gebhart/patrepeval huggingface dataset:
Differential effects of statins on relevant functions of human monocyte-derived dendritic cells (2005)

Statins were shown to possess immunomodulating properties, but the mechanisms of statin effects on the immune system are poorly understood. We analyzed the influence of statins on professional antigen-presenting dendritic cells (DC). Immature DC were cultivated from monocytes of healthy donors. DC maturation was induced by lipopolysaccharide (LPS; 1 microg/mL). Unstimulated and LPS-stimulated DC were treated with simvastatin or atorvastatin (0.1-1 microM). The expression of CD40, CD83, CD86, and human leukocyte antigen-DR on unstimulated and LPS-stimulated DC was reduced significantly by statins, and the expression of Toll-like receptor 2 (TLR2) and TLR4 on LPS-stimulated DC was enhanced temporarily. Statins caused a significant reduction of endocytosis of fluorescein isothiocyanate-dextran by DC. Statins significantly inhibited the basal secretion of interleukin (IL)-6, IL-8, IL-12, and tumor necrosis factor alpha from unstimulated DC, and their release from LPS-stimulated DC was enhanced. In mixed leukocyte reaction, preincubation of LPS-stimulated DC with statins significantly suppressed their clustering with T cells and their ability to induce T cell proliferation, CD71, and CD25 up-regulation on T cells and the secretion of interferon-gamma and IL-2 from T cells. In conclusion, this study showed that statins suppressed endocytosis, basal secretion of proinflammatory cytokines, and the ability of DC to induce T cell proliferation, activation, and T helper cell type 1 differentiation. However, statin preincubation of LPS-stimulated DC caused a further increase in their secretion of proinflammatory cytokines.
Tunable polarisation-maintaining filter based on liquid crystal photonic bandgap fibre (2008)

A tunable and polarisation-maintaining all-in-fibre filter based on a liquid crystal photonic bandgap fibre is demonstrated. Its polarisation extinction ratio reaches 14 dB at 1550 nm wavelength. Its spectral tunability range spans over 250 nm in the temperature range 30–70°C. The measured transmission spectrum is compared with that obtained through finite element simulations.
Whole-exome sequencing reveals a recurrent mutation in the cathepsin C gene that causes Papillon–Lefevre syndrome in a Saudi family (2015)

Papillon-Lefevre syndrome (PALS) is a rare, autosomal recessive disorder characterized by periodontitis and hyperkeratosis over the palms and soles. Mutations in the cathepsin C gene (CTSC) have been recognized as the cause of PALS since the late 1990s. More than 75 mutations in CTSC have been identified, and phenotypic variability between different mutations has been described. Next generation sequencing is widely used for efficient molecular diagnostics in various clinical practices. Here we investigated a large consanguineous Saudi family with four affected and four unaffected individuals. All of the affected individuals suffered from hyperkeratosis over the palms and soles and had anomalies of both primary and secondary dentition. For molecular diagnostics, we combined whole-exome sequencing and genome-wide homozygosity mapping procedures, and identified a recurrent homozygous missense mutation (c.899G>A; p.Gly300Asp) in exon 7 of CTSC. Validation of all eight family members by Sanger sequencing confirmed co-segregation of the pathogenic variant (c.899G>A) with the disease phenotype. This is the first report of whole-exome sequencing performed for molecular diagnosis of PALS in Saudi Arabia. Our findings provide further insights into the genotype-phenotype correlation of CTSC pathogenicity in PALS.
PGH1, the Precursor for the Anti-Inflammatory Prostaglandins of the 1-series, Is a Potent Activator of the Pro-Inflammatory Receptor CRTH2/DP2 (2012)

Prostaglandin H(1) (PGH(1)) is the cyclo-oxygenase metabolite of dihomo-γ-linolenic acid (DGLA) and the precursor for the 1-series of prostaglandins which are often viewed as "anti-inflammatory". Herein we present evidence that PGH(1) is a potent activator of the pro-inflammatory PGD(2) receptor CRTH2, an attractive therapeutic target to treat allergic diseases such as asthma and atopic dermatitis. Non-invasive, real time dynamic mass redistribution analysis of living human CRTH2 transfectants and Ca(2+) flux studies reveal that PGH(1) activates CRTH2 as PGH(2), PGD(2) or PGD(1) do. The PGH(1) precursor DGLA and the other PGH(1) metabolites did not display such effect. PGH(1) specifically internalizes CRTH2 in stable CRTH2 transfectants as assessed by antibody feeding assays. Physiological relevance of CRTH2 ligation by PGH(1) is demonstrated in several primary human hematopoietic lineages, which endogenously express CRTH2: PGH(1) mediates migration of and Ca(2+) flux in Th2 lymphocytes, shape change of eosinophils, and their adhesion to human pulmonary microvascular endothelial cells under physiological flow conditions. All these effects are abrogated in the presence of the CRTH2 specific antagonist TM30089. Together, our results identify PGH(1) as an important lipid intermediate and novel CRTH2 agonist which may trigger CRTH2 activation in vivo in the absence of functional prostaglandin D synthase.
High-density optical interconnects within large-scale systems (2003)

Next-generation high-end data processing systems such as Internet switches or servers are approaching aggregate bandwidths in excess of 1 Terabit per second. In the case of Internet switches, the increase of fiber bandwidth that is caused by the introduction of Dense Wavelength Division Multiplexing leads to an increase of system size from single-shelf to multi-rack configurations. Intra-system interconnects will therefore span from centimeters (on-board) up to tens of meters (rack-to-rack). The task of providing hundreds of individual links at speeds in excess of 10 Gigabit per second over these distances becomes increasingly difficult for conventional copper-based technology. Using a packet switch system as an example application, we define a set of interconnect requirements for future large-scale systems. Distinguishing three interconnect classes (on-board, card-to-card over a backplane, rack-to-rack), we study the expected limits of copper-based solutions from an application point of view. After an overview of the state of the art in optical interconnect technology, we compare available technologies with the initially defined requirements. From this, we deduct key focus areas for future optical interconnect research. Finally, we present some of our recent activities in the field of waveguide and free-space based board-to-board interconnects.
Expression and role of PAICS, a de novo purine biosynthetic gene in prostate cancer (2018)

The authors regret that the printed version of the above article contained an inadvertent error where a wrong tumor xenograft study was represented due to a mistaken labeling of PC3 prostate lines in another file. We have now repeated the in vivo experiments with PAICS knockdown cells and with a non-targeting shRNA as a control, and added the correct Figures 3E and F.
Prognostic implications of admission inflammatory profile in acute ischemic neurological events (2002)

Admission inflammatory markers have long-term prognostic implications in patients with acute ischemic neurological events. These findings are relevant in view of the new therapeutic interventions now available for reducing the inflammatory response.
Characterization of the gene structure, functional significance, and clinical application of RNF180, a novel gene in gastric cancer (2011)

RNF180 is a novel potential tumor suppressor in gastric carcinogenesis and has potential clinical utility as a biomarker for gastric cancer patients.
Low-Rank Nonlinear Decoding of $μ$-ECoG from the Primary Auditory Cortex (2020)

This paper considers the problem of neural decoding from parallel neural measurements systems such as micro-electrocorticography ($μ$-ECoG). In systems with large numbers of array elements at very high sampling rates, the dimension of the raw measurement data may be large. Learning neural decoders for this high-dimensional data can be challenging, particularly when the number of training samples is limited. To address this challenge, this work presents a novel neural network decoder with a low-rank structure in the first hidden layer. The low-rank constraints dramatically reduce the number of parameters in the decoder while still enabling a rich class of nonlinear decoder maps. The low-rank decoder is illustrated on $μ$-ECoG data from the primary auditory cortex (A1) of awake rats. This decoding problem is particularly challenging due to the complexity of neural responses in the auditory cortex and the presence of confounding signals in awake animals. It is shown that the proposed low-rank decoder significantly outperforms models using standard dimensionality reduction techniques such as principal component analysis (PCA).
Restrictions on the Importation of Zebrafish into Canada Associated with Spring Viremia of Carp Virus (2016)

The zebrafish model system is helping researchers improve the health and welfare of people and animals and has become indispensable for advancing biomedical research. As genetic engineering is both resource intensive and time-consuming, sharing successfully developed genetically modified zebrafish lines throughout the international community is critical to research efficiency and to maximizing the millions of dollars in research funding. New restrictions on importation of zebrafish into Canada based on putative susceptibility to infection by the spring viremia of carp virus (SVCV) have been imposed on the scientific community. In this commentary, we review the disease profile of SVCV in fish, discuss the findings of the Canadian government's scientific assessment, how the interpretations of their assessment differ from that of the Canadian research community, and describe the negative impact of these regulations on the Canadian research community and public as it pertains to protecting the health of Canadians.
The role of the histone H3 variant CENPA in prostate cancer (2020)

Overexpression of centromeric proteins has been identified in a number of human malignancies, but the functional and mechanistic contributions of these proteins to disease progression have not been characterized. The centromeric histone H3 variant centromere protein A (CENPA) is an epigenetic mark that determines centromere identity. Here, using an array of approaches, including RNA-sequencing and ChIP-sequencing analyses, immunohistochemistry-based tissue microarrays, and various cell biology assays, we demonstrate that CENPA is highly overexpressed in prostate cancer in both tissue and cell lines and that the level of CENPA expression correlates with the disease stage in a large cohort of patients. Gain-of-function and loss-of-function experiments confirmed that CENPA promotes prostate cancer cell line growth. The results from the integrated sequencing experiments suggested a previously unidentified function of CENPA as a transcriptional regulator that modulates expression of critical proliferation, cell-cycle, and centromere/kinetochore genes. Taken together, our findings show that CENPA overexpression is crucial to prostate cancer growth.
Design and analysis of a soft mobile robot composed of multiple thermally activated joints driven by a single actuator (2010)

Soft robotic systems have applications in industrial, medical, and security applications. Many applications require these robots to be small and lightweight. One challenge in developing a soft robotic system is to drive multiple degrees-of-freedom (DOF) with few actuators, thereby reducing system size and weight. This paper presents the analysis and design of an inchworm-like mobile robot that consists of multiple, independent thermally activated joints but is driven by a single actuator. To realize control of this under-actuated system, a solder-based locking mechanism has been developed to selectively activate individual joints without requiring additional actuators. The design and performance analysis of a prototype mobile robot that is capable of inchworm-like translational and steering motion is described. The design of novel “feet” with anisotropic friction properties is also described.
Distortion correction in diffusion‐weighted imaging of the breast: Performance assessment of prospective, retrospective, and combined (prospective + retrospective) approaches (2016)

Combined prospective and retrospective distortion correction can provide an efficient way to reduce susceptibility-induced image distortions and enhance the reliability of breast DWI exams. Magn Reson Med 78:247-253, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Evolution of an Ensemble of Nanoparticles in a Colloidal Solution:  Theoretical Study (2001)

The evolution of a nanosized particle in colloidal solution has been studied theoretically. The model developed is based on the size dependence of the activation energies of the growth and dissolution processes and takes into account the mass transport dynamics. Using this model, Monte Carlo simulations of the evolution of an ensemble of growing nanoparticles during Ostwald ripening have been performed, and conditions leading to either “focusing” or “defocusing” of the particle size distribution were found. The stationary particle size distribution inherent to the Ostwald ripening process in ensembles of nanoparticles less than 5 nm in radius is narrower and more symmetric than that predicted by the Lifshitz−Slyozov−Wagner theory valid for ensembles of larger (>20 nm in radius) colloidal particles. The growth of nanoparticles in the diffusion-controlled regime results in better final size distributions as compared with those grown in the reaction-controlled regime. The dependence of the particle size distribution on a number of external and internal ensemble characteristics is studied and possible ways of controlling the particle size distribution are discussed.
Composite pulse excitation in quadrupole echo spectroscopy (1986)

An examination of several composite pulse quadrupole echo sequences designed for the broadband excitation of I=1 systems shows that these sequences reduce but do not eliminate finite pulse width effects. It is demonstrated both experimentally and theoretically that these sequences can also introduce additional distortions. The origin of these distortions and several aspects of the evaluation of broadband excitation sequences are discussed. It is shown that these distortions can be eliminated by employing higher order composite pulses. Finally the viability of composite pulse excitation for systems undergoing chemical exchange is discussed.
Alignment strategy for metal layers after W-CMP (1999)

CMP of Tungsten (W) in the wafer process flow pose a major challenge for robust stepper alignment, particularly at tighter design rules for 0.25 micron and beyond. Traditional alignment strategies based on optical diffraction often fail to provide alignment accuracy and consistency, as dictated by the tighter overlay budgets. Intensity based image analysis methods prove to be more successful in the alignment of metal CMP layers. In addition the noise reduction and signal processing capabilities of alignment sensors, the condition of the mark after W-CMP is vital for achieving good alignment. In this paper we report results from various alignment mark designs. The marks are designed to reduce the impact of CMP process variations on stepper alignment. Three types of alignment methods using laser diffraction, bright field imaging and laser interferometry techniques were investigated. The brightfield imaging alignment schemes provide the best results using a narrow trench mark separated by wider islands. Details of stepper alignment signals and overlay measurement results corresponding to some of the relevant mark design sand process variations are included in the paper.
Electric-field distribution in composite media (1998)

Spatial fluctuations of the local electric field induced by a constant applied electric field in composite media are studied analytically and numerically. It is found that the density of states for the fields exhibit sharp peaks and abrupt changes in the slope at certain critical points which are analogous to van Hove singularities in the density of states for phonons and electrons in solids. As in solids, these singularities are generally related to saddle and inflection points in the field spectra and are useful in characterizing field fluctuations. The critical points are very prominent in dispersions with a regular, ``crystal-like,'' structure. However, they broaden and eventually disappear as the disorder increases.
Genetics: Scenario for a Crisis (2009)

Genetics is a novel science, its foundations only being laid in 1865 by Johann Gregor Mendel. It is a discipline which studies the way hereditary characteristics are transmitted, it is, together with the virtually contemporaneous theory of evolution, responsible for major scientific, sociological, philosophical and political upheavals. As such, it is par excellence the science of past, present and future crisis.
Development of KABISA (2006)

KABISA is a computer-based program for training in diagnostic problems in (sub-) tropical regions. It challenges the individual student with a randomly generated case, for which he should try to find the diagnosis, asking questions, performing a physical examination, and ordering tests. The built-in tutor follows the student’s input with complex logical algorithms and mathematical computations, gives comments and support, and accepts the final diagnosis if sufficient evidence has been built up. Several problems arose with the development. In the first place, the evolution in the teaching of clinical logic is always ahead of the program, so regular updating of the computer logic is necessary. Secondly, the choice of MS Access as computer language has provoked problems of stability, especially the installation of an MSAccess runtime. Thirdly, and most importantly, scholars want proof of the added value of computer programs over classical teaching. Moreover, the concept of a pedagogical “game” is often regarded as childish. Finally, the planning and financing of an “open-ended” pedagogical project is questioned by deciders, as is the case with all operational research.
HybridAxes: An Immersive Analytics Tool With Interoperability Between 2D and Immersive Reality Modes (2022)

Throughout the visual analytics process, users create visualizations with different dimensionalities. Research shows that in this process users benefit from being able to simultaneously see 2D and 3D modes of their data visualizations. Towards supporting this potential need, we introduce HybridAxes, an immersive visual analytics tool that allows the users to conduct their analysis at either end of the Reality-Virtuality continuum - either in 2D on desktop monitors or 3D in an immersive AR/VR environment - while enabling them to seamlessly switch between the two modes. We believe that by using our system, users will find it easier and faster to understand and analyze multi-dimensional data. An initial pilot test indicates positive trends in terms of users' performance time and usability metrics compared to the standalone desktop or AR/VR counterparts. Our preliminary results also suggest that users experience a lower cognitive load while task-switching between these virtuality modes. This reduction in mental effort causes them to perceive the system to be unobtrusive and pleasant to work with. Going forward, we plan to conduct more rigorous studies to verify our claims and to explore other research questions on this topic.
[NEt4][AuCl2][AuCl3]: Solid‐State Evidence of Essentially Y‐Shaped Jahn–Teller‐Distorted AuCl3 (2006)

Zwischen zwei Geometrien gefangen: Die Festkörperstruktur von [NEt4][AuCl2][AuCl3] (siehe Bild) zeigt für AuCl3 eine Geometrie, die typisch für einen Y-förmigen Übergangszustand als Folge einer Jahn-Teller-Verzerrung ist. Nach den Ergebnissen von Rechnungen ist die beobachtete Orientierung eine mittlere Geometrie zwischen zwei T-förmigen Strukturen mit C2v-Symmetrie.
Nontemplate Polymerization of Free Nucleotides Into Genetic Elements by Thermophilic DNA Polymerase in vitro (2011)

DNA synthesis is the cornerstone of all life forms and is required to replicate and restore the genetic information. Usually, DNA synthesis is carried out only by DNA polymerases semiconservatively to copy preexisting DNA templates. We report here that DNA strands were synthesized ab initio in the absence of any DNA or RNA template by thermophilic DNA polymerases at (a) a constant high temperature (74°C), (b) alternating temperatures (94°C/60°C/74°C), or (c) physiological temperatures (37°C). The majority of the ab initio synthesized DNA represented short sequence blocks, repeated sequences, intergenic spacers, and other unknown genetic elements. These results suggest that novel DNA elements could be synthesized in the absence of a nucleic acid template by thermophilic DNA polymerases in vitro. Biogenesis of genetic information by thermophilic DNA polymerase-mediated nontemplate DNA synthesis may explain the origin of genetic information and could serve as a new way of biosynthesis of genetic information that may have facilitated the evolution of life.
Chemiosmotic systems in bioenergetics: H+-cycles and Na+-cycles (1991)

The development of membrane bioenergetic studies during the last 25 years has clearly demonstrated the validity of the Mitchellian chemiosmotic H+ cycle concept. The circulation of H+ ions was shown to couple respiration-dependent or light-dependent energy-releasing reactions to ATP formation and performance of other types of membrane-linked work in mitochondria, chloroplasts, some bacteria, tonoplasts, secretory granules and plant and fungal outer cell membranes. A concrete version of the direct chemiosmotic mechanism, in which H+ potential formation is a simple consequence of the chemistry of the energy-releasing reaction, is already proved for the photosynthetic reaction centre complexes. Recent progress in the studies on chemiosmotic systems has made it possible to extend the coupling-ion principle to an ion other than H+. It was found that, in certain bacteria, as well as in the outer membrane of the animal cell, Na+ effectively substitutes for H+ as the coupling ion (the chemiosmotic Na+ cycle). A precedent is set when the Na+ cycle appears to be the only mechanism of energy production in the bacterial cell. In the more typical case, however, the H+ and Na+ cycles coexist in one and the same membrane (bacteria) or in two different membranes of one and the same cell (animals). The sets of delta mu H+ and delta mu Na+ generators as well as delta mu H+ and delta mu Na+ consumers found in different types of biomembranes, are listed and discussed.
Room‐Temperature Quantum Transport Signatures in Graphene/LaAlO3/SrTiO3 Heterostructures (2017)

High mobility graphene field-effect devices, fabricated on the complex-oxide heterostructure LaAlO<sub>3</sub> /SrTiO<sub>3</sub> , exhibit quantum interference signatures up to room temperature. The oxide material is believed to play a critical role in suppressing short-range and phonon contributions to scattering. The ability to maintain pseudospin coherence at room temperature holds promise for the realization of new classical and quantum information technologies.