gebhart/patrepeval huggingface dataset:
Correlated Components Analysis - Extracting Reliable Dimensions in Multivariate Data (2019)

How does one find dimensions in multivariate data that are reliably expressed across repetitions? For example, in a brain imaging study one may want to identify combinations of neural signals that are reliably expressed across multiple trials or subjects. For a behavioral assessment with multiple ratings, one may want to identify an aggregate score that is reliably reproduced across raters. Correlated Components Analysis (CorrCA) addresses this problem by identifying components that are maximally correlated between repetitions (e.g. trials, subjects, raters). Here we formalize this as the maximization of the ratio of between-repetition to within-repetition covariance. We show that this criterion maximizes repeat-reliability, defined as mean over variance across repeats, and that it leads to CorrCA or to multi-set Canonical Correlation Analysis, depending on the constraints. Surprisingly, we also find that CorrCA is equivalent to Linear Discriminant Analysis for zero-mean signals, which provides an unexpected link between classic concepts of multivariate analysis. We present an exact parametric test of statistical significance based on the F-statistic for normally distributed independent samples, and present and validate shuffle statistics for the case of dependent samples. Regularization and extension to non-linear mappings using kernels are also presented. The algorithms are demonstrated on a series of data analysis applications, and we provide all code and data required to reproduce the results.
Comparison of Adaptive Neuro-Fuzzy Inference Systems and Echo State Networks for PV Power Prediction (2015)

Use of photo-voltaic (PV) power as a source of electricity has been rapidly growing. Integration of large PV power into the grid operation introduces several challenges. Uncertainty of PV power generation causes frequency fluctuations and power system instabilities. Due to this, short term PV power prediction has become an important area of study. Short term PV power prediction supports proper decision-making in control centers. Power generation output of a PV plant is highly dependent on different weather conditions such as solar irradiance, temperature and cloud covers. Weather data analysis and prediction can be considered as big data due to its complexity and dynamically changing characteristics. In this paper, an adaptive neuro-fuzzy inference system (ANFIS) is developed and compared with an echo state network (ESN) for short term PV power prediction. The ANFIS approach consists of three ANFIS modules for predicting solar irradiance and temperature, and then estimating the PV power, respectively. The ESN on the other hand predicts the PV power based on current weather parameters. A weather database containing data sampled every second is used in developing the ANFIS and ESN based PV power prediction systems. Results are compared under different Clemson, SC weather conditions with the two approaches.
Gravity‐Independent Grain Size Segregation in Experimental Granular Shear Flows as a Mechanism of Layer Formation (2018)

Abstract Fine grain bands in faults are normally interpreted as indicative of slip localization. However, grains can migrate systematically during shear resulting in nonintuitive effects on the final structure. Here we report the results of shear experiments performed on natural granular materials and discuss their possible implications for natural shear systems. We sheared dry grains in a rheometer over a range of velocities, followed the structural evolution with video during shear, and characterized the final structures. Fine particles comminuted during high‐velocity shear migrated from the highest shear rate regions to a layer where shear rate is near zero. This migration is an example of shear segregation that is driven by grain‐inertia effects. The segregation forms an apparent shear band displaced from the principal slip surface and has a stabilizing effect on subsequent flow. This shear segregation may result in fine‐particle layers and slip localization in natural shear zones.
Le paysage visible de la promenade des Anglais à Nice : essai de cartographie dynamique (2007)

International audience
Peptide Mimicry of the Polysaccharide Capsule ofCryptococcus neoformans (2014)

Organisms that possess a polysaccharide capsule, such as Streptococcus pneumoniae, Haemophilus influenzae type b, Neisseria meningitidis, and Cryptococcus neoformans, are extremely important clinically because they are responsible for a majority of serious infections and for most deaths from meningitis. The reasons for searching for a peptide mimic of a carbohydrate structure are many-fold. In comparison to peptide chemistry, which is well-defined and relatively easy to manipulate, carbohydrate chemistry is more complex. C. neoformans is an environmentally ubiquitous encapsulated yeast that causes a life-threatening meningoencephalitis in 8% of AIDS patients in the United States and as many as 30% of HIV-infected people in Africa; it is the most common cause of central nervous system infections in New York City. Peptide binding monoclonal antibodies (MAbs) were obtained from mice immunized with P601E with the hope that their molecular structure would provide an explanation as to why they did not bind to glucuronoxylomannan (GXM). The antibody binding site of MAb 2H1 is a hydrophobic pocket delimited by CDR2 and CDR3 of the heavy chain and CDR1 and CDR3 of the light chain. The crystal structure of one of the peptides bound to MAb 2H1, combined with the molecular structure of the antipeptide MAbs elicited by another one of the peptides, provided a clue as to why our peptides were not good mimotopes. The 2H1 antibody does not change its conformation when it interacts with the peptide mimic, making it unlikely that changes in the site occur when it interacts with GXM.
Osteomyelitis Associated With Pressure Sores (1994)

Clinical evaluation for osteomyelitis is often inaccurate. Pathologic examination of bone tissue is required for definitive diagnosis of osteomyelitis. Quantitative bone cultures do not help differentiate osteomyelitis from infection or colonization of adjacent soft tissue. It is possible that treatment of osteomyelitis may improve the outcome of associated pressure sores.
Patient-derived cancer organoid tracking with wide-field one-photon redox imaging to assess treatment response (2021)

Wide-field one-photon redox imaging can monitor metabolic and morphological changes on a single organoid-level, providing an accessible, non-destructive tool to screen drugs in patient-matched samples.
Long-lived tissue resident HIV-1 specific memory CD8+ T cells are generated by skin immunization with live virus vectored microneedle arrays (2017)

The generation of tissue resident memory (T<sub>RM</sub>) cells at the body surfaces to provide a front line defence against invading pathogens represents an important goal in vaccine development for a wide variety of pathogens. It has been widely assumed that local vaccine delivery to the mucosae is necessary to achieve that aim. Here we characterise a novel micro-needle array (MA) delivery system fabricated to deliver a live recombinant human adenovirus type 5 vaccine vector (AdHu5) encoding HIV-1 gag. We demonstrate rapid dissolution kinetics of the microneedles in skin. Moreover, a consequence of MA vaccine cargo release was the generation of long-lived antigen-specific CD8<sup>+</sup> T cells that accumulate in mucosal tissues, including the female genital and respiratory tract. The memory CD8<sup>+</sup> T cell population maintained in the peripheral mucosal tissues was attributable to a MA delivered AdHu5 vaccine instructing CD8<sup>+</sup> T cell expression of CXCR3<sup>+</sup>, CD103<sup>+,</sup> CD49a<sup>+</sup>, CD69<sup>+</sup>, CD127<sup>+</sup> homing, retention and survival markers. Furthermore, memory CD8<sup>+</sup> T cells generated by MA immunization significantly expanded upon locally administered antigenic challenge and showed a predominant poly-functional profile producing high levels of IFNγ and Granzyme B. These data demonstrate that skin vaccine delivery using microneedle technology induces mobilization of long lived, poly-functional CD8<sup>+</sup> T cells to peripheral tissues, phenotypically displaying hallmarks of residency and yields new insights into how to design and deliver effective vaccine candidates with properties to exert local immunosurveillance at the mucosal surfaces.
Learning innovation at scale (2014)

The rapid developments in online education raise new issues for the future of learning and universities, practical questions about what counts as good design, and new opportunities for research. This workshop brings together practitioners, learning platform innovators, and researchers who draw on a multi-disciplinary range of theory and methodology. We will share insights about the current state and next directions for research and practice in online learning and technology.
Plasmonic Photovoltaic and Photonic Switching Devices (2008)

Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text H. Atwater, "Plasmonic Photovoltaic and Photonic Switching Devices," in Frontiers in Optics 2008/Laser Science XXIV/Plasmonics and Metamaterials/Optical Fabrication and Testing, OSA Technical Digest (CD) (Optica Publishing Group, 2008), paper MThD1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Adapting the Ceramics Process with Creative Problem-Solving (2021)

Madeline Kaczmarczyk, a ceramics sculptor based in Rockford, MI, provided the cover art for the Fall 2021 edition of The Open Journal of Occupational Therapy (OJOT). The piece is a wall vase made from clay, luster glaze, and glass beads. Madeline has been creating decorative ceramics for over four decades. In recent years, Madeline has found creative ways to adapt the ceramics process so she can continue creating beautiful works of art. For Madeline, ceramics is more than a means to make a living. This meaningful activity brings focus to her life.
Supplementary Figure S1 from Circulating Mitochondrial DNA Level, a Noninvasive Biomarker for the Early Detection of Gastric Cancer (2023)

&lt;p&gt;Supplementary Figure S1 : Effect of H. pylori infection on the levels of mtDNA in leukocytes of NAG and GC spatients as compared to healthy blood donors in cohort 1. MtDNA was determined by quantitaive PCR and the presence of H. pylori infection by serology as described in material and methods. H. pylori infected patients are represented in black symbols and non-infected in gray symbols. Each symbol represents a single patient, bars correspond to mean{plus minus}SEM. Each samples was tested in triplicate in three independent experiments. *p-value&lt;0.05; ***p-value&lt;0.001.&lt;/p&gt;
Speckle reduction in digital holography with resampling ring masks (2018)

One-shot digital holographic imaging has the advantages of high stability and low temporal cost. However, the reconstruction is affected by the speckle noise. Resampling ring-mask method in spectrum domain is proposed for speckle reduction. The useful spectrum of one hologram is divided into several sub-spectra by ring masks. In the reconstruction, angular spectrum transform is applied to guarantee the calculation accuracy which has no approximation. N reconstructed amplitude images are calculated from the corresponding sub-spectra. Thanks to speckle’s random distribution, superimposing these N uncorrelated amplitude images would lead to a final reconstructed image with lower speckle noise. Normalized relative standard deviation values of the reconstructed image are used to evaluate the reduction of speckle. Effect of the method on the spatial resolution of the reconstructed image is also quantitatively evaluated. Experimental and simulation results prove the feasibility and effectiveness of the proposed method.
A Phase 1 Dose-Escalation Study of the Novel Cell Cycle Active Agent SNS-595 in Advanced Leukemias. (2006)

Abstract SNS-595 is a novel, cell cycle active cytotoxic naphthyridine analog that induces G2 arrest in a variety of preclinical tumor models. We initiated an escalating-dose phase 1 trial of SNS-595, administered as a weekly x 3 (arm A) or twice weekly x 2 bolus (arm B), in patients with advanced or refractory acute leukemias. Objectives: The primary objectives were to:establish safety, tolerability, and MTD of SNS-595 given on each schedule,characterize pharmacokinetics (PK) of SNS-595 when given on these schedules. Secondary objectives were:assessment of clinical activity,exploration of potential biomarkers. Methods: SNS-595 was administered as a slow IV push on days 1, 8, 15 (arm A) or days 1, 4, 8, 11 (arm B). Minimum cycle length was 42 days (arm A) and 39 days (arm B). Additional cycles were permitted if patients achieved stable disease or better. The starting dose was 18 mg/m2/d on arm A, and 9 mg/m2/d on arm B and escalated by cohort using a modified Fibonacci schema. PK analyses for SNS-595 were performed on plasma samples collected during cycle 1. Pretreatment peripheral blood and bone marrow aspirate samples were collected for exploratory analyses of the level and functional activity of the DNA damage repair proteins DNA-PK and MSH2. Results: To date, 21 patients have been enrolled and are evaluable in the live database, including 13 patients assigned to arm A and 8 assigned to arm B, 12 males and 9 females with a median age of 64 years. Diagnoses included AML (19 patients) and ALL (2 patients). All patients had disease refractory to or relapsed from prior therapy (median 3 prior regimens (range 1–6)). Dose escalation has proceeded to 50 mg/m2/d (arm A) and 19 mg/m2/d (arm B). No dose-limiting toxicities have been observed to date. Non-dose limiting toxicities included nausea/vomiting, diarrhea, and mucositis . Grade 4 neutropenic fever was observed in only one patient. Plasma exposures at the first two dose levels in each arm increased linearly, resulting in AUCs of 5.5 – 17.8 ughr/mL for 9–27 mg/m2 doses. CL, Vss, and terminal half-lives were similar to those reported previously in solid tumor patients, and averaged ~2 L/hr/m2, 58 L/m2, and 23 hr, respectively. No patients have achieved complete response to date, although 6 patients (distributed across all dosing groups) experienced &gt;50% reductions in peripheral blasts following cycle 1. Conclusion: SNS-595 appears to be well-tolerated in patients with advanced leukemias, with preliminary and promising signs of clinical activity as measured by decreases in leukemic blasts. Bone marrow ablation has not yet been achieved; patient accrual and dose-escalation are ongoing.
The neurotrophins and CNTF: specificity of action towards PNS and CNS neurons. (1991)

The availability of relatively large amounts of nerve growth factor (NGF) has allowed extensive in vitro and in vivo characterization of the neuronal specificity of this neurotrophic factor. The restricted neuronal specificity of NGF (sympathetic neurons, neural crest-derived sensory neurons, basal forebrain cholinergic neurons) has long predicted the existence of other neurotrophic factors possessing different neuronal specificities. Whereas there have been many reports of activities distinct from NGF, full characterization of such molecules has been hampered by their extremely low abundance. The recent molecular cloning of brain-derived neurotrophic factor (BDNF) revealed that this protein is closely related to NGF and suggested that these two factors might be members of an even larger gene family. A PCR cloning strategy based on homologies between NGF and BDNF has allowed us to identify and clone a third member of the NGF family which we have termed neurotrophin-3 (NT-3). The establishment of suitable expression systems has now made available sufficient quantities of these proteins to allow us to begin to establish the neuronal specificity of each member of the neurotrophin family, and the role of each in development, maintenance and repair of the PNS and CNS. Using primary cultures of various PNS and CNS regions of the developing chick and rat, and Northern blot analysis, we describe novel neuronal specificities of BDNF, NT-3 and an unrelated neurotrophic factor-ciliary neurotrophic factor (CNTF).
ChemInform Abstract: Concise Total Synthesis of Cruentaren A. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
PD32-06 THE ROLE OF PRESEPSIN AS PREDICTIVE FACTOR FOR SEPSIS IN PATIENTS WITH URINARY TRACT INFECTION ASSOCIATED WITH URINARY CALCULI (2022)

You have accessJournal of UrologyCME1 May 2022PD32-06 THE ROLE OF PRESEPSIN AS PREDICTIVE FACTOR FOR SEPSIS IN PATIENTS WITH URINARY TRACT INFECTION ASSOCIATED WITH URINARY CALCULI Yeong Uk Kim, Jong Gyun Ha, Jae Youn Jang, Jae Young Choi, Young Hwii Ko, Phil Hyun Song, Ki Hak Moon, and Hee Chang Jung Yeong Uk KimYeong Uk Kim More articles by this author , Jong Gyun HaJong Gyun Ha More articles by this author , Jae Youn JangJae Youn Jang More articles by this author , Jae Young ChoiJae Young Choi More articles by this author , Young Hwii KoYoung Hwii Ko More articles by this author , Phil Hyun SongPhil Hyun Song More articles by this author , Ki Hak MoonKi Hak Moon More articles by this author , and Hee Chang JungHee Chang Jung More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002583.06AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail WITHDRAWN © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e548 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information Yeong Uk Kim More articles by this author Jong Gyun Ha More articles by this author Jae Youn Jang More articles by this author Jae Young Choi More articles by this author Young Hwii Ko More articles by this author Phil Hyun Song More articles by this author Ki Hak Moon More articles by this author Hee Chang Jung More articles by this author Expand All Advertisement PDF DownloadLoading ...
Fiber Optic Sensors for Biomedical Applications (2008)

Biomedicine is surely the area where the optical fibre sensors can play an important role. Thanks to their potential miniaturisation and their easy handling they are offering unique performances in invasive or minimally invasive applications. The immunity to electromagnetic interference and the absence of electrical contact make the optical fibres useful also in the case of non invasive applications for the setting of the interrogation optoelectronic unit in a safer location, keeping only the sensing element close to the patients bedside. As a matter of fact, there are many optical fibre sensors designed for biomedical applications and described in the literature, but the greater part of them stops at the prototype level, without entering the hospital. The clinical validation, which is the necessary step after the characterisation of the laboratory prototype, is often an insurmountable obstacle due to the requirements of compliance with the European Directives on Medical Devices or with the regulations of the Food and Drug Administration. The strategy followed for the clinical validation in the case of optical fibre sensors developed at the Institute of Applied Physics for the detection of bile-containing refluxes, gastric carbon dioxide and interstitial pH is described. An example for potential non-invasive applications in point of care testing is also given with a novel optical platform for the interrogation of optical biochips.
Lack of Association between Mannose Binding Lectin and Antibody Responses after Acellular Pertussis Vaccinations (2014)

This study indicates that MBL polymorphisms do not affect the production and persistence of antibodies after acellular pertussis vaccination. Our finding also suggests that MBL might not be involved in modulating antibody responses to the vaccines made of purified bacterial proteins.
Platelet Apoptosis Events Can Be Triggered by Shear Stresses and Chemical Agonists. (2005)

Abstract Apoptosis, or programmed cell death, is appreciated as the main physiologic mechanism that regulates cell life-span and serves for controlled deletion of unwanted cells. Since its discovery in 1972, apoptosis was long attributed exclusively to nucleate cells. It took more than 20 years to recognize apoptosis in enucleated cells cytoplasts and anucleate platelets. During the following years, apoptosis has been demonstrated in platelets treated with natural and artificial agonists, in platelet concentrates aged during storage under standard blood banking conditions, and in animal models of suppressed thrombopoiesis and thrombocytopenia. Other studies documented that mechanical forces (shear stresses) stimulate platelet activation and signaling in the absence of exogenous chemical stimuli. We analysed whether shear stresses can trigger platelet apoptosis, a question that has not yet been studied. Using a cone-and-plate viscometer (CAP-2000, Brookfield Engineering Labs, Inc., Middleboro, MA), we exposed human platelet-rich plasma to different shear stresses, ranging from physiologic arterial and arterioles levels (10-44 dynes/cm2) to pathologic high levels (117–388 dynes/cm2) occurring in stenosed coronary, peripheral or cerebral arteries. We found that pathologic shear stresses induce not only platelet activation (P-selectin upregulation and GPIbα downregulation) but also trigger apoptosis events, including mitochondrial transmembrane potential depolarization, caspase 3 activation, phosphatidylserine exposure, and platelet shrinkage and fragmentation into microparticles, whereas physiologic shear stresses are not effective. Platelets subjected to pathologic shear stresses are characterized by impaired platelet function as shown by the absence of ADP-induced platelet aggregation. Apoptosis changes were also induced by the treatment of platelets with calcium ionophore A23187 (10 μM) and thrombin (1 U/mL). Thus, in the present work, we have demonstrated that platelet apoptosis can be induced by chemical stimuli and by mechanical rheological forces (pathologic high shear stresses). Most of shear-induced activation and apoptosis events occur inside of the platelet, including translocation of CD62 from α-granules to the platelet surface, depolarization of mitochondrial inner membrane potential, activation of cytosolic enzyme caspase 3, and translocation of phosphatidylserine from the inner to the outer plasma membrane leaflet. These data suggest that the effects of shear stress on platelet activation and apoptosis are mediated by mechanoreceptor(s) that transmit activation and apoptosis signals to the cell interior. The platelet paradigm of apoptosis induced by chemical agonists and shear stresses suggests that apoptotic cytoplasmic machinery may function without nuclear participation.