gebhart/patrepeval huggingface dataset:
CRISPR/Cas9 + AAV-mediated Intra-embryonic Gene Knocking in Mice (2019)

Intra-embryo genome editing by CRISPR/Cas9 has enabled rapid generation of gene knockout animals. However, large fragment knock-in directly into embryos' genome is still difficult, especially without microinjection of donor DNA. Viral vectors are good transporters of knock-in donor DNA for cell lines, but seemed unsuitable for pre-implantation embryos with zona pellucida, glycoprotein membrane surrounding early embryos. We found adeno-associated virus (AAV) can infect zygotes of various mammals through intact zona pellucida. AAV-mediated donor DNA delivery following Cas9 ribonucleoprotein electroporation enables large fragment knock-in without micromanipulation.
Supp Legends and Table S1 and S2 from <i>Frizzled-7</i> Is Required for Wnt Signaling in Gastric Tumors with and Without <i>Apc</i> Mutations (2023)

&lt;p&gt;Supplemental Figure Legends. And Supp Table S1. List of Antibodies used. Table S2. Differential expression of genes in gp130 gastric adenomas compared to wild-type and following deletion of Fzd7.&lt;/p&gt;
Chemical Genetics Reveals an RGS/G-Protein Role in the Action of a Compound (2006)

We report here on a chemical genetic screen designed to address the mechanism of action of a small molecule. Small molecules that were active in models of urinary incontinence were tested on the nematode Caenorhabditis elegans, and the resulting phenotypes were used as readouts in a genetic screen to identify possible molecular targets. The mutations giving resistance to compound were found to affect members of the RGS protein/G-protein complex. Studies in mammalian systems confirmed that the small molecules inhibit muscarinic G-protein coupled receptor (GPCR) signaling involving G-alphaq (G-protein alpha subunit). Our studies suggest that the small molecules act at the level of the RGS/G-alphaq signaling complex, and define new mutations in both RGS and G-alphaq, including a unique hypo-adapation allele of G-alphaq. These findings suggest that therapeutics targeted to downstream components of GPCR signaling may be effective for treatment of diseases involving inappropriate receptor activation.
HIGHER HDL CHOLESTEROL LEVELS DECREASE SUSCEPTIBILITY TO COVID-19 INFECTION (2023)

ASCVD/CVD Risk Factors Host cell-membrane cholesterol, an important player in viral infections, is in constant interaction with serum lipids, such as high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C). Recent meta-analyses have shown an association between low serum lipid levels at hospital admission and COVID-19 severity. However, the effect of antecedent serum lipid levels on the risk of COVID-19 infection has not been explored previously. Our retrospective cohort from the Arkansas Clinical Data Repository included all adults with lipid levels available within the 2 years antecedent to COVID-19 testing. We assessed the association of trajectories of lipid levels antecedent to COVID-19 testing, identified using group-based-trajectory-modeling with the risk of COVID-19 infection using multivariable log-binomial regression. We used mixed-effects linear regression to assess the trends in serum lipid levels followed up to the time of, and 2-months after COVID-19 testing. Among the 11001 individuals, 1340 (12.2%) tested positive for COVID-19. The median age was 59 years (IQR 46-70) and 40.8% were males. Log-binomial regression showed that the highest trajectory for antecedent serum HDL-C level was associated with a lower risk for COVID-19 infection (RR 0.63, 95% CI 0.46-0.86). Antecedent serum LDL-C, total cholesterol (TC), and triglycerides (TG) levels showed no independent association with COVID-19 infection risk. But the COVID-19 infection risk was the highest in the subgroup with lower HDL-C (Trajectory 1) and higher LDL-C or higher TG (Trajectory 3). In COVID-19 patients, at the time of testing, serum HDL-C (-7.7, 95% CI -9.8 to -5.5 mg/dL), LDL-C (-6.29, 95% CI -12.2 to -0.37 mg/dL) and TC (-11.71, 95%CI -18.9 to -4.5 mg/dL), but not TG levels, were lower. These returned to pre-infection values by 2-months following COVID-19 testing. Higher antecedent serum HDL-C, but not LDL-C, TC, and TG levels, were associated with a lower COVID-19 infection risk. Serum HDL-C, LDL-C, and TC levels declined transiently at the time of diagnosis, returning to pre-infection levels during follow-up. The results of our study could provide the impetus for clinical trials aimed at increasing HDL-C, such as CETP inhibitors, in the prevention and amelioration of COVID-19 infection or infections in general.
Energy-dependent quantum detective efficiency (QDE) measurements of a photon-counting CdTe detector array used for the scanning-beam digital x-ray (SBDX) system (2003)

The Scanning-Beam Digital X-ray (SBDX) system utilizes a scanning x-ray pencil beam and a small-area detector array for low-dose cardiac angiography with tomographic imaging capabilities. For the system to provide adequate signal-to-noise ratios, the multi-element detector must be highly efficient and capable of high photon count rates. Cadmium telluride (CdTe) is well suited to these purposes. The CdTe SBDX detector is a direct-conversion photon-counting device consisting of 2304 elements. The efficiency of the detector is a function of several factors including the incident photon energy, the fluorescence properties of CdTe, and the discriminator threshold that determines whether sufficient energy was deposited in an element to register a count. For maximum efficiency, the discriminator threshold must be set low enough to detect CdTe k-fluorescence photons (23-31 keV), but not so low as to register false counts from electronic noise. The purpose of this investigation was to evaluate the energy-dependent quantum detective efficiency (QDE) of a new lower-noise SBDX detector design and to determine whether adequately low thresholds can be achieved. Experiments were performed using metal fluorescer foils to generate quasi-monochromatic x-ray beams with energies of 17.5, 25.3, and 46.0 keV. The resulting spectral purities were high, although fluence rates were low. The measured QDE values at 17.5, 25.3, and 46.0 keV were 60%, 76%, and 86% repsectively.
Gene Therapy for Ocular Neovascularization (2007)

Ocular neovascularization is a major cause of blindness and visual disability in developed countries. There has been considerable recent progress identifying molecular signals that participate in ocular neovascularization and it appears that imbalances between stimulatory and inhibitory proteins contribute. Re-establishing balance by ocular gene transfer to block stimulators or increase expression of endogenous inhibitors is an appealing therapeutic approach, because it provides a potential means to achieve sustained intraocular effects with little impact on the rest of the body. Proof-of-concept has been provided in animal models using several vector systems and several transgenes and completion of a phase I study testing intraocular injection of an adenoviral vector expressing pigment epithelium-derived factor is an important milestone that will help to accelerate future progress. It is likely that additional vectors and transgenes will enter clinical trials in the near future. This report discusses the rationale and experimental evidence regarding several candidate transgenes.
Continuous-Flow Electrokinetic-Assisted Plasmapheresis by Using Three-Dimensional Microelectrodes Featuring Sidewall Undercuts (2016)

We present a novel plasmapheresis device designed for a fully integrated point-of-care blood analysis microsystem. In the device, fluidic microchannels exhibit a characteristic cross-sectional profile arising from distinct three-dimensional (3D) microelectrodes featuring sidewall undercuts readily integrated through a single-mask process. The structure leverages mainly electrothermal convective rolls that efficiently manifest themselves in physiological fluids and yet have received inadequate attention for the application of plasmapheresis due to concerns over Joule heating. Using this device, we show that such convective rolls not only lead to plasma extraction at a high yield and purity but also deliver plasma at an acceptable quality with no evidence of hemolytic stress or protein denaturation. Specifically, plasma from 1.5 μL of whole blood diluted to 4% hematocrit in a high-conductivity buffer (1.5 S/m) is extracted in a continuous flow at a fraction of 70% by using a peak voltage of ±10 Vp applied at 650 kHz; the extracted plasma is nearly 99% pure, as shown by a rigorous assessment using flow cytometry. The plasmas obtained using this device and using conventional centrifugation and sedimentation are of comparable quality as revealed by absorbance and circular dichroism spectra despite thermal gradients; however, these gradients effectively drive electrothermal bulk flows, as assessed using the microparticle image velocity technique. The device achieves high target molecule recovery efficiency, delivering about 97% of the proteins detected in the plasma obtained using sedimentation. The utility of the extracted plasma is further validated based on the detection of prostate-specific antigen at clinically relevant levels.
Synthesis of 8-methoxy- and 8-methoxy-6-methylhomophthalic anhydrides, key intermediates for the synthesis of anthracyclinones and peri-hydroxylated polycyclic aromatic compounds. (1984)

A novel synthesis of 8-methoxy-(1a) and 8-methoxy-6-methylhomophthalic anhydrides (1b) is described. Oxidative aromatization of methyl 2-(2-carbomethoxy-3-oxocyclohex-1-enyl) acetate (2) using 2, 3-dichloro-5, 6-dicyano-1, 4-benzoquinone (DDQ) or sublimed sulfur followed by methylation gave methyl (2-carbomethoxy-3-methoxyphenyl) acetate (4) (method A). Diels-Alder reaction of 6-methoxy-4-methyl-2-pyrone (5) with 1, 3-dicarboalkoxyallenes occurred with the loss of carbon dioxide to give alkyl (2-carboalkoxy-3-methoxy-5-methylphenyl) acetates (6 and 7) (method B). These esters (4, 6, and 7) were converted to the corresponding 8-methoxyhomophthalic anhydrides (1a, b) by a usual alkaline hydrolysis followed by dehydrative cyclization with acetyl chloride in dry acetone.
McbR/YncC: Implications for the Mechanism of Ligand and DNA Binding by a Bacterial GntR Transcriptional Regulator Involved in Biofilm Formation (2014)

MqsR-controlled colanic acid and biofilm regulator (McbR, also known as YncC) is the protein product of a highly induced gene in early Escherichia coli biofilm development and has been regarded as an attractive target for blocking biofilm formation. This protein acts as a repressor for genes involved in exopolysaccharide production and an activator for genes involved in stress response. To better understand the role of McbR in governing the switch from exponential growth to the biofilm state, we determined the crystal structure of McbR to 2.1 Å. The structure reveals McbR to be a member of the FadR C-terminal domain (FCD) family of the GntR superfamily of transcriptional regulators (this family was named after the first identified member, GntR, a transcriptional repressor of the gluconate operon of Bacillus subtilis). Previous to this study, only six of the predicted 2800 members of this family had been structurally characterized. Here, we identify the residues that constitute the McbR effector and DNA binding sites. In addition, comparison of McbR with other members of the FCD domain family shows that this family of proteins adopts highly distinct oligomerization interfaces, which has implications for DNA binding and regulation.
Proximal-to-Distal Sequencing Behavior and Motor Cortex (2010)

Proximal-to-distal sequencing of limb segments is characteristic of a number of motor behaviors, including throwing, hitting, jumping, and perhaps even reach-to-grasp. Moreover, shoulder- and elbow-related neurons in the primary motor cortex (MI) have been shown to activate earlier than wrist- and finger-related neurons in monkeys performing a button-press task. It was recently discovered that β frequency oscillations in the local field potential (LFP) spontaneously propagate as travelling waves across the surface of the motor cortex along a rostral-to-caudal axis while monkeys perform a variety of visuomotor tasks. This chapter hypothesizes that these propagating LFP waves may promote proximal-to-distal recruitment of motor cortical neurons. This is consistent with a number of intracortical microstimulation experiments in the MI demonstrating a topographic gradient, such that proximal movements of the shoulder and elbow are evoked more rostrally on the precentral gyrus, while wrist and finger movements are elicited more caudally including within the bank of the central sulcus.
Chemical Methods from PPT1 Promotes Tumor Growth and Is the Molecular Target of Chloroquine Derivatives in Cancer (2023)

&lt;p&gt;Chemical Methods&lt;/p&gt;
High-Resolution Hierarchical Beam Alignment with Segmented Beams (2019)

We propose a high-resolution hierarchical beam alignment algorithm that learns millimeter wave channel space using segmented beams obtained from feasible phase shifted sum of given hierarchical basis. To be specific, at each stage, the segmented beam is designed using a linear combination of given training beam basis instead of just choosing a beam among them. Then, the designed beam is used to determine the subset of higher resolution training beam candidates for the next stage which is referred to as the over-complete dictionary embracing even partially overlapped beams as elements. At the next stage, the proposed beam alignment can focus only on the most promising directions associated with finer grids. The simulation results demonstrate that the proposed beam alignment framework can remedy the limitations of the existing grid-of-beams method and achieve favorable beam alignment performance with reduced training time.
ChemInform Abstract: Synthesis and Biological Activity of C‐3 Direct Heterocyclylcarbon‐ Substituted Novel Cephalosporins (1996)

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.
Speaker Diarization: A Review of Recent Research (2010)

Abstract—Speaker diarization is the task of determining “who spoke when? ” in an audio or video recording that contains an unknown amount of speech and also an unknown number of speakers. Initially, it was proposed as a research topic related to automatic speech recognition, where speaker diarization serves as an upstream processing step. Over recent years, however, speaker diarization has become an important key technology for many tasks, such as navigation, retrieval, or higher-level inference on audio data. Accordingly, many important improvements in accuracy and robustness have been reported in journals and conferences in the area. The application domains, from broadcast news, to lectures and meetings, vary greatly and pose different problems, such as having access to multiple microphones and multimodal information or overlapping speech. The most recent review of existing technology dates back to 2006 and focuses on the broadcast news domain. In this paper we review the current state-of-the-art, focusing on research developed since 2006 that relates predominantly to speaker diarization for conference meetings. Finally, we present an analysis of speaker diarization performance as reported through the NIST Rich Transcription evaluations on meeting data and identify important areas for future research. Index Terms—Speaker diarization, rich transcription, meetings I.
Review 1: "Omicron-induced interferon signalling prevents influenza A virus infection" (2022)

The authors demonstrate differential interferon-signaling in SARS-CoV-2 Delta and Omicron variants, which is correlated with the ability of Omicron infection, but not Delta infection, to protect in vitro cell cultures from subsequent influenza A virus co-infection.
Generalized multiprotocol label switching: an overview of signaling enhancements and recovery techniques (2001)

Generalized multiprotocol label switching (GMPLS), also referred to as multiprotocol lambda switching, is a multipurpose control plane paradigm that supports not only devices that perform packet switching, but also devices that perform switching in the time, wavelength, and space domains. The development of GMPLS necessitates enhancements to existing IP signaling and routing protocols. We present enhancements to two commonly used IP signaling protocols, RSVP and LDP, to support GMPLS. We illustrate the concept of hierarchical label switched path setup with an example, discuss mechanisms for bidirectional LSP setup, and describe the applications of suggested labels. We also discuss the important problem of protection and restoration in the GMPLS context. Finally, we describe how various recovery mechanisms can be implemented within the GMPLS framework.
Synthesis of a Novel Series of Tricyclic Dihydrofuran Derivatives: Discovery of 8,9-Dihydrofuro[3,2-c]pyrazolo[1,5-a]pyridines as Melatonin Receptor (MT1/MT2) Ligands (2011)

Novel tricyclic dihydrofuran derivatives were designed, synthesized, and evaluated as melatonin receptor (MT(1)/MT(2)) ligands based on the previously reported 1,6-dihydro-2H-indeno[5,4-b]furan 1a. By screening the central tricyclic cores, we identified 8,9-dihydrofuro[3,2-c]pyrazolo[1,5-a]pyridine as a potent scaffold with a high ligand-lipophilicity efficiency (LLE) value. Subsequent optimization of the side chains led to identification of the potent MT(1)/MT(2) agonist 4d (MT(1), K(i) = 0.062 nM; MT(2), K(i) = 0.420 nM) with good oral absorption and blood-brain barrier (BBB) penetration in rats. The oral administration of compound 4d exhibited a sleep-promoting action in freely moving cats at 0.1 mg/kg.
Phase-Resolved Laser Diagnostic Measurements of a Downscaled, Fuel-Staged Gas Turbine Combustor at Elevated Pressure and Comparison to LES Predictions (2006)

A technical gas turbine combustor has been studied in detail with optical diagnostics for validation of large-eddy simulations (LES). OH* chemiluminescence, OH laser-induced fluorescence (LIF) and particle image velocimetry (PIV) have been applied to stable and pulsating flames up to 8 bar. The combination of all results yielded good insight into the combustion process with this type of burner and forms a database that was used for the validation of complex numerical combustion simulations. LES, including radiation, convective cooling, and air cooling, were combined with a reduced chemical scheme that predicts NOx emissions. Good agreement of the calculated flame position and shape with experimental data was found.
Sensitivity of quantum conductance fluctuations and of 1/f noise to time reversal symmetry (1992)

We have measured 50 magnetoconductance curves corresponding to 50 microscopic disorder configurations in a single mesoscopic GaAs:Si wire at T=45 mK. This permits to establish that the universal conductance fluctuation decreases by a factor-of-two when one breaks time reversal symmetry by application of the magnetic field which destroys the weak-localisation correction to the mean conductance. We have also observed the same factor of reduction for the 1/f noise power in a gated GaAs:Si wire at T=45 mK, that indicates the quantum interference origin of this noise at least at very low temperature.
Bilayer Interdiffused Heterojunction Organic Photodiodes Fabricated by Double Transfer Stamping (2016)

A novel double transfer stamping method for the fabrication of a bilayer, interdiffused organic photodetector is demonstrated. The concept leads to a device having both a low dark current density of 7.7 nA cm−2 and high external quantum efficiency of 60% through optimized segregation of electron donor and acceptor materials within the active layer. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to 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.
<title>Comparison of sampling methods for time and frequency domain signals in Monte Carlo simulations of light migration in turbid material</title> (1998)

We compare two methods to evaluate the time dependence in Monte Carlo simulations of photon migration: sampling of the pulse response in time and evaluation of the transfer function at discrete points in the frequency domain. We show that these two methods differ in accuracy due to quantization and sampling errors, while the statistical error is the same for both methods. From our analysis we also derive alternative techniques to sample the time-domain pulse response with reduced quantization and sampling error.
Immunogold Electron Microscopic Localization of the Cross–Reactive Two–EF–Hand Calcium–Binding Birch Pollen Allergen Bet v 4 in Dry and Rehydrated Birch Pollen (1999)

Bet v 4 represents an intracellular pollen protein which, following hydration of pollen grains, rapidly migrates to the pollen surface (exine) and is washed out. This behavior explains how Bet v 4, being primarily an intracellular pollen protein, becomes available to sensitize patients.
RELIGION AND THE COMMUNITY COLLEGE (1973)

If universities can teach about religion, the community colleges cannot be far behind. Here are some impelling reasons
A Rapid Synthesis Method for Au, Pd, and Pt Aerogels Via Direct Solution-Based Reduction (2018)

A Rapid Synthesis Method For Au Pd And Pt Aerogels Via Direct Solution-based Reduction - Video. JoVE publishes peer-reviewed scientific video protocols to accelerate biological, medical, chemical and physical research. Watch our scientific video articles. JoVE is the world-leading producer and provider of science videos with the mission to improve scientific research, scientific journals, and education. Millions of scientists, educators and students at thousands of universities, colleges, hospitals and biopharmaceutical companies worldwide use JoVE for their research, teaching and learning.
Discriminating electromagnetic radiation based on angle of incidence (2023)

The present invention provides systems, articles, and methods for discriminating electromagnetic radiation based upon the angle of incidence of the electromagnetic radiation. In some cases, the materials and systems described herein can be capable of inhibiting reflection of electromagnetic radiation (e.g., the materials and systems can be capable of transmitting and/or absorbing electromagnetic radiation) within a given range of angles of incidence at a first incident surface, while substantially reflecting electromagnetic radiation outside the range of angles of incidence at a second incident surface (which can be the same as or different from the first incident surface). A photonic material comprising a plurality of periodically occurring separate domains can be used, in some cases, to selectively transmit and/or selectively absorb one portion of incoming electromagnetic radiation while reflecting another portion of incoming electromagnetic radiation, based upon the angle of incidence. In some embodiments, one domain of the photonic material can include an isotropic dielectric function, while another domain of the photonic material can include an anisotropic dielectric function. In some instances, one domain of the photonic material can include an isotropic magnetic permeability, while another domain of the photonic material can include an anisotropic magnetic permeability. In some embodiments, non-photonic materials (e.g., materials with relatively large scale features) can be used to selectively absorb incoming electromagnetic radiation based on angle of incidence.