gebhart/patrepeval huggingface dataset:
Dynamic organization of visual cortical networks inferred from massive spiking datasets (2023)

ABSTRACT Complex cognitive functions in a mammalian brain are distributed across many anatomically and functionally distinct areas and rely on highly dynamic routing of neural activity across the network. While modern electrophysiology methods enable recording of spiking activity from increasingly large neuronal populations at a cellular level, development of probabilistic methods to extract these dynamic inter-area interactions is lagging. Here, we introduce an unsupervised machine learning model that infers dynamic connectivity across the recorded neuronal population from a synchrony of their spiking activity. As opposed to traditional population decoding models that reveal dynamics of the whole population, the model produces cellular-level cell-type specific dynamic functional interactions that are otherwise omitted from analysis. The model is evaluated on ground truth synthetic data and compared to alternative methods to ensure quality and quantification of model predictions. Our strategy incorporates two sequential stages – extraction of static connectivity structure of the network followed by inference of temporal changes of the connection strength. This two-stage architecture enables detailed statistical criteria to be developed to evaluate confidence of the model predictions in comparison with traditional descriptive statistical methods. We applied the model to analyze large-scale in-vivo recordings of spiking activity across mammalian visual cortices. The model enables the discovery of cellular-level dynamic connectivity patterns in local and long-range circuits across the whole visual cortex with temporally varying strength of feedforward and feedback drives during sensory stimulation. Our approach provides a conceptual link between slow brain-wide network dynamics studied with neuroimaging and fast cellular-level dynamics enabled by modern electrophysiology that may help to uncover often overlooked dimensions of the brain code.
Claw toes after tibial fracture in children (2009)

We described five patients with a claw toe deformity following a tibia fracture associated with adhesions of the flexor hallucis longus (FHL) and flexor digitorum longus (FDL) muscles to the surrounding structures under or just proximal to the flexor retinaculum. It is the authors' opinion that this condition may be related to a subclinical compartment syndrome localized in the distal part of the deep posterior compartment. Soft-tissue release without tendon lengthening allowed recovery in all patients.
Correlating the silicon surface passivation to the nanostructure of low-temperature a-Si:H after rapid thermal annealing (2017)

Using an inductively coupled plasma, hydrogenated amorphous silicon (a-Si:H) films have been prepared at very low temperatures (&amp;lt;50 °C) to provide crystalline silicon (c-Si) surface passivation. Despite the limited nanostructural quality of the a-Si:H bulk, a surprisingly high minority carrier lifetime of ∼4 ms is demonstrated after a rapid thermal annealing treatment. Besides the excellent level of surface passivation, the main advantage of the low-temperature approach is the facile suppression of undesired epitaxial growth. The correlation between the a-Si:H nanostructure and the activation of a-Si:H/c-Si interface passivation, upon annealing, has been studied in detail. This yields a structural model that qualitatively describes the different processes that take place in the a-Si:H films during annealing. The presented experimental findings and insights can prove to be useful in the further development of very thin a-Si:H passivation layers for use in silicon heterojunction solar cells.
Ultrafast Dynamics in Helium Nanodroplets Probed by Femtosecond Time-Resolved EUV Photoelectron Imaging (2010)

The dynamics of electronically excited helium nanodroplets are studied by femtosecond time-resolved photoelectron imaging. EUV excitation into a broad absorption band centered around 23.8 eV leads to an indirect photoemission process that generates ultraslow photoelectrons. A 1.58 eV probe pulse transiently depletes the indirect photoemission signal for pump-probe time delays &lt;200 fs and enhances the signal beyond this delay. The depletion is due to suppression of the indirect ionization process by the probe photon, which generates a broad, isotropically emitted photoelectron band. Similar time scales in the decay of the high energy photoelectron signal and the enhancement of the indirect photoemission signal suggest an internal relaxation process that populates states in the range of a lower energy droplet absorption band located just below the droplet ionization potential (IP {approx} 23.0 eV). A nearly 70% enhancement of the ultraslow photoelectron signal indicates that interband relaxation plays a more dominant role for the droplet de-excitation mechanism than photoemission.
Measurements of the production cross section of a $$Z$$ Z boson in association with jets in pp collisions at $$\sqrt{s} = 13$$ s = 13 TeV with the ATLAS detector (2017)

Measurements of the production cross section of a [Formula: see text] boson in association with jets in proton-proton collisions at [Formula: see text] TeV are presented, using data corresponding to an integrated luminosity of 3.16 fb[Formula: see text] collected by the ATLAS experiment at the CERN Large Hadron Collider in 2015. Inclusive and differential cross sections are measured for events containing a [Formula: see text] boson decaying to electrons or muons and produced in association with up to seven jets with [Formula: see text] GeV and [Formula: see text]. Predictions from different Monte Carlo generators based on leading-order and next-to-leading-order matrix elements for up to two additional partons interfaced with parton shower and fixed-order predictions at next-to-leading order and next-to-next-to-leading order are compared with the measured cross sections. Good agreement within the uncertainties is observed for most of the modelled quantities, in particular with the generators which use next-to-leading-order matrix elements and the more recent next-to-next-to-leading-order fixed-order predictions.
Abstract 521: The Thrombotic Potential of the Endothelium Is Regulated by Hemodynamic Flow (2012)

BACKGROUND: Vascular wall mechanisms underlying human arterial and venous thrombosis are still evolving. TNFα and other cytokines have been shown to be potent mediators of endothelial cell-derived tissue factor in vitro, which mediates fibrin deposition in the vascular wall. Circulating levels of TNFα detected in humans with cardiovascular disease are approximately 0.05 ng/ml. METHODS: Human endothelial cells were co-cultured with or without smooth muscle cells in the presence or absence of human-derived, region-specific hemodynamics. Endothelial cells were exposed to TNFα at various concentrations and incubated in human, platelet-free-plasma supplemented by Alexa 488-labeled fibrinogen. Conversion of A488-fibrinogen to A488-fibrin and deposition on the endothelium was quantified by confocal microscopy. RESULTS: In static cultures, samples treated with 1ng/ml TNFα demonstrated minimal fibrin deposition whereas samples treated with 10ng/ml or 20ng/ml exhibited dense fibrin networks (1.17e5 vs. 2.69e7 vs. 3.61e7 mean fluorescence intensity, respectively). Fibrin deposition was tissue factor-dependent. In contrast, endothelial/smooth muscle cell co-cultures primed with inflammatory-prone hemodynamics derived from the internal carotid sinus and 0.05ng/ml TNFα deposited a dense fibrin network (1.9e7 mean fluorescence intensity). Identical experiments in which only endothelial cells were cultured yielded similar results demonstrating the result is hemodynamic-specific and not a consequence of the presence of smooth muscle cells. CONCLUSIONS: Hemodynamic priming of endothelial cells in vitro shifts the dose-dependent fibrin deposition response to TNFα into a more human physiological range, two orders of magnitude below that required to induce fibrin deposition in static endothelial cell cultures. Similar approaches can be used to investigate the differential mechanisms underlying vascular wall-mediated venous and arterial thrombosis.
Measurement of vectorial response of IQ modulator using optical interference (2016)

We propose a new measurement method of modulator response in phasor domain for Mach-Zehnder modulators embedded in IQ modulator using simple equipments. The modulation curve with extinction ratio of 14.7 and 22 dB were measured.
Design and identification of a novel, functionally subtype selective GABAApositive allosteric modulator (PF-06372865). (2019)

The design, optimization, and evaluation of a series of novel imidazopyridazine-based subtype-selective positive allosteric modulators (PAMs) for the GABA<sub>A</sub> ligand-gated ion channel are described. From a set of initial hits multiple subseries were designed and evaluated based on binding affinity and functional activity. As designing in the desired level of functional selectivity proved difficult, a probability-based assessment was performed to focus the project's efforts on a single subseries that had the greatest odds of delivering the target profile. These efforts ultimately led to the identification of two precandidates from this subseries, which were advanced to preclinical safety studies and subsequently to the identification of the clinical candidate PF-06372865.
ChemInform Abstract: Chiral Synthesis of an α‐Tetrasubstituted Proline Derivative. (2011)

Abstract Starting from D‐proline (I), an improved gram‐scale synthesis of the potential triple reuptake inhibitor (VIII) is presented.
ChemInform Abstract: C‐C Bond Formation with Chelated Alkene‐Carbene and Allyl‐Carbene Complexes. Novel Pathways to Functionalized Alkadienes, Carbo‐, and Heterocycles (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Oxygen Affinity of Hemoglobin Regulates O2Consumption, Metabolism, and Physical Activity (2003)

The oxygen affinity of hemoglobin is critical for gas exchange in the lung and O(2) delivery in peripheral tissues. In the present study, we generated model mice that carry low affinity hemoglobin with the Titusville mutation in the alpha-globin gene or Presbyterian mutation in the beta-globin gene. The mutant mice showed increased O(2) consumption and CO(2) production in tissue metabolism, suggesting enhanced O(2) delivery by mutant Hbs. The histology of muscle showed a phenotypical conversion from a fast glycolytic to fast oxidative type. Surprisingly, mutant mice spontaneously ran twice as far as controls despite mild anemia. The oxygen affinity of hemoglobin may control the basal level of erythropoiesis, tissue O(2) consumption, physical activity, and behavior in mice.
<title>Micro-optics design, fabrication, and integration for fiber optic devices</title> (2001)

Micro-Optics have begun to play a key role in micro-photonic systems and devices. This is largely due to the fact that semiconductor processing has enabled one to incorporate complex optical functions and integration features into the actual optical substrates. In this paper, key application areas of micro-optics are demonstrated for mode matching, gain equalization, and spectral filtering.
820 Linear DNA amplicons as a novel antiviral and cancer vaccine strategy (2022)

<h3>Background</h3> DNA-based vaccines represent a simple, safe and promising strategy for harnessing the immune system to fight infectious diseases as well as various forms of cancer and thus are considered an important tool in the cancer immunotherapy toolbox. Nonetheless, the manufacture of plasmid DNA vaccines has several drawbacks, including long lead times and the need to remove impurities from bacterial cultures. Here we report the development of polymerase chain reaction (PCR)-produced amplicon expression vectors as DNA vaccines and their <i>in vivo</i> application to elicit antigen-specific immune responses in animal cancer models.<sup>1</sup> <h3>Methods</h3> Plasmid DNA and amplicon expression was assessed both <i>in vitro</i>, by Hela cells transfection, and <i>in vivo</i>, by evaluating luciferase expression in mice through optical imaging. Immunogenicity induced by DNA amplicons was assessed by vaccinating mice, cats and ferrets against SARS-CoV-2 Spike protein. Similarly, amplicons encoding a tumor-associated antigen (Telomerase Reverse Transcriptase, TERT) and neoantigens were tested to evaluate the antitumoral effect of DNA amplicons in murine cancer models in combination with immune-checkpoint inhibitors (ICIs). <h3>Results</h3> Amplicons encoding Spike Receptor Binding Domain (RBD) were strongly immunogenic in all models and were able to confer antiviral effects. DNA vaccines encoding tumor-associated-antigens, such as telomerase reverse transcriptase or neoantigens expressed by murine tumor cell lines were able to elicit antigen-specific immune responses and proved to significantly impact tumor growth when administered in combination with ICIs. <h3>Conclusions</h3> These results strongly support the further exploration of the use of PCR-based amplicons as an innovative immunotherapeutic approach to viral diseases and cancer treatment. <h3>Reference</h3> Conforti A, <i>et al</i>. Linear DNA amplicons as a novel cancer vaccine strategy. <i>J Exp Clin Cancer Res</i> 2022 Jun 6;<b>41</b>(1):195. doi: 10.1186/s13046-022-02402-5. <h3>Ethics Approval</h3> All animal experiments were performed according to the guidelines for the care and use of laboratory animals and were approved by the ethical committee of the Italian Ministry of Health, with authorization #1166/2020-PR
Production of wires and coils from high-temperature superconducting materials (1989)

Coils of high-T/sub c/ superconductors, which are essential for the development of highly efficient motors and generators, have been fabricated by plastic extrusion. Wires have been extruded in long continuous lengths, wrapped into coils, and subsequently sintered. Coils, 2 cm in diameter and comprising up to 30 turns, have been made with critical current densities of about 200 A/cm/sup 2/ at 77 K. Critical current density has been found to be dependent on both sintered density and wire geometry. 5 refs., 2 figs.
Characterization of blue- and red- very small aperture lasers for hybrid recording (2005)

The characterization of a rectangular aperture on a very small aperture laser (VSAL) is described and the parameters of interest to hybrid recording technology is quantified. VSALs based on blue laser diodes (LDs) (/spl lambda/ = 405 nm) and red-LDs (/spl lambda/ = 658 nm) with 100 nm /spl times/ 200 nm rectangular apertures milled into 50 nm thick aluminum by focused ion beam etching (FIBE) are fabricated and their slope efficiencies (SE) captured by a NA 0.65 objective lens in the far field (FF) measured. SE is defined as the-ratio of the measured optical power to the input current. The background SEs (BSE) were measured after coating with Al but prior to forming the aperture for reference. The SEs of these blue and red lasers with apertures were 2.7 mW/A (BSE = 1.3 mW/A) and 3.8 mW/A (BSE = 0.3 mW/A), respectively. Detailed characterization of both lasers before and after aperture fabrication indicate that this greater SE of the red VSAL is primarily due to greater efficiency of coupling between the laser and the aperture, /spl eta//sub coupling/, and greater transmission efficiency of the aperture, /spl eta//sub aperture/, in the red. It is not due to difference in the SBs of the two LDs themselves. Near field simulation of the apertures using the finite difference time domain (FDTD) method supports the above conclusions.
3P1-P06 Force Measurement on the Spike Pin in Running(Sense, Motion and Measurement (2)) (2014)

In this paper, we report a method to measure the force of a spike pin in running. To measure the force of the spike pin, we fabricated a spike-pin-shaped sensor using MEMS (Micro Electro Mechanical Systems) 3-axis force sensor chip. The sensor consisted of a 2 mm square 3-axis force sensor chip and spike-pin-shaped epoxy resin which covered the sensor chip. The sensor was attached on a position of big toe on the right spike shoe to measure 3-axis forces when the subject was walking at 4.0 km/h and 5.2 km/h, and running at 9.2 km/h. Among 3-axis forces, the vertical component was the largest, the propulsive component was second largest, and left-right component was the smallest. The direction of impulse was upward, forward, and leftward. The faster the gait speed was, the larger the resultant force was.
Solid-State Phosphorus-31 Nuclear Magnetic Resonance Differentiation of Bone Mineral and Synthetic Apatite Used to Fill Bone Defects (1991)

Bioabsorption of synthetic apatite compounds used to promote bone healing and remodeling has been difficult to evaluate. In this study, solid-state phosphorus-31 nuclear magnetic resonance (NMR) has been used to characterize and quantitate bone mineral and a synthetic apatite in order to establish a model for bioabsorption studies. Pulverized solid samples of cortical rabbit bone and a synthetic fluoridated apatite were examined in vitro at variable degrees of hydration. A 9.4 T superconducting spectrometer was used to obtain 31P magic angle spinning NMR spectra and T1 relaxation times. Quantitation was attempted in mixed samples using T1 recovery data. Bone mineral and synthetic apatite could be distinguished by chemical shift and T1 relaxation time in variable hydration states, and were readily differentiated in mixtures by their T1 relaxation time. NMR estimates of relative proportions of components in mixed samples were accurate within 2% of evaluations based on weight. Solid-state 31P NMR therefore provides a suitable method for monitoring the bioabsorption of synthetic apatites.
Ego-motion and omnidirectional cameras (2002)

Recent research in image sensors has produced cameras with very large fields of view. A n area of computer vision research which will benefit from this technology is the computation of camera motion (ego-motion)from a sequence of images.Traditional cameras suffer from the problem that the direction of translation may lie outside of the field of view, making the computation of camera motion sensitive to noise.In this paper, we present a method for the recovery of ego-motion using omnidirectional cameras.Noting the relationship between spherical projection and wide-angle imaging devices, we propose mapping the image velocity vectors to a sphere, using the Jacobian of the transformation between the projection model of the camera and spherical projection.Once the velocity vectors are mapped to a sphere, we show how existing ego-motion algorithms can be applied and present some experimental results.These results demonstrate the ability to compute egomotion with omnidirectional cameras.
Effect of food additives on key bacterial taxa and the mucosa-associated microbiota in Crohn’s disease. The ENIGMA study (2023)

Food additives have been linked to the pro-inflammatory microbial dysbiosis associated with Crohn's disease (CD) but the underlying ecological dynamics are unknown. Here, we examine how selection of food additives affects the growth of multiple strains of a key beneficial bacterium (<i>Faecalibacterium prausnitzii</i>), axenic clinical isolates of proinflammatory bacteria from CD patients (<i>Proteus, Morganella</i>, and <i>Klebsiella</i> spp.), and the consortia of mucosa-associated microbiota recovered from multiple Crohn's disease patients. Bacterial growth of the axenic isolates was evaluated using a habitat-simulating medium supplemented with either sodium sulfite, aluminum silicate, carrageenan, carboxymethylcellulose, polysorbate 80, saccharin, sucralose, or aspartame, intended to approximate concentrations found in food. The microbial consortia recovered from post-operative CD patient mucosal biopsy samples were challenged with either carboxymethylcellulose and/or polysorbate 80, and the bacterial communities compared to unchallenged consortia by 16S rRNA gene amplicon profiling. Growth of all <i>F. prausnitzii</i> strains was arrested when either sodium sulfite or polysorbate 80 was added to cultures at baseline or mid-exponential phase of growth, and the inhibitory effects on the Gram-negative bacteria by sodium sulfite were conditional on oxygen availability. The effects from polysorbate 80, saccharin, carrageenan, and/or carboxymethylcellulose on these bacteria were strain-specific. In addition to their direct effects on bacterial growth, polysorbate 80 and/or carboxymethylcellulose can drive profound changes in the CD mucosa-associated microbiota via niche expansion of <i>Proteus</i> and/or <i>Veillonellaceae</i> - both implicated in early Crohn's disease recurrence. These studies on the interaction of food additives with the enteric microbiota provide a basis for dietary management in Crohn's disease.
Fault scanner for reconfigurable logic (2002)

We propose a technique for online built-in self-test of Field Programmable Gate Arrays (FPGAs). The goal of this system is to detect deviations from the intended functionality of an FPGA without using special-purpose hardware, hardware external to the device, and without interrupting system operation. A system that solves these problems would be useful for mission-critical applications with resource constraints. We present here a fault detection system which solves these problems through an online fault scanning methodology. Resources internal to the device are configured to test for faults. Testing scans across an FPGA, checking a section at a time. The viability and effectiveness of such a system is supported through simulation of the system on a model FPGA.
A complete and continuous map of the Lattice Isometry Space for all 3-dimensional lattices (2021)

This paper extends the recently obtained complete and continuous map of the Lattice Isometry Space (LISP) to the practical case of dimension 3. A periodic 3-dimensional lattice is an infinite set of all integer linear combinations of basis vectors in Euclidean 3-space. Motivated by crystal structures determined in a rigid form, we study lattices up to rigid motion or isometry, which is a composition of translations, rotations and reflections. The resulting space LISP consists of infinitely many isometry classes of lattices. In dimension 3, we parameterise this continuous space LISP by six coordinates and introduce new metrics satisfying the metric axioms and continuity under all perturbations. This parameterisation helps to visualise hundreds of thousands of real crystal lattices from the Cambridge Structural Database for the first time.
Data Supplement from A Search for Novel Cancer/Testis Antigens in Lung Cancer Identifies VCX/Y Genes, Expanding the Repertoire of Potential Immunotherapeutic Targets (2023)

&lt;p&gt;Supplementary Figure S2. Methylation levels of CpG sites for VCX/Y genes.&lt;/p&gt;
Total Synthesis and Structure Revision of the Marine Metabolite Palmerolide A (2007)

We describe a highly convergent and flexible synthesis of the novel antarctic marine metabolite palmerolide Aan effort leading to a reformulation of palmerolide A as ent-24, the enantiomer of the C19,C20-bis-epimer of the original proposed structure 1. Our total synthesis features a highly stereoselective vinylogous Mukaiyama aldol reaction to introduce the C19,C20-stereodiad, an efficient Suzuki cross-coupling to install the endocyclic diene unit, and an intramolecular Horner−Wadsworth−Emmons olefination to close the macrocycle. Starting from fragments 2, 3 (ent-3), and 13 (prepared in five to eight steps each, 38−70% overall yield) the synthesis of the proposed structure 1 and the enantiomer of palmerolide A (24) was completed in an additional 14 steps (22 steps longest linear sequence).