gebhart/patrepeval huggingface dataset:
Advanced in vivo fluorescence microscopy of neural electronic interface (2023)

Abstract Neuroelectronic devices are essential tools in neuroscience research, diagnosis, and/or treatment of neurological diseases, as well as in neuro-prosthetics and brain–computer interfaces. Despite a long history of application, neuroelectronic devices are still facing challenges of unsatisfactory chronic stability and a lack of understanding of cellular mechanisms for recording and stimulation. To improve the information transfer between the neural tissue and electronic devices, a comprehensive understanding of the biological activities around the neural electrode is critical. In vivo fluorescent microscopy technologies are rapidly developing and have revolutionized our understanding of cellular dynamics in response to neural interfacing materials. Here, we will provide an overview of the in vivo fluorescence microscopy systems and imaging configurations for studying the neural electronic interface, as well as recent findings in biological mechanisms learned using these advanced optical imaging modalities. Finally, we will discuss the current challenges and future directions. Graphical abstract
A Market Mechanism for Electric Vehicle Charging Under Network Constraints (2015)

The increasing impact of electric vehicles on distribution networks can be alleviated by smart charging-the shifting of electric vehicle load to times when there is available capacity in the network. This work presents a market mechanism for smart charging that optimally allocates available charging capacity in a way that ensures network stability, while at the same time allowing vehicles to express individual preferences regarding their charging rates. Those who want higher rates can receive these, but must pay a higher price. The mechanism takes into account network-specific constraints such as total network load, voltage drop, and phase unbalance. However, since vehicles have differing impacts on these constraints, this leads to unequal access to the available resources (i.e., charging capacity), resulting in an unfair market. An additional constraint can be introduced to level the playing field for all users, but it leads to a reduction in aggregate performance. The mechanism is shown to be efficient and strategy-proof, so users cannot gain an unfair advantage by misrepresenting their preferences. A series of simulations demonstrate the mechanism's behavior and properties. The results open the door to multi-tiered user plans by demand response aggregators.
Necroptosis-based CRISPR knockout screen reveals Neuropilin-1 as a critical host factor for early stages of murine cytomegalovirus infection (2020)

Herpesviruses are ubiquitous human pathogens that cause a wide range of health complications. Currently, there is an incomplete understanding of cellular factors that contribute to herpesvirus infection. Here, we report an antiviral necroptosis-based genetic screen to identify novel host cell factors required for infection with the β-herpesvirus murine cytomegalovirus (MCMV). Our genome-wide CRISPR-based screen harnessed the capacity of herpesvirus mutants that trigger antiviral necroptotic cell death upon early viral gene expression. Vascular endothelial growth factor (VEGF) and semaphorin-binding receptor Neuropilin-1 (Nrp-1) emerge as crucial determinants of MCMV infection. We find that elimination of Nrp-1 impairs early viral gene expression and reduces infection rates in endothelial cells, fibroblasts, and macrophages. Furthermore, preincubation of virus with soluble Nrp-1 dramatically inhibits infection by reducing virus attachment. Thus, Nrp-1 is a key determinant of the initial phase of MCMV infection.
An algebraic model for asynchronous circuits verification (1988)

An algebraic methodology for comparing switch-level circuits with higher-level specifications is presented. Switch-level networks, 'user' behavior, and input constraints are modeled as asynchronous machines. The model is based on the algebraic theory of characteristic functions (CF). An asynchronous automation is represented by a pair of CFs, called a dynamic CF (DCF): the first CF describes the potential stable states, and the second CF describes the possible transitions. The set of DCFs is a Boolean algebra. Machine composition and internal variables abstraction correspond, respectively, to the product and sum operations of the algebra. Internal variables can be abstracted under the presence of a domain constraint. The constraint is validated by comparison to the outside behavior. The model is well suited for speed-independent circuits for which the specification is given as a collection of properties. Verification reduces to the validation of Boolean inequalities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Generalized synchronization of chaos in directionally coupled chaotic systems (1995)

Synchronization of chaotic systems is frequently taken to mean actual equality of the variables of the coupled systems as they evolve in time. We explore a generalization of this condition, which equates dynamical variables from one subsystem with a function of the variables of another subsystem. This means that synchronization implies a collapse of the overall evolution onto a subspace of the system attractor in full space. We explore this idea in systems where a response system y(t) is driven with the output of a driving system x(t), but there is no feedback to the driver. We lose generality but gain tractability with this restriction. To investigate the existence of the synchronization condition y(t)=\ensuremath{\varphi}(x(t)) we introduce the idea of mutual false nearest neighbors to determine when closeness in response space implies closeness in driving space. The synchronization condition also implies that the response dynamics is determined by the drive alone, and we provide tests for this as well. Examples are drawn from computer simulations on various known cases of synchronization and on data from nonlinear electrical circuits. Determining the presence of generalized synchronization will be quite important when one has only scalar observations from the drive and from the response systems since the use of time delay (or other) embedding methods will produce ``imperfect'' coordinates in which strict equality of the synchronized variables is unlikely to transpire.
Chromatic dispersion measurement in the 1-2 μm spectral region using a high brightness supercontinuum fiber laser source (2002)

We demonstrate a novel, diode-pumped ytterbium-doped fiber laser, which combines the unique characteristics of a high brightness supercontinuum together with simplicity of operation and compactness for application in dispersion measurement using both time delay and interferometric techniques and has considerable potential for implementation into a simple yet highly practical apparatus for dispersion measurement. The high brightness and intensity of the source is particularly applicable to nondestructive dispersion-distribution measurements as well as real time control of dispersion during fiber drawing. The potential of these have been examined.
Probiotic Therapy as a Novel Approach for Allergic Disease (2012)

The prevalence of allergic disease has increased dramatically in Western countries over the past few decades. The hygiene hypothesis, whereby reduced exposure to microbial stimuli in early life programs the immune system toward a Th2-type allergic response, is suggested to be a major mechanism to explain this phenomenon in developed populations. Such microbial exposures are recognized to be critical regulators of intestinal microbiota development. Furthermore, intestinal microbiota has an important role in signaling to the developing mucosal immune system. Intestinal dysbiosis has been shown to precede the onset of clinical allergy, possibly through altered immune regulation. Existing treatments for allergic diseases such as eczema, asthma, and food allergy are limited and so the focus has been to identify alternative treatment or preventive strategies. Over the past 10 years, a number of clinical studies have investigated the potential of probiotic bacteria to ameliorate the pathological features of allergic disease. This novel approach has stemmed from numerous data reporting the pleiotropic effects of probiotics that include immunomodulation, restoration of intestinal dysbiosis as well as maintaining epithelial barrier integrity. In this mini-review, the emerging role of probiotics in the prevention and/or treatment of allergic disease are discussed with a focus on the evidence from animal and human studies.
ChemInform Abstract: 4‐Substituted‐5(3)‐carbamoyl‐3(5)‐(2‐deoxy‐β‐D‐ribofuranosyl) pyrazoles. Application of Palladium Catalyzed Glycal Coupling Methodology to the Synthesis of Pyrazofurin Analogues. (1997)

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.
Madrid Quantum Communication Infrastructure: a testbed for assessing QKD technologies into real production networks (2021)

We report on the Madrid Quantum Communication Infrastructure, which demonstrates that a telecommunications network can also host quantum communications in a unified, logical and physical infrastructure. Using new Quantum Key Distribution systems paired with modern networking paradigms, we demonstrate a high technology readiness level of QKD installing the network in production facilities and running relevant use cases.
Vaccinia-based oncolytic immunotherapy Pexastimogene Devacirepvec in patients with advanced hepatocellular carcinoma after sorafenib failure: a randomized multicenter Phase IIb trial (TRAVERSE) (2019)

Pexastimogene devacirepvec (Pexa-Vec) is a vaccinia virus-based oncolytic immunotherapy designed to preferentially replicate in and destroy tumor cells while stimulating anti-tumor immunity by expressing GM-CSF. An earlier randomized Phase IIa trial in predominantly sorafenib-naïve hepatocellular carcinoma (HCC) demonstrated an overall survival (OS) benefit. This randomized, open-label Phase IIb trial investigated whether Pexa-Vec plus Best Supportive Care (BSC) improved OS over BSC alone in HCC patients who failed sorafenib therapy (TRAVERSE). 129 patients were randomly assigned 2:1 to Pexa-Vec plus BSC vs. BSC alone. Pexa-Vec was given as a single intravenous (IV) infusion followed by up to 5 IT injections. The primary endpoint was OS. Secondary endpoints included overall response rate (RR), time to progression (TTP) and safety. A high drop-out rate in the control arm (63%) confounded assessment of response-based endpoints. Median OS (ITT) for Pexa-Vec plus BSC vs. BSC alone was 4.2 and 4.4 months, respectively (HR, 1.19, 95% CI: 0.78-1.80; p = .428). There was no difference between the two treatment arms in RR or TTP. Pexa-Vec was generally well-tolerated. The most frequent Grade 3 included pyrexia (8%) and hypotension (8%). Induction of immune responses to vaccinia antigens and HCC associated antigens were observed. Despite a tolerable safety profile and induction of T cell responses, Pexa-Vec did not improve OS as second-line therapy after sorafenib failure. The true potential of oncolytic viruses may lie in the treatment of patients with earlier disease stages which should be addressed in future studies. <b>ClinicalTrials.gov</b>: NCT01387555.
Data from Identification of Existing Drugs That Effectively Target <i>NTRK1</i> and <i>ROS1</i> Rearrangements in Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Efforts to discover drugs that overcome resistance to targeted therapies in patients with rare oncogenic alterations, such as &lt;i&gt;NTRK1&lt;/i&gt; and &lt;i&gt;ROS1&lt;/i&gt; rearrangements, are complicated by the cost and protracted timeline of drug discovery.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; In an effort to identify inhibitors of NTRK1 and ROS1, which are aberrantly activated in some patients with non–small cell lung cancer (NSCLC), we created and screened a library of existing targeted drugs against Ba/F3 cells transformed with these oncogenes.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; This screen identified the FDA-approved drug cabozantinib as a potent inhibitor of &lt;i&gt;CD74–ROS1&lt;/i&gt;-transformed Ba/F3, including the crizotinib-resistant mutants G2032R and L2026M (IC&lt;sub&gt;50&lt;/sub&gt; = 9, 26, and 11 nmol/L, respectively). Cabozantinib inhibited &lt;i&gt;CD74–ROS1&lt;/i&gt;-transformed Ba/F3 cells more potently than brigatinib (wild-type/G2032R/L2026M IC&lt;sub&gt;50&lt;/sub&gt; = 30/170/200 nmol/L, respectively), entrectinib (IC&lt;sub&gt;50&lt;/sub&gt; = 6/2,200/3,500 nmol/L), and PF-06463922 (IC&lt;sub&gt;50&lt;/sub&gt; = 1/270/2 nmol/L). Cabozantinib inhibited ROS1 autophosphorylation and downstream ERK activation in transformed Ba/F3 cells and in patient-derived tumor cell lines. The IGF-1R inhibitor BMS-536924 potently inhibited &lt;i&gt;CD74–NTRK1&lt;/i&gt;-transformed compared with parental Ba/F3 cells (IC&lt;sub&gt;50&lt;/sub&gt; = 19 nmol/L vs. &gt; 470 nmol/L). A patient with metastatic &lt;i&gt;ROS1&lt;/i&gt;-rearranged NSCLC with progression on crizotinib was treated with cabozantinib and experienced a partial response.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; While acquired resistance to targeted therapies is challenging, this study highlights that existing agents may be repurposed to overcome drug resistance and identifies cabozantinib as a promising treatment of ROS1-rearranged NSCLC after progression on crizotinib. &lt;i&gt;Clin Cancer Res; 23(1); 204–13. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
ChemInform Abstract: CRYSTAL STRUCTURE AND POLARIZED ELECTRONIC SPECTRA OF A (μ‐SUPEROXO)DICOBALT(III) COMPLEX: (((NH3)5CO)2O2)(NO3)2CL3.2H2O (1984)

Abstract Die Titelverbindung kristallisiert orthorhombisch, RG Pnnm mit Z=2.
X-ray structural studies on three analogues of the α-anomer of the antitumour antibiotic showdomycin. Different ring-puckering effects of hydroxyl sugar substituents in lyxo and arabino configurations (1990)

The crystal structures of three a-analogues of the anititumour antibiotic showdomycin (1) have been determined at room temperature. They are 2-(a-D-2'- deoxyribofuranosyl)maleimide (2), 2-(a-D-arabinofuranosyl) maleimide (3) and 2-(a-D-lyxofuranosyl)- maleimide (4). The structures were refined to R factors of 0-039, 0-042 and 0-029 for 971, 1025 and 716 observed reflections. The conformational properties of the sugar rings are discussed in detail, in relation to the differing hydroxyl group substitutions. Compounds (2) and (3) have CY-endo, C4-exo and CY-endo ring puckers, whereas (3) has C2-endo, C l'-exo puckers. Compound (3) has an intramolecular hydrogen bond between the 05' and 02' hydroxyl groups. This and the sugar pucker difference are in accord with NMR chemical shift data for the O5' and O2' protons. Crystal data: compound (2), C9H11NOs, orthorhombic, P212~21, a = 5-916 (1), b = 8-191 (1), c = 19.691 (3) A, Z = 4; compound (3), C9HIINO6, orthorhombic, P212121, a = 6.785 (1), b = 8.006 (1), c = 17.564 (2) A, Z= 4; compound (4), C9HI1NO6, monoclinic, P2~, a = 8.681 (1), b = 5.135 (1), c= 11-364 (1) A, Z= 2.
Fenofibrate induced PPAR alpha expression was attenuated by oestrogen receptor alpha overexpression in Hep3B cells (2017)

The physiological regulation of Oestrogen receptor α (ERα) and peroxisome proliferator-activated receptor alpha (PPARα) in Hepatocellular carcinoma (HCC) remains unknown. The present study we first treat the cells with fenofibrate and further investigated the possible mechanisms of 17β-estradiol (E<sub>2</sub> ) and/or ERα on regulating PPARα expression. We also found higher PPARα expression in the tumor area than adjacent areas and subsequently compared PPARα expression in four different hepatic cancer cell lines. Hep3B cells were found to express more PPARα than the other cell lines. Using the PPARα agonist fenofibrate, we found that fenofibrate increased Hep3B cell proliferation efficiency by increasing cell cycle proteins, such as cyclin D1 and PCNA, and inhibiting p27 and caspase 3 expressions. Next, we performed transient transfections and immuno-precipitation studies using the pTRE2/ERα plasmid to evaluate the interaction between ERα and PPARα. ERα interacted directly with PPARα and negatively regulated its function. Moreover, in Tet-on ERα over-expressed Hep3B cells, E<sub>2</sub> treatment inhibited PPARα, its downstream gene acyl-CoA oxidase (ACO), cyclin D1 and PCNA expression and further increased p27 and caspase 3 expressions. However, over-expressed ERα plus 17-β-estradiol (10<sup>-8</sup> M) reversed the fenofibrate effect and induced apoptosis, which was blocked in ICI/melatonin/fenofibrate-treated cells. This study illustrates that PPARα expression and function were negatively regulated by ERα expression in Hep3B cells.
Free Radical Chain Reactions and Polyunsaturated Fatty Acids in Brain Lipids (2022)

Polyunsaturated fatty acyl chains (PUFAs) concentrate in the brain and give rise to numerous oxidative chemical degradation products. It is widely assumed that these products are the result of free radical chain reactions, and reactions of this type have been demonstrated in preparations where a single PUFA substrate species predominates. However, it is unclear whether such reactions can occur in the biologically complex milieu of lipid membranes where PUFA substrates are a minority species, and where diverse free radical scavengers or other quenching mechanisms are present. It is of particular interest to know whether they occur in brain, where PUFAs are concentrated and where PUFA oxidation products have been implicated in the pathogenesis of neurodegenerative disorders. To ascertain whether free radical chain reactions can occur in a complex brain lipid mixture, mouse brain lipids were extracted, formed into vesicles, and treated with a fixed number of hydroxyl radicals under conditions wherein the concentrations and types of PUFA-containing phospholipids were varied. Specific phospholipid species in the mixture were assayed by tandem mass spectrometry to quantify the oxidative losses of endogenous PUFA-containing phospholipids. Results reveal crosstalk between the oxidative degradation of ω3 and ω6 PUFAs that can only be explained by the occurrence of free radical chain reactions. These results demonstrate that PUFAs in a complex brain lipid mixture can participate in free radical chain reactions wherein the extent of oxidative degradation is not limited by the number of reactive oxygen species available to initiate such reactions. These reactions may help explain otherwise puzzling in vivo interactions between ω3 and ω6 PUFAs in mouse brain.
Ultra-compact acousto-optic modulator of a fibre Bragg grating in a highly birefringent suspended core fibre (2021)

Highly efficient and compact acousto-optic modulator of a fibre Bragg grating is reported for the first time. The device is composed of millimetre scaled components and a 1 cm grating inscribed in a four air holes birefringent suspended core fibre. The reflection of the orthogonal polarization modes is tuned by a sinusoidal electrical signal at the resonance frequency of 469 kHz. A significant modulation depth of 45% is achieved at a maximum drive voltage of 10 V. The demonstrated 4 cm long all-fibre modulator is 60% shorter compared to previous similar setups, indicating new possibilities for stable and fast switching of fibre-integrated photonic devices.
Joint design and test consideration in high frequency circuits (1997)

Radiofrequency (RF) systems technology is continually pushing maximum operating frequencies upward. This constrains manufacturers of RF products to specify their circuits in terms of scattering parameters. Integrating design and test is one of the highly desirable analog systems requirements. In this paper, a frequency domain analysis of RF systems is performed. This analysis is intended to ameliorate the design performances and to facilitate the test of a given product especially integrated circuits. It helps a design engineer to determine parameters that influence the circuit performance and the best topology that can be used to help improve this performance. On the other hand, it helps a test engineer to plan test strategy and to predict which elements can be isolated by a given test set. By this analysis, we determine the correlation between the different components in a circuit and their conjoint influence on the output. © 1997 John Wiley & Sons, Inc. Microwave Opt Technol Lett 16: 132–138, 1997.
Large-Scale Categorization of Japanese Product Titles Using Neural Attention Models (2017)

Yandi Xia, Aaron Levine, Pradipto Das, Giuseppe Di Fabbrizio, Keiji Shinzato, Ankur Datta. Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 2, Short Papers. 2017.
Rethinking block storage encryption with virtual disks (2022)

Disk encryption today uses standard encryption methods that are length preserving and do not require storing any additional information with an encrypted disk sector. This significantly simplifies disk encryption management as the disk mapping does not change with encryption. On the other hand, it forces the encryption to be deterministic when data is being overwritten and it disallows integrity mechanisms, thus lowering security guarantees. Moreover, because the most widely used standard encryption methods (like AES-XTS) work at small sub-blocks of no more than 32 bytes, deterministic overwrites form an even greater security risk. Overall, today's standard practice forfeits some security for ease of management and performance considerations. This shortcoming is further amplified in a virtual disk setting that supports versioning and snapshots so that overwritten data remains accessible.