gebhart/patrepeval huggingface dataset:
A unique and evolutionarily conserved retinal interneuron relays rod and cone input to the inner plexiform layer (2020)

Abstract Neurons in the CNS are distinguished from each other by their morphology, the types of the neurotransmitter they release, their synaptic connections, and their genetic profiles. While attempting to characterize the retinal bipolar cell (BC) input to retinal ganglion cells (RGCs), we discovered a previously undescribed type of interneuron in mice and primates. This interneuron shares some morphological, physiological, and molecular features with traditional BCs, such as having dendrites that ramify in the outer plexiform layer (OPL) and axons that ramify in the inner plexiform layer (IPL) to relay visual signals from photoreceptors to inner retinal neurons. It also shares some features with amacrine cells, particularly Aii amacrine cells, such as their axonal morphology and possibly the release of the inhibitory neurotransmitter glycine, along with the expression of some amacrine cell specific markers. Thus, we unveil an unrecognized type of interneuron, which may play unique roles in vision. Significance Statement Cell types are the building blocks upon which neural circuitry is based. In the retina, it is widely believed that all neuronal types have been identified. We describe a cell type, which we call the Campana cell, that does not fit into the conventional neuronal retina categories but is evolutionarily conserved. Unlike retinal bipolar cells, the Campana cell receives synaptic input from both rods and cones, has broad axonal ramifications, and may release an inhibitory neurotransmitter. Unlike retinal amacrine cells, the Campana cell receives direct photoreceptor input has bipolar-like ribbon synapses. With this discovery, we open the possibility for new forms of visual processing in the retina.
Ultrafast frequency-selective optical switching based on thin self-assembled organic chromophoric films with a large second-order nonlinear response (2002)

Thin films consisting of self-assembled chromophoric superlattices exhibit very large second-order nonlinear responses [χ(2)]. Using such films, a “static” diffraction grating is created by the interference of two coherent infrared beams from a pulsed yttritium–aluminum–garnet laser. This grating is used to switch the second-harmonic and third-harmonic “signal” beams (generated from the fundamental “pump” beam or mixed within the chromophoric superlattice) into different channels (directions). Ultrafast switching response as a function of the time overlap of the pumping beams is demonstrated. It is suggested that such devices can be used to spatially and temporally separate signal trains consisting of pulses having different frequencies and arrival times.
Modeling of sparse aperture telescope image quality (2001)

Sparse aperture imaging systems are mathematically modeled so that high fidelity image simulations can be produced. These simulations are used to better understand the image quality issues, such as low MTF and noise amplification, with sparse aperture systems.
Supplementary Figure 1 from Combining ABCG2 Inhibitors with IMMU-132, an Anti–Trop-2 Antibody Conjugate of SN-38, Overcomes Resistance to SN-38 in Breast and Gastric Cancers (2023)

&lt;p&gt;Molecular structure of fumitremorgin C&lt;/p&gt;
Lamellar Envelopes of Semiconductor Nanocrystals (2009)

We report the solution-phase formation of ordered lamellar nanocrystal (NC) arrays. These semiconductor lamellae exhibit structural integrity and temporal stability, without recourse to chemical cross-linking. They are many micrometers in diameter yet only two or three nanocrystal layers in thickness. We show that these structures can integrate a cargo of water-soluble ions, molecules, metal nanoparticles, or biomolecules. Encapsulation of gold nanoparticles is found to cause photoluminescence enhancement of the host CdSe nanocrystals. These easily prepared nanocrystal "envelopes" promise properties modulated through the integration of a vast array of water-soluble species. Our approach marks a step toward ordered, compartmentalized, NC-based complexes with controlled architectures.
Supplementary Figure Legends 2A and 2B from Cancer Immunotherapy Based on Killing of <i>Salmonella</i>-Infected Tumor Cells (2023)

Supplementary Figure Legends 2A and 2B from Cancer Immunotherapy Based on Killing of &lt;i&gt;Salmonella&lt;/i&gt;-Infected Tumor Cells
RAProp (2013)

The increasing popularity of Twitter renders improved trust- worthiness and relevance assessment of tweets much more important for search. However, given the limitations on the size of tweets, it is hard to extract measures for ranking from the tweets? content alone. We present a novel ranking method called RAProp, which combines two orthogonal measures of relevance and trustworthiness of a tweet. The first, called Feature Score, measures the trustworthiness of the source of the tweet by extracting features from a 3-layer Twitter ecosystem consisting of users, tweets and webpages. The second measure, called agreement analysis, estimates the trustworthiness of the content of a tweet by analyzing whether the content is independently corroborated by other tweets. We view the candidate result set of tweets as the vertices of a graph, with the edges measuring the estimated agreement between each pair of tweets. The feature score is propagated over this agreement graph to compute the top-k tweets that have both trustworthy sources and independent corroboration. The evaluation of our method on 16 million tweets from the TREC 2011 Microblog Dataset shows that for top-30 precision, we achieve 53% better precision than the current best performing method on the data set, and an improvement of 300% over current Twitter Search.
Initial experimental results on a superconducting-qubit reset based on photon-assisted quasiparticle tunneling (2022)

We present here our recent results on qubit reset scheme based on a quantum-circuit refrigerator (QCR). In particular, we use the photon-assisted quasiparticle tunneling through a superconductor–insulator–normal-metal–insulator–superconductor junction to controllably decrease the energy relaxation time of the qubit during the QCR operation. In our experiment, we use a transmon qubit with dispersive readout. The QCR is capacitively coupled to the qubit through its normal-metal island. We employ rapid, square-shaped QCR control voltage pulses with durations in the range of 2–350 ns and a variety of amplitudes to optimize the reset time and fidelity. Consequently, we reach a qubit ground-state probability of roughly 97% with 80-ns pulses starting from the first excited state. The qubit state probability is extracted from averaged readout signal, where the calibration is based on Rabi oscillations, thus not distinguishing the residual thermal population of the qubit.
Dog breeds and body conformations with predisposition to osteosarcoma in the UK: a case-control study (2021)

This study provides evidence of strong breed-associated osteosarcoma risk and protection, suggesting a genetic basis for osteosarcoma pathogenesis. It highlights that breeds selected for long legs/large body mass are generally overrepresented amongst at-risk breeds, whilst those selected for short leg length/small body mass are generally protected. These findings could inform genetic studies to identify osteosarcoma risk alleles in canines and humans; as well as increasing awareness amongst veterinarians and owners, resulting in improved breeding practices and clinical management of osteosarcoma in dogs.
Highly multiplexed single-cell quantitative PCR (2018)

We present a microfluidic device for rapid gene expression profiling in single cells using multiplexed quantitative polymerase chain reaction (qPCR). This device integrates all processing steps, including cell isolation and lysis, complementary DNA synthesis, pre-amplification, sample splitting, and measurement in twenty separate qPCR reactions. Each of these steps is performed in parallel on up to 200 single cells per run. Experiments performed on dilutions of purified RNA establish assay linearity over a dynamic range of at least 104, a qPCR precision of 15%, and detection sensitivity down to a single cDNA molecule. We demonstrate the application of our device for rapid profiling of microRNA expression in single cells. Measurements performed on a panel of twenty miRNAs in two types of cells revealed clear cell-to-cell heterogeneity, with evidence of spontaneous differentiation manifested as distinct expression signatures. Highly multiplexed microfluidic RT-qPCR fills a gap in current capabilities for single-cell analysis, providing a rapid and cost-effective approach for profiling panels of marker genes, thereby complementing single-cell genomics methods that are best suited for global analysis and discovery. We expect this approach to enable new studies requiring fast, cost-effective, and precise measurements across hundreds of single cells.
Tolterodine for overactive bladder: time to onset of action, preferred dosage, and 9-month follow-up. (1999)

This is a prospective study of 28 patients who had urinary frequency (>8 times/day) and either urgency or urge incontinence (>1 time/day). After a 2-week run-in period (visit 1), the patients were started on tolterodine 1 mg twice a day (bid) (visit 2). They were followed at 4 and 8 weeks (visits 3 and 4). The patients were contacted by telephone 1 week after visit 2. Tolterodine was increased to 2 mg bid if the patient had incomplete improvement at either the initial phone call or during visit 3. Evaluation criteria were daily micturition charts including urinary frequency, nocturia, leakage episodes, average urine volume per day, and average voided volume. Tolterodine was well tolerated without side effects in 20 (80%) of 28 patients. Eight patients (20%) dropped out after enrollment because of side effects in 3, no improvement in 2, and missing visits (>1) in 3. Drug dosage in the 20 patients who tolerated tolterodine was 1 mg bid in 3 and 2 mg bid in 17 (85%). According to micturition charts, urinary frequency, nocturia, and leakage episodes decreased significantly after tolterodine treatment, whereas average urine volume per day and average voided volume did not change significantly. There were no electrocardiographic or biochemical abnormalities due to tolterodine treatment. Mean follow-up was 9.4 months. All 20 patients who tolerated tolterodine continue to take the medication without significant side effects. We conclude that tolterodine is well tolerated and effective for overactive bladders. Two milligrams bid is the dosage preferred by the majority of patients and the onset of action is seen within 1 week of treatment. Long-term compliance and efficacy are excellent, with no dropout in >9 months of follow-up.
Effects of three avocado/soybean unsaponifiable mixtures on human chondrocytes metabolism (1996)

peer reviewed
Refinement of Visual Hulls for Human Performance Capture (2012)

This section summarizes related works on 3D model refinement. The spatial and the temporal domain approaches are orthogonal and are independent of each other. They can be combined to generate more accurate 3D models, although this is out of the scope of this chapter.
Biocatalytic synthesis of acrylates in supercritical fluids: tuning enzyme activity by changing pressure. (1993)

Supercritical fluids are a unique class of nonaqueous media in which biocatalytic reactions can occur. The physical properties of supercritical fluids, which include gas-like diffusivities and liquid-like densities, can be predictably controlled with changing pressure. This paper describes how adjustment of pressure, with the subsequent predictable changes of the dielectric constant and Hildebrand solubility parameter for fluoroform, ethane, sulfur hexafluoride, and propane, can be used to manipulate the activity of lipase in the transesterification of methylmethacrylate with 2-ethyl-1-hexanol. Of particular interest is that the dielectric constant of supercritical fluoroform can be tuned from approximately 1 to 8, merely by increasing pressure from 850 to 4000 psi (from 5.9 to 28 MPa). The possibility now exists to predictably alter both the selectivity and the activity of a biocatalyst merely by changing pressure.
Gene expression profile by inhibiting Raf-1 protein kinase in breast cancer cells (2006)

Raf-1 protein serine-threonine kinase plays an important role in cell growth, proliferation, and cell survival. Previously, we and others have demonstrated that antisense raf oligonucleotide-mediated inhibition of Raf-1 expression leads to tumor growth arrest, radiosensitization and chemosensitization in vivo. Raf-1 inhibition is also associated with apoptotic cell death. In this study, we inhibited Raf-1 using an antisense raf oligonucleotide (AS-raf-ODN) to identify downstream targets of Raf-1 using microarray gene expression analysis. Treatment of MDA-MB-231 breast cancer cells with 250 nM AS-raf-ODN led to significant inhibition of Raf-1 protein (75.2 +/- 9.6%) and c-raf-1 mRNA levels (86.2 +/- 3.3%) as compared to untreated control cells. The lipofectin control or mismatch oligonucleotide had no effect on Raf-1 expression. To determine the changes in gene expression profiles that were due to inhibition of Raf-1, we simultaneously compared the gene expression patterns in AS-raf-ODN treated cells with untreated control cells and cells treated with lipofectin alone or MM-ODN. A total of 17 genes (4 upregulated and 13 down-regulated) including c-raf-1 were identified that were altered after AS-raf-ODN treatment. Functional clustering analysis revealed genes involved in apoptosis (Bcl-XL), cell adhesion (paxillin, plectin, Rho GDIalpha, CCL5), metabolism (GM2A, SLC16A3, PYGB), signal transduction (protein kinase C nu), and transcriptional regulation (HMGA1), and membrane-associated genes (GNAS, SLC16A3). Real-time PCR, Northern analysis and Western analysis confirmed the microarray findings. Our study provides insight into Raf-1 related signaling pathways and a model system to identify potential target genes.
Promoter Domains Required for Expression of Plasmid-Borne Copies of the Herpes Simplex Virus Thymidine Kinase Gene in Virus-Infected Mouse Fibroblasts and Microinjected Frog Oocytes (1985)

A transient expression assay was used to measure the relative template activities of mutated tk genes in mouse L cells induced in trans by herpes simplex virus (HSV). In this assay, expression of the wild-type HSV type 1 tk gene is induced at least 200-fold by the superinfecting virus. Genetic lesions that were assayed include 5' deletions, clustered base substitutions, single base substitutions, intrapromoter inversions, and intrapromoter recombinants with the HSV type 2 tk gene. Roughly half of the mutations that were tested were found to weaken tk expression efficiency, and the remaining mutations did not alter expression. The spatial distribution of mutations that reduce expression efficiency in trans-induced mouse fibroblasts facilitated the construction of a map of promoter domains. The most gene-proximal promoter domain is located between 16 and 32 base pairs (bp) upstream of the tk mRNA cap site and contains a TATA homology. Two more distally located promoter domains were mapped to discrete locations upstream from the TATA homology. One of these distal domains is located between 47 and 79 bp upstream from the mRNA cap site, and the other is located between 84 and 105 bp upstream from the tk gene. The boundaries of these three promoter domains, with one exception, coincided with the set of domains delineated previously in a frog oocyte microinjection assay. The concordant behavior of tk promoter mutants in microinjected frog oocytes and trans-induced mouse fibroblasts leads us to propose that recognition and activation of the HSV tk promoter is mediated by cellular transcription factors that are common to frogs and mice.
Step-to-Step Variability in Tibiofemoral Contact Force During Walking Measured by an Instrumented Knee Implant (2009)

Understanding the dynamic loading at the knee can provide critical information for characterizing normal as well as pathologic conditions. However, measuring or predicting this loading from extrinsic measurement remains an unmet challenge. Part of the complexity of generalizing the tibiofemoral loading is that contact force patterns are largely subject specific and vary within subjects based on the activity performed and the specific muscle activation patterns exhibited [1]. While several studies have quantified the intra-subject variability in extrinsic knee kinematics and kinetics during repetitive activities of daily living [2,3], changes in patterns of muscle contraction can yield substantial step-to-step variability in tibiofemoral contact force with minimal changes in extrinsic kinetics due to the potential influence of muscle co-contraction. Knowledge of this step-to-step tibiofemoral loading variability could play an integral role in improving the interpretation of analytical contact force predictions.
Interaction of L2 with -Actin Directs Intracellular Transport of Papillomavirus and Infection (2003)

Viruses that replicate in the nucleus, including the primary causative agent of cervical cancer, human papillomavirus type 16 (HPV16), must first cross the cytoplasm. We compared the uptake of HPV16 virus-like particles (VLPs) either with or without the minor capsid protein L2. Whereas VLPs containing only the major capsid protein L1 were diffusely distributed within the cytoplasm even 6 h post-infection, VLPs comprising both L1 and L2 exhibited a radial distribution in the cytoplasm and accumulated in the perinuclear region of BPHE-1 cells within 2 h. L2 of HPV16 or bovine papillomavirus was shown to bind to a 43-kDa cellular protein that was subsequently identified as beta-actin by matrix-assisted laser desorption ionization time-of-flight analysis. A conserved domain comprising residues 25-45 of HPV16 L2 was sufficient for interaction with beta-actin. HPV16 L2 residues 25-45 fused to green fluorescent protein, but not green fluorescent protein alone, colocalized with actin and caused cell retraction and disruption of the microfilament network. Finally, wild-type L2, but not L2 with residues 25-45 deleted, facilitated HPV16 pseudovirion infection. Thus, binding of beta-actin by L2 residues 25-45 facilitates transport of HPV16 across the cytoplasm during infection, and blockade of this novel interaction may be useful for prophylaxis.
Relating cone penetration resistance to sand state using the material point method (2022)

Cone penetration tests (CPTs) can quantitatively inform about the mechanical state of a sand. However, relating measured cone resistance values to sand state requires complex back-analysis of the processes occurring in the soil during the test. This paper provides new evidence of the value added in this area by modern large-deformation modelling based on the material point method (MPM). It is shown that accurate simulation of the relationship between cone resistance and sand state can be achieved, on condition that the constitutive behaviour of the soil – and especially its critical state features – is adequately modelled over a wide range of confining pressures. This study relies on the predictive capabilities of the critical state NorSand model, and shows how previous calibrations endeavours from the literature (based on triaxial test results) can support the MPM simulation of unrelated CPT results obtained through calibration chamber tests. MPM CPT simulations of ever-increasing quality will positively impact the state of the art of CPT interpretation procedures, to date still largely based on simplified cavity expansion theories.
High-temperature characteristics and tunability of long-wavelength vertical-cavity semiconductor optical amplifiers (2003)

We investigate the high-temperature characteristics and the temperature tuning of long-wavelength vertical-cavity semiconductor optical amplifiers (VCSOA). The temperature shift of the peak-signal gain is shown to depend on the mirror reflectivity of the VCSOA. Experimental results of temperature tuning of a 1.3-μm VCSOA are presented. We demonstrate 10 dB of fiber-to-fiber gain over a tuning range of approximately 8 nm.
A tunable S-band erbium-doped fiber ring laser (2003)

In this paper, we experimentally investigate and demonstrate an S-band erbium-doped fiber (EDF) ring laser based on an erbium-doped silica fiber and 980-nm pumping laser. Widely tunable range from 1480 to 1522 nm, and the sidemode suppression ratio (SMSR) of >30 dB/0.1 nm and the output power of >-2 dBm in the operating range from 1482 nm to 1517 nm have been achieved for this ring laser. Under the constant power control, the output power variation less than /spl plusmn/0.05 dB can also be accomplished over the tuning range from 1482 to 1517 nm. This S-band EDF ring laser is promising for the future S-band applications.
Pharmaceutical Development and Safety Evaluation of a GMP-Grade Fucoidan for Molecular Diagnosis of Cardiovascular Diseases (2019)

The adhesion molecule P-selectin is present on the cell surface of both activated endothelium and activated platelets. The present study describes the pharmaceutical development, safety evaluation, and preclinical efficacy of a micro-dosed radiotracer. The macromolecular nanoscale assembly consisted of a natural compound made of a sulfated fucose-rich polysaccharides (fucoidan) and a radionuclide (technetium-99m) for the detection of <i>P</i>-selectin expression in cardiovascular diseases. After extraction and fractionation from brown seaweeds, the good manufacturing practice (GMP) production of a low molecular weight (LMW) fucoidan of 7 kDa was achieved and full physicochemical characterization was performed. The regulatory toxicology study in rats of the GMP batch of LMW fucoidan revealed no adverse effects up to 400 μg/kg (×500 higher than the expected human dose) and pseudoallergy was not seen as well. In a myocardial ischemia-reperfusion model in rats, the GMP-grade LMW fucoidan labeled with technetium-99m detected <i>P</i>-selectin upregulation in vivo. The present study supports the potential of using <sup>99m</sup>Tc-fucoidan as an imaging agent to detect activated endothelium in humans.
A protocol family approach to survivable storage infrastructures (2004)

A protocol family supports a variety of fault models with a single client-server protocol and a single server implementation. Protocol families shift the decision of which types of faults to tolerate from system design time to data creation time. With a protocol family based on a common survivable storage infrastructure, each data-item can be protected from different types and numbers of faults. Thus, a single implementation can be deployed in different environments. Moreover, a single deployment can satisfy the specific survivability requirements of different data for costs commensurate with its requirements.
Apollo window meteoroid experiment (1972)

The Apollo window meteoroid experiment is described which uses the Apollo command module heat shield window surfaces to obtain information about the flux of meteoroids with masses of 10 to the minus 7th power g and less; to examine the residue and the morphology of the craters produced by these meteoroid; to obtain information regarding the dynamic and physical properties of the meteoroids; and to discover possible correlations with the lunar-rock-crater studies. Photographs are included.