gebhart/patrepeval huggingface dataset:
An open-source toolbox for automated phenotyping of mice in behavioral tasks (2014)

Classifying behavior patterns in mouse models of neurological, psychiatric and neurodevelopmental disorders is critical for understanding disease causality and treatment. However, complete characterization of behavior is time-intensive, prone to subjective scoring, and often requires specialized equipment. Although several reports describe automated home-cage monitoring and individual task scoring methods, we report the first open source, comprehensive toolbox for automating the scoring of several common behavior tasks used by the neuroscience community. We show this new toolbox is robust and achieves equal or better consistency when compared to manual scoring methods. We use this toolbox to study the alterations in behavior that occur following blast-induced traumatic brain injury (bTBI), and study if these behavior patterns are altered following genetic deletion of the transcription factor Ets-like kinase 1 (Elk-1). Due to the role of Elk-1 in neuronal survival and proposed role in synaptic plasticity, we hypothesized that Elk-1 deletion would improve some neurobehavioral deficits, while impairing others, following blast exposure. In Elk-1 knockout (KO) animals, deficits in open field, spatial object recognition (SOR) and elevated zero maze performance after blast exposure disappeared, while new significant deficits appeared in spatial and associative memory. These are the first data suggesting a molecular mediator of anxiety deficits following bTBI, and represent the utility of the broad screening tool we developed. More broadly, we envision this open-source toolbox will provide a more consistent and rapid analysis of behavior across many neurological diseases, promoting the rapid discovery of novel pathways mediating disease progression and treatment.
L'oxycombustion pour la valorisation de gaz à bas pouvoir calorifique (2017)

National audience
An Overview Of Evaluations Using Augmented Reality For Assembly Training Tasks (2017)

Augmented Reality (AR) is a strong growing research topic in different training domains such as medicine, sports, military, education and industrial use cases like assembly and maintenance tasks. AR claims to improve the efficiency and skill-transfer of training tasks. This paper gives a comprehensive overview of evaluations using AR for assembly and maintenance training tasks published between 1992 and 2017. We search in a structured way in four different online databases and get 862 results. We select 17 relevant articles focusing on evaluating AR-based training applications for assembly and maintenance tasks. This paper also indicates design guidelines which are necessary for creating a successful application for an AR-based training. We also present five scientific limitations in the field of AR-based training for assembly tasks. Finally, we show our approach to solve current research problems using Design Science Research (DSR).
Repeatability and Reproducibility of ADC Histogram Metrics from the ACRIN 6698 Breast Cancer Therapy Response Trial (2020)

Mean tumor apparent diffusion coefficient (ADC) of breast cancer showed excellent repeatability but only moderate predictive power for breast cancer therapy response in the ACRIN 6698 multicenter imaging trial. Previous single-center studies have shown improved predictive performance for alternative ADC histogram metrics related to low ADC dense tumor volume. Using test/retest (TT/RT) 4 b-value diffusion-weighted imaging acquisitions from pretreatment or early-treatment time-points on 71 ACRIN 6698 patients, we evaluated repeatability for ADC histogram metrics to establish confidence intervals and inform predictive models for future therapy response analysis. Histograms were generated using regions of interest (ROIs) defined separately for TT and RT diffusion-weighted imaging. TT/RT repeatability and intra- and inter-reader reproducibility (on a 20-patient subset) were evaluated using wCV and Bland-Altman limits of agreement for histogram percentiles, low-ADC dense tumor volumes, and fractional volumes (normalized to total histogram volume). Pearson correlation was used to reveal connections between metrics and ROI variability across the sample cohort. Low percentiles (15th and 25th) were highly repeatable and reproducible, wCV < 8.1%, comparable to mean ADC values previously reported. Volumetric metrics had higher wCV values in all cases, with fractional volumes somewhat better but at least 3 times higher than percentile wCVs. These metrics appear most sensitive to ADC changes around a threshold of 1.2 μm<sup>2</sup>/ms. Volumetric results were moderately to strongly correlated with ROI size. In conclusion, Lower histogram percentiles have comparable repeatability to mean ADC, while ADC-thresholded volumetric measures currently have poor repeatability but may benefit from improvements in ROI techniques.
In-vivo continuous monitoring of mixed venous oxygen saturation by photoacoustic transesophageal echocardiography (Conference Presentation) (2016)

Mixed venous oxygen saturation (SvO2), measured from pulmonary arteries, is a gold-standard measure of the dynamic balance between the oxygen supply and demand in the body. In critical care, continuous monitoring of SvO2 plays a vital role in early detection of circulatory shock and guiding goal-oriented resuscitation. In current clinical practice, SvO2 is measured by invasive pulmonary artery catheters (PAC), which are associated with a 10% risk of severe complications. To address the unmet clinical need for a non-invasive SvO2 monitor, we are developing a new technology termed photoacoustic transesophageal echocardiography (PA-TEE). PA-TEE integrates transesophageal echocardiography with photoacoustic oximetry, and enables continuous assessment of SvO2 through an esophageal probe that can be inserted into the body in a minimally invasive manner. We have constructed a clinically translatable PA-TEE prototype, which features a mobile OPO laser, a modified ultrasonography console and a dual-modality esophageal probe. Comprised of a rotatable acoustic array detector, a flexible optical fiber bundle and a light-integrating acoustic lens, the oximetric probe has an outer diameter smaller than 15 mm and will be tolerable for most patients. Through custom-made C++/Qt software, our device acquires and displays ultrasonic and photoacoustic images in real time to guide the deployment of the probe. SvO2 is calculated on-line and updated every second. PA-TEE has now been used to evaluate SvO2 in living swine. Our findings show that changing the fraction of oxygen in the inspired gas modulates SvO2 measured by PA-TEE. Statistic comparison between SvO2 measurements from PA-TEE in vivo the gold-standard laboratorial analysis on blood samples drawn from PACs will be presented.
Deep learning integrates histopathology and proteogenomics at a pan-cancer level (2023)

We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.
Reliability of MIM HAO capacitor for 70NM DRAM (2005)

In order to verify the package reliability of a MIM HAO capacitor module, mass production 256M DDR processes with 0.1 /spl mu/m design rule were adopted. The capacitor dielectrics used were HAH and Hf/sub x/Al/sub y/O/sub z/ and showed Tox.eq of 12/spl Aring/ and Lc of<0.2 fA/cell, respectively. With proper thermal compensation for adjusting the cell Vt, we could get a high probe test yield, and high package yield when a MIM HAO capacitor was introduced instead of an SIS Al/sub 2/O/sub 3/ capacitor. With package samples, the refresh time of the device did not degrade after IR and EFR stresses, and finally, we could confirm the reliability of MIM HAO capacitors at package level through long term operation lifetime testing.
Experimental automatic calibration of a semi-active suspension controller via Bayesian Optimization (2021)

The End-of-Line (EoL) calibration of semi-active suspension systems for road vehicles is usually a critical and expensive task, needing a team of vehicle and control experts as well as many hours of professional driving. In this paper, we propose a purely data-based tuning method enabling the automatic calibration of the parameters of a proprietary suspension controller by relying on little experimental time and exploiting Bayesian Optimization tools. A detailed methodology on how to select the most critical degrees of freedom of the algorithm is also provided. The effectiveness of the proposed approach is assessed on a commercial multi-body simulator as well as on a real car.
Distortion-free high-resolution fMRI at 9.4 T (2012)

SNR benefits allow for significantly higher resolution in BOLD fMRI at ultra-high fields. On the flip side, faster T2* relaxation leads to blurring and increased B0 field inhomogeneities aggravate distortion artifacts in EPI BOLD imaging at higher fields. In this work, a single-echo gradient-echo sequence is presented, that is optimized for high BOLD SNR by combining the concept of echo-shifting with an interleaved slice order. The method is demonstrated in finger tapping experiments on a human 9.4T system. The result is a BOLD activation map with 1mm isotropic resolution virtually free from distortions.
Synthesis of 1,3,4-Oxadiazoles from Carboxylic Hydrazides and of 1,2-Oxazin-6-ones from α-(Hydroxyimino)carboxylic Esters with Keteneylidene Triphenylphosphorane (1997)

In a one-pot procedure 1,3,4-oxadiazoles 8 are prepared from carboxylic hydrazides 2 and keteneylidene triphenylphosphorane 1 via an untypical intermolecular Wittig olefination of a carbamate type carbonyl group. Under similar conditions, reaction of 1 and α-(hydroxyimino) carboxylic esters 9 furnishes 1,2-oxazin-6-ones 11 by a different process including an intramolecular olefination step.
Novel alignment technique for 0.1-micron lithography using the wafer rear surface and canceling tilt effect (1993)

A new wafer rear surface alignment (RSA) technique using a rear surface and canceling tilt effect (RECT) for wafer steppers is proposed. RECT alignment can provide the alignment accuracies of less than 0.03 μm (3σ) that are required for 0.1-μm lithography. The accuracy is almost the same as the resolution limit in the alignment sensor; therefore, position detection errors, which are caused by multi-interference in resist films and the asymmetric profile of marks deformed during manufacturing processes, must be decreased until they can be neglected. The concept of wafer RSA has provided a breakthrough to obtain higher overlay accuracy by fabricating alignment marks on the wafer rear surface. RSA, however, has the disadvantage of a position detection error ε caused by a thickness between the wafer surface and the rear surface, which strongly depends on the wafer tilt. To overcome this problem, RECT consists of two-beam-illumination optics to cancel the error ε. The diffracted beams that are reflected from two separate points on the grating mark include information on both mark positions and light-path difference due to wafer tilt. Thus, the wafer-tilt-induced error can be automatically canceled by processing this information. In an experiment using a six-axis fine positioning stage, it was proven that alignment accuracy can be minimized to as small as 0.015 μm (3σ) for a wafer-tilt angle range of ±50 μrad.
Growth and Laboratory Maintenance of Staphylococcus aureus (2013)

Staphylococcus aureus is a facultative anaerobic Gram-positive coccus and a member of the normal skin flora as well as the nasal passages of humans. S. aureus is also the etiological agent of suppurative abscesses, as first described by Sir Alexander Ogston in 1880. Ever since, studies on S. aureus have focused on the complex battery of virulence factors and regulators that allow for its swift transition between commensalism and pathogenic states and escape from host immune defenses. The success of this pathogen is further evidenced by its ability to acquire antibiotic resistance traits through mechanisms that often remain poorly understood.
Visual plasticity induced by short-term monocular deprivation recovers without visual input (2018)

Short-term monocular deprivation in adults has been shown to temporarily strengthen the contribution of the patched eye to a fused percept. In adults, the effect of monocular deprivation disappears within 30 minutes after the patch has been taken off (Zhou et al., doi: 10.1155/2017/4780876). Here we investigate whether visual deprivation (sitting in the dark) after patching would preserve the effect of monocular deprivation. We patched six adults with normal vision for two hours with a translucent eyepatch. We used a binocular phase combination task to measure each eye's contribution to a fused percept. For the control condition, subjects performed two rounds of baseline tests, were patched for two hours, then performed post-patching measurements at 0, 3, 6, 12, 24, 48, 60 and 96 minutes after patch removal. For the visual deprivation condition, the subjects sat in darkness after patching with both eyes covered for one hour. Subjects then performed the post-patching tests. Each subject completed two sessions for every condition. There was a significant difference (Wilcoxon Signed-Rank, P< 0.05, Cohen's d = 1.5) in the effect of monocular deprivation between the darkness and control conditions. Subjects recovered from monocular deprivation even when sitting in the dark. This result suggests that recovery from the patching effect does not require visual input. Meeting abstract presented at VSS 2018
An automatic fluidic system for the rapid detection of soil nutrients (2008)

Low-cost, rapid and reliable detection technologies for soil nutrients can improve the effectiveness of data collection for site-specific management of soil fertility. In this study, an automated fluidic control system was developed for rapid detection of soil nutrients. Micro pump and valves, controlled by a lap-top computer, delivered a sequence of test solutions to a test chamber where ion selective electrodes are mounted. A 90 seconds test time with acceptable accuracy was demonstrated. This automated soil nutrient fluidic system can further be miniaturized and may be useful for in-field rapid detection of soil nutrients.
Summary description schemes for efficient video navigation and browsing (2000)

The Summary Description Scheme (DS) in MPEG-7 aims at providing a summary of an audio-visual program that offers the effective mechanism for efficient access to the program by abstracting the contents. In this paper, we present, in details, the Summary DS proposed to MPEG-7 that allows for efficient navigation and browsing to the contents of interest as well as overview of the overall content in an incorporated way. This efficiency is achieved by a unified description framework that combines static summary based on key frames and key sounds with dynamic summary based on a series of highlights. The proposed DS also allows efficient description for the event-based summarization by specifying summary criteria. In this paper, we also show the usefulness of the Summary DS in real applications largely based on the results of the Validation and Core Experiments we performed in MPEG-7 activities. We also describe a methodology for the automated generation of a dynamic summary.
Generation and Characterization of New Fluoro-Substituted Carbenes (2004)

Singlet fluorocarbenes substituted with diphenylphosphanyl, phenylsulfanyl, and trimethylsilyl groups were generated upon photolysis of the corresponding tricyclo[4.3.1.0]decadiene precursors 1a−c. Diphenylphosphanyl fluoro carbene 2a was directly observed by transient UV−Vis spectroscopy. Its lifetime in several solvents ranged from 1 to 10 μs. A study of its reactivity toward methyl acrylate and tetramethylethylene along with DFT calculations did not indicate specific solvation of the carbene center. Fluorothiophenyl carbene 2b and fluorotrimethylsilyl carbene 2c were studied by their reaction with pyridine to form ylides and have lifetimes of 1 μs (cyclohexane) and 33 ns (carbon tetrachloride), respectively, at room temperature. Transient UV−Vis spectroscopy supported by DFT calculations showed that, in the case of fluorothiophenyl carbene 2b, carbene formation is in competition with the generation of the diradical intermediate formed by the cleavage of only a single C−C bond of the cyclopropane ring of the precursor.
A study of surface acoustic wave pressure sensor in ZnO/quartz (2006)

It was previously reported that a Rayleigh wave propagating on a zinc oxide film has a relatively low temperature coefficient of frequency (TCF) and a large electromechanical coupling factor (K/sup 2/). In this study we investigate the performance of a SAW pressure sensor using ZnO/quartz structure. Y-cut is preferred in our study due to its positive TCF value permitting a zero TCF when combined with ZnO. ZnO thickness was determined to achieve a zero TCF and to improve the electromechanical coupling coefficient (K/sup 2/=1%) seven times higher than that of quartz Y-cut X propagating direction. The development of the optimal structure to be used is presented followed by the operating frequency effect and ZnO film contribution to the pressure sensitivity.
Web on the wall (2012)

New sensing technologies like Microsoft's Kinect provide a low-cost way to add interactivity to large display surfaces, such as TVs. In this paper, we interview 25 participants to learn about scenarios in which they would like to use a web browser on their living room TV. We then conduct an interaction-elicitation study in which users suggested speech and gesture interactions for fifteen common web browser functions. We present the most popular suggested interactions, and supplement these findings with observational analyses of common gesture and speech conventions adopted by our participants. We also reflect on the design of multimodal, multi-user interaction-elicitation studies, and introduce new metrics for interpreting user-elicitation study findings.
Kinetic and Structural Analysis of a New Group of Acyl-CoA Carboxylases Found in Streptomyces coelicolor A3(2) (2002)

Two acyl-CoA carboxylases from Streptomyces coelicolor have been successfully reconstituted from their purified components. Both complexes shared the same biotinylated alpha subunit, AccA2. The beta and the epsilon subunits were specific from each of the complexes; thus, for the propionyl-CoA carboxylase complex the beta and epsilon components are PccB and PccE, whereas for the acetyl-CoA carboxylase complex the components are AccB and AccE. The two complexes showed very low activity in the absence of the corresponding epsilon subunits; addition of PccE or AccE dramatically increased the specific activity of the enzymes. The kinetic properties of the two acyl-CoA carboxylases showed a clear difference in their substrate specificity. The acetyl-CoA carboxylase was able to carboxylate acetyl-, propionyl-, or butyryl-CoA with approximately the same specificity. The propionyl-CoA carboxylase could not recognize acetyl-CoA as a substrate, whereas the specificity constant for propionyl-CoA was 2-fold higher than for butyryl-CoA. For both enzymes the epsilon subunits were found to specifically interact with their carboxyltransferase component forming a beta-epsilon subcomplex; this appears to facilitate the further interaction of these subunits with the alpha component. The epsilon subunit has been found genetically linked to several carboxyltransferases of different Streptomyces species; we propose that this subunit reflects a distinctive characteristic of a new group of acyl-CoA carboxylases.
Sustained Local Release of Methylprednisolone From a Thiol-Acrylate Poly(Ethylene Glycol) Hydrogel for Treating Chronic Compressive Radicular Pain (2015)

N/A.
On Immunologists and Microbiologists: Ground Zero in the Battle for Interdisciplinary Knowledge (2010)

The individual disciplines of microbiology and immunology are exploding with new information necessary for understanding host-pathogen relationships, infectious diseases, cancer, and autoimmunity. Because of overlapping scientific interests, immunologists and microbiologists often share common academic affiliations. The coexistence is uneasy. Significant problems arise because the groups have evolved different intellectual traditions. Pressures are intensified by sporadic changes in perceptions of their relative worth. As the mixing of microbiologists and immunologists can be likened to ground zero in the fight for interdisciplinary knowledge, it is useful, at this time of escalating data acquisition and growing appreciation for multidisciplinary research, to examine their histories, the challenges to amalgamation, and the advantages of their association for the advancement of knowledge and the delivery of protection against disease. The exploration supports a recommitment to integration of the disciplines and a proposal to facilitate this by inclusion of expertise bridging the areas.
ChemInform Abstract: Synthesis and Anticancer Activity of Oxindole Derived Imidazo[1,5‐a]pyridines (VIII). (2011)

Abstract Among all the title compounds (VIII) (18 examples) synthesized, compound (VIIIc) shows significant and selective anticancer activity.
Si-LDMOS high power amplifier RFIC with integrated analogue pre-distorter (2008)

A simple approach to improve the linearity of silicon (Si) laterally diffused metal oxide semiconductor (LDMOS) base-station power amplifiers (PAs) by integrating an analogue pre-distorter (APD) is presented. The Si-LDMOS APD utilises an unequal power divider/combiner and Si-LDMOS field effect transistors to provide inverse distortion characteristics. Measurement shows that this method compensates for the nonlinear gain and phase compressions of the PA, thereby resulting in a 1.5 dB increase of the 1 dB compressed output power (P−1 dB)