gebhart/patrepeval huggingface dataset:
Snow Water Equivalent of Dry Snow Derived From GNSS Carrier Phases (2018)

Snow water equivalent (SWE) is a key variable for various hydrological applications. It is defined as the depth of water that would result upon complete melting of a mass of snow. However, until now, continuous measurements of the SWE are either scarce, expensive, labor-intense, or lack temporal or spatial resolution especially in mountainous and remote regions. We derive the SWE for dry-snow conditions using carrier phase measurements from the Global Navigation Satellite System (GNSS) receivers. Two static GNSS receivers are used, whereby one antenna is placed below the snow and the other antenna is placed above the snow. The carrier phase measurements of both receivers are combined in double differences (DDs) to eliminate clock offsets and phase biases and to mitigate atmospheric errors. Each DD carrier phase measurement depends on the relative position between both antennas, an integer ambiguity due to the periodic nature of the carrier phase signal, and the SWE projected into the direction of incidence. The relative positions of the antennas are determined under snow-free conditions with millimeter accuracy using real-time kinematic positioning. Subsequently, the SWE and carrier phase integer ambiguities are jointly estimated with an integer least-squares estimator. We tested our method at an Alpine test site in Switzerland during the dry-snow season 2015-2016. The SWE derived solely by the GNSS shows very high correlation with conventionally measured snow pillow (root mean square error: 11 mm) and manual snow pit data. This method can be applied to dense low-cost GNSS receiver networks to improve the spatial and temporal information on snow.
Vibrational relaxation in the A1A′(1B1) electronic state of 4-methyl-1,2,4-triazoline-3,5-dione (1974)

The fluorescence decay rate from selected vibronic levels of the A1A′(1B1) excited electronic state of 4-methyl-1,2,4-triazoline-3,5-dione has been examined as a function of added inert gas pressure. A simple, physically reasonable model is presented from which vibrational relaxation rates may be explicitly determined. The relaxation rate constants have been found to be 6.3×105 Torr−1 sec−1 for collisions with helium, 7×105 Torr−1 sec−1 for argon, 2.5×106 Torr−1 sec−1 for CCl4, 15×105 Torr−1 sec−1 for O2, and 75×105 Torr−1 sec−1 for cyclohexane.
How do Lyme Borrelia Organisms Cause Disease? The Quest for Virulence Determinants (2012)

Lyme disease Borrelia are invasive, nontoxigenic, persistent pathogens, and little is known about their mechanisms of pathogenesis. In our laboratory, a signature-tagged mutagenesis (STM) library of over 4,000 Borrelia burgdorferi transposon mutants has been constructed and is being screened for infectivity in mice. In this manner, a global view of the virulence determinants (factors required for full infectivity) is being developed. Additionally, the mechanisms of immune evasion involving the VMP-like system (vls) are under analysis, and cryo-electron microscopy is providing a detailed view of the three-dimensional structure of B. burgdorferi. These approaches will contribute to the improved understanding of how Lyme disease Borrelia cause disease.
Aromatic Cytokinin Arabinosides Promote PAMP-like Responses and Positively Regulate Leaf Longevity (2020)

Cytokinins are plant hormones with biological functions ranging from coordination of plant growth to the regulation of biotic and abiotic stress-related responses and senescence. The components of the plant immune system can learn from past elicitations by microbial pathogens and herbivores and adapt to new threats. It is known that plants can enter the primed state of enhanced defense induced by either natural or synthetic compounds. While the involvement of cytokinins in defense priming has been documented, no comprehensive model of their action has been provided to date. Here, we report the functional characterization of two aromatic cytokinin derivatives, 6-benzylaminopurine-9-arabinosides (BAPAs), 3-methoxy-BAPA and 3-hydroxy-BAPA, that proved to be effective in delaying senescence in detached leaves while having low interactions with the cytokinin pathway. An RNA-seq profiling study on <i>Arabidopsis</i> leaves treated with 3-methoxy-BAPA revealed that short and extended treatments with this compound shifted the transcriptional response markedly toward defense. Both treatments revealed upregulation of genes involved in processes associated with plant innate immunity such as cell wall remodeling and upregulation of specific MAP kinases, most importantly <i>MPK11</i>, which is a MAPK module involved in stress-related signaling during the pathogen-associated molecular patterns (PAMPs) response. In addition, elevated levels of JA and its metabolites, jasmonate/ethylene-driven upregulation of <i>PLANT DEFENSIN 1.2</i> (<i>PDF1.2</i>) and other defensins, and also temporarily elevated levels of reactive oxygen species marked the plant response to 3-methoxy-BAPA treatment. Synergistic interactions were observed when plants were cotreated with 3-hydroxy-BAPA and the flagellin-derived bacterial PAMP peptide (flg22), leading to the enhanced expression of the PAMP-triggered immunity (PTI) marker gene <i>FRK1</i>. Our data collectively show that some BAPAs can sensitively prime the PTI responses in a low micromolar range of concentrations while having no observable negative effects on the overall fitness of the plant.
Quantifying identifiability to choose and audit $\epsilon$ in differentially private deep learning (2021)

Differential privacy allows bounding the influence that training data records have on a machine learning model. To use differential privacy in machine learning, data scientists must choose privacy parameters $(\epsilon,\delta)$. Choosing meaningful privacy parameters is key, since models trained with weak privacy parameters might result in excessive privacy leakage, while strong privacy parameters might overly degrade model utility. However, privacy parameter values are difficult to choose for two main reasons. First, the theoretical upper bound on privacy loss $(\epsilon,\delta)$ might be loose, depending on the chosen sensitivity and data distribution of practical datasets. Second, legal requirements and societal norms for anonymization often refer to individual identifiability, to which $(\epsilon,\delta)$ are only indirectly related. We transform $(\epsilon,\delta)$ to a bound on the Bayesian posterior belief of the adversary assumed by differential privacy concerning the presence of any record in the training dataset. The bound holds for multidimensional queries under composition, and we show that it can be tight in practice. Furthermore, we derive an identifiability bound, which relates the adversary assumed in differential privacy to previous work on membership inference adversaries. We formulate an implementation of this differential privacy adversary that allows data scientists to audit model training and compute empirical identifiability scores and empirical $(\epsilon,\delta)$.
Cytochrome c conformations resolved by the photon counting histogram: Watching the alkaline transition with single-molecule sensitivity (2005)

We apply the photon counting histogram (PCH) model, a fluorescence technique with single-molecule sensitivity, to study pH-induced conformational changes of cytochrome c. PCH is able to distinguish different protein conformations based on the brightness of a fluorophore sensitive to its local environment. We label cytochrome c through its single free cysteine with tetramethylrhodamine-5-maleimide (TMR), a fluorophore with specific brightnesses that we associate with specific protein conformations. Ensemble measurements demonstrate two different fluorescence responses with increasing pH: (i) a decrease in fluorescence intensity caused by the alkaline transition of cytochrome c (pH 7.0-9.5), and (ii) an increase in intensity when the protein unfolds (pH 9.5-10.8). The magnitudes of these two responses depend strongly on the molar ratio of TMR used to label cytochrome c. Using PCH we determine that this effect arises from the proportion of a nonfunctional conformation in the sample, which can be differentiated from the functional conformation. We further determine the causes of each ensemble fluorescence response: (i) during the alkaline transition, the fluorophore enters a dark state and discrete conformations are observed, and (ii) as cytochrome c unfolds, the fluorophore incrementally brightens, but discrete conformations are no longer resolved. Moreover, we also show that functional TMR-cytochrome c undergoes a response of identical magnitude regardless of the proportion of nonfunctional protein in the sample. As expected for a technique with single-molecule sensitivity, we demonstrate that PCH can directly observe the most relevant conformation, unlike ensemble fluorometry.
Aggregation and Fibrillation Study of .ALPHA.-synuclein Under Applied Voltage (2008)

The application of voltage has been used to control the movement of charged molecule such as DNA, some proteins and phospholipid in recent year. In this study, we first applied voltage to amyloidogenic protein, α-synuclein, which is related to Parkinson’s disease. To offer the new approach using electric field and new insight into aggregation and fibrillation mechanism of α-synuclein, we tried to control the aggregation of α-synuclein, which has a negative charge, by applying voltage to it. The aggregation of α-synuclein without conformational change occurred rapidly when a voltage of 1 V was applied. The protein did not form amyloid-like fibrils, but it did form small aggregates. These results demonstrate that this technique might be useful not only to efficiently control aggregation of α-syn but also to understand the mechanism of aggregation and fibrillation of α-syn.
Mitochondrial dysfunction and neurodegeneration in multiple sclerosis (2013)

Multiple sclerosis (MS) has traditionally been considered an autoimmune inflammatory disorder leading to demyelination and clinical debilitation as evidenced by our current standard anti-inflammatory and immunosuppressive treatment regimens. While these approaches do control the frequency of clinical relapses, they do not prevent the progressive functional decline that plagues many people with MS. Many avenues of research indicate that a neurodegenerative process may also play a significant role in MS from the early stages of disease, and one of the current hypotheses identifies mitochondrial dysfunction as a key contributing mechanism. We have hypothesized that pathological permeability transition pore (PTP) opening mediated by reactive oxygen species (ROS) and calcium dysregulation is central to mitochondrial dysfunction and neurodegeneration in MS. This focused review highlights recent evidence supporting this hypothesis, with particular emphasis on our in vitro and in vivo work with the mitochondria-targeted redox enzyme p66ShcA.
Maritime hyperspectral imaging and coastal bathymetry from space (2005)

Spaceborne maritime hyperspectral imagery promises to be a powerful technique for the retrieval of coastal bathymetry and other environmental parameters worldwide. In hyperspectral imaging, a contiguous spectrum of the light leaving each ground sample is recorded. Bathymetry retrievals are performed by modeling the water-leaving spectral radiance of sunlight scattered by the water column and bottom, and matching the modeled data to the measured spectra. This can be done using a look-up-table (LUT) in which modeled spectra are stored for many combinations of water and bottom parameters, which are then searched to find the modeled spectrum that best matches the measured data for each ground sample. This method is applied to 4 m resolution airborne hyperspectral imagery of the Indian River Lagoon in Florida, and the retrieved bathymetry is compared to 30 m resolution ground validation data. LUT bathymetry retrievals for regions identified as a having uniform bottom type correlated well with measured bathymetry to a depth of 5 m. These preliminary results suggest that the LUT method has the potential for accurate bathymetry determination from space.
Multi-shaped beam proof of lithography (2010)

In this paper a full package high throughput multi electron-beam approach, called Multi Shaped Beam (MSB), for applications in mask making as well as direct write will be presented including complex proof-of-lithography results. The basic concept enables a significant exposure shot count reduction for advanced patterns compared to standard Variable Shaped Beam (VSB) systems and allows full pattern flexibility by concurrently using MSB, VSB and Cell Projection (CP). Proof of lithography results will be presented, which have been performed using a fully operational electron-beam lithography system including data path and substrate scanning by x/y-stage movement.
Increased activity of mitochondrial respiratory chain complex in noise-damaged rat cochlea (2012)

The hearing threshold level changed depending on the exposure time in both the noise-exposed groups. In the 1 h group, hearing was improved after 1 day, and in the 5 h group, hearing was measured after 7 days. Changes in SDH activity were observed at the third day in the 1 h group and at the seventh day in the 5 h group. The expression level of MRC complex V was increased after noise exposure. TEM showed mitochondrial damage.
Formal [4 + 2] Cycloaddition Reactions of N‐Sulfonyl‐2,2′‐biindoles: Synthesis of Indolo[2,3‐a]carbazoles and Indigo Azines. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Killer cells: lytic signalling pathways and regulation (2004)

Les cellules de l’immunite a mediation cellulaire, lymphocytes T et cellules tueuses naturelles (NK), jouent un role cle dans la reponse de l’hote contre les agents infectieux et les cellules tumorales. Les strategies anti-tumorales se fondent, pour la plupart, sur le caractere immunogene de la tumeur et de l’activation de la reponse lymphocytaire T specifique. Cependant, cette reponse immunitaire n’est pas toujours suffisamment efficace pour prevenir l’apparition et limiter la croissance des tumeurs. Les cellules cancereuses sont alors tolerees par le systeme immunitaire. L’echappement tumoral a l’immunosurveillance concerne a la fois la cellule tumorale mais egalement le systeme immunitaire et implique differents mecanismes : la voie perforine/granzymes et la voie des recepteurs a domaines de mort. Une meilleure comprehension de ces mecanismes de tolerance est un defi majeur pour faire progresser l’immunotherapie.
Crystalline linkage and defect structures in bulk zone melt textured YBa2Cu3O7 observed by transmission electron microscopy (1993)

The microstructural features of zone melt textured wires of YBa2Cu3O7 (123) with and without additions of Y2BaCuO5 have been examined by transmission electron microscopy. The 123 phase is observed to form well aligned platelets, which are of limited extent along [001], but extremely long in the perpendicular directions. Although platelet boundaries are wetted by a second phase, junctions are commonly observed to interconnect the plates. This suggests the possibility that the wires are actually highly defective single crystals. High densities of stacking faults are also observed, particularly at Y2BaCuO5/YBa2Cu3O7 interfaces and at dislocation arrays. It is suggested that these result from a drive for phase conversion to YBa2Cu4O8, and that they may be associated with flux pinning.
Magnetic Nanoparticles: Design and Characterization, Toxicity and Biocompatibility, Pharmaceutical and Biomedical Applications (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMagnetic Nanoparticles: Design and Characterization, Toxicity and Biocompatibility, Pharmaceutical and Biomedical ApplicationsL. Harivardhan Reddy†‡, José L. Arias§, Julien Nicolas†, and Patrick Couvreur*†View Author Information† Laboratoire de Physico-Chimie, Pharmacotechnie et Biopharmacie, Université Paris-Sud XI, UMR CNRS 8612, Faculté de Pharmacie, IFR 141, 5 rue Jean-Baptiste Clément, F-92296 Châtenay-Malabry, France§ Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Campus Universitario de Cartuja s/n, Universidad de Granada, 18071 Granada, Spain‡ Pharmaceutical Sciences Department, Sanofi, 13 Quai Jules Guesdes, F-94403 Vitry-sur-Seine, France*Phone: (+33) 1 46 83 53 96. Fax: (+33) 1 46 61 93 34. E-mail: [email protected]Cite this: Chem. Rev. 2012, 112, 11, 5818–5878Publication Date (Web):October 9, 2012Publication History Received16 February 2012Published online9 October 2012Published inissue 14 November 2012https://pubs.acs.org/doi/10.1021/cr300068phttps://doi.org/10.1021/cr300068preview-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views42314Altmetric-Citations1697LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Anatomy,Cells,Magnetic properties,Nanoparticles,Tumors Get e-Alerts
Limited Cross-Protection Provided by Prior Infection Contributes to High Prevalence of Influenza D Viruses in Cattle (2020)

Since its detection in swine, influenza D virus (IDV) has been shown to be present in multiple animal hosts, and bovines have been identified as its natural reservoir. However, it remains unclear how IDVs emerge, evolve, spread, and maintain in bovine populations. Through multiple years of virological and serological surveillance in a single order-buyer cattle facility in Mississippi, we showed consistently high seroprevalence of IDVs in cattle and recovered a total of 32 IDV isolates from both healthy and sick animals, including those with antibodies against IDV. Genomic analyses of these isolates along with those isolated from other areas showed that active genetic reassortment occurred in IDV and that five reassortants were identified in the Mississippian facility. Two antigenic groups were identified through antigenic cartography analyses for these 32 isolates and representative IDVs from other areas. Remarkably, existing antibodies could not protect cattle from experimental reinfection with IDV. Additional phenotypic analyses demonstrated variations in growth dynamics and pathogenesis in mice between viruses independent of genomic constellation. In summary, this study suggests that, in addition to epidemiological factors, the ineffectiveness of preexisting immunity and cocirculation of a diverse viral genetic pool could facilitate its high prevalence in animal populations.<b>IMPORTANCE</b> Influenza D viruses (IDVs) are panzootic in multiple animal hosts, but the underlying mechanism is unclear. Through multiple years of surveillance in the same order-buyer cattle facility, 32 IDV isolates were recovered from both healthy and sick animals, including those with evident antibodies against IDV. Active reassortment occurred in the cattle within this facility and in those across other areas, and multiple reassortants cocirculated in animals. These isolates are shown with a large extent of phenotypic diversity in replication efficiency and pathogenesis but little in antigenic properties. Animal experiments demonstrated that existing antibodies could not protect cattle from experimental reinfection with IDV. This study suggests that, in addition to epidemiological factors, limited protection from preexisting immunity against IDVs in cattle herds and cocirculation of a diverse viral genetic pool likely facilitate the high prevalence of IDVs in animal populations.
Electrical stimulation of gut motility guided by anin silicomodel (2017)

This work demonstrates an in silico GI neuromuscular model to enable GI neuromodulation parameter optimization and suggests that low frequency sinusoidal currents may improve the efficacy of GI pacing.
Real-world flash glucose monitoring patterns and associations between self-monitoring frequency and glycaemic measures: A European analysis of over 60 million glucose tests (2017)

In real-world conditions, flash glucose monitoring allows frequent glucose checks with higher rates of scanning linked to improved glycaemic markers, including increased time in range and reduced time in hyper and hypoglycaemia.
Novel strategies for liver therapy using stem cells (2014)

TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
High Mutability of the Tumor Suppressor Genes RASSF1 and RBSP3 (CTDSPL) in Cancer (2009)

This is the first report of high frequencies of somatic mutations in RASSF1 and RBSP3 in different cancers suggesting it may underlay the mutator phenotype of cancer. Somatic hypermutations in tumor suppressor genes involved in major human malignancies offer a novel insight in cancer development, progression and spread.
Accurate tracking of tumor volume change during radiotherapy by CT-CBCT registration with intensity correction (2016)

In this paper, we propose a CT-CBCT registration method to accurately predict the tumor volume change based on daily cone-beam CTs (CBCTs) during radiotherapy. CBCT is commonly used to reduce patient setup error during radiotherapy, but its poor image quality impedes accurate monitoring of anatomical changes. Although physician’s contours drawn on the planning CT can be automatically propagated to daily CBCTs by deformable image registration (DIR), artifacts in CBCT often cause undesirable errors. To improve the accuracy of the registration-based segmentation, we developed a DIR method that iteratively corrects CBCT intensities by local histogram matching. Three popular DIR algorithms (B-spline, demons, and optical flow) with the intensity correction were implemented on a graphics processing unit for efficient computation. We evaluated their performances on six head and neck (HN) cancer cases. For each case, four trained scientists manually contoured the nodal gross tumor volume (GTV) on the planning CT and every other fraction CBCTs to which the propagated GTV contours by DIR were compared. The performance was also compared with commercial image registration software based on conventional mutual information (MI), VelocityAI (Varian Medical Systems Inc.). The volume differences (mean±std in cc) between the average of the manual segmentations and automatic segmentations are 3.70&plusmn;2.30 (B-spline), 1.25&plusmn;1.78 (demons), 0.93&plusmn;1.14 (optical flow), and 4.39&plusmn;3.86 (VelocityAI). The proposed method significantly reduced the estimation error by 9% (B-spline), 38% (demons), and 51% (optical flow) over the results using VelocityAI. Although demonstrated only on HN nodal GTVs, the results imply that the proposed method can produce improved segmentation of other critical structures over conventional methods.