gebhart/patrepeval huggingface dataset:
Overexpression of Spexin 1 in the Dorsal Habenula Reduces Anxiety in Zebrafish (2019)

Spexin (SPX) is an evolutionarily conserved neuropeptide that is expressed in the mammalian brain and peripheral tissue. Two orthologs are present in the teleost, SPX1 and SPX2. SPX1 is involved in reproduction and food intake. Recently, SPX1 neurons have been found to be located in the specific nuclei of dorsal habenula (dHb) and to project into the interpeduncular nucleus (IPN), in which galanin receptor 2a/2b (GALR2a/2b) expression was also observed. This indicates that habenula SPX1 neurons may interact with GALR2a/2b in the IPN; however, the function of SPX1 in the dHb-IPN neuronal circuit remains unknown. To determine the role of SPX1 in the dHb-IPN neural circuit, we generated transgenic zebrafish overexpressing SPX1 specifically in the dHb. We found that transgenic zebrafish overexpressing SPX1 in the dHb had anxiolytic behaviors compared with their wildtype siblings. Furthermore, quantitative PCR revealed that mRNA expression of <i>galr2a</i> and <i>galr2b</i> in the IPN and serotonin-related genes in the raphe was upregulated in the brains of transgenic zebrafish. Taken together, our data suggest that SPX1 function in the dHb-IPN neural circuits is implicated in the regulation of anxiety behaviors <i>via</i> modulation of the serotoninergic system in zebrafish.
Differential Regulation of Caspase-1 Activation, Pyroptosis, and Autophagy via Ipaf and ASC in Shigella-Infected Macrophages (2007)

Shigella infection, the cause of bacillary dysentery, induces caspase-1 activation and cell death in macrophages, but the precise mechanisms of this activation remain poorly understood. We demonstrate here that caspase-1 activation and IL-1beta processing induced by Shigella are mediated through Ipaf, a cytosolic pattern-recognition receptor of the nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family, and the adaptor protein apoptosis-associated speck-like protein containing a C-terminal caspase recruitment domain (ASC). We also show that Ipaf was critical for pyroptosis, a specialized form of caspase-1-dependent cell death induced in macrophages by bacterial infection, whereas ASC was dispensable. Unlike that observed in Salmonella and Legionella, caspase-1 activation induced by Shigella infection was independent of flagellin. Notably, infection of macrophages with Shigella induced autophagy, which was dramatically increased by the absence of caspase-1 or Ipaf, but not ASC. Autophagy induced by Shigella required an intact bacterial type III secretion system but not VirG protein, a bacterial factor required for autophagy in epithelial-infected cells. Treatment of macrophages with 3-methyladenine, an inhibitor of autophagy, enhanced pyroptosis induced by Shigella infection, suggesting that autophagy protects infected macrophages from pyroptosis. Thus, Ipaf plays a critical role in caspase-1 activation induced by Shigella independently of flagellin. Furthermore, the absence of Ipaf or caspase-1, but not ASC, regulates pyroptosis and the induction of autophagy in Shigella-infected macrophages, providing a novel function for NLR proteins in bacterial-host interactions.
Cognitive Aspect of Diagnostic Errors (2013)

Diagnostic errors can result in tangible harm to patients. Despite our advances in medicine, the mental processes required to make a diagnosis exhibits shortcomings, causing diagnostic errors. Cognitive factors are found to be an important cause of diagnostic errors. With new understanding from psychology and social sciences, clinical medicine is now beginning to appreciate that our clinical reasoning can take the form of analytical reasoning or heuristics. Different factors like cognitive biases and affective influences can also impel unwary clinicians to make diagnostic errors. Various strategies have been proposed to reduce the effect of cognitive biases and affective influences when clinicians make diagnoses; however evidence for the efficacy of these methods is still sparse. This paper aims to introduce the reader to the cognitive aspect of diagnostic errors, in the hope that clinicians can use this knowledge to improve diagnostic accuracy and patient outcomes.
Supplementary Figure S1 from The discovery and mechanism of action of novel tumor-selective and apoptosis-inducing 3,5-diaryl-1,2,4-oxadiazole series using a chemical genetics approach (2023)

&lt;p&gt;Expression profile&lt;/p&gt;
Positive Allosteric Modulation of α5-GABAA Receptors Reverses Stress-Induced Alterations in Dopamine System Function and Prepulse Inhibition of Startle (2022)

Our results demonstrate that pharmacological intervention augmenting α5-GABAAR function, but not α5 overexpression in itself, can reverse stress-induced deficits related to PTSD in a rodent model, providing a potential site of therapeutic intervention to treat comorbid psychosis in PTSD.
More Efficient Off-Policy Evaluation through Regularized Targeted\n Learning (2019)

We study the problem of off-policy evaluation (OPE) in Reinforcement Learning\n(RL), where the aim is to estimate the performance of a new policy given\nhistorical data that may have been generated by a different policy, or\npolicies. In particular, we introduce a novel doubly-robust estimator for the\nOPE problem in RL, based on the Targeted Maximum Likelihood Estimation\nprinciple from the statistical causal inference literature. We also introduce\nseveral variance reduction techniques that lead to impressive performance gains\nin off-policy evaluation. We show empirically that our estimator uniformly wins\nover existing off-policy evaluation methods across multiple RL environments and\nvarious levels of model misspecification. Finally, we further the existing\ntheoretical analysis of estimators for the RL off-policy estimation problem by\nshowing their $O_P(1/\\sqrt{n})$ rate of convergence and characterizing their\nasymptotic distribution.\n
Phase-shifting point-diffraction interferometry at EUV wavelengths (1997)

A novel phase-shifting point-diffraction interferometer (PS/PDI) operating at the Advanced Light Source (ALS) is being used to perform wavefront-measuring metrology at 13.4-nm wavelength to characterize aberrations in a multilayer-coated 10x Schwarzschild objective designed for extreme ultraviolet (EUV) projection lithography experiments. To achieve 0.1-micron critical dimension pattern transfer with EUV projection lithography at 13.4-nm wavelength, nearly diffraction-limited all-reflective multilayer-coated optical systems with 0.1 numerical aperture are required. The EUV wavefront, determined by the mirror surfaces and the reflective multilayer coatings, is measurable only at the operational wavelength of the system. The authors goal is to measure the EUV wavefront to an accuracy of 0.01 waves rms (0.13 nm). The PS/PDI is a type of point-diffraction interferometer, modified for significantly improved throughput and phase-shifting capability. The interferometer design utilizes a grating beamsplitter and pinhole spatial filters in the object and image planes of the optical system under test. The 10x-reduction Schwarzschild objective, with image-side numerical aperture of 0.08, is illuminated by a sub-micron pinhole in the object plane. A coarse, 20-micron pitch grating placed between the illumination pinhole and the Schwarzschild system serves a dual role as a small-angle beam-splitter and a phase-shifting element. The first-order diffracted beam from the grating is spatially filtered in the image plane of the Schwarzschild with a sub-100-nm pinhole and becomes the `D reference` wave in the interferometer. The zero-order beam is the `test` wave, and it passes unobstructed through a 4.5-{mu}m window in the image plane. The test and reference beams are separated by several microns in the image plane to minimize beam overlap. The interference fringes are recorded with a CCD detector placed about 12 cm from the Schwarzschild image plane.
Haploid Genetic Screen Reveals a Profound and Direct Dependence on Cholesterol for Hantavirus Membrane Fusion (2015)

Although hantaviruses cause important human diseases worldwide, no specific antiviral treatments are available. One of the major obstacles to the development of new therapies is a lack of understanding of how hantaviruses hijack our own host factors to enter cells. Here, we identified multiple cellular genes that control the levels of cholesterol in cellular membranes to be important for hantavirus entry. Our findings suggest that high concentrations of cholesterol in cellular membranes are required at a specific step in the entry process-fusion between viral and cellular membranes-that allows escape of the hantavirus genome into the host cell cytoplasm to initiate infection. Our findings uncover a fundamental feature of the hantavirus infection mechanism and point to cholesterol-lowering drugs as a potential new treatment of hantaviral infections.
Cardiac Subsarcolemmal and Interfibrillar Mitochondria Display Distinct Responsiveness to Protection by Diazoxide (2012)

These results provide evidence for the distinct sensitivity of cardiac SSM and IFM toward Ca²⁺-dependent metabolic stress and the protective effect of diazoxide on mitochondrial energetics.
A coherent minimum-output-energy receiver with a Kalman channel predictor for DS-CDMA systems (2002)

In this paper, we develop a Kalman channel predictor based receiver for DS-CDMA systems. In particular, we develop and analyze the performance of a minimum-output-energy (MOE) receiver with short spreading codes, when fast Rayleigh flat fading channels are predicted by the Kalman filter. For comparison, we also derive the performance of a matched filter receiver with long spreading codes. It is shown by analysis and simulation that in a fast fading environment, MOE with short spreading codes is better than matched filter with long spreading codes.
Access-Network-Identifier Option in DHCP (2016)

This document specifies the format and mechanism that is to be used for encoding Access-Network Identifiers in DHCPv4 and DHCPv6 messages by defining new Access-Network-Identifier options and sub-options.
STED-FLCS: An Advanced Tool to Reveal Spatiotemporal Heterogeneity of Molecular Membrane Dynamics (2015)

Heterogeneous diffusion dynamics of molecules play an important role in many cellular signaling events, such as of lipids in plasma membrane bioactivity. However, these dynamics can often only be visualized by single-molecule and super-resolution optical microscopy techniques. Using fluorescence lifetime correlation spectroscopy (FLCS, an extension of fluorescence correlation spectroscopy, FCS) on a super-resolution stimulated emission depletion (STED) microscope, we here extend previous observations of nanoscale lipid dynamics in the plasma membrane of living mammalian cells. STED-FLCS allows an improved determination of spatiotemporal heterogeneity in molecular diffusion and interaction dynamics via a novel gated detection scheme, as demonstrated by a comparison between STED-FLCS and previous conventional STED-FCS recordings on fluorescent phosphoglycerolipid and sphingolipid analogues in the plasma membrane of live mammalian cells. The STED-FLCS data indicate that biophysical and biochemical parameters such as the affinity for molecular complexes strongly change over space and time within a few seconds. Drug treatment for cholesterol depletion or actin cytoskeleton depolymerization not only results in the already previously observed decreased affinity for molecular interactions but also in a slight reduction of the spatiotemporal heterogeneity. STED-FLCS specifically demonstrates a significant improvement over previous gated STED-FCS experiments and with its improved spatial and temporal resolution is a novel tool for investigating how heterogeneities of the cellular plasma membrane may regulate biofunctionality.
[3H]CGP-12177, A β-Adrenergic Ligand Suitable for Measuring Cell Surface Receptors (1983)

[3H]CGP-12177, in contrast to lipophilic ligands like [3H] Dihydroalprenolol, shows very little non-specific binding to intact cells. It also differs from lipophilic ligands in that it can be completely displaced from the receptors on intact cells by isoproterenol. Furthermore, binding sites for this ligand disappear rapidly upon exposure of cells to agonists. These binding sites reappear rapidly upon removal of the agonist, if any possible interaction with residual traces of the agonist are prevented. These results indicate that [3H]CGP-12177 binds only to. cell surface receptors and that agonist causes a rapid and reversible shift of receptors from the cell surface to the interior of the cell
Polyacetylenic Compounds, ACAT Inhibitors from the Roots of Panax ginseng (2005)

Acyl-CoA: cholesterol acyltransferase (ACAT), which plays a role in the absorption, storage, and production of cholesterol, has been explored as a potential target for pharmacological intervention of hyperlipidemia and atherosclerotic disease. In our search for ACAT inhibitors from natural sources, the petroleum ether extract of Panax ginseng showed moderate inhibition of ACAT enzyme from rat liver microsomes. Bioactivity-guided fractionations led to the isolation of one new polyacetylenic compound, (9R,10S)-epoxy-16-heptadecene-4, 6-diyne-3-one (1), in addition to the previously reported polyacetylenic compounds 2 and 3. Their chemical structures were elucidated on the basis of spectroscopic evidence (UV, IR, NMR, and MS). The compounds 1, 2, and 3 showed significant ACAT inhibition with IC(50) values of 35, 47, and 21 microM, respectively.
Overhead-constrained rate-allocation for scalable video transmission over networks (2003)

Summary form only given. Forward error correction (FEC) based schemes are use widely to address the packet loss problem for Internet video. Given total available bandwidth, finding optimal bit allocation is very important in FEC-based video, because the FEC bit rate limits the rate available to compress video. We want to give proper protection to the source, but also prevent unwanted FEC rate expansion. The rate of packet headers is often ignored in allocating bit rate. We show that this packetization overhead has significant influence on system performance in many cases. Decreasing packet size increases the rate of packet headers, thus reducing the available rate for the source and its FEC codes. On the other hand, smaller packet size allows a larger number of packets, in which case it can be shown that the efficiency of FEC codes improves. We show that packet size should be optimized to balance the effect of packet headers and the efficiency of FEC codes. We develop a probabilistic framework for the solution of rate allocation problem in the presence of packet overhead. We implement our solution on the MPEG-4 fine granularity scalability (FGS) mode. To show the flexibility of our technique, we use an unequal error protection scheme with FGS. Experimental results show that our overhead-constrained method leads to significant improvements in reconstructed video quality.
Engineered Ferritin for Magnetogenetic Manipulation of Proteins and Organelles Inside Living Cells (2017)

Magnetogenetics is emerging as a novel approach for remote-controlled manipulation of cellular functions in tissues and organisms with high spatial and temporal resolution. A critical, still challenging issue for these techniques is to conjugate target proteins with magnetic probes that can satisfy multiple colloidal and biofunctional constraints. Here, semisynthetic magnetic nanoparticles are tailored based on human ferritin coupled to monomeric enhanced green fluorescent protein (mEGFP) for magnetic manipulation of proteins inside living cells. This study demonstrates efficient delivery, intracellular stealth properties, and rapid subcellular targeting of those magnetic nanoparticles via GFP-nanobody interactions. By means of magnetic field gradients, rapid spatial reorganization in the cytosol of proteins captured to the nanoparticle surface is achieved. Moreover, exploiting efficient nanoparticle targeting to intracellular membranes, remote-controlled arrest of mitochondrial dynamics using magnetic fields is demonstrated. The studies establish subcellular control of proteins and organelles with unprecedented spatial and temporal resolution, thus opening new prospects for magnetogenetic applications in fundamental cell biology and nanomedicine.
Technological and safety properties of newly isolated GABA-producing Lactobacillus futsaii strains (2016)

This study focuses on the technological and safety characteristics of Lact. futsaii CS3 and CS5 including their high GABA-producing capacity for the first time. This provides a way of replacing chemical GABA by natural GABA using a GABA-producing starter culture candidate, at the same time offering the consumer new attractive food products.
Quadratic hyperpolarizabilities of fluorinated sulfonyl and carbonyl aromatics: optimization of nonlinearity and transparency trade-off (1990)

We present electric-field induced second-harmonic generation measurement results on the
hyperpolarizabilities of donor-acceptor substituted aromatics. Those with strongly inductive
accepting groups, such as the fluoromethyl carbonyl, perfluoroalkyl sulfonyl, and
perfluoroalkyl sulfonylsulfimide groups, afford favorable trade-off between quadratic optical
nonlinearity and optical transparency. Their relatively large molecular dipole moment and
hyperpolarizability products (4) as well as high transparency in the visible region suggest
promising applications in the frequency conversion of short wavelength diode lasers. The
inductive contribution is found to be short ranged, being most effective in the relatively compact
benzene derivatives but less so in the extended stilbene structures. Dispersive enhancements of
hyperpolarizabiities at 1064 and 810 nm are also reported.
Innate immune mediators in cancer: between defense and resistance (2016)

Chronic inflammation in the tumor microenvironment and evasion of the antitumor effector immune response are two of the emerging hallmarks required for oncogenesis and cancer progression. The innate immune system not only plays a critical role in perpetuating these tumor-promoting hallmarks but also in developing antitumor adaptive immune responses. Thus, understanding the dual role of the innate system in cancer immunology is required for the design of combined immunotherapy strategies able to tackle established tumors. Here, we review recent advances in the understanding of the role of cell populations and soluble components of the innate immune system in cancer, with a focus on complement, the adapter molecule Stimulator of Interferon Genes, natural killer cells, myeloid cells, and B cells.
Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum. (1996)

Plasmodium falciparum is the major causative agent of malaria, a disease of worldwide importance. Resistance to current drugs such as chloroquine and mefloquine is spreading at an alarming rate, and our antimalarial armamentarium is almost depleted. The malarial parasite encodes two homologous aspartic proteases, plasmepsins I and II, which are essential components of its hemoglobin-degradation pathway and are novel targets for antimalarial drug development. We have determined the crystal structure of recombinant plasmepsin II complexed with pepstatin A. This represents the first reported crystal structure of a protein from P. falciparum. The crystals contain molecules in two different conformations, revealing a remarkable degree of interdomain flexibility of the enzyme. The structure was used to design a series of selective low molecular weight compounds that inhibit both plasmepsin II and the growth of P. falciparum in culture.
ChemInform Abstract: SYNTHESIS AND CHARACTERIZATION OF DIETHYLMETHYLENE DIPHOSPHONATO METAL COMPLEXES (1974)

Abstract Die Umsetzung von Tetraäthyl‐methylendiphosphonat mit den entsprechenden Metallchloriden führt zu den thermisch beständigen Titelkomplexen (I)‐(III).
Pathological Findings Following Slow Pathway Ablation for AV Nodal Reentrant Tachycardia (1996)

Ablation of the slow pathway to cure AV nodal reentrant tachycardia does not produce any gross or histologic damage to the AV node, suggesting that the AV nodal reentrant circuit does not exist in its entirety in the AV node.
Bilayer Graphene Tunneling FET for Sub-0.2 V Digital CMOS Logic Applications (2014)

We propose a bilayer graphene (BLG) tunneling field-effect-transistor (TFET) suitable for digital CMOS logic circuits. The ultimate performance limit of this structure is evaluated by solving the quantum transport equations in nonequilibrium Green's function framework. A bandgap opening is induced in BLG using both vertical electric field and top-bottom asymmetric chemical doping. To overcome the limitations of nonabrupt p-i-n junctions using practical process methods, source/drain regions are created using work-function engineered metal-graphene contacts. We evaluate the performance of BLG-TFET by taking doping gradient due to contact induced doping into account. Our BLG-TFET exhibits a subthreshold slope as low as 35 mV/dec, and ION/IOFF as high as 2910 for a supply voltage of 0.2 V. The proposed BLG-TFET shows promise for ultralow-power applications, particularly in low to medium speed applications.
Two-Photon Three-Dimensional Microfabrication of Poly(Dimethylsiloxane) Elastomers (2004)

Three-dimensional microfabrication by two-photon-initiated polymerization is used to prepare poly(dimethylsiloxane) microstructures. Both radical and hydrosilylation photocuring chemistries were studied. These elastomeric structures may prove useful for modifying microfluidic channels to add a higher level of functionality or building complex microfluidic networks.
Improving Bluetooth Security: What IT Managers and Mobile Device Users Can Do (2006)

Abstract Bluetooth wireless technology is becoming ubiquitous. According to the Bluetooth Special Interest Group (SIG), Bluetooth weekly shipments passed the 5 million unit mark in the second quarter of 2005, up from 3 million in the third quarter of 2004. Most of this growth has been in the mobile phone and PDA markets; in fact, 20 percent of mobile phones now ship with Bluetooth. In high-end business phones, the penetration rate is even higher, and many business-class phones include Bluetooth.
Full-vector multi-mode fiber modeling for short reach serdes links of 112Gbps and beyond (2016)

A rigorous full-vector multi-mode fiber (MMF) model is proposed. It is believed to be the first comparative study of vector and scalar MMF model in terms of differential mode delay (DMD), mode power distribution (MPD), transfer functions as well as eye diagrams. It shows that the vector nature of fiber modes cannot be ignored even though the refractive index difference can be as small as 1%. A standard-compliant methodology for MMF characterization is introduced. The impact of fiber parameters on bandwidth is studied. The statistical transfer function model of OM3 and OM4 fiber is provided. These transfer functions can be applied to the MMF link modeling. Rigorous full-vector MMF model is an essential tool for research and development of MMF link transceivers and standard development of 112Gbps and beyond.