gebhart/patrepeval huggingface dataset:
Selective retention of virus-specific tissue-resident T cells in healed skin after recovery from herpes zoster (2022)

Herpes zoster is a localized skin infection caused by reactivation of latent varicella-zoster virus. Tissue-resident T cells likely control skin infections. Zoster provides a unique opportunity to determine if focal reinfection of human skin boosts local or disseminated antigen-specific tissue-resident T cells. Here, we show virus-specific T cells are retained over one year in serial samples of rash site and contralateral unaffected skin of individuals recovered from zoster. Consistent with zoster resolution, viral DNA is largely undetectable on skin from day 90 and virus-specific B and T cells decline in blood. In skin, there is selective infiltration and long-term persistence of varicella-zoster virus-specific T cells in the rash site relative to the contralateral site. The skin T cell infiltrates express the canonical tissue-resident T cell markers CD69 and CD103. These findings show that zoster promotes spatially-restricted long-term retention of antigen-specific tissue-resident T cells in previously infected skin.
Opsonization of HIV with Complement Enhances Infection of Dendritic Cells and Viral Transfer to CD4 T Cells in a CR3 and DC-SIGN-Dependent Manner (2007)

In the present study, we demonstrated that opsonization of primary HIV-1 with human complement enhances infection of immature monocyte-derived dendritic cells (iDC) and transmission in trans of HIV to autologous CD4(+) T lymphocytes. Infection of iDC by opsonized primary R5- and X4-tropic HIV was increased 3- to 5-fold as compared with infection by the corresponding unopsonized HIV. Enhancement of infection was dependent on CR3 as demonstrated by inhibition induced by blocking Abs. The interaction of HIV with CCR5 and CXCR4 on iDC was affected by opsonization. Indeed, stromal-derived factor-1 was more efficient in inhibiting infection of iDC with opsonized R5-tropic HIV-1(BaL) (45%) than with heat-inactivated complement opsonized virus and similarly RANTES inhibited more efficiently infection of iDC with opsonized X4-tropic HIV-1(NDK) (42%) than with heat-inactivated complement opsonized virus. We also showed that attachment of complement-opsonized virus to DC-specific ICAM-grabbing nonintegrin (DC-SIGN) molecule on iDC and HeLa DC-SIGN(+) CR3(-) cells was 46% and 50% higher compared with heat-inactivated complement opsonized virus, respectively. Hence, Abs to DC-SIGN suppressed up to 80% and 60% the binding of opsonized virus to HeLa cells and iDC, respectively. Furthermore, Abs to DC-SIGN inhibited up to 70% of the infection of iDC and up to 65% of infection in trans of autologous lymphocytes with opsonized virus. These results further demonstrated the role of DC-SIGN in complement opsonized virus uptake and infection. Thus, the virus uses complement to its advantage to facilitate early steps leading to infection following mucosal transmission of HIV.
Chaotic attractor learning and how to deal with nonlinear singularities (2002)

In linear regression it is common practice to use principal component analysis (PCA) to find and remove directions in the input space that are not covered by the observed data. PCA fails to identify these 'singular directions' if the data lie on a lower dimensional nonlinear subspace. Typically, this is the case for data observed from deterministic chaotic systems. In this paper we present a viable nonlinear counterpart for principal component regression, and show why this algorithm can learn stable models for chaotic dynamics where other approaches often fail. The algorithm is applied to an experimental chaotic bubble column, with data highly contaminated with system noise and measurement errors.
A Practical Synthesis of (±)-α-Isosparteine from a Tetraoxobispidine Core (2005)

[reaction: see text] The title alkaloid was synthesized in racemic form from 3,7-diallyl-2,4,6,8-tetraoxo-3,7-diazabicyclo[3.3.1]nonane (7) by a regioselective diallylation reaction followed by double ring-closing olefin metathesis and exhaustive reduction. Tetraoxobispidine 7 was itself prepared in three simple operations from dimethyl malonate. The entire sequence to alpha-isosparteine was conducted on a multigram scale and proceeded without recourse to chromatography.
Trois questions sur les départements au bord de la faillite (Interview) (2015)

Premier paragraphe :\nDominique Bussereau tire la sonnette d'alarme. Le président de l'Assemblée des départements de France (ADF) estime qu'un à cinq départements "risquent de se déclarer en faillite d'ici à la fin de l'année si rien n'est fait", dans une interview publiée par Les Echos, lundi 27 juillet. Un constat inquiétant qui serait, en partie, le résultat d'une hausse des prestations sociales et d'une baisse des recettes provenant de l'Etat, selon le président (Les Républicains) du conseil départemental de Charente-Maritime.
Increased Sequence Diversity Coverage Improves Detection of HIV-Specific T Cell Responses (2007)

The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss responses to regions where test set and infecting virus differ. In this study, we report the design of a peptide test set with significantly increased coverage of HIV sequence diversity by including alternative amino acids at variable positions during the peptide synthesis step. In an IFN-gamma ELISpot assay, these "toggled" peptides detected HIV-specific CD4(+) and CD8(+) T cell responses of significantly higher breadth and magnitude than matched consensus peptides. The observed increases were explained by a closer match of the toggled peptides to the autologous viral sequence. Toggled peptides therefore afford a cost-effective and significantly more complete view of the host immune response to HIV and are directly applicable to other variable pathogens.
Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K oligo microarray. I. Top differentially expressed genes (2011)

Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated. Pooled RNA samples (n = 6/phenotype) labeled with cyanine 3 or cyanine 5 fluorescent dyes to generate cRNA probes were hybridized on a 4 × 44K chicken oligo microarray. Local polynomial regression normalization was applied to background-corrected red and green intensities with a moderated t-statistic. Corresponding P-values were computed and adjusted for multiple testing by false discovery rate to identify differentially expressed genes. Microarray validation was carried out by comparing findings with quantitative reverse-transcription PCR. A 1.3-fold difference in gene expression was set as a cutoff value, which encompassed 20% (782 of 4,011) of the total number of genes that were differentially expressed between FE phenotypes. Using an online software program (Ingenuity Pathway Analysis), the top 10 upregulated genes identified by Ingenuity Pathway Analysis in the high-FE group were generally associated with anabolic processes. In contrast, 7 of the top 10 downregulated genes in the high-FE phenotype (upregulated in the low-FE phenotype) were associated with muscle fiber development, muscle function, and cytoskeletal organization, with the remaining 3 genes associated with self-recognition or stress-responding genes. The results from this study focusing on only the top differentially expressed genes suggest that the high-FE broiler phenotype is derived from the upregulation of genes associated with anabolic processes as well as a downregulation of genes associated with muscle fiber development, muscle function, cytoskeletal organization, and stress response.
Doping of 6H–SiC by selective diffusion of boron (2000)

Experimental evidence of selective boron doping of 6H–SiC via diffusion is given. Selective diffusion has been realized at 1800–2100 °C using graphite film as a protecting mask. Cathodoluminescence measurements as well as an anodic oxidation technique have been employed to identify the local doped regions. In addition, a diffused planar p–n diode based on the local p-type emitter region was fabricated. The ideality factor extracted from current–voltage characteristics was 1.97, which indicates that the Shockley–Hall–Read recombination is the dominant mechanism in the conduction region. The value of breakdown voltage for this diode measured at room temperature was a little greater than 800 V, and a leakage current density of 5.7×10−6 A/cm2 at 800 V was achieved.
MEMS-Electronic-Photonic Heterogeneous Integrated FMCW Ladar Source (2015)

Abstract : The goal of this project is to develop a modular, heterogeneous integration process to combine III-V tunable VCSELs, silicon photonic integrated circuits, and CMOS ICs in a seamless manner, and demonstrate a single-chip FMCW (Frequency-Modulated Continuous-Wave) LADAR source. In Phase 2, we have successfully developed through-silicon-vias (TSVs) on Si photonics at wafer level, and stacking the Si photonic dies on top of CMOS at die level. Electrical and mechanical properties of the bonded systems were characterized. FPGA and CMOS programming using a custom graphical user interface have been implemented, and optical and electrical interfacing to the system has been achieved.
In VitroBACE-1 Inhibitory Activity of Resveratrol Oligomers from the Seed Extract ofPaeonia lactiflora (2010)

A new resveratrol oligomer (1) together with eight related components (2- 9) were isolated from the seed extract of Paeonia lactiflora (Paeoniaceae) as active principles responsible for the inhibition of beta-site APP-cleaving enzyme 1 (BACE-1) in vitro. The chemical structure of 1 was established as (-)-7a,8a- CIS- ε-viniferin with the aid of spectroscopic analyses including NOESY experiments. All isolated resveratrol oligomers (1- 9) demonstrated significant inhibition on baculovirus-expressed BACE-1 in a dose-dependent manner, which was assessed by the FRET assay using Rh-EVNLDAEFK as a substrate in vitro.
Revealing the uniaxial to biaxial nematic liquid crystal phase transition via distinctive electroconvection (2009)

Electroconvection (EC) phenomena are reported in the uniaxial and biaxial nematic phases of a bent-core liquid crystal. Two EC instabilities are observed. Prewavy_1, which exists only in the uniaxial phase, has stripes parallel to the rubbing direction, a periodicity of order of the device thickness, and an onset voltage that diverges near the uniaxial to biaxial transition. The prewavy_2 instability, characterized by stripes perpendicular to the rubbing direction and a periodicity of twice the device thickness, exists across the entire nematic regime. Our observations are explained through changes in the electrical conductivity anisotropy at the uniaxial to biaxial transition.
Early lineage specification defines alveolar epithelial ontogeny in the murine lung (2019)

During the stepwise specification and differentiation of tissue-specific multipotent progenitors, lineage-specific transcriptional networks are activated or repressed to orchestrate cell specification. The gas-exchange niche in the lung contains two major epithelial cell types, alveolar type 1 (AT1) and AT2 cells, and the timing of lineage specification of these cells is critical for the correct formation of this niche and postnatal survival. Integrating cell-specific lineage tracing studies, spatially specific mRNA transcript and protein expression, and single-cell RNA-sequencing analysis, we demonstrate that specification of alveolar epithelial cell fate begins concomitantly with the proximal-distal specification of epithelial progenitors and branching morphogenesis earlier than previously appreciated. By using a newly developed dual-lineage tracing system, we show that bipotent alveolar cells that give rise to AT1 and AT2 cells are a minor contributor to the alveolar epithelial population. Furthermore, single-cell assessment of the transcriptome identifies specified AT1 and AT2 progenitors rather than bipotent cells during sacculation. These data reveal a paradigm of organ formation whereby lineage specification occurs during the nascent stages of development coincident with broad tissue-patterning processes, including axial patterning of the endoderm and branching morphogenesis.
Immunohistochemical Characterization of Neurotransmitters in the Episcleral Circulation in Rats (2019)

These findings indicate that there is neuronal input to the episcleral circulation. ChAT and VIP as well as dopamine-β-hydroxylase suggest parasympathetic and sympathetic innervation. Further studies are needed on whether the positively-stained structures are of functional significance for the regulation of the episcleral venous pressure and thereby IOP.
mGlu1 potentiation enhances prelimbic somatostatin interneuron activity to rescue schizophrenia-like physiological and cognitive deficits (2021)

Evidence for prefrontal cortical (PFC) GABAergic dysfunction is one of the most consistent findings in schizophrenia and may contribute to cognitive deficits. Recent studies suggest that the mGlu<sub>1</sub> subtype of metabotropic glutamate receptor regulates cortical inhibition; however, understanding the mechanisms through which mGlu<sub>1</sub> positive allosteric modulators (PAMs) regulate PFC microcircuit function and cognition is essential for advancing these potential therapeutics toward the clinic. We report a series of electrophysiology, optogenetic, pharmacological magnetic resonance imaging, and animal behavior studies demonstrating that activation of mGlu<sub>1</sub> receptors increases inhibitory transmission in the prelimbic PFC by selective excitation of somatostatin-expressing interneurons (SST-INs). An mGlu<sub>1</sub> PAM reverses cortical hyperactivity and concomitant cognitive deficits induced by N-methyl-d-aspartate (NMDA) receptor antagonists. Using in vivo optogenetics, we show that prelimbic SST-INs are necessary for mGlu<sub>1</sub> PAM efficacy. Collectively, these findings suggest that mGlu<sub>1</sub> PAMs could reverse cortical GABAergic deficits and exhibit efficacy in treating cognitive dysfunction in schizophrenia.
A Measurement Rate-MSE Tradeoff for Compressive Sensing Through Partial Support Recovery (2014)

We consider the problem of estimating sparse vectors from noisy linear measurements in the high dimensionality regime. For a fixed number k of nonzero entries, we study the fundamental relationship between two relevant quantities: the measurement rate, which characterizes the asymptotic behavior of the dimensions of the measurement matrix in terms of the ratio m/log n (with m being the number of measurements and n the dimension of the sparse vector), and the estimation mean square error. First, we use an information-theoretic approach to derive sufficient conditions on the measurement rate to reliably recover a part of the support set that represents a certain fraction of the total vector power. Second, we characterize the mean square error of an estimator that uses partial support set information. Using these two parts, we derive a tradeoff between the measurement rate and the mean-square error. This tradeoff is achievable using a two-step approach: first support set recovery, and then estimation of the active components. Finally, for both deterministic and random vectors, we perform a numerical evaluation to verify the advantages of the methods based on partial support set recovery.
Dynamic Interference Steering in Heterogeneous Cellular Networks (2018)

With the development of diverse wireless communication technologies, interference has become a key impediment in network performance, thus making effective interference management (IM) essential to accommodate a rapidly increasing number of subscribers with diverse services. Although there have been numerous IM schemes proposed thus far, none of them are free of some form of cost. It is, therefore, important to balance the benefit brought by and cost of each adopted IM scheme by adapting its operating parameters to various network deployments and dynamic channel conditions. We propose a novel IM scheme, called <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dynamic interference steering</i> (DIS), by recognizing the fact that interference can be not only suppressed or mitigated but also steered in a particular direction. Specifically, DIS exploits both channel state information and the data contained in the interfering signal to generate a signal that modifies the spatial feature of the original interference to partially or fully cancel the interference appearing at the victim receiver. By intelligently determining the strength of the steering signal, DIS can steer the interference in an optimal direction to balance the transmitter’s power used for interference steering and the desired signal’s transmission. DIS is shown via simulation to be able to make better use of the transmit power, hence enhancing users’ spectral efficiency effectively.
An improved method for rapid objective measurement of gamma camera resolution (2000)

An improved method for an easy, rapid measurement of the intrinsic spatial resolution of a gamma camera is presented. A simplified model was previously developed based solely on mean and standard deviation measurements taken from a region of interest in bar pattern images. This led to an estimate of the modulation transfer function and the full width at half maximum (FWHM) of a line spread function (LSF). The improved method involved expanding the simplified model to incorporate input modulation, square wave input versus the assumed sinusoidal input, aperture (pixel) size, and scatter from the plastic in the bar pattern. The input square wave modulation was calculated to be unity for the typical bar patterns used for gamma camera quality control assessment. For the typical range of bar sizes available, in combination with the typical resolving capabilities of gamma cameras, the sinusoidal approximation of the bar pattern was found to be valid (<1% contribution to the measured resolution from higher harmonic frequencies present in a square wave input with an effective input modulation greater than unity by a factor of 4/pi). The aperture correction factor was calculated for numerous bar and pixel size combinations. Applying the aperture correction factor results in an improvement in the accuracy of the calculated FWHM values, especially for large apertures (pixel sizes). For a camera with a specified FWHM value of 3.5 mm, the simplified model predicts values ranging from 3.2 to 4.1 mm, when the acquisition matrix varies from 128(2) to 512(2). When the expanded model is used with the aperture correction applied, this range was reduced to 3.6-3.9 mm. The scatter correction further improved the calculated FWHM (from 3.6 to 3.8 mm). It is suggested that the expanded model should be used when more accurate measurements are desired, such as in acceptance testing.
Ferroelectric behavior of orthogonal smectic phase made of bent-core molecules (2011)

Ferroelectric behavior in the recently reported orthogonal ferroelectric Sm-A(d)P(F) phase in an unsymmetric bent-core molecule with a carbosilane terminal group was studied. The ferroelectricity of the Sm-A(d)P(F) phase was unambiguously confirmed by optical second-harmonic generation activity in the absence of an electric field, ferroelectric response, and high dielectric strength. The long-range polar order is a consequence of weakened interlayer coupling due to the formation of carbosilane sublayers, which allows for the parallel order of dipole moments of bent-core molecules in the neighboring layers. It develops in the system gradually through the second-order phase transition from the orthogonal Sm-A(d) phase. In the Sm-A(d)P(F) phase the strong surface anchoring results in the splay of polarization across the sample thickness. The polar surface anchoring also brings about strongly thickness-dependent polar fluctuations, as proved by the dielectric measurements (Goldstone-like mode). The relaxation frequency and dielectric strength vary more than one order of magnitude with cell thickness; in particular the dielectric strength attains more than 2000 in a 25 μm-thick cell and continues to increase for thicker cells. Simple theory developed qualitatively explains the experimental results, supporting the polarization splay model proposed.
AR and lidar applications enabled by beam and image steering by MEMS SLM (2023)

Micro Mechanical Electronics System based Spatial Light Modulators (MEMS-SLM) enables unique capability “Just in time photon delivery” or steering beam images to where and when they are needed. The beam and image steering solves challenges commonly found in both lidar and AR optical engines dominated by classical tradeoffs, such as image FOV, resolution and SLM size or form factor of optical engine. As a novel beam and image steering device, we transformed Texas Instruments Digital Micromirror Device (TI-DMD) into a diffractive beam and image steering device. TI-DMD is known as a binary spatial light modulator. Micromirros’ tilt re-directs light into on- or off-states. Without modifying TIDMD, but with employing a nano-second pulse illumination synchronized to the transitional movement of micromirrors between the of- and off-states turns DMD into a diffractive beam and image steering device.
Human interleukin 4. (1991)

Human IL-4 is a mature 129 AA glycoprotein, mostly secreted by activated T cells. It is a pleiotropic cytokine which acts on T and B lymphocytes, monocytes, polymorphonuclear cells, fibroblasts and endothelial cells. In addition it acts at various stages of cell differentiation and its effects are also dependent on the cytokine environment. In particular, IL-4 blocks some of the effects of IL-2 whereas interferon gamma blocks some of the effects of IL-4. In vitro and in vivo experiments in mouse and in vitro experiments in man have shown that IL-4 plays a crucial role in the induction of IgE production, whereas interferons counteract this effect. Human IL-4 binds to a high affinity receptor which is composed at least of one 130-kDa glycoprotein of 800 AA, a member of the newly described hematopoietin receptor superfamily. IL-4 may prove useful as an antitumoral and antiinflammatory agent.
Pre-clinical Safety and Off-Target Studies to Support Translation of AAV-Mediated RNAi Therapy for FSHD (2017)

RNAi emerged as a prospective molecular therapy nearly 15 years ago. Since then, two major RNAi platforms have been under development: oligonucleotides and gene therapy. Oligonucleotide-based approaches have seen more advancement, with some promising therapies that may soon reach market. In contrast, vector-based approaches for RNAi therapy have remained largely in the pre-clinical realm, with limited clinical safety and efficacy data to date. We are developing a gene therapy approach to treat the autosomal-dominant disorder facioscapulohumeral muscular dystrophy. Our strategy involves silencing the myotoxic gene <i>DUX4</i> using adeno-associated viral vectors to deliver targeted microRNA expression cassettes (miDUX4s). We previously demonstrated proof of concept for this approach in mice, and we are now taking additional steps here to assess safety issues related to miDUX4 overexpression and sequence-specific off-target silencing. In this study, we describe improvements in vector design and expansion of our miDUX4 sequence repertoire and report differential toxicity elicited by two miDUX4 sequences, of which one was toxic and the other was not. This study provides important data to help advance our goal of translating RNAi gene therapy for facioscapulohumeral muscular dystrophy.