gebhart/patrepeval huggingface dataset:
An investigation of the structural, connectional, and functional subspecialization in the human amygdala (2012)

Although the amygdala complex is a brain area critical for human behavior, knowledge of its subspecialization is primarily derived from experiments in animals. We here employed methods for large-scale data mining to perform a connectivity-derived parcellation of the human amygdala based on whole-brain coactivation patterns computed for each seed voxel. Voxels within the histologically defined human amygdala were clustered into distinct groups based on their brain-wide coactivation maps. Using this approach, connectivity-based parcellation divided the amygdala into three distinct clusters that are highly consistent with earlier microstructural distinctions. Meta-analytic connectivity modelling then revealed the derived clusters' brain-wide connectivity patterns, while meta-data profiling allowed their functional characterization. These analyses revealed that the amygdala's laterobasal nuclei group was associated with coordinating high-level sensory input, whereas its centromedial nuclei group was linked to mediating attentional, vegetative, and motor responses. The often-neglected superficial nuclei group emerged as particularly sensitive to olfactory and probably social information processing. The results of this model-free approach support the concordance of structural, connectional, and functional organization in the human amygdala and point to the importance of acknowledging the heterogeneity of this region in neuroimaging research.
Elucidating the Mechanisms Behind Sonoporation with Adeno-Associated Virus-Loaded Microbubbles (2011)

Microbubbles are Food and Drug Administration (FDA) approved contrast agents for ultrasound imaging. It has been reported that applying ultrasound on drug-loaded microbubbles facilitates drug uptake by cells, due to so-named sonoporation. However, the biophysics behind sonoporation are not fully understood. It is believed that sonoporation results in a "direct" delivery of drugs in the cytoplasm of cells, though it has been suggested as well that sonoporation facilitates endocytosis which would improve the internalization of drugs by cells. To get a better understanding of sonoporation, this study reports on the ultrasound assisted delivery of adeno-associated virus (AAV) loaded on the surface of microbubbles. AAVs rely on endocytosis for efficient transduction of cells and are, consequently, an elegant tool to evaluate whether endocytosis is involved in ultrasound-induced sonoporation. Applying ultrasound on AAV-loaded microbubbles clearly improved the internalization of AAVs by cells, though transduction of the cells did not occur, indicating that by sonoporation substances become directly delivered in the cytosol of cells.
Synthesis of an l-proline modified mimetic of the A83586C antitumour cyclodepsipeptideElectronic supplementary information (ESI) available: characterisation data. See http://www.rsc.org/suppdata/cc/b2/b204018b/ (2002)

A mimetic of the A83586C cyclodepsipeptide has been synthesised via a three-segment coupling protocol involving dipeptides 9, 8 and 7; in contrast to our previous synthesis of A83586C, where the HATU-mediated macrolactamisation proceeded in 25% yield, the corresponding macro-lactamisation of seco-amino acid 18 occurred in ca. 78% yield.
Activity of Anti-epidermal Growth Factor Receptor Monoclonal Antibody C225 against Glioblastoma Multiforme (2002)

Blocking EGFR in GBM cells that overexpress this receptor significantly changes tumor cell biology by promoting apoptosis while decreasing proliferation and vascular endothelial growth factor expression. This approach holds great promise for the treatment of patients with GBMs.
Composition dependence of electro-mechanical properties and field induced phase transformations in [001]CPIN–PMN–PT single crystals (2014)

The compositional dependence of the electro-mechanical properties of [001]C cut and poled relaxor ferroelectric lead indium niobate—lead magnesium niobate—lead titanate, xPb(In1/2Nb1/2)O3-(1–x−y)Pb(Mg1/3Nb2/3)O3-yPbTiO3 (PIN–PMN–PT) single crystals was characterized under combined stress and electric field loading. Increasing the PIN and PT concentrations in compositions near the morphotropic phase boundary affected the piezoelectric, dielectric, and compliance coefficients, and the ferroelectric, pyroelectric, and thermal expansion coefficients, as well as the ferroelectric rhombohedral to ferroelectric orthorhombic phase transformation thresholds. The combinations of stress and electric field that induced the phase transformations were determined as a function of temperature. The results indicate that the linear response regime can be increased by modifying the composition, but this reduces the piezoelectric, dielectric, and compliance coefficients. This may be a desirable trade off in device design where linearity and low loss are important to the application.
A bifunctional palladium/acid solid catalyst performs the direct synthesis of cyclohexylanilines and dicyclohexylamines from nitrobenzenes (2013)

Nitroderivatives are transformed to cyclohexylanilines at room temperature in good yields and selectivity via a hydrogenation-amine coupling cascade reaction using Pd nanoparticles on carbon as a catalyst and a Brönsted acid.
Integration and Evaluation of Antenna Systems for 5G mmWave Mobile Device (2019)

Critical aspects on millimeter wave (mmWave) antenna integration and performance characterization for 5th generation (5G) mobile device have been reviewed in this paper. The influence of the device housing on the antenna performance is presented, and the corresponding performance characterization from 3GPP has been given. A practical example of an antenna system for a mobile device will also be shown at the end of the paper.
Explicit Navier-Stokes Computation of Turbomachinery Flows (1991)

A new three-dimensional explicit Navier-Stokes procedure has been developed for computation of turbomachinery flows. Several numerical strategies and modelling techniques have been developed and incorporated which enable convergent and accurate predictions of high Reynolds number flowfields across a wide range of Mach numbers. These include incorporation of a compressible low Reynolds number form of the turbulence transport model and other physical and solution parameters, eigenvalue and local velocity artificial dissipation scalings, a compact flux evaluation procedure and a hybrid low Reynolds number ke/algebraic Reynolds stress model. Detailed stability and order of magnitude analyses are performed on the discrete system of seven governing equations. Conclusions are drawn concerning the influence of system rotation and turbulence transport source terms, implicit source term treatment and the coupling of the discrete mean flow equation system to the turbulence model equations and its effect on the stability of the numerical scheme. Three-dimensional validation is provided by the results of an incompressible curved duct flow computation. A high Reynolds number axial rotor flow, for which extensive' experimental data is also available, was computed. A backswept transonic centrifugal compressor flow, for which L2F meridional passage velocity measurements are available, is computed. Full Navier-Stokes solutions are presented which are shown to capture detailed viscous dominated flow features, including tip clearance and curvature induced and rotation induced secondary motions, with good accuracy.
Incorporating Stimuli-Responsive Bacteria in Microfluidic Droplets (2015)

Model cellular membranes respond to chemical and electrical stimuli, regulating transport and exchange between two neighboring aqueous droplets. This regulated exchange may prove useful for controlling aqueous micro-environments for studying stimuli-responsive encapsulated bacteria. This concept is explored in this work, focusing on characterizing the bacterial response within a synthetic cellular environment. In the droplet interface bilayer (DIB) approach, aqueous micro-droplets deposited in an oil reservoir with dissolved lipids are coated with lipid monolayers and arranged into artificial cellular networks. This approach has been explored for potential use as a biologically-inspired smart material, but new material transduction pathways are necessary. This may be accomplished by combining this bottom-up approach to synthetic biology with living organisms such as stimuli-responsive bacteria. Bacteria encapsulation within the microfluidic droplets begins with a strain of Escherichia coli (E. coli), XL1-Blue. These flagellated bacteria naturally respond and move towards chemoattractants such as casamino acids, and their motion may be tracked through differential interference contrast (DIC) and fluorescent microscopy. Chemotaxis of XL1-Blue was assessed through low-flow perfusion of the chemoattractant (casamino acids) into a buffer solution containing the bacteria through a tailored capillary tube. Next, the response of bacteria within asymmetric DIB networks separating the bacteria and the chemoattractant were studied.
Fibroblast growth factor-2 protects entorhinal layer II glutamatergic neurons from axotomy-induced death (1996)

The entorhinal cortex is a major relay between the hippocampus and other cortical and subcortical regions. Glutamatergic axons from layer II neurons form the entorhinal cortical projection to the hippocampus via the perforant pathway. We have demonstrated previously that lesion of the perforant pathway causes the death of approximately 30% of entorhinal layer II (ECL2) neurons. To elucidate mechanisms contributing to neuronal death and to investigate strategies preventing it, we identified the phenotype of the vulnerable neuronal population. Sections were immunolabeled with antibodies to the neuronal markers NeuN, glutamate, and calbindin-D28k, and to receptors for fibroblast growth factor-2 (FGFR1) and NMDA (NMDAR1) and were examined using confocal microscopy. Calbindin immunoreactivity was strikingly lamina-specific to ECL2, where one-third of all ECL2 neurons were calbindin-positive. Localization of glutamate revealed that half of the glutamatergic ECL2 neurons coexpressed calbindin. Quantification using unbiased stereology at 9 weeks after lesion of the perforant pathway revealed that the only ECL2 neuronal population that experienced a significant (70%) loss (20% of the total) was the population of glutamatergic ECL2 neurons that did not coexpress calbindin. All ECL2 neurons expressed FGFR1; therefore, we tested the role of FGF-2 in the survival of glutamatergic ECL2 neurons. We grafted fibroblasts genetically engineered to express nerve growth factor or FGF-2 and found that only FGF-2 grafts prevented loss of the vulnerable glutamatergic/calbindin-negative neurons. We present a hypothesis for the selective vulnerability of these glutamatergic/calbindin-negative ECL2 neurons and address the role of FGF-2 in neuronal rescue.
Efforts in fighting against cancer in Croatia have to be focused on the primary health care. (2008)

This manuscript is a comprehensive review of the long-lasting tradition and the state-of-the-art in the prevention and early detection of cancer in Croatia. Compared with other European countries, Croatia holds a high and unfavourable position in cancer morbidity and mortality. Global experience in implementation of national programmes for the early detection of cancer clearly shows that such approach is the most successful and in the long-term the least expensive method for fighting against cancer. In Croatia, numerous separate actions in cancer care have been taken, but never systematically, nor included in a health care policy. The National Programme for the Prevention and Early Detection of Cancer of the common localizations for which effective screening tests are available (breast, uterine cervix, colon and prostate) has recently been launched. Local long-standing experience of the Osijek-Baranja County in implementation of programmes of cancer care contributed significantly to these initiatives. In this review, draft National Programme and the early results of its implementation were presented. In addition, preparations for the research project "Model of early cancer detection integrated in a practice of family physician", recently set up by the Department of Family Medicine of the School of Medicine, University of Osijek, were described. In this project, the programme of the early detection of cancer in which family physicians take responsibility for the programme implementation is suggested. Possible advantages of this model, compared with the model proposed by the National Programme, centrally directed and mostly supplied by the public services, are pointed out.
Dilute magnetic semiconductors based on InN (2006)

Abstract We present growth and characterization of Cr-doped InN by plasma assisted molecular beam epitaxy. The films were grown on c-plane sapphire substrates, employing GaN intermediate layers to accommodate the lattice mismatch between InN and sapphire. X-ray diffraction and Hall measurements were used for structural and electrical characterization of the films. The magnetic properties were measured using superconducting quantum interference device magnetometry. Cr : InN displayed long range ferromagnetic order up to room temperature without indications of phase separation. A optimal Cr-doping regime was found around 1–2% where the effective magnetic moment per Cr atom was maximal and the paramagnetic background signal of the samples was minimal. Keywords: Dilute magnetic semiconductorsIndium nitrideMagnetic hysteresis Acknowledgements We want to thank A. Kellock for the RBS measurements and V. Deline for the SIMS characterization. We are grateful to G. Solomon for the growth of the GaN buffer layers. A. N. wants to thank the Alexander-von-Humboldt foundation for financial support.
The Benchmark Lottery (2021)

The world of empirical machine learning (ML) strongly relies on benchmarks in order to determine the relative effectiveness of different algorithms and methods. This paper proposes the notion of "a benchmark lottery" that describes the overall fragility of the ML benchmarking process. The benchmark lottery postulates that many factors, other than fundamental algorithmic superiority, may lead to a method being perceived as superior. On multiple benchmark setups that are prevalent in the ML community, we show that the relative performance of algorithms may be altered significantly simply by choosing different benchmark tasks, highlighting the fragility of the current paradigms and potential fallacious interpretation derived from benchmarking ML methods. Given that every benchmark makes a statement about what it perceives to be important, we argue that this might lead to biased progress in the community. We discuss the implications of the observed phenomena and provide recommendations on mitigating them using multiple machine learning domains and communities as use cases, including natural language processing, computer vision, information retrieval, recommender systems, and reinforcement learning.
Chitinase gene expression in transgenic plants: a molecular approach to understanding plant defence responses (1993)

Abstract Recent studies suggest that the production of enzymes capable of degrading the cell walls of invading phytopathogenic fungi may be an important component of the defence response of plants. In this chapter, we summarize recent progress on the isolation and characterization of chitinolytic enzymes from higher plants. Emphasis is placed on experiments designed to study the regulation of chitinase gene expression in response to ethylene treatment or pathogen ingress and on determining the role of this enzyme in plant defence. The production of transgenic plants with enhanced resistance to attack by the fungal pathogen Rhizodonia solani is discussed.
Mucociliary Transport Deficiency and Disease Progression in Syrian Hamsters with SARS-CoV-2 Infection (2022)

Substantial clinical evidence supports the notion that ciliary function in the airways plays an important role in COVID-19 pathogenesis. Although ciliary damage has been observed in both <i>in vitro</i> and <i>in vivo</i> models, consequent impaired mucociliary transport (MCT) remains unknown for the intact MCT apparatus from an <i>in vivo</i> model of disease. Using golden Syrian hamsters, a common animal model that recapitulates human COVID-19, we quantitatively followed the time course of physiological, virological, and pathological changes upon SARS-CoV-2 infection, as well as the deficiency of the MCT apparatus using micro-optical coherence tomography, a novel method to visualize and simultaneously quantitate multiple aspects of the functional microanatomy of intact airways. Corresponding to progressive weight loss up to 7 days post-infection (dpi), viral detection and histopathological analysis in both the trachea and lung revealed steadily descending infection from the upper airways, as the main target of viral invasion, to lower airways and parenchymal lung, which are likely injured through indirect mechanisms. SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 dpi, largely due to diminished motile ciliation coverage, but not airway surface liquid depth, periciliary liquid depth, or cilia beat frequency of residual motile cilia. Further analysis indicated that the fewer motile cilia combined with abnormal ciliary motion of residual cilia contributed to the delayed MCT. The time course of physiological, virological, and pathological progression suggest that functional deficits of the MCT apparatus predispose to COVID-19 pathogenesis by extending viral retention and may be a risk factor for secondary infection. As a consequence, therapies directed towards the MCT apparatus deserve further investigation as a treatment modality.
Aliphatic Polyester Block Polymer Design (2016)

Aliphatic polyester block polymers constitute a highly useful and amazingly versatile class of self-assembled materials. Analogous to styrenic block polymers in both design and function, the property profiles of these degradable materials can be precisely tailored by altering the chemical structure of the components. Driven by this ideal, we have examined the impact of n-alkyl substituents on the polymerization thermodynamics and kinetics of substituted δ-valerolactone monomers and developed guiding design principles based on critical structure–property relationships in the resulting aliphatic polyesters. Under bulk room temperature conditions the polymerization rate depends strongly on substituent position and exhibits a more modest dependence on alkyl length (from –CH<sub>3</sub> to –(CH<sub>2</sub>)<sub>8</sub>CH<sub>3</sub>). The enthalpy and entropy of polymerization are significantly influenced by substituent position, but both are largely insensitive to n-alkyl length. However, the physical properties of the resulting aliphatic polyesters depend much more on substituent length than on substituent position. Notably, we demonstrate that polymer entanglement molar mass and solubility parameter can be systematically tuned by changing the substituent length. We discuss how these key structure property relationships can be used to inform the design of advanced sustainable materials for future technologies important in the arena of environmentally friendly materials.
Siglec-9 defines and restrains a natural killer subpopulation highly cytotoxic to HIV-infected cells (2021)

Siglec-9 is an MHC-independent inhibitory receptor expressed on a subset of natural killer (NK) cells. Siglec-9 restrains NK cytotoxicity by binding to sialoglycans (sialic acid-containing glycans) on target cells. Despite the importance of Siglec-9 interactions in tumor immune evasion, their role as an immune evasion mechanism during HIV infection has not been investigated. Using in vivo phenotypic analyses, we found that Siglec-9+ CD56dim NK cells, during HIV infection, exhibit an activated phenotype with higher expression of activating receptors and markers (NKp30, CD38, CD16, DNAM-1, perforin) and lower expression of the inhibitory receptor NKG2A, compared to Siglec-9- CD56dim NK cells. We also found that levels of Siglec-9+ CD56dim NK cells inversely correlate with viral load during viremic infection and CD4+ T cell-associated HIV DNA during suppressed infection. Using in vitro cytotoxicity assays, we confirmed that Siglec-9+ NK cells exhibit higher cytotoxicity towards HIV-infected cells compared to Siglec-9- NK cells. These data are consistent with the notion that Siglec-9+ NK cells are highly cytotoxic against HIV-infected cells. However, blocking Siglec-9 enhanced NK cells' ability to lyse HIV-infected cells, consistent with the known inhibitory function of the Siglec-9 molecule. Together, these data support a model in which the Siglec-9+ CD56dim NK subpopulation is highly cytotoxic against HIV-infected cells even whilst being restrained by the inhibitory effects of Siglec-9. To harness the cytotoxic capacity of the Siglec-9+ NK subpopulation, which is dampened by Siglec-9, we developed a proof-of-concept approach to selectively disrupt Siglec/sialoglycan interactions between NK and HIV-infected cells. We achieved this goal by conjugating Sialidase to several HIV broadly neutralizing antibodies. These conjugates selectively desialylated HIV-infected cells and enhanced NK cells' capacity to kill them. In summary, we identified a novel, glycan-based interaction that may contribute to HIV-infected cells' ability to evade NK immunosurveillance and developed an approach to break this interaction.
Investigation on the Effects of Process Parameters on Defect Formation in Friction Stir Welded Samples Via Predictive Numerical Modeling and Experiments (2017)

Setting optimum process parameters is very critical in achieving a sound friction stir weld joint. Understanding the formation of defects and developing techniques to minimize them can help in improving the overall weld strength. The most common defects in friction stir welding (FSW) are tunnel defects, cavities, and excess flash formation, which are caused due to incorrect tool rotational or advancing speed. In this paper, the formation of these defects is explained with the help of an experimentally verified 3D finite element (FE) model. It was observed that the asymmetricity in temperature distribution varies for different types of defects formed during FSW. The location of the defect also changes based on the shoulder induced flow and pin induced flow during FSW. Besides formation of defects like excess flash, cavity defects, tunnel/wormhole defects, two types of groove like defects are also discussed in this paper. By studying the different types of defects formed, a methodology is proposed to recognize these defects and counter them by modifying the process parameters to achieve a sound joint for a displacement-based FSW process.
Efficient Reduction of Esters to Aldehydes through Iridium‐Catalyzed Hydrosilylation (2012)

DIBALH wird übertrumpft: Eine neue Methode für die Reduktion von Estern zu Aldehyden über Silylacetal-Zwischenstufen umfasst eine einstufige Hydrosilylierung mit dem leicht verfügbaren Iridium-Komplex [{Ir(coe)2Cl}2] als Katalysator (siehe Schema; coe=Cycloocten). Durch die geringen Katalysatormengen, milden Reaktionsbedingungen, hohen Umsätze und das breite Substratspektrum ist die Methode eine überlegene Alternative zur Esterreduktion mit DIBALH. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.