gebhart/patrepeval huggingface dataset:
High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response (2022)

Suppression of the host innate immune response is a critical aspect of viral replication. Upon infection, viruses may introduce one or more proteins that inhibit key immune pathways, such as the type I interferon pathway. However, the ability to predict and evaluate viral protein bioactivity on targeted pathways remains challenging and is typically done on a single-virus or -gene basis. Here, we present a medium-throughput high-content cell-based assay to reveal the immunosuppressive effects of viral proteins. To test the predictive power of our approach, we developed a library of 800 genes encoding known, predicted, and uncharacterized human virus genes. We found that previously known immune suppressors from numerous viral families such as <i>Picornaviridae</i> and <i>Flaviviridae</i> recorded positive responses. These include a number of viral proteases for which we further confirmed that innate immune suppression depends on protease activity. A class of predicted inhibitors encoded by <i>Rhabdoviridae</i> viruses was demonstrated to block nuclear transport, and several previously uncharacterized proteins from uncultivated viruses were shown to inhibit nuclear transport of the transcription factors NF-κB and interferon regulatory factor 3 (IRF3). We propose that this pathway-based assay, together with early sequencing, gene synthesis, and viral infection studies, could partly serve as the basis for rapid <i>in vitro</i> characterization of novel viral proteins. <b>IMPORTANCE</b> Infectious diseases caused by viral pathogens exacerbate health care and economic burdens. Numerous viral biomolecules suppress the human innate immune system, enabling viruses to evade an immune response from the host. Despite our current understanding of viral replications and immune evasion, new viral proteins, including those encoded by uncultivated viruses or emerging viruses, are being unearthed at a rapid pace from large-scale sequencing and surveillance projects. The use of medium- and high-throughput functional assays to characterize immunosuppressive functions of viral proteins can advance our understanding of viral replication and possibly treatment of infections. In this study, we assembled a large viral-gene library from diverse viral families and developed a high-content assay to test for inhibition of innate immunity pathways. Our work expands the tools that can rapidly link sequence and protein function, representing a practical step toward early-stage evaluation of emerging and understudied viruses.
Demonstration of ultra-compact setup for synthesis of space-time wave packets (2023)

We introduce an ultra-compact and robust system to generate space-time wave packets based on chirped volume Bragg gratings to spatially resolve the spectrum, which reduced the volume of the synthesis setup down to 25 × 25 × 8 mm 3 .
An optical tweezers study of nanosecond duration DNA conformations through DNA-surface binding distance measurements (2010)

Optical tweezers have been widely used to study DNA properties including time dependent changes in conformation; however, such studies have emphasized direct fluorescent observation of the conformations of dyed DNA molecules. In this work we explore DNA conformations that allow undyed DNA to link to spatially separated surfaces. In one set of experiments, we used optical tweezers to hold a polystyrene bead at a fixed distance from the sample capillary wall and measured the probability of the binding as a function of the separation between the polystyrene bead and the capillary, where the beads were fully confined in liquid. In a separate magnetic crystal experiment, we used magnetic forces to control the separation between magnetic beads in a hexagonal lattice at an air-water interface and measured the probability of linking to beads in the crystal. In both types of experiments peak binding occurs at a surface separation several times longer than the radius of gyration of the DNA. These experiments provide fundamental information on elusive, but significant DNA conformations, as well as technologically useful information on the probability of the DNA binding that will link two surfaces.
Faster than Nyquist PDM-16QAM Modulation with Low Resolution and Low Speed DAC (2022)

We experimentally demonstrated an error free modulation and demodulation of 100GBaud PDM-16QAM signal using a 92GSa/s low-power digital-to-analog converter as 4bit resolution enabled by the advanced digital-signal-processing of Tomlinson Harashima pre-coding and digital resolution enhancer.
Neuroimaging evidence implicating cerebellum in the experience of hypercapnia and hunger for air (2001)

Recent neuroimaging and neurological data implicate cerebellum in nonmotor sensory, cognitive, vegetative, and affective functions. The present study assessed cerebellar responses when the urge to breathe is stimulated by inhaled CO(2). Ventilation changes follow arterial blood partial pressure CO(2) changes sensed by the medullary ventral respiratory group (VRG) and hypothalamus, entraining changes in midbrain, pons, thalamus, limbic, paralimbic, and insular regions. Nearly all these areas are known to connect anatomically with the cerebellum. Using positron emission tomography, we measured regional brain blood flow during acute CO(2)-induced breathlessness in humans. Separable physiological and subjective effects (air hunger) were assessed by comparisons with various respiratory control conditions. The conjoint physiological effects of hypercapnia and the consequent air hunger produced strong bilateral, near-midline activations of the cerebellum in anterior quadrangular, central, and lingula lobules, and in many areas of posterior quadrangular, tonsil, biventer, declive, and inferior semilunar lobules. The primal emotion of air hunger, dissociated from hypercapnia, activated midline regions of the central lobule. The distributed activity across the cerebellum is similar to that for thirst, hunger, and their satiation. Four possible interpretations of cerebellar function(s) here are that: it subserves implicit intentions to access air; it provides predictive internal models about the consequences of CO(2) inhalation; it modulates emotional responses; and that while some cerebellar regions monitor sensory acquisition in the VRG (CO(2) concentration), others influence VRG to adjust respiratory rate to optimize partial pressure CO(2), and others still monitor and optimize the acquisition of other sensory data in service of air hunger aroused vigilance.
GPU conversion of quad meshes to smooth surfaces (2008)

We convert any quad manifold mesh into an at least C1 surface consisting of bi-cubic tensor-product splines with localized perturbations of degree bi-5 near non-4-valent vertices. There is one polynomial piece per quad facet, regardless of the valence of the vertices. Particular care is taken to derive simple formulas so that the surfaces are computed efficiently in parallel and match up precisely when computed independently on the GPU.
Study of Nasal Enzyme Activity towards Insulin. In Vitro. (1991)

The possibility of insulin being enzymatically degraded in contact with the nasal mucosa has been studied in vitro. The insulin concentration was followed during 3 h incubation at 37 degrees C with freshly collected human nasal wash, isolated enzymes from pig and rabbit nasal mucosal tissue, leucine aminopeptidase and microsomal aminopeptidase, respectively. The rate of degradation with human nasal wash was found to be less than or equal to 0.02 microgram/min, which indicates that less than 0.5% of an intranasally applied insulin dose may be destroyed by local enzymes during the time of absorption. The observed degradation was not found to be limiting for an intranasal application of insulin.
Effect of Squealer Geometry Arrangement on a Gas Turbine Blade Tip Heat Transfer (2002)

Abstract This study investigates the effect of a squealer tip geometry arrangement on heat transfer coefficient and static pressure distributions on a gas turbine blade tip in a five-bladed stationary linear cascade. A transient liquid crystal technique is used to obtain detailed heat transfer coefficient distribution. The test blade is a linear model of a tip section of the GE E3 high-pressure turbine first stage rotor blade. Six tip geometry cases are studied: (1) squealer on pressure side, (2) squealer on mid camber line, (3) squealer on suction side, (4) squealer on pressure and suction sides, (5) squealer on pressure side plus mid camber line, and (6) squealer on suction side plus mid camber line. The flow condition during the blowdown tests corresponds to an overall pressure ratio of 1.32 and exit Reynolds number based on axial chord of 1.1×106. Results show that squealer geometry arrangement can change the leakage flow and results in different heat transfer coefficients to the blade tip. A squealer on suction side provides a better benefit compared to that on pressure side or mid camber line. A squealer on mid camber line performs better than that on a pressure side.
Preparations for extreme ultraviolet interferometry of the 0.3 numerical aperture Micro Exposure Tool optic (2003)

An at-wavelength interferometer is being created for the measurement and alignment of the 0.3 numerical aperture Micro Exposure Tool (MET) projection optic at extreme ultraviolet (EUV) wavelengths. The prototype MET system promises to provide early learning from EUV lithographic imaging down to 20 nm feature size. The threefold increase to 0.3 NA in the image-side numerical aperture presents several challenges for the extension of ultrahigh-accuracy interferometry, including pinhole fabrication and the calibration and removal of systematic error sources.
Consequences of Soil Crude Oil Pollution on Some Wood Properties of Olive Trees (2014)

To enlighten the extent of crude oil pollution effects on some anatomical characteristics of olive plant (Olea europaea ). Two years - old seedlings were chosen to grow under 5 levels of pollution (0.0, 0.5, 1.0, 2.0, and 3.0, liter/ plant). The experiment has been conducted in the experimental field of Natural History Research Center and Museum, University of Baghdad. It was designed as CRD experiment. Testing wood specimens were prepared after 2.5 years of growth. Fiber length, width, wall thickness, and wood specific gravity were measured. Results showed that olive plants could not resist the highest level ( 3 liters / plant ) of pollution .Fiber length was the most affected property by treatment. All fiber dimensions were decreased with the increase of pollution level. The reduction was unsystematic. 12% of the fiber length was reduced as a result of pollution. Wood specific gravity of polluted plants showed few higher values than that of control. Lower parts of stem seemed to be more affected, that may be because these parts are fare away from crown ( the source of oxen ).
Microcavity VCSELs (1993)

Microcavity lasers potentially will have ultra-low thresholds in the micro ampere range or even lower. The vertical-cavity surface-emitting laser (VCSEL) structure represents the most straightforwardly produceable device which can scale down to ultra-small cavity dimensions and active material volumes. By a simple scaling, one can calculate that a single-quantum-well (SQW) microcavity VCSEL, given a 100 A/cm 2 threshold current density, would have a 200 nA threshold if scaled down to a 0.5 μm diameter. This calculated threshold does not rely on any enhancement of spontaneous emission, which could further reduce the threshold. The spontaneous emission factor in a GaAs/AlAs microcavity VCSEL of this diameter is predicted to be greater than 0.1, even at room temperature, compared to ~10 -4 for conventional laser diodes [1], or ~10 -2 for cryogenic-temperature planar microcavity VCSELs [2]. It is questionable, however, whether such a device is feasible. A SQW microlaser cavity must have extremely low loss, well under 1 % per pass. At some minimum diameter, almost certainly above 0.2 μm, diffraction and scattering due to sidewall roughness and the mirror-layer interfaces will cause losses to be excessively high. For an ultra-small microlaser to be electrically pumped with practical efficiency formidable fabrication challenges must be overcome.
Supplementary Table 1 from Vitamin D<sub>3</sub> Metabolism in Human Glioblastoma Multiforme: Functionality of CYP27B1 Splice Variants, Metabolism of Calcidiol, and Effect of Calcitriol (2023)

Supplementary Table 1 from Vitamin D&lt;sub&gt;3&lt;/sub&gt; Metabolism in Human Glioblastoma Multiforme: Functionality of CYP27B1 Splice Variants, Metabolism of Calcidiol, and Effect of Calcitriol
The Gonadotropin-Releasing Hormone Pituitary Receptor Interacts with a Guanosine Triphosphate Binding Protein: Differential Effects of Guanyl Nucleotides on Agonist and Antagonist Binding* (1989)

Binding of the GnRH agonist [DAla6,NMe-Leu7,Pro9Net]GnRH to bovine anterior pituitary membranes is inhibited by guanyl nucleotides. The effect of guanyl nucleotides is temperature dependent, in that significant binding inhibition is observed when the receptor-hormone interaction is measured at 37 C, and no inhibition is seen at 4 C. Micromolar concentrations of the nonhydrolyzable GTP analog 5′-guanylylimidodiphosphate [Gpp(NH)p] displace the bound agonist in a dosedependent manner, with half-maximal displacement occurring in a concentration range of 0.1–0.5 μM, and maximum displacement occurring at a concentration of 50 fiM Gpp(NH)p. At a concentration of 50 nM, the other nucleotides GTP and GDP inhibit binding to a lesser extent, while GMP, cGMP, 5′- adenylylimidodiphosphate [App(NH)p], ATP, and cAMP have no effect on the binding. At 37 C, Gpp(NH)p reduces the affinity of the agonist by a factor of 6 and increases its dissociation rate. In the presence of Gpp(NH)p at 37 C, there is also a 2-fold increase in the total number of binding sites. Under the same conditions as those used for the agonist, there is no displacement of the bound antagonist [Ac-D2Nal1, 4ClDPhe2,D3Pal3,DLys6,Lys8,DAla10]-GnRH by doses up to 50 fiM Gpp(NH)p. The modulation of the binding of the agonist, but not that of the antagonist, by guanyl nucleotides is characteristic of receptors that are coupled to GTP-binding proteins. Thus, the GnRH receptor appears to be coupled to a GTPbinding protein that may play a role in the mechanism of action of GnRH at the pituitary. (Endocrinology124: 798–804, 1989)
A common genetic variant of fucosyltransferase 2 correlates with serum carcinoembryonic antigen levels and affects cancer screening in patients with primary sclerosing cholangitis (2015)

CEA is interesting for biliary-malignancy screening in PSC patients, especially in patients who do not express CA19-9. This is the first study to show that the combined use of CEA measurement and FUT genotyping is clinically beneficial and that it might enhance the early detection of biliary malignancy in clinical practice. This approach could also be effective when screening for other common gastrointestinal malignancies.
Parkinsonian daytime sleep-wake classification using deep brain stimulation lead recordings (2022)

Excessive daytime sleepiness is a recognized non-motor symptom that adversely impacts the quality of life of people with Parkinson's disease (PD), yet effective treatment options remain limited. Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an effective treatment for PD motor signs. Reliable daytime sleep-wake classification using local field potentials (LFPs) recorded from DBS leads implanted in STN can inform the development of closed-loop DBS approaches for prompt detection and disruption of sleep-related neural oscillations. We performed STN DBS lead recordings in three nonhuman primates rendered parkinsonian by administrating neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Reference sleep-wake states were determined on a second-by-second basis by video monitoring of eyes (eyes-open, wake and eyes-closed, sleep). The spectral power in delta (1-4 Hz), theta (4-8 Hz), low-beta (8-20 Hz), high-beta (20-35 Hz), gamma (35-90 Hz), and high-frequency (200-400 Hz) bands were extracted from each wake and sleep epochs for training (70% data) and testing (30% data) a support vector machines classifier for each subject independently. The spectral features yielded reasonable daytime sleep-wake classification (sensitivity: 90.68 ± 1.28; specificity: 88.16 ± 1.08; accuracy: 89.42 ± 0.68; positive predictive value; 88.70 ± 0.89, n = 3). Our findings support the plausibility of monitoring daytime sleep-wake states using DBS lead recordings. These results could have future clinical implications in informing the development of closed-loop DBS approaches for automatic detection and disruption of sleep-related neural oscillations in people with PD to promote wakefulness.
Acute and Chronic Shear Stress Differently Regulate Endothelial Internalization of Nanocarriers Targeted to Platelet-Endothelial Cell Adhesion Molecule-1 (2012)

Intracellular delivery of nanocarriers (NC) is controlled by their design and target cell phenotype, microenvironment, and functional status. Endothelial cells (EC) lining the vascular lumen represent an important target for drug delivery. Endothelium in vivo is constantly or intermittently (as, for example, during ischemia-reperfusion) exposed to blood flow, which influences NC-EC interactions by changing NC transport properties, and by direct mechanical effects upon EC mechanisms involved in NC binding and uptake. EC do not internalize antibodies to marker glycoprotein PECAM(CD31), yet internalize multivalent NC coated with PECAM antibodies (anti-PECAM/NC) via a noncanonical endocytic pathway distantly related to macropinocytosis. Here we studied the effects of flow on EC uptake of anti-PECAM/NC spheres (~180 nm diameter). EC adaptation to chronic flow, manifested by cellular alignment with flow direction and formation of actin stress fibers, inhibited anti-PECAM/NC endocytosis consistent with lower rates of anti-PECAM/NC endocytosis in vivo in arterial compared to capillary vessels. Acute induction of actin stress fibers by thrombin also inhibited anti-PECAM/NC endocytosis, demonstrating that formation of actin stress fibers impedes EC endocytic machinery. In contrast, acute flow without stress fiber formation, stimulated anti-PECAM/NC endocytosis. Anti-PECAM/NC endocytosis did not correlate with the number of cell-bound particles under flow or static conditions. PECAM cytosolic tail deletion and disruption of cholesterol-rich plasmalemma domains abrogated anti-PECAM/NC endocytosis stimulation by acute flow, suggesting complex regulation of a flow-sensitive endocytic pathway in EC. The studies demonstrate the importance of the local flow microenvironment for NC uptake by the endothelium and suggest that cell culture models of nanoparticle uptake should reflect the microenvironment and phenotype of the target cells.
Tunable FPGA Bitstream Obfuscation with Boolean Satisfiability Attack Countermeasure (2020)

Field Programmable Gate Arrays (FPGAs) are seeing a surge in usage in many emerging application domains, where the in-field reconfigurability is an attractive characteristic for diverse applications with dynamic design requirements, such as cloud computing, automotive, IoT, and aerospace. The security of the FPGA configuration file, or bitstream , is critical, especially for devices with long in-field lifetimes, where attackers may attempt to extract valuable Intellectual Property (IP) from within. In this article, we propose a tunable obfuscation approach that protects IP from typical bitstream attacks while enabling designers to trade off security with acceptable overhead. We also consider two potential attacks on this protection mechanism: Boolean SAT Attacks on the obfuscation and removal attacks on the protection circuitry. The obfuscation and SAT countermeasure are integrated in a custom CAD framework within a commercial FPGA toolflow and together provide mathematically strong protection against common bitstream attacks. Further, we quantify the difficulty of a removal attack on the protection circuitry through pattern matching and direct bitstream manipulation. The average area, power, and delay overhead for obfuscation with 95% mismatch probability are 18%, 16%, and 8%, respectively, for small combinational circuits, and 1%, 2%, and 5% for larger arithmetic modules.
Cellular bias on the microscale: probing the effects of digital microfluidic actuation on mammalian cell health, fitness and phenotype (2013)

The potential benefits of using new technologies such as microfluidics for life science applications are exciting, but it is critical to understand and document potential biases imposed by these technologies on the observed results. Here, we report the first study of genome-level effects on cells manipulated by digital microfluidics. These effects were evaluated using a broad suite of tools: cell-based stress sensors for heat shock activation, single-cell COMET assays to probe changes in DNA integrity, and DNA microarrays and qPCR to evaluate changes in genetic expression. The results lead to two key observations. First, most DMF operating conditions tested, including those that are commonly used in the literature, result in negligible cell-stress or genome-level effects. Second, for DMF devices operated at high driving frequency (18 kHz) and with large driving electrodes (10 mm × 10 mm), there are significant damage to DNA integrity and differential genomic regulation. We hypothesize that these effects are caused by droplet heating. We recommend that for DMF applications involving mammalian cells that driving frequencies be kept low (≤ 10 kHz) and electrode sizes be kept small (≤ 5 mm) to avoid detrimental effects.
Halogen‐Bonding‐Donor Catalyzed Cyanosilylation of Aldehydes (2021)

Abstract Although halogen‐bonding has been utilized as an emerging means for activation of substrates, the use of the interaction for activation of relatively low Lewis basic electrophiles such as carbonyl compounds is still limited. Herein, we developed the halogen‐bonding‐donor donor catalyzed cyanosilylation of aldehydes via a synergistic activation mechanism, which were supported by a combined computational and experimental approach. The substrate scope for the reaction and the chemoselectivity of cationic XB‐donors are described.
Structural studies by electron microscopy: coherent intergrowth of the ReO3and tetragonal tungsten bronze structure types in the system Nb2O5–WO3 (1974)

High-resolution lattice images from WO3-rich compositions in the system Nb2O5-WO3 contain direct evidence for the coherent intergrowth of extensive domains of several orientations of the ReO3-type structure with the more complex tetragonal tungsten bronze-type structure. A model for the transformation between the two structure types is proposed.
Structure–Relaxivity Relationships among Targeted MR Contrast Agents (2012)

Paramagnetic gadolinium(III) complexes are widely used to increase contrast in magnetic resonance (MR) images. Contrast enhancement depends on the concentration of the gadolinium complex and on its relaxivity, an inherent property of the complex. Increased relaxivity results in greater image contrast or the ability to detect the contrast agent at a lower concentration. Increasing relaxivity enables imaging of abundant molecular targets.Relaxivity depends on the structure of the complex, kinetics of inner-sphere and second sphere water exchange, and on the rotational dynamics of the molecule. The latter, and in some cases the former, properties of the complex change when it is bound to its target. All of these properties can be rationally tuned to enhance relaxivitry. In this Microreview we summarize our efforts in understanding and optimizing the relaxivity of contrast agents targeted to serum albumin and to fibrin.