gebhart/patrepeval huggingface dataset:
Cerebellar Contributions to Adaptive Control of Saccades in Humans (2009)

The cerebellum may monitor motor commands and through internal feedback correct for anticipated errors. Saccades provide a test of this idea because these movements are completed too quickly for sensory feedback to be useful. Earlier, we reported that motor commands that accelerate the eyes toward a constant amplitude target showed variability. Here, we demonstrate that this variability is not random noise, but is due to the cognitive state of the subject. Healthy people showed within-saccade compensation for this variability with commands that arrived later in the same saccade. However, in people with cerebellar damage, the same variability resulted in dysmetria. This ability to correct for variability in the motor commands that initiated a saccade was a predictor of each subject's ability to learn from endpoint errors. In a paradigm in which a target on the horizontal meridian jumped vertically during the saccade (resulting in an endpoint error), the adaptive response exhibited two timescales: a fast timescale that learned quickly from endpoint error but had poor retention, and a slow timescale that learned slowly but had strong retention. With cortical cerebellar damage, the fast timescale of adaptation was effectively absent, but the slow timescale was less impaired. Therefore, the cerebellum corrects for variability in the motor commands that initiate saccades within the same movement via an adaptive response that not only exhibits strong sensitivity to previous endpoint errors, but also rapid forgetting.
Impairment of Couple Relationship in Male Patients with Sexual Dysfunction is Associated with Overt Hypogonadism (2009)

Our data suggest that, in subjects consulting for sexual dysfunction, a deterioration of the couple's relationship is associated with impairment in sexual activities, which, in turn, can lead to a mild hypogonadism. Any speculation on pathogenetic relationships should be confirmed through prospective studies or intervention trials.
Gefügetomografie mit Ionen- und Elektronenstrahlen: ein Werkzeug zur Aufklärung komplexer Gefügebildung und lokaler Gefügedegradation∗ (2009)

Kurzfassung Neben der Analyse komplexer Geometrien können auch lokale Phänomene, bei denen eine 2-D-Analyse versagt, mit Hilfe der FIB/REM-Gefügetomografie aufgeklärt werden. Am Beispiel von silberbasierten Kontaktwerkstoffen wird der Einfluss einer elektrischen Entladung auf die Größe, Form und Verteilung der Oxidpartikel und Poren im Material gezeigt und mit der effektiven elektrischen Leitfähigkeit korreliert.
New developments in frontotemporal dementia and parkinsonism linked to chromosome 17 (2002)

Hopefully, the identification of responsible genetic defects and associated proteins will be helpful in improving our understanding of the role of the tau protein in the common neurodegenerative process of frontotemporal degeneration.
Combining E-Graphs with Abstract Interpretation (2023)

E-graphs are a data structure that compactly represents equivalent expressions. They are constructed via the repeated application of rewrite rules. Often in practical applications, conditional rewrite rules are crucial, but their application requires the detection -- at the time the e-graph is being built -- that a condition is valid in the domain of application. Detecting condition validity amounts to proving a property of the program. Abstract interpretation is a general method to learn such properties, traditionally used in static analysis tools. We demonstrate that abstract interpretation and e-graph analysis naturally reinforce each other through a tight integration because (i) the e-graph clustering of equivalent expressions induces natural precision refinement of abstractions and (ii) precise abstractions allow the application of deeper rewrite rules (and hence potentially even greater precision). We develop the theory behind this intuition and present an exemplar interval arithmetic implementation, which we apply to the FPBench suite.
9,10-Bis(7-fluoro-2,5-dioxaheptyl)triptycene (1996)

The structure of the title compound, C 30 H 32 F 2 O 4 , exhibits C-H...π-arene hydrogen bonding.
Multi-element Germanium Detectors for Synchrotron Applications (2018)

We have developed a series of monolithic multi-element germanium detectors, based on sensor arrays produced by the Forschungzentrum Julich, and on Application-specific integrated circuits (ASICs) developed at Brookhaven. Devices have been made with element counts ranging from 64 to 384. These detectors are being used at NSLS-II and APS for a range of diffraction experiments, both monochromatic and energy-dispersive. Compact and powerful readout systems have been developed, based on the new generation of FPGA system-on-chip devices, which provide closely coupled multi-core processors embedded in large gate arrays. We will discuss the technical details of the systems, and present some of the results from them.
Synthesis of New α,ω‐Olefinic Silicon‐Containing Compounds via Cross‐Metathesis (2000)

We studied the synthesis of a new generation of silicon compounds containing two or four terminal double bonds. The synthesis was realized via transition-metal-catalyzed cross-metathesis of silicon-containing cycloolefins with ethylene (ethenolysis). Silicon-containing α, ω-dienes may be useful, e.g. as crosslinking agents in polymers and as precursors for α,ω-difunctional compounds. In general, the problem in the cross-metathesis of cycloolefins with acyclic olefins (here: ethylene) is the occurence of side reactions which lead to homo-metathesis products besides the desired cross-metathesis products. Therefore, the choice of a suitable catalyst and a cycloolefin for which ring-opening is energetically favorable as well as the optimization of the reaction conditions are crucial for the selectivity of the cross-metathesis.
New Results in Colloid Display Technology (1983)

&lt;div class="htmlview paragraph"&gt;Recent improvements in the synthesis procedure for colloidal suspensions have led to reproducible suspensions and a reduced production time.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In the past year, the previous disadvantages of high drive voltage, slow response at low temperatures and restricted operating lifetime have been substantially reduced. Present displays operate at 18 volts (CMOS compatible) with response times substantially less than 500 ms at -30°C and also have improved lifetimes under both storage and operating conditions.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;New test methods have been developed to assist the understanding of the degradation process under operating conditions.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The latest technical data for colloidal displays are presented.&lt;/div&gt;
Multiomics Data Integration for Gene Regulatory Network Inference with Exponential Family Embeddings (2021)

The advent of omics technologies have enabled the generation of huge, complex, heterogeneous, and high-dimensional omics data. Imposing numerous challenges in data integration, these data could lead to a better understanding of the organism's cellular system. Omics data are typically represented as networks to study relations between biological entities, such as protein-protein interaction, gene regulation, and signal transduction. To this end, network embedding approaches allow us to learn latent feature representations for nodes of a graph structure. In this study, we propose a new methodology to learn embeddings by modeling the underlying interactions among biological entities (nodes) with exponential family distributions from a well chosen set of omics modalities. We evaluate our proposed method based on the gene regulatory network (GRN) inference problem. As the ground truth for evaluation, we use GRN available in public databases and demonstrate its effectiveness by comparing to other network integration approaches.
Design and implementation of a second prototype intelligent alarm system in anesthesia (1990)

In today's operating room (OR), a number of monitors is connected to both patient and equipment.Each individual monitor is equipped with its own, usually rather unspecific, alarms.Therefore, there is a clear need for an integrated alarm system that, by combining data from all monitors, generates useful and intelligent alarm messages about possible abnormalities occurring in patient and/or equipment.A first prototype of such a system, combining data from three different monitors to detect mechanical malfunctions in the breathing circuit, was tested on an anesthesia simulator and in the OR.During tests with the simulator, the system identified 88% of the introduced malfunctions correctly within 30 seconds.No false alarms were recorded in the OR, although the signals were often disturbed.A second prototype was designed to adapt automatically to adjustments in one or more of the control settings on the anesthesia machine or the anesthesia ventilator during surgery.Furthermore, a user-friendly interface screen was designed for this system.During tests on the simulator, 95.5% of the malfunctions was detected correctly.The system could keep up with high pediatric respiratory rates.After some additional refinements and improvements, the system can be the platform for the development of a completely integrated intelligent alarm system for patient as well as equipment during anesthesia.
Improved rectangular cavity for EPR in TE102 mode (1987)

Usually the side walls of a rectangular cavity are less than one skin depth thick at the field-modulation frequency. Eddy current creates an opposing magnetic field to the incoming modulation field, which tends to reduce the field at the center of the cavity. Moreover if the walls of the cavity are kept thin, interaction of eddy currents and the static magnetic field will create mechanical vibrations that will modulate the microwave frequency, thus generating spurious signals at the output of the amplifier. In this note a cavity for X band (in 9–10 GHz) is described in which the above problems have been overcome by corrugating the cavity walls in a precise manner. In comparison with a thin sidewall, the EMF that drives the eddy currents remains unchanged, but because the resistance increases, the eddy currents decrease.
Role of microRNA221 in regulating normal mammary epithelial hierarchy and breast cancer stem-like cells (2015)

Increasing evidence suggests that lineage specific subpopulations and stem-like cells exist in normal and malignant breast tissues. Epigenetic mechanisms maintaining this hierarchical homeostasis remain to be investigated. In this study, we found the level of microRNA221 (miR-221) was higher in stem-like and myoepithelial cells than in luminal cells isolated from normal and malignant breast tissue. In normal breast cells, over-expression of miR-221 generated more myoepithelial cells whereas knock-down of miR-221 increased luminal cells. Over-expression of miR-221 stimulated stem-like cells in luminal type of cancer and the miR-221 level was correlated with clinical outcome in breast cancer patients. Epithelial-mesenchymal transition (EMT) was induced by overexpression of miR-221 in normal and breast cancer cells. The EMT related gene ATXN1 was found to be a miR-221 target gene regulating breast cell hierarchy. In conclusion, we propose that miR-221 contributes to lineage homeostasis of normal and malignant breast epithelium.
Supporting collaborative activity (2005)

We describe here the properties of a mutant of Chinese hamster ovary cells that expresses a conditional-lethal mutation affecting dense lysosomes. This mutant, termed V.24.1, is a member of the End4 complementation group of temperature-sensitive mutants selected for resistance to protein toxins (Colbaugh, P. A., C.-Y. Kao, S.-P. Shia, M. Stookey, and R. K. Draper. 1988. Somatic Cell Mol. Genet. 14:499-507). Vesicles present in postnuclear supernatants prepared from V.24.1 cells harvested at the restrictive temperature had a 50% reduction in acidification activity, assessed by the ATP-stimulated accumulation of the dye acridine orange in acidic vesicles. To investigate whether specific populations of vesicles were impaired in acidification, we measured acidification activity in three subcellular fractions prepared from Percoll gradients: one containing endosomal and Golgi markers, one containing buoyant lysosomes, and the third containing dense lysosomes. Activity in dense lysosomes was reduced by 90%, activity in the buoyant lysosome fraction was unaffected, and activity in the endosome-Golgi fraction was mildly reduced. The activity of three lysosomal enzymes--beta-hexosaminidase, beta-galactosidase, and beta-glucocerebrosidase--was also reduced in dense lysosomes but nearly normal in the buoyant lysosome fraction. However, beta-hexosaminidase and beta-glucocerebrosidase activity was increased two- to threefold in the endosome-Golgi fraction. We conclude that the lesion selectively impairs dense lysosomes but has little effect on properties of buoyant lysosomes.
Murine Salivary Functional Assessment via Pilocarpine Stimulation Following Fractionated Radiation (2018)

Hyposalivation is commonly observed in the autoimmune reaction of Sjögren's syndrome or following radiation injury to the major salivary glands. In these cases, questions remain regarding disease pathogenesis and effective interventions. An optimized technique that allows functional assessment of the salivary glands is invaluable for investigating exocrine gland biology, dysfunction, and therapeutics. Here, we present a step by step approach to performing pilocarpine stimulated saliva secretion, including tracheostomy and the dissection of the three major murine salivary glands. We also detail the appropriate murine head and neck anatomy accessed during these techniques. This approach is scalable, allowing for multiple mice to be processed simultaneously, thus improving the efficiency of the work flow. We aim to improve the reproducibility of these methods, each of which has further applications within the field. In addition to saliva collection, we discuss metrics for quantifying and normalizing functional capacity of these tissues. Representative data are included from submandibular glands with depressed salivary gland function 2 weeks following fractionated radiation (4 doses of 6.85 Gy).
Zero-bias optically controlled RF switch in 0.13 µm CMOS technology (2011)

International audience
Rowing effort meter (1991)

While involved in ‘coxing’ a girls four, I came across the problem of determining the amount of effort being contributed by each crew member. This is necessary because any one crew member could be applying, for instance, only 80% of the required effort and it would be almost impossible for the cox to know this. To solve this problem I designed and built a rowing training aid which:
Illustration and Photography Inspired Visualization of Flows and Volumes (2006)

Understanding and analyzing complex volumetrically varying data is a difficult problem. Many computational visualization techniques have had only limited success in succinctly portraying the structure of three-dimensional turbulent flow. Motivated by both the extensive history and success of illustration and photographic flow visualization techniques, we have developed a new interactive volume rendering and visualization system for flows and volumes that simulates and enhances traditional illustration, experimental advection, and photographic flow visualization techniques. Our system uses a combination of varying focal and contextual illustrative styles, new advanced two-dimensional transfer functions, enhanced Schlieren and shadowgraphy shaders, and novel oriented structure enhancement techniques to allow interactive visualization, exploration, and comparative analysis of scalar, vector, and time-varying volume datasets. Both traditional illustration techniques and photographic flow visualization techniques effectively reduce visual clutter by using compact oriented structure information to convey three-dimensional structures. Therefore, a key to the effectiveness of our system is using one-dimensional (Schlieren and shadowgraphy) and two-dimensional (silhouette) oriented structural information to reduce visual clutter, while still providing enough three-dimensional structural information for the user's visual system to understand complex three-dimensional flow data. By combining these oriented feature visualization techniques with flexible transfer function controls, we can visualize scalar and vector data, allow comparative visualization of flow properties in a succinct, informative manner, and provide continuity for visualizing time-varying datasets.
Anaerobic guilds responsible for mercury methylation in boreal wetlands of varied trophic status serving as either a methylmercury source or sink (2020)

Wetlands are common sites of active Hg methylation by anaerobic microbes; however, the amount of methylmercury produced varies greatly, as Hg methylation is dependent upon both the availability of Hg and the composition and activity of the microbial community involved. In this study, we identified the major microbial guilds responsible for Hg methylation along a trophic gradient composed of two sites and three different types of wetlands: a bog-fen peatland gradient and a black alder swamp, serving as net sources and a sink for methylmercury respectively. Iron-reducing bacteria in the Geobacteraceae were important Hg methylators across all wetlands and seasons examined, as evidenced by abundant 16S rRNA and hgcA transcripts clustering with this family. Molybdate inhibited Hg methylation more efficiently in the peatlands than in the swamp, suggesting an increasing role of sulfate-reducing bacteria and/or related syntrophs in the methylation of Hg with decreasing trophic status. Sulfate addition failed to increase Hg methylation rates in the peatlands, suggesting that SRBs/syntrophs were instead likely metabolizing alternative substrates such as syntrophic fermentation of organic compounds with methanogens. These results highlight the interconnectivity of anaerobic metabolism and importance of community dynamics on the methylation of Hg in wetlands with different trophic status.
Abstract 579: Multiplex digital PCR combined with melting curve analysis for detecting KRAS mutations towards pancreatic cancer diagnosis (2021)

Abstract Background Digital PCR (dPCR) is a promising method for liquid biopsies and is able to quantify nucleic acids more sensitively than real-time PCR. However, dPCR has a large fluctuation in the fluorescence intensity of the droplets or wells due to insufficient PCR in the small partitions, limiting the multiplexing capability of using the fluorescence intensity. In this study, we propose a measurement method that combines dPCR with melting curve analysis for highly multiplexed genotyping. Methods A sample is digitized into a silicon chip with up to ~104 wells in which asymmetric PCR was performed to obtain more single-stranded amplicons that are complimentary to molecular beacon probes. Fluorescence images were captured while controlling the temperature of the chip, and melting curve was measured for each well. Then, genotyping was performed by using the fluorescence intensity, dye color of the probe, and melting temperature (Tm). Because the Tm of the PCR products does not considerably depend on the amplification efficiency of PCR, genotyping accuracy is improved by using Tm values, enabling highly multiplexed genotyping. Results The concept was confirmed by simultaneously identifying wild-type KRAS, BRAF and, eight mutants of these genes (G12D, G12R, G12V, G13D, G12A, G12C, G12S, and V600E) through four-color melting curve analysis. G12D, G12V and G12R-mutant KRAS alleles were detected with FAM-labeled probes, G13D-mutant KRAS allele and wildtype KRAS allele were detected with HEX-labeled probes, G12S and G12C-mutant KRAS alleles were detected with Cy5-labeled probes, and V600E-mutant BRAF allele and wildtype BRAF allele were detected with CAL Fluor Red 610-labeled probes. The results showed that the peaks of the Tm distributions of the DNA groups were separated by 3.5 °C on average, while the standard deviation of the Tm distributions was 0.23 °C on average. The difference in Tm was 15 times larger than the standard deviation, enabling more accurate genotyping than when using the fluorescence intensity. Conclusion We have proposed a measurement method that combines dPCR with melting curve analysis, and successfully performed the multiplexed genotyping assay. We plan to evaluate the effect of this method on measurement using clinical specimens of pancreatic cancer patients in the future. Citation Format: Junko Tanaka, Tatsuo Nakagawa, Takeshi Ishida, Yoshio Kamura, Akiko Shiratori, Kunio Harada, Chihiro Uematsu. Multiplex digital PCR combined with melting curve analysis for detecting KRAS mutations towards pancreatic cancer diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 579.
Supplementary Figure S4 from Targeting BET Proteins Downregulates miR-33a To Promote Synergy with PIM Inhibitors in CMML (2023)

&lt;p&gt;Supplemental Figure 4 contains data related to miR-33a regulation in BETi treated cells.&lt;/p&gt;
Deep Brain Polarization Sensitive Optical Coherence Tomography: Depth Resolved Retardance and Optic Axis Measurement (2023)

We present improved reconstruction of depth-resolved optic axis orientation in catheter-based polarization-sensitive optical coherence tomography, by using the intrinsic retardance of the catheter-sheath as reference, and image white matter fiber bundles in sheep brain.
Robust and secure image hashing (2006)

Image hash functions find extensive applications in content authentication, database search, and watermarking. This paper develops a novel algorithm for generating an image hash based on Fourier transform features and controlled randomization. We formulate the robustness of image hashing as a hypothesis testing problem and evaluate the performance under various image processing operations. We show that the proposed hash function is resilient to content-preserving modifications, such as moderate geometric and filtering distortions. We introduce a general framework to study and evaluate the security of image hashing systems. Under this new framework, we model the hash values as random variables and quantify its uncertainty in terms of differential entropy. Using this security framework, we analyze the security of the proposed schemes and several existing representative methods for image hashing. We then examine the security versus robustness tradeoff and show that the proposed hashing methods can provide excellent security and robustness.
On Integer-Forcing Precoding for the Gaussian MIMO Broadcast Channel (2017)

Integer-forcing (IF) precoding, also known as downlink IF, is a promising new approach to communication over multiple-input multiple-output (MIMO) broadcast channels. Inspired by the integer-forcing linear receiver for multiple-access channels, it generalizes linear precoding by inducing an effective channel matrix that is approximately integer, rather than approximately identity. Combined with lattice encoding and a pre-inversion of the channel matrix at the transmitter, the scheme has the potential to outperform any linear precoding scheme, despite enjoying similar low complexity. In this paper, a specific IF precoding scheme, called diagonally scaled exact IF (DIF), is proposed and shown to achieve maximum spatial multiplexing gain. For the special case of two receivers, in the high SNR regime, an optimal choice of parameters is derived analytically, leading to an almost closed-form expression for the achievable sum rate. In particular, it is shown that the gap to the sum capacity is upper bounded by 0.27 bits for any channel realization. For general SNR, a regularized version of DIF (RDIF) is proposed. Numerical results for two receivers under Rayleigh fading show that RDIF can achieve performance superior to optimal linear precoding and very close to the sum capacity.