gebhart/patrepeval huggingface dataset:
Near-Infrared Genetically Encoded Positive Calcium Indicator Based on GAF-FP Bacterial Phytochrome (2019)

A variety of genetically encoded calcium indicators are currently available for visualization of calcium dynamics in cultured cells and in vivo. Only one of them, called NIR-GECO1, exhibits fluorescence in the near-infrared region of the spectrum. NIR-GECO1 is engineered based on the near-infrared fluorescent protein mIFP derived from bacterial phytochromes. However, NIR-GECO1 has an inverted response to calcium ions and its excitation spectrum is not optimal for the commonly used 640 nm lasers. Using small near-infrared bacterial phytochrome GAF-FP and calmodulin/M13-peptide pair, we developed a near-infrared calcium indicator called GAF-CaMP2. In vitro, GAF-CaMP2 showed a positive response of 78% and high affinity (K<sub>d</sub> of 466 nM) to the calcium ions. It had excitation and emission maxima at 642 and 674 nm, respectively. GAF-CaMP2 had a 2.0-fold lower brightness, 5.5-fold faster maturation and lower pH stability compared to GAF-FP in vitro. GAF-CaMP2 showed 2.9-fold higher photostability than smURFP protein. The GAF-CaMP2 fusion with sfGFP demonstrated a ratiometric response with a dynamic range of 169% when expressed in the cytosol of mammalian cells in culture. Finally, we successfully applied the ratiometric version of GAF-CaMP2 for the simultaneous visualization of calcium transients in three organelles of mammalian cells using four-color fluorescence microscopy.
Functional connectivity in the resting‐state motor networks influences the kinematic processes during motor sequence learning (2014)

Neuroimaging studies support the involvement of the cerebello-cortical and striato-cortical motor loops in motor sequence learning. Here, we investigated whether the gain of motor sequence learning could depend on a-priori resting-state functional connectivity (rsFC) between motor areas and structures belonging to these circuits. Fourteen healthy subjects underwent a resting-state functional magnetic resonance imaging session. Afterward, they were asked to reproduce a verbally-learned sequence of finger opposition movements as fast and as accurately as possible. All subjects increased their movement rate with practice, by reducing the touch duration and/or intertapping interval. The rsFC analysis showed that, at rest, the left and right primary motor cortex (M1) and left and right supplementary motor area (SMA) were mainly connected with other motor areas. The covariate analysis taking into account the different kinematic parameters indicated that the subjects achieving greater movement rate increase were those showing stronger rsFC of the left M1 and SMA with the right lobule VIII of the cerebellum. Notably, the subjects with greater intertapping interval reduction showed stronger rsFC of the left M1 and SMA with the association nuclei of the thalamus. Conversely, the regression analysis with the right M1 and SMA seeds showed only a few significant clusters for the different covariates not located in the cerebellum and thalamus. No common clusters were found between the right M1 and SMA. All of these findings indicated important functional connections at rest of those neural circuits responsible for motor learning improvement, involving the motor areas related to the hemisphere directly controlling the finger movements, the thalamus and cerebellum.
Crystallographic Microstructure Analyses below Cleavage Triggers in Bainitic Low Carbon Steels (2016)

Microstructures at the cleavage triggers were investigated in Bainitic steels. Bainitic steels with different Austenite grain size and second phase were prepared, and the fracture absorbed energies in cleavage fracture were examined under static loading with Charpy type bend specimens. Cleavage trigger point was identified on each fracture surface by fractography, and was exposed into an etching process. The correspondence of cleavage facets around a trigger with Bainite microstructural unit was investigated. Bainite packet boundaries were frequently observed on a continuous cleavage facet. Fracture surfaces were sectioned, and the cross sections which included a trigger were polished. These cross sections were exposed onto EBSD observations, and the correspondence of cleavage facets with Bainite microstructure was crystallographically investigated. Optically observed microstructure boundary did not always act as a resistance against a cleavage cracking, and EBSD analyses suggested that the crystalline orientation units such as a Bain group controlled a cleavage facet unit.
Effects of Chain Length on Adhesive Force between Gold Tip and Gold Substrate Covered with Alkanethiol Self-Assembled Monolayers (2004)

The effects of chain length on adhesive force between a gold-coated tip and a Au(111) substrate covered with alkanethiol self-assembled monolayers (SAMs) were studied. By microcontact printing (µ-CP), we prepared a patterned surface covered with two types of n -alkanethiol that have the same CH 3 -terminal functional group but different chain lengths. As a method for mapping adhesive force, pulsed-force-mode atomic force microscopy (PFM-AFM) was used. PFM-AFM enables the simultaneous imaging of surface topography and adhesive force. Regardless the use of the same CH 3 -terminal functional group to modify a surface, a difference in adhesive force corresponding to the printed pattern was observed. The adhesive force on a printed region covered with a longer alkanethiol SAM was slightly smaller than that of an unprinted region covered with a shorter alkanethiol SAM chemisorbed from solution after µ-CP. The possible molecular mechanisms for the difference in the observed adhesive force were discussed in detail.
Detection of Explosives via Photolytic Cleavage of Nitroesters and Nitramines (2011)

The nitramine-containing explosive RDX and the nitroester-containing explosive PETN are shown to be susceptible to photofragmentation upon exposure to sunlight. Model compounds containing nitroester and nitramine moieties are also shown to fragment upon exposure to UV irradiation. The products of this photofragmentation are reactive, electrophilic NO(x) species, such as nitrous and nitric acid, nitric oxide, and nitrogen dioxide. N,N-Dimethylaniline is capable of being nitrated by the reactive, electrophilic NO(x) photofragmentation products of RDX and PETN. A series of 9,9-disubstituted 9,10-dihydroacridines (DHAs) are synthesized from either N-phenylanthranilic acid methyl ester or a diphenylamine derivative and are similarly shown to be rapidly nitrated by the photofragmentation products of RDX and PETN. A new (turn-on) emission signal at 550 nm is observed upon nitration of DHAs due to the generation of fluorescent donor-acceptor chromophores. Using fluorescence spectroscopy, the presence of ca. 1.2 ng of RDX and 320 pg of PETN can be detected by DHA indicators in the solid state upon exposure to sunlight. The nitration of aromatic amines by the photofragmentation products of RDX and PETN is presented as a unique, highly selective detection mechanism for nitroester- and nitramine-containing explosives and DHAs are presented as inexpensive and impermanent fluorogenic indicators for the selective, standoff/remote identification of RDX and PETN.
A multicentric evaluation of the recombinant Leishmania infantum antigen-based immunochromatographic assay for the serodiagnosis of canine visceral leishmaniasis (2014)

The recombinant antigens rLci1A and rLci2B represent promising candidates for use in a multi-antigen rapid test for CVL. The inclusion of novel antigens to the DPP rLci1A/rLci2B prototype model could offer additionally enhanced sensitivity to detect animals infected by L. infantum.
CowClip: Reducing CTR Prediction Model Training Time from 12 hours to 10 minutes on 1 GPU (2022)

The click-through rate (CTR) prediction task is to predict whether a user will click on the recommended item. As mind-boggling amounts of data are produced online daily, accelerating CTR prediction model training is critical to ensuring an up-to-date model and reducing the training cost. One approach to increase the training speed is to apply large batch training. However, as shown in computer vision and natural language processing tasks, training with a large batch easily suffers from the loss of accuracy. Our experiments show that previous scaling rules fail in the training of CTR prediction neural networks. To tackle this problem, we first theoretically show that different frequencies of ids make it challenging to scale hyperparameters when scaling the batch size. To stabilize the training process in a large batch size setting, we develop the adaptive Column-wise Clipping (CowClip). It enables an easy and effective scaling rule for the embeddings, which keeps the learning rate unchanged and scales the L2 loss. We conduct extensive experiments with four CTR prediction networks on two real-world datasets and successfully scaled 128 times the original batch size without accuracy loss. In particular, for CTR prediction model DeepFM training on the Criteo dataset, our optimization framework enlarges the batch size from 1K to 128K with over 0.1% AUC improvement and reduces training time from 12 hours to 10 minutes on a single V100 GPU. Our code locates at https://github.com/bytedance/LargeBatchCTR.
ChemInform Abstract: Evaporation‐Induced Self‐Assembly: Nanostructures Made Easy (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Identifying thermal phase transitions of lignin–solvent mixtures using electrochemical impedance spectroscopy (2015)

A new approach to measuring the phase-transition temperature of lignin–solvent systems using electrochemical impedance spectroscopy is reported.
Abstract P114: Interaction of Dietary n-3 Fatty Acids on Cardiac Risk by J-point Elevation in Japanese Men: NIPPON DATA80 (2012)

Background: Early repolarization, characterized by an elevation of QRS-ST junction (J-point) on a 12-lead electrocardiography, has recently been considered an independent predictor of cardiac or sudden death. Meanwhile, protective effects of n-3 fatty acids (FAs) on cardiovascular diseases have been demonstrated in epidemiologic studies and clinical trials. Therefore, we assessed the hypothesis that an increased dietary intake of n-3 FAs may reduce poor prognosis of J-point elevation (JpE). Methods: A total of 4443 community-dwelling men (mean age of 49.5 years) without previous cardiovascular diseases from randomly selected areas across Japan were included for the analysis. The primary endpoint was cardiac death during a mean follow-up of 20.4±6.1 years. JpE was defined as an elevation of J-point at least one lead: ≥0.2mV in V 1-4 leads or ≥0.1mV in other leads. Dietary intakes of n-3 FAs were calculated by a combined method using household-based food-weighing records and an approximation of the proportions of each dish or food shared in the household. The hazard ratios (HRs) (95% confidence interval [95%CI]) of JpE for cardiac death were estimated by Cox proportional hazard models adjusted for age, sex, body mass index, systolic blood pressure, total cholesterol, diabetes mellitus, smoking status, drinking habits, medication status, cohort, heart rate, dietary sodium, dietary fiber, dietary saturated fatty acids, high R wave on electrocardiography (based on Minnesota Codes 3.1 and 3.3), and suspected coronary heart disease on electrocardiography (based on Minnesota Codes 1.1 to 1.3, 5.1 to 5.2, 4.1 to 4.3, 7.1, and 7.4). Results: JpE were present in 153 of 2176 (7.0%) and 187 of 2267 (8.2%) individuals in low (&lt;the median n-3 FAs level of 1.06%kcal) and high (≥1.06%kcal) n-3 FAs groups, respectively. During follow-up period, the number of deaths from cardiac causes in low and high n-3 FAs groups were 128 (5.9%) and 85 (3.7%), respectively. In the low n-3 FAs group, individuals with JpE had a significantly higher HR of cardiac death than those without JpE (2.77; 95%CI, 1.60-4.82; P=0.001). In contrast, in the high n-3 FAs group, a HR was not significantly increased (0.85; 95%CI, 0.37-1.97; P=0.711) (P for n-3 FAs-JpE interaction = 0.032). Conclusions: An increased risk of cardiac death related to JpE was attenuated in individuals with higher dietary intake of n-3 FAs, suggesting that a higher n-3 FAs intake may prevent long-term cardiac risk associated with JpE
Astrocytic pathology in the immune‐mediated motor neuron injury (2007)

Reactive astrogliosis has been found in the cerebral cortex and spinal cord in amyotrophic lateral sclerosis, whereas astrocytic pathology in immune‐mediated motor neuron injury has not been reported. On the basis of the establishment of an immune‐mediated motor neuron injury model, histological, immunohistochemical and ultrastructural studies on astrocytes were carried out. Reactive astrogliosis in spinal cord anterior horn was observed, and the increase of GFAP‐positive astrocytes may occur prior to the clinical manifestations. Reactive astrocytes could show pathological changes similar to those of motor neurons, such as swollen mitochondria and dilated endoplasmic reticulum. Of special interest are crystallized inclusions that were frequently observed in the reactive astrocytes in the bovine ventral horn homogenate‐immunized anterior horn. The precise nature and origin of these inclusions deserve to be elucidated.
Effects of gamma-Radiation on Select Lipids and Antioxidants (2006)

Radiation encountered on an extended duration space mission (estimates of 3 Sieverts for a mission to Mars) poses a threat not only to human health, but also to the quality, nutritional value, and palatability of the food system. Free radicals generated by radiation interaction with foods may initiate many unwanted reactions including: 1) autoxidation in lipids that alters flavor, odor, and concentrations of essential fatty acids, and 2) depletion of antioxidants food products and dietary supplements. Studies have shown that antioxidants may provide long term health protection from oxidative stress caused by radiation exposure; therefore, consumption of antioxidants will be important. Stability of essential fatty acids is also important for astronauts long-term health status. The objectives of this study were to characterize the effects of low dose gamma-radiation on lipids and antioxidants by monitoring oxidation and reducing power, respectively, in model systems. Select oils and antioxidants were exposed to levels of gamma-radiation ranging from 0 to 1000 Gy (1 Gy = 1 Sv) using a Gammacell 220 and stored at ambient or elevated temperatures (65 C) for up to 3 months prior to analysis. A Fricke dosimeter was used to verify differences between the radiation doses administered. Primary and secondary products of lipid oxidation in soybean and peanut oils were monitored using conjugated diene and 2-thiobarbituric acid (TBARs) assays. Changes in fatty acid composition and formation and vitamin E levels were also measured. The reducing power of antioxidant compounds, including vitamins C and E and beta-carotene, was determined using the ferric reducing antioxidant power (FRAP) assay. Significant differences (alpha =0.05) were present between all radiation doses tested using the Fricke dosimeter. Increasing radiation doses above 3 Sv resulted in significantly (alpha =0.05) elevated levels of oxidation and free fatty acids in soybean and peanut oils. Decreases in concentrations of essential fatty acids upon increasing radiation doses were also observed. Increasing radiation doses caused significant (alpha =0.05) decreases in reducing power and hence the effectiveness of vitamins C and E as well as beta-carotene. This work establishes a need for quantifying the effects of space relevant radiation doses in the development of a food system for an extended duration mission and for identifying threshold radiation levels that will impact the useful shelf-life of the variety of foods that will be sent. Eventual rancidity of lipids and the loss of antioxidant bioprotective effects are major concerns for the acceptability and nutritional profile of a food system.
Optimal pattern search for database systems (2013)

Many time series database applications require processing and analyzing database sequences where the focus is on finding the patterns and trends in sequence data. In this paper, the approach carried out is based on the observation that finding sequential patterns in databases is somehow similar to searching for a phrase in the text. However instead of searching for sequence of letters usually from finite alphabet, we search for sequence of tuple with rich structure and infinite possibilities from both ends of the sequential database. We take the algorithm of Boyer moore used for text and generalize it to search for complex sequence patterns of interest in a given database by exploiting the logical interdependencies between the elements of a sequential pattern having constraints.
Can MiRBase Provide Positive Data for Machine Learning for the Detection of MiRNA Hairpins? (2013)

Summary Experimental detection and validation of miRNAs is a tedious, time-consuming, and expensive process. Computational methods for miRNA gene detection are being developed so that the number of candidates that need experimental validation can be reduced to a manageable amount. Computational methods involve homology-based and ab inito algorithms. Both approaches are dependent on positive and negative training examples. Positive examples are usually derived from miRBase, the main resource for experimentally validated miRNAs. We encountered some problems with miRBase which we would like to report here. Some problems, among others, we encountered are that folds presented in miRBase are not always the fold with the minimum free energy; some entries do not seem to conform to expectations of miRNAs, and some external accession numbers are not valid. In addition, we compared the prediction accuracy for the same negative dataset when the positive data came from miRBase or miRTarBase and found that the latter led to more precise prediction models. We suggest that miRBase should introduce some automated facilities for ensuring data quality to overcome these problems.
Development of a Sound Coding Strategy based on a Deep Recurrent Neural Network for Monaural Source Separation in Cochlear Implants (2016)

Comunicació presentada a la 12th ITG Conference on Speech Communication, celebrada els dies 5 a 7 d'octubre de 2016 a Paderborn, Alemanya.
ChemInform Abstract: Hydroboration. Part 90. Synthesis of 2‐Isobutyl‐ and 2‐ Isopropylapopinenes. Rates and Stoichiometry of the Hydroboration of 2‐ Organylapopinenes with Borane‐Methyl Sulfide and Borane‐ Tetrahydrofuran. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Application of Haptic Feedback to Robotic Surgery (2004)

Robotic surgical systems have greatly contributed to the advancement of minimally invasive endoscopic surgery. However, current robotic systems do not provide tactile or haptic feedback to the operating surgeon. Under certain circumstances, particularly with the manipulation of delicate tissues and suture materials, this may prove to be a significant irritation. We hypothesize that haptic feedback, in the form of sensory substitution, facilitates the performance of surgical knot tying. This preliminary study describes evidence that visual sensory substitution permits the surgeon to apply more consistent, precise, and greater tensions to fine suture materials without breakage during robot-assisted knot tying.
A probabilistic framework for the spatio-temporal segmentation of multiple sclerosis lesions in MR images of the brain (2003)

In this paper we describe the application of a novel statistical image-sequence (video) modeling scheme to sequences of multiple sclerosis (MS) images taken over time. A unique key feature of the proposed framework is the analysis of the image-sequence input as a single entity as opposed to a sequence of separate frames. The extracted space-time regions allow for the detection and identification of disease events and processes, such as the appearance and progression of lesions. According to the proposed methodology, coherent space-time regions in the feature space, and corresponding coherent segments in the video content are extracted by unsupervised clustering via Gaussian mixture modeling (GMM). The parameters of the GMM are determined via the maximum likelihood principle and the Expectation-Maximization (EM) algorithm. The clustering of the image sequence yields a collection of regions (blobs) in a four-dimensional feature space (including intensity, position (x,y), and time). Regions corresponding to MS lesions are automatically identified based on criteria regarding the mean intensity and the size variability over time. The proposed methodology was applied to a registered sequence of 24 T2-weighted MR images acquired from an MS patient over a period of approximately a year. Examples of preliminary qualitative results are shown.
Monolithic integration of a 3-level DCM-operated low-floating-capacitor buck converter for DC-DC step-down donversion in standard CMOS (2008)

This paper addresses the fully monolithic integration of a 3-level 2-phase buck converter for DC-DC step-down conversion in standard CMOS. First it is shown a design-oriented analysis of the converter considering DCM mode (due to PFM operation for low output currents) and with low values of the floating capacitor (to improve integrability). At transistor-level, a self-driving scheme is proposed which allows supplying the tapered buffer drivers from the floating capacitor, thereby reducing the voltage across the power MOSFETs gate dielectric and improving efficiency. The presented converter exhibits enhanced degrees of freedom in the design space defined by the switching frequency, inductor and capacitors values, which have an impact on the achievable efficiency, occupied silicon area and output ripple. An optimized design exploration is carried out for V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">bat</sub> = 3.6 V, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> = 1 V, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> = 100 mA, DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> = 50 mV, which yields a converter with the following main characteristics: L = 20.9 nH, C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> = 18.6 nF, C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> = 3.8 nF and/s = 51.79 MHz (for I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> = 100 mA), a power efficiency of 68.51 % and a occupied area of 3.77 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , which results in a clear improvement when the same structured design method is applied to classical buck converter. However, finally a lower switching frequency design is selected to be implemented to allow control loops operation (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> = 37.28 MHz). After providing details of the layout design, full-transistor level simulation results validate the improved performance and the efficiency model. Experimental results from an implemented IC validate the time-domain functionality of the on-chip converter.