gebhart/patrepeval huggingface dataset:
Encrypted Three-dimensional Dynamic Imaging using Snapshot Time-of-flight Compressed Ultrafast Photography (2015)

Compressed ultrafast photography (CUP), a computational imaging technique, is synchronized with short-pulsed laser illumination to enable dynamic three-dimensional (3D) imaging. By leveraging the time-of-flight (ToF) information of pulsed light backscattered by the object, ToF-CUP can reconstruct a volumetric image from a single camera snapshot. In addition, the approach unites the encryption of depth data with the compressed acquisition of 3D data in a single snapshot measurement, thereby allowing efficient and secure data storage and transmission. We demonstrated high-speed 3D videography of moving objects at up to 75 volumes per second. The ToF-CUP camera was applied to track the 3D position of a live comet goldfish. We have also imaged a moving object obscured by a scattering medium.
The HER-2-Targeting Antibodies Trastuzumab and Pertuzumab Synergistically Inhibit the Survival of Breast Cancer Cells (2004)

Trastuzumab (herceptin) and pertuzumab (Omnitarg, 2C4) are recombinant humanized monoclonal antibodies that target different extracellular regions of the HER-2 tyrosine kinase receptor. We explored combination effects of these agents in the HER-2-overexpressing BT474 breast cancer cell line. Trastuzumab and 2C4 synergistically inhibited the survival of BT474 cells, in part, because of increased apoptosis. Trastuzumab increased 2C4-mediated disruption of HER-2 dimerization with the epidermal growth factor receptor and HER-3. Combination drug treatment reduced levels of total and phosphorylated HER-2 protein and blocked receptor signaling through Akt but did not affect mitogen-activated protein kinase. These results suggest that combining HER-2-targeting agents may be a more effective therapeutic strategy in breast cancer rather than treating with a single HER-2 monoclonal antibody.
Constitutive Activation of G Protein-Coupled Receptors as a Result of Selective Substitution of a Conserved Leucine Residue in Transmembrane Helix III (2000)

Whereas numerous mutations of the human lutropin receptor (hLHR) and human TSH receptor (hTSHR) have been shown to cause constitutive activation of these receptors, it has been suggested that either the hFSHR as a whole, or the i3/TM VI region of the hFSHR, is less susceptible to mutation-induced constitutive activation. However, as shown herein, substitution of a highly conserved leucine residue in transmembrane III (TM III) of the hFSHR (Leu 111.18) with arginine causes a 5-fold increase in basal cAMP in transfected cells, consistent with a strong constitutive activation of the hFSHR. Interestingly, this mutant is unresponsive to further hormonal stimulation. Substitutions of hFSHR(L460) with lysine, alanine, or aspartate show that only arginine causes constitutive activation. However, all result in decreased FSH responsiveness, suggesting a role for L460 in FSH-stimulated cAMP production by the hFSHR. Because Leu 111.18 is highly conserved in rhodopsin-like G protein-coupled receptors (GPCRs), we tested the effects of substitution of the comparable leucine in the human beta2-adrenergic receptor (hbeta2-AR). Substitution of L124 in the hbeta2-AR with arginine, lysine, or alanine resulted in constitutive activation as evidenced by increased basal levels of cAMP that could be attenuated by an inverse agonist. In all cases, isoproterenol-stimulated cAMP was unaffected. Taken altogether, our data support a model whereby Leu 111.18 may play a general role in GPCRs by stabilizing them in an inactive state. Constitutive activation may arise by both a disruption of Leu 111.18 as well as the introduction of a specific residue that serves to stabilize the active state of the receptor.
Epigenetics and human disease: translating basic biology into clinical applications (2006)

Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an "extra" layer of transcriptional control that regulates how genes are expressed. These mechanisms are critical components in the normal development and growth of cells. Epigenetic abnormalities have been found to be causative factors in cancer, genetic disorders and pediatric syndromes as well as contributing factors in autoimmune diseases and aging. In this review, we examine the basic principles of epigenetic mechanisms and their contribution to human health as well as the clinical consequences of epigenetic errors. In addition, we address the use of epigenetic pathways in new approaches to diagnosis and targeted treatments across the clinical spectrum.
Correction of phase offset errors in main pulmonary artery flow quantification (2005)

The method significantly reduces phase offset errors in pulmonary artery flow.
Metabolic Engineering of Escherichia coli for Production of Enantiomerically Pure ( R )-(−)-Hydroxycarboxylic Acids (2003)

A heterologous metabolism of polyhydroxyalkanoate (PHA) biosynthesis and degradation was established in Escherichia coli by introducing the Ralstonia eutropha PHA biosynthesis operon along with the R. eutropha intracellular PHA depolymerase gene. By with this metabolically engineered E. coli, enantiomerically pure (R)-3-hydroxybutyric acid (R3HB) could be efficiently produced from glucose. By employing a two-plasmid system, developed as the PHA biosynthesis operon on a medium-copy-number plasmid and the PHA depolymerase gene on a high-copy-number plasmid, R3HB could be produced with a yield of 49.5% (85.6% of the maximum theoretical yield) from glucose. By integration of the PHA biosynthesis genes into the chromosome of E. coli and by introducing a plasmid containing the PHA depolymerase gene, R3HB could be produced without plasmid instability in the absence of antibiotics. This strategy can be used for the production of various enantiomerically pure (R)-hydroxycarboxylic acids from renewable resources.
Role of calcium in the thermal stability of thermolysin (1976)

The effect of calcium ion on the thermal stability of thermolysin has been investigated. The native protein undergoes an irreversible structural change and autolysis at high temperature. Analysis of the calcium ion dependence of the apparent melting temperature observed spectroscopically gives an apparent deltaH of -x (130 kcal/mol) where x is either 1 or 2. Neither zinc ion, where bound at the active site, nor terbium ion, which binds very tightly to the double calcium binding site, shows a stabilizing effect. These sites are therefore presumably not coupled to the transition which leads to autolysis. Removal of calcium ion from the native enzyme at temperatures below 50 degrees C results in inactivation but not major autolysis. The addition of 1 equiv of terbium before calcium removal results in a protein species which is 40% active and is no longer subject to thermal stabilization by calcium. These results suggest a pathway for the thermal inactivation of the enzyme which involves an irreversible structural change at one or both of the single calcium ion sites. This change propagates to the active site and results in inactivation. The binding of calcium ion to either or both single sites completely inhibits this structural change. The structural change is apparently cooperative and may correspond to a localized denaturation of the native structure.
Polycomb homologs are involved in teratogenicity of valproic acid in mice (2004)

We propose that, during embryonic development, VPA may affect the gene silencing pathway mediated by the Polycomb group complex. The epigenetic mechanism of VPA teratogenicity on anteroposterior patterning is suspected.
Large-scale simultaneous measurement of epitopes and transcriptomes in single cells (2017)

Recent high-throughput single-cell sequencing approaches have been transformative for understanding complex cell populations, but are unable to provide additional phenotypic information, such as protein levels of cell-surface markers. Using oligonucleotide-labeled antibodies, we integrate measurements of cellular proteins and transcriptomes into an efficient, sequencing-based readout of single cells. This method is compatible with existing single-cell sequencing approaches and will readily scale as the throughput of these methods increase.
Flow cytometer and imaging device used in combination (1995)

This report presents a flow cytometer devised by the authors and equipped with a CCD camera to obtain images of selected particles. Each image is linked to a point in the scattergram from which it can be retrieved from memory. The system uses an argon ion laser for flow-cytometric analysis and a diode-pumped pulse laser (532nm) to generate CCD images. Aggregated platelets in a blood sample and casts in a urine sample can be detected by this system. A fast flow rate is suitable for efficient flow-cytometric detection, and image resolution is sufficiently adequate for recognizing aggregated platelets and casts. Flow-cytometric and morphological data are used together to distinguish different types of cells in the same region on the scattergram and identify cells present in extremely small numbers among the majority.
A Fast Transform Domain Based Algorithm for H.264/AVC Intra Prediction (2007)

Directional intra prediction is one of the new features adopted in H.264/AVC standard. In contrast to some previous coding standards, the prediction is performed in the spatial domain. Two types of intra prediction for luma - Intra16times16 and Intra4times4 are included in each profile. For high profile, there is an additional type - Intra8times8. Intra 16x16 and Intra4times4 support four and nine modes respectively. As a result, the encoder complexity is increased dramatically. In this paper we proposed a fast intra prediction algorithm using transform domain features of the target block to filter out the majority of candidate modes. Extensive simulations verify that the proposed method speeds up the intra prediction process by 67.5% on average without sacrificing the picture quality and compression ratio. A comparison between the proposed algorithm and others is also provided.
Image Difference Threshold Strategies and Shadow Detection. (1995)

The paper considers two problems associated with the detection and classification of motion in image sequences obtained from a static camera. Motion is detected by differencing a reference and the ``current&amp;apos;&amp;apos; image frame, and therefore requires a suitable reference image and the selection of an appropriate detection threshold. Several threshold selection methods are investigated, and an algorithm based on hysteresis thresholding is shown to give acceptably good results over a number of test image sets. The second part of the paper examines the problem of detecting shadow regions within the image which are associated with the object motion. This is based on the notion of a shadow as a semi-transparent region in the image which retains a (reduced contrast) representation of the underlying surface pattern, texture or grey value. The method uses a region growing algorithm which uses a growing criterion based on a fixed attenuation of the photometric gain over the shadow region, in comparison to the reference image.
Transgenic alteration of ethylene biosynthesis increases grain yield in maize under field drought‐stress conditions (2014)

A transgenic gene-silencing approach was used to modulate the levels of ethylene biosynthesis in maize (Zea mays L.) and determine its effect on grain yield under drought stress in a comprehensive set of field trials. Commercially relevant transgenic events were created with down-regulated ACC synthases (ACSs), enzymes that catalyse the rate-limiting step in ethylene biosynthesis. These events had ethylene emission levels reduced approximately 50% compared with nontransgenic nulls. Multiple, independent transgenic hybrids and controls were tested in field trials at managed drought-stress and rain-fed locations throughout the US. Analysis of yield data indicated that transgenic events had significantly increased grain yield over the null comparators, with the best event having a 0.58 Mg/ha (9.3 bushel/acre) increase after a flowering period drought stress. A (genotype × transgene) × environment interaction existed among the events, highlighting the need to better understand the context in which the down-regulation of ACSs functions in maize. Analysis of secondary traits showed that there was a consistent decrease in the anthesis-silking interval and a concomitant increase in kernel number/ear in transgene-positive events versus nulls. Selected events were also field tested under a low-nitrogen treatment, and the best event was found to have a significant 0.44 Mg/ha (7.1 bushel/acre) yield increase. This set of extensive field evaluations demonstrated that down-regulating the ethylene biosynthetic pathway can improve the grain yield of maize under abiotic stress conditions.
Neurogenesis in dentate subgranular zone and rostral subventricular zone after focal cerebral ischemia in the rat (2001)

Because neurogenesis persists in the adult mammalian brain and can be regulated by physiological and pathological events, we investigated its possible involvement in the brain's response to focal cerebral ischemia. Ischemia was induced by occlusion of the middle cerebral artery in the rat for 90 min, and proliferating cells were labeled with 5-bromo-2'-deoxyuridine-5'-monophosphate (BrdUrd) over 2-day periods before sacrificing animals 1, 2 or 3 weeks after ischemia. Ischemia increased the incorporation of BrdUrd into cells in two neuroproliferative regions-the subgranular zone of the dentate gyrus and the rostral subventricular zone. Both effects were bilateral, but that in the subgranular zone was more prominent on the ischemic side. Cells labeled with BrdUrd coexpressed the immature neuronal markers doublecortin and proliferating cell nuclear antigen but did not express the more mature cell markers NeuN and Hu, suggesting that they were nascent neurons. These results support a role for ischemia-induced neurogenesis in what may be adaptive processes that contribute to recovery after stroke.
Inherited genetic markers discovered to date are able to identify a significant number of men at considerably elevated risk for prostate cancer (2010)

SNPs discovered to date are suitable for risk prediction while additional SNPs discovered in the future may identify more subjects at higher risk. Men identified as high risk by SNP-based testing may be targeted for PCa screening or chemoprevention. The clinical impact on improving the effectiveness of these interventions can be and should be assessed.
The Quantum Coherent Mechanism for Singlet Fission: Experiment and Theory (2013)

The absorption of one photon by a semiconductor material usually creates one electron-hole pair. However, this general rule breaks down in a few organic semiconductors, such as pentacene and tetracene, where one photon absorption may result in two electron-hole pairs. This process, where a singlet exciton transforms to two triplet excitons, can have quantum yields as high as 200%. Singlet fission may be useful to solar cell technologies to increase the power conversion efficiency beyond the so-called Shockley-Queisser limit. Through time-resolved two-photon photoemission (TR-2PPE) spectroscopy in crystalline pentacene and tetracene, our lab has recently provided the first spectroscopic signatures in singlet fission of a critical intermediate known as the multiexciton state (also called a correlated triplet pair). More importantly, we found that population of the multiexciton state rises at the same time as the singlet state on the ultrafast time scale upon photoexcitation. This observation does not fit with the traditional view of singlet fission involving the incoherent conversion of a singlet to a triplet pair. However, it provides an experimental foundation for a quantum coherent mechanism in which the electronic coupling creates a quantum superposition of the singlet and the multiexciton state immediately after optical excitation. In this Account, we review key experimental findings from TR-2PPE experiments and present a theoretical analysis of the quantum coherent mechanism based on electronic structural and density matrix calculations for crystalline tetracene lattices. Using multistate density functional theory, we find that the direct electronic coupling between singlet and multiexciton states is too weak to explain the experimental observation. Instead, indirect coupling via charge transfer intermediate states is two orders of magnitude stronger, and dominates the dynamics for ultrafast multiexciton formation. Density matrix calculation for the crystalline tetracene lattice satisfactorily accounts for the experimental observations. It also reveals the critical roles of the charge transfer states and the high dephasing rates in ensuring the ultrafast formation of multiexciton states. In addition, we address the origins of microscopic relaxation and dephasing rates, and adopt these rates in a quantum master equation description. We show the need to take the theoretical effort one step further in the near future by combining high-level electronic structure calculations with accurate quantum relaxation dynamics for large systems.
Democratic Integration: Self-Organized Integration of Adaptive Cues (2001)

Sensory integration or sensor fusion -- the integration of information from different modalities, cues, or sensors -- is among the most fundamental problems of perception in biological and artificial systems. We propose a new architecture for adaptively integrating different cues in a self-organized manner. In Democratic Integration different cues agree on a result, and each cue adapts toward the result agreed on. In particular, discordant cues are quickly suppressed and recalibrated, while cues having been consistent with the result in the recent past are given a higher weight in the future. The architecture is tested in a face tracking scenario. Experiments show its robustness with respect to sudden changes in the environment as long as the changes disrupt only a minority of cues at the same time, although all cues may be disrupted at one time or another.
Cholesteryl nitrolinoleate, a nitrated lipid present in human blood plasma and lipoproteins (2003)

Nitric oxide (*NO) and *NO-derived reactive species (e.g., peroxynitrite anion, nitrogen dioxide radical) react with lipids containing unsaturated fatty acids to generate nitrated species. In the present work, we synthesized, characterized, and detected a nitrated derivative of cholesteryl linoleate (Ch18:2) in human blood plasma and lipoproteins using a high-pressure liquid chromatography coupled to electrospray ionization tandem mass spectrometry method. It was synthesized by a reaction of Ch18:2 with nitronium tetrafluoroborate, yielding a species with m/z 711, which is characteristic of the cholesteryl nitrolinoleate (Ch18:2NO2) ammonium adduct. The presence of the nitro group was confirmed by using [15N]nitrite, which gave a product with m/z 712, with the same chromatographic and spectrometric characteristics of those of m/z 711. Furthermore, a C-NO2 structure was also demonstrated in Ch18:2NO2 by infrared analysis (Vmax 1549, 1374 cm-1). A stable product with m/z of 711, showing the same chromatographic characteristics and fragmentation pattern as those of synthesized standard, was found in human blood plasma and lipoproteins of normolipidemic subjects. The presence of this novel nitrogen-containing lipid product in human plasma and lipoproteins could represent a potential indicator of the oxidative/nitrative roles that *NO or its metabolites play during in vivo lipid oxidation, generating a compensatory mechanism of protection in vascular disease.
Design Considerations of a Direct Drive Brushless Machine With Concentrated Windings (2008)

This paper discusses the performance attributes of the open-slot, modular-wound, external-rotor, topology of electrical machine. Combinations of pole and slot numbers are presented for which the winding factor is maximal and torque ripple is minimal. An optimization of the magnetic circuit design of six promising pole-slot configurations is undertaken using a parametric finite element model (FEM) combined with a genetic algorithm (GA). These designs are benchmarked against a conventional 1.5 slots/pole external-rotor brushless dc machine. These candidate electrical machine versions are characterized by having the same external-rotor diameter, total slot area available for the winding and by equal volumes of permanent magnet (PM). Based on the analysis, the most promising motor structure was selected and a prototype wheel-hub motor has been built for application in a small electrical vehicle. Test data from the prototype is used to validate the findings of the initial analyses and practically demonstrate the attributes of the topology.
Behavioral Recovery in a Primate Model of Parkinson's Disease by Triple Transduction of Striatal Cells with Adeno-Associated Viral Vectors Expressing Dopamine-Synthesizing Enzymes (2002)

One potential strategy for gene therapy of Parkinson's disease (PD) is the local production of dopamine (DA) in the striatum induced by restoring DA-synthesizing enzymes. In addition to tyrosine hydroxylase (TH) and aromatic-L-amino-acid decarboxylase (AADC), GTP cyclohydrolase I (GCH) is necessary for efficient DA production. Using adeno-associated virus (AAV) vectors, we previously demonstrated that expression of these three enzymes in the striatum resulted in long-term behavioral recovery in rat models of PD. We here extend the preclinical exploration to primate models of PD. Mixtures of three separate AAV vectors expressing TH, AADC, and GCH, respectively, were stereotaxically injected into the unilateral putamen of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated monkeys. Coexpression of the enzymes in the unilateral putamen resulted in remarkable improvement in manual dexterity on the contralateral to the AAV-TH/-AADC/-GCH-injected side. Behavioral recovery persisted during the observation period (four monkeys: 48 days, 65 days, 50 days, and >10 months, each). TH-immunoreactive (TH-IR), AADC-IR, and GCH-IR cells were present in a large region of the putamen. Microdialysis demonstrated that concentrations of DA in the AAV-TH/-AADC/-GCH-injected putamen were increased compared with the control side. Our results show that AAV vectors efficiently introduce DA-synthesizing enzyme genes into the striatum of primates with restoration of motor functions. This triple transduction method may offer a potential therapeutic strategy for PD.
Stress and mind-body impact on the course of inflammatory bowel diseases. (1999)

At present, the medical management of inflammatory bowel diseases (IBD) including Crohn's disease and ulcerative colitis, are focused on topical, locally active antiinflammatories and systemic immunosuppressives, which are thought to exert their targeted effects in the gastrointestinal mucosa. There is a paucity of controlled trials assessing the impact of mind, central nervous system (CNS), and neuromodulation on the overly active immune response in the intestinal mucosa. Patients and their physicians have long been aware of a strong association between attitude, stress, and flares of their IBD. Although reports to date remain mostly anecdotal, the degree to which mind-body influences and stress impact levels of local inflammation deserves closer attention with the aim of identifying contributing mechanisms, which may highlight new therapeutic interventions, as well as assist in identifying particular subsets of patients that may respond to novel forms of adjunctive treatments for IBD, including hypnosis, meditation, neuropeptide receptor modulation, and cortisol-releasing factor (CRF) modulation.