAR) data is examined and compared to the fast-convolution algorithm. The algorithms, called basic spectral analysis and the step transform, use the properties of the linear FM signal to achieve some significant performance improvements. The algorithms are evaluated on the basis of their ability to deal with problems peculiar to the SAR application, such as multilooking, range-cell migration, and variations in the FM rate of the input signal. Computation rates are also derived as a function of resolution and target return signal aperture. It is shown that no one algorithm is optimal for all cases. The basic-spectral-analysis algorithm has the lowest computation rate at low resolutions, but has an output data rate which varies with the FM rate and cannot correct for nonlinear data shifts called range curvature. The step transform has the most efficient computation rate at high resolutions. It also has a constant output data rate and can correct for range curvature. The fast-convolution algorithm has a lower computation rate than the step transform at low resolutions and can meet all of the SAR requirements mentioned. All of the algorithms are able to perform multilook processing.
Talaromyces marneffei Infection: Virulence, Intracellular Lifestyle and Host Defense Mechanisms (2022)

Talaromycosis (Penicilliosis) is an opportunistic mycosis caused by the thermally dimorphic fungus <i>Talaromyces</i> (<i>Penicillium</i>) <i>marneffei</i>. Similar to other major causes of systemic mycoses, the extent of disease and outcomes are the results of complex interactions between this opportunistic human pathogen and a host's immune response. This review will highlight the current knowledge regarding the dynamic interaction between <i>T. marneffei</i> and mammalian hosts, particularly highlighting important aspects of virulence factors, intracellular lifestyle and the mechanisms of immune defense as well as the strategies of the pathogen for manipulating and evading host immune cells.
Decapping Scavenger Enzyme Activity toward N2-Substituted 5′ End mRNA Cap Analogues (2019)

mRNA degradation is a key mechanism of gene expression regulation. In the 3' → 5' decay pathway, mRNA is degraded by the exosome complex and the resulting cap dinucleotide or short-capped oligonucleotide is hydrolyzed mainly by a decapping scavenger enzyme (DcpS)-a member of the histidine triad family. The decapping mechanism is similar for DcpS from different species; however, their respective substrate specificities differ. In this paper, we describe experiments exploring DcpS activity from human (hDcps), <i>Caenorhabditis elegans</i> (CeDcpS), and <i>Ascaris suum</i> (AsDcpS) toward dinucleotide cap analogues modified at the N2 position of 7-methylguanosine. Various alkyl substituents were tested, and cap analogues with a longer than three-carbon chain were nonhydrolyzable by hDcpS and CeDcpS. Resistance of the modified cap analogues to hDcpS and CeDcpS may be associated with their weaker binding with enzymes.
Intelligent Alarms Reduce Anesthesiologist's Response Time to Critical Faults (1992)

The proliferation of monitors and alarms in the operating room may lead to increased confusion and misdiagnosis unless the information provided is better organized. Intelligent alarm systems are being developed to organize these alarms, on the assumption that they will shorten the time anesthesiologists need to detect and correct faults. This study compared the human response time (the time between the sounding of an alarm and the resolution of a fault) when anesthesiologists used a conventional alarm system and when they used an intelligent alarm system. In a simulated operating room environment, we asked 20 anesthesiologists to resolve seven breathing circuit faults as quickly as possible. Human response time was 62% faster, decreasing from 45 to 17 s, when the intelligent alarm system was used. The standard deviations in response time were only half as large for the intelligent alarm system. It appears that the computer-based neural network in the intelligent alarm system diagnosed faults more rapidly and consistently than did the anesthesiologists. This study indicates that breathing circuit faults may be more rapidly corrected when the anesthesiologist is guided by intelligent alarms.
Molecular Analysis of Gene-Polymorphisms Affecting the Host Response to Infection (2003)

The genetic regulation of the host response to infection is crucial for understanding susceptibility to and outcome of meningococcal disease. The initial host response depends on the innate immune system, after which specific immunity is attained when antibodies from the adaptive immune system appear. The comparison of genetic markers in patients who have suffered from the disease, their families, and appropriate control populations thus identifies components of the host response that are key to combat meningococcal infection. A similar reasoning can be followed when studying susceptibility to or when studying outcome of meningococcal disease. A better understanding of the host response at a molecular level also allows for estimating individual risk. This accumulating knowledge can be used to develop new preventive and therapeutic interventions and to vary these strategies dependent on risk profiles.
Physical bound on the excluded-volume exponent of a polymer (1978)

A simple physical argument restricts the value of the excluded-volume exponent nu of a polymer. The result is nu <2/3 in three dimensions.
Techniques for fast stereoscopic MRI (2001)

Stereoscopic MRI can impart 3D perception with only two image acquisitions. This economy over standard multiplanar 3D volume renderings allows faster frame rates, which are needed for real-time imaging applications. Real-time 3D perception may enhance the appreciation of complex anatomical structures, and may improve hand-eye coordination while manipulating a medical device during an image-guided interventional procedure. To this goal, a system is being developed to acquire and display stereoscopic MR images in real-time. A clinically used, fast gradient-recalled echo-train sequence has been modified to produce stereo image pairs. Features have been added for depth cueing, view sharing, and bulk signal suppression. A workstation was attached to a clinical MR scanner for fast data extraction, image reconstruction and stereoscopic image display.
Progress in Aptamer-Mediated Drug Delivery Vehicles for Cancer Targeting and Its Implications in Addressing Chemotherapeutic Challenges (2014)

Aptamers are novel oligonucleotides with flexible three-dimensional configurations that recognize and bind to their cognate targets, including tumor surface receptors, in a high-affinity and highly specific manner. Because of their unique intrinsic properties, a variety of aptamer-mediated nanovehicles have been developed to directionally transport anti-cancer drugs to tumor sites to minimize systemic cytotoxicity and to enhance permeation by these tumoricidal agents. Despite advances in the selection and synthesis of aptamers and in the conjugation and self-assembly of nanotechnologies, current chemotherapy and drug delivery systems face great challenges. These challenges are due to the limitations of aptamers and vehicles and because of complicated tumor mechanisms, including heterogeneity, anti-cancer drug resistance, and hypoxia-induced aberrances. In this review, we will summarize current approaches utilizing tumor surface hallmarks and aptamers and their roles and mechanisms in therapeutic nanovehicles targeting tumors. Delivery forms include nanoparticles, nanotubes, nanogels, aptamer-drug conjugates, and novel molecular trains. Moreover, the obstacles posed by the aforementioned issues will be highlighted, and possible solutions will be acknowledged. Furthermore, future perspectives will be presented, including cutting-edge integration with RNA interference nanotechnology and personalized chemotherapy, which will facilitate innovative approaches to aptamer-based therapeutics.
Selective 5-Hydroxytryptamine 2C Receptor Agonists Derived from the Lead Compound Tranylcypromine: Identification of Drugs with Antidepressant-Like Action (2009)

We report here the design, synthesis, and pharmacological properties of a series of compounds related to tranylcypromine (9), which itself was discovered as a lead compound in a high-throughput screening campaign. Starting from 9, which shows modest activity as a 5-HT(2C) agonist, a series of 1-aminomethyl-2-phenylcyclopropanes was investigated as 5-HT(2C) agonists through iterative structural modifications. Key pharmacophore feature of this new class of ligands is a 2-aminomethyl-trans-cyclopropyl side chain attached to a substituted benzene ring. Among the tested compounds, several were potent and efficacious 5-HT(2C) receptor agonists with selectivity over both 5-HT(2A) and 5-HT(2B) receptors in functional assays. The most promising compound is 37, with 120- and 14-fold selectivity over 5-HT(2A) and 5-HT(2B), respectively (EC(50) = 585, 65, and 4.8 nM at the 2A, 2B, and 2C subtypes, respectively). In animal studies, compound 37 (10-60 mg/kg) decreased immobility time in the mouse forced swim test.
Abstract 449: The H2 Domain in the Connexin43 Carboxyl Terminus Regulates Cardioprotection From Ischemia Reperfusion Injury (2017)

Cardiac ischemia-reperfusion (IR) injury occurs in patients with acute coronary syndromes undergoing percutaneous intervention to re-establish blood flow in blocked or narrowed arteries. Presently, there are no therapies approved to prevent the loss of heart muscle, scar tissue formation and contractile dysfunction that result from IR injury. We have previously reported that α CT1, a Connexin 43 (Cx43) mimetic peptide currently in Phase III testing in humans (GAIT1; NCT02667327) as a therapy for chronic skin wounds (PMID:27856288; 25072595), improves contractile function of mouse hearts following injury in association with increases in PKCε-mediated phosphorylation of Cx43 at serine 368 (S368) (PMID: 21273554). Here, we report that induction of S368 phosphorylation and cardioprotection from IR injury by α CT1 involves direct protein-protein interaction of α CT1 with a short alpha-helical sequence within the Cx43 carboxyl terminus (CT) termed the H2 domain. The interacting protein domains involved in Cx43 S368 phosphorylation were identified and validated by a combination of techniques including tandem mass spectroscopy, surface plasmon resonance, immunoprecipitation and thermal shift assays. These studies indicated that α CT1 induced S368 phosphorylation (pS368) via a novel mechanism involving interaction between a pair of positively charged lysines (K344, K345) in the Cx43 CT H2 domain and a cluster of negatively charged amino acids i α CT1. It is further shown that the known ability of α CT1 to interact with Zonula Occludens-1 (ZO-1), has no direct role in either the induction of S368 phosphorylation or protection from IR injury. Finally, we identify a small, novel variant of α CT1 ( α CT11 - RPRPDDLEI, Mr 1110) that penetrates myocyte membranes, induces S368 phosphorylation and robustly preserves ventricular contractile function and cardiac muscle when administered after ischemic injury. Data on Cx43 hemichannel dependence of α CT11 uptake by cells will be presented. Our results indicate that selective targeting of the secondary structure and phospho-status of the Cx43 CT by small peptidergic drugs may provide a novel and potent pharmacological approach to preservation of cardiac muscle following IR injury.
Umbilical Cord Mannan‐Binding Lectin and Infections in Early Childhood (2003)

To investigate whether mannan-binding lectin (MBL) in umbilical cord blood (UCB) is associated with the incidence rate of hospitalizations for infections during early childhood. A follow-up study from birth to 31 months of age, with endpoint data from the Danish National Hospital Discharge Registry. The concentration of MBL and immunoglobulin A (IgA) in UCB was measured in a time-resolved immunofluorometric assay. Information on possible confounding factors was obtained from questionnaires completed by mothers during their pregnancy, and characteristics of the child at birth were registered by a midwife on a structured coding sheet. A total of 2104 infants born in the period between 1 February 1990 and 25 May 1991 to mothers living in the municipality of Aarhus. Concentration of MBL and IgA in UCB, gestational age, birth weight, number of siblings less than 3 years old, mother's smoking habits, alcohol and coffee consumption, educational and marital status and previous spontaneous abortions and stillbirths. Of 2104 children, 626 were hospitalized at least once, and 346 of these were hospitalized with infection. The hazard ratio (HR) of hospitalization with infections in children with low levels of MBL (<120 ng/ml) was 1.4 (95% confidence interval (CI), 1.0-1.8), which was similar to our findings on hospitalization because of other diseases. The HR of hospitalization for viral infections was 2.8 (CI, 1.3-5.9). Low levels of MBL in UCB were associated with hospitalization in general and particularly with hospitalization for viral infections.