gebhart/patrepeval huggingface dataset:
Accurate Concentration Measurements Using Surface-Enhanced Raman and Deuterium Exchanged Dye Pairs (2008)

Quantitative applications of surface-enhanced resonance Raman scattering (SERRS) are often limited by the reproducibility of SERRS intensities, given the difficulty of controlling analyte-substrate interactions and the associated local field enhancement. As demonstrated here, SERRS from dye molecules even within the same structural class that compete with similar substrates display distinct spectral intensities that are not proportional to analyte concentrations, which limits their use as internal standardization probes and/or for multiplex analysis. Recently, we demonstrated that isotopic variants of rhodamine 6G (R6G), namely R6G-d0 and R6G-d4, can be used for internal standards in SERRS experiments with a linear optical response from picomolar to micromolar concentrations (of total analytes). Here we extend these results by describing a straightforward method for obtaining isotopomeric pairs of other Raman active dyes by hydrogen-deuterium exchange conditions for substitution at electron rich aromatic heterocycles. Most of the known SERRS active probes can be converted into the corresponding isotopomeric molecule by this exchange method, which significantly expands the scope of the isotopic edited internal standard (IEIS) approach. The relative quantification using IEIS enables accurate, reproducible (residual standard deviation+/-2.2%) concentration measurements over a range of 200 pM to 2 microM. These studies enable easy access to a variety of isotopically substituted Raman active dyes and establish the generality of the methodology for quantitative SERRS measurements. For the first time, three rhodamine 6G isotopomers have been created and show distinct Raman spectra, demonstrating the principle of the approach for application as a multiplex technique in biomolecular detection/quantification.
Recent advances in the treatment of cystinosis (1995)

Cysteamine bitartrate capsules (Cystagon) have been approved by the US Food and Drug Administration for use in patients with nephropathic cystinosis. Plasma cysteamine concentrations were virtually identical at various times following ingestion of either cysteamine hydrochloride or Cystagon capsules in 24 normal control subjects. A transfer study was done with eight cystinosis patients who had been receiving either cysteamine hydrochloride or phosphocysteamine for many years. The plasma cysteamine concentration was significantly higher 2h after Cystagon and the leukocyte cystine content was significantly lower at all times after Cystagon compared to older forms of the drug. These differences are probably the result of greater patient compliance in taking the capsules compared to the older, liquid forms of the drug. A new method for following the course of renal glomerular deterioration in diseases such as cystinosis has been published recently. This method was used to re-analyse data on the efficacy of cysteamine treatment and to re-analyse new data on treating cystinosis patients with either of two doses of cysteamine (1.30 g/m2 per day and 1.95 g/m2 per day). This new method agrees well with other methods and shows that both doses of drug are equally effective in maintaining glomerular function.
Supplementary Figure 3 from Mechanisms by which E-Selectin Regulates Diapedesis of Colon Cancer Cells under Flow Conditions (2023)

Supplementary Figure 3 from Mechanisms by which E-Selectin Regulates Diapedesis of Colon Cancer Cells under Flow Conditions
EXPERIMENTAL STUDIES OF CAPSIZING OF INTACT SHIPS IN HEAVY SEAS (1972)

Abstract : Experiments intended to shed light on the mechanism of the capsizing of an intact ship in heavy seas are described. These experiments were carried out in San Francisco Bay using a radio controlled model of a cargo liner. Three capsizing modes were observed: low cycle resonance, pure stability loss, and broaching. All modes are seen to be strongly influenced by the effect of quartering or following seas in attenuating the ship's stability. Some conclusions are reached concerning the value of such experiments in predicting minimum stability standards.
Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting (2015)

The goal of precipitation nowcasting is to predict the future rainfall intensity in a local region over a relatively short period of time. Very few previous studies have examined this crucial and challenging weather forecasting problem from the machine learning perspective. In this paper, we formulate precipitation nowcasting as a spatiotemporal sequence forecasting problem in which both the input and the prediction target are spatiotemporal sequences. By extending the fully connected LSTM (FC-LSTM) to have convolutional structures in both the input-to-state and state-to-state transitions, we propose the convolutional LSTM (ConvLSTM) and use it to build an end-to-end trainable model for the precipitation nowcasting problem. Experiments show that our ConvLSTM network captures spatiotemporal correlations better and consistently outperforms FC-LSTM and the state-of-the-art operational ROVER algorithm for precipitation nowcasting.
Communication et lien social : usages des machines à communiquer (1992)

Actes du colloque organise a Paris en 1991 par l'Association Descartes et la Cite des sciences et de l'industrie
Glial Dysfunction in the Mouse Habenula Causes Depressive-Like Behaviors and Sleep Disturbance (2014)

The lateral habenula (LHb) regulates the activity of monoaminergic neurons in the brainstem. This area has recently attracted a surge of interest in psychiatry because studies have reported the pathological activation of the habenula in patients with major depression and in animal models. The LHb plays a significant role in the pathophysiology of depression; however, how habenular neurons are activated to cause various depression symptoms, such as reduced motivation and sleep disturbance, remain unclear. We hypothesized that dysfunctional astrocytes may cause LHb hyperactivity due to the defective uptake activity of extracellular glutamate, which induces depressive-like behaviors. We examined the activity of neurons in habenular pathways and performed behavioral and sleep analyses in mice with pharmacological and genetic inhibition of the activity of the glial glutamate transporter GLT-1 in the LHb. The habenula-specific inhibition of GLT-1 increased the neuronal firing rate and the level of c-Fos expression in the LHb. Mice with reduced GLT-1 activity in the habenula exhibited a depressive-like phenotype in the tail suspension and novelty-suppressed feeding tests. These animals also displayed increased susceptibility to chronic stress, displaying more frequent avoidant behavior without affecting locomotor activity in the open-field test. Intriguingly, the mice showed disinhibition of rapid eye movement sleep, which is a characteristic sleep pattern in patients with depression. These results provide evidence that disrupting glutamate clearance in habenular astrocytes increases neuronal excitability and depressive-like phenotypes in behaviors and sleep.
Advanced-generation breeding strategies - breeding population size, structure and management. (2007)

This chapter describes the factors that should be considered when developing long-term tree breeding strategies. Topics covered include: (1) the general concepts of advanced-generation breeding strategies; (2) breeding population size; (3) breeding population structure; (4) mating designs for advanced-generation breeding; and (5) making advanced-generation selections.
The Factor Graph Approach to Model-Based Signal Processing (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The message-passing approach to model-based signal processing is developed with a focus on Gaussian message passing in linear state-space models, which includes recursive least squares, linear minimum-mean-squared-error estimation, and Kalman filtering algorithms. Tabulated message computation rules for the building blocks of linear models allow us to compose a variety of such algorithms without additional derivations or computations. Beyond the Gaussian case, it is emphasized that the message-passing approach encourages us to mix and match different algorithmic techniques, which is exemplified by two different approaches—steepest descent and expectation maximization—to message passing through a multiplier node. </para>
Towards just-in-time middleware architectures (2005)

Middleware becomes increasingly important in building distributed applications. Today, conventional middleware systems are designed, implemented, and packaged prior to their applications. We argue that with this middleware construction paradigm it is often difficult to meet the challenges imposed by application specific customization requirements. We propose to reverse this paradigm by automatically synthesizing middleware structures as the result of reasoning about the distribution needs of the user application of middleware. We term this type of post-postulated middleware Just-in-time middleware (JiM). In this paper, we present our initial design and present an evaluation of the JiM paradigm through Abacus, a CORBA middleware implementation based on the aspect oriented refactoring of an industrial strength object request broker. In addition, we present Arachne, the Abacus synthesizer, which integrates source analysis, feature inference, and implementation synthesis. Our evaluations show that, through automatic synthesis alone, Abacus is able to support diversified application domains with very flexible architectural compositions and versatile resource requirements as compared to conventional pre-postulated approaches.
Nanostructured biohybrid material with wide-ranging antiviral action (2023)

Respiratory pathogens kill more people than any other infectious agent each year worldwide. Development of novel, economically friendly, sustainable, and highly efficient materials against viruses is a major challenge. Herein, we describe a nanostructured material composed of very small crystalline phosphate copper nanoparticles synthesized using a new biohybrid technology that employs a biological agent for its formation at room temperature in aqueous media. The evaluation of different enzymes in the final preparation of the nanomaterial or even in synthetic methods was performed. Biochemical characterization revealed the formation of Cu species in the protein network. The best biomaterial synthesized using a lipase called BioCuNPs showed excellent inhibition capacity against functional proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); for example, assent 3-chymotrypsin like protease (3CLpro) complete inhibition was achieved by using 5 µg/mL, or acetone (ACE)–spike protein interaction was inhibited by more than 80% in the presence of 400 µg/mL of BioCuNPs. Taking these in vitro results into account, an efficacy analysis against human coronavirus 229E (HCoV-E229) coronavirus was performed. A virus reduction of 99% was obtained in 5 min. Additionally, SARS-CoV-2 virus was tested to demonstrate high efficiency, with > 99% inhibition in 15 min using 500 microgram of material. To determine the wide applicability of this nanohybrid against viruses, an evaluation was carried out against a non-enveloped virus such as Human Rhinovirus (HRV-14), obtaining a virus reduction of 99.9% in 5 min. Finally, the virucidal capacity against different bacteriophages was also evaluated, obtaining an excellent inhibition effect against Phage ϕX174 (99.999% reduction in 5 min).
System-level cost analysis and design exploration for three-dimensional integrated circuits (3D ICs) (2009)

Three-dimensional integrated circuit (3D IC) is emerging as an attractive option for overcoming the barriers in interconnect scaling. The majority of the existing 3D IC research is focused on how to take advantage of the performance, power, smaller form-factor, and heterogeneous integration benefits that offered by 3D integration. However, all such advantages ultimately have to translate into cost savings when a design strategy has to be decided: Is 3D integration a cost effective technology for a particular IC design? Consequently, system-level cost analysis at the early design stage is imperative to help the decision making on whether 3D integration should be adopted. In this paper, we study the design estimation method for 3D ICs at the early design stage, and propose a cost analysis model to study the cost implication for 3D ICs, and address the following cost-related problems related to 3D IC design: (1) Do all the benefits of 3D IC design come with a much higher cost? (2) How can 3D integration be achieved in a cost-effective way? (3) Are there any design options to compensate the extra 3D bonding cost? A cost-driven 3D IC design flow is also proposed to guide the design space exploration for 3D ICs toward a cost-effective direction.
Resonance reflector for suppressing undesired rotational lines from TEA CO2 lasers (1974)

A resonant reflector made of germanium is reported which allows selection of one single rotational line out of a TEA CO2 laser. The reflector has to be temperature stabilized within ± 0.1 °C. Selection of one, two or three rotational lines simultaneously is possible by varying the temperature.
Cell types as species: Exploring a metaphor (2022)

The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.
Language Identification using Warping and the Shifted Delta Cepstrum (2005)

This paper proposes the novel use of feature warping for automatic language identification, in combination with the shifted delta cepstrum (SDC) and perceptual linear predictive coefficients in a Gaussian mixture model (GMM) based system. Experimental results on various configurations of front-end techniques reported herein demonstrate that, besides providing robustness against channel mismatch and noise as found in existing literature, feature warping is useful more generally as a technique for pre-mapping data for improved compatibility with a GMM back-end. The configuration reported in this paper provides a language identification performance of 76.4% using the OGI/NIST database, a 46.5% relative reduction in error rate when compared with a benchmark system employing Mel frequency cepstral coefficients and the SDC
Determination of the Absolute Configuration of u-fac-[Co(ida)(mdien)]+ by 1H NMR Spectroscopy (1987)

Abstract Iminodiacetic acid containing asymmetric carbon with S chirality (H2ida(Cs); HOOCCH2NHC*HDCOOH) was prepared by stereospecific deuteration of (−)563CD-mer(O)cis(Nc)-[Co(ida)(edma)]. Using this H2ida(Cs), u-fac-[Co(ida(Cs))(mdien)]+ was prepared and optically resolved. On the basis of the 1H NMR spectra of the chelating ida(Cs), the absolute configuration of the (−)550CD isomer was assigned to ΔΛΔ.
Supplementary Methods from Resistance Mechanisms to SYK Inhibition in Acute Myeloid Leukemia (2023)

&lt;p&gt;Computational analysis methods for RNAseq, WES, synergy analyse, Masspec information used for phosphoproteomic studies.&lt;/p&gt;
Authenticity and provenance in long term digital preservation: modeling and implementation in preservation aware storage (2009)

A growing amount of digital objects is designated for long term preservation- a time scale during which technologies, formats and communities are very likely to change. Specialized approaches, models and technologies are needed to guarantee the long-term understandability of the preserved data. Maintaining the authenticity (trustworthiness) and provenance (history of creation, ownership, accesses and changes) of the preserved objects for the long term is of great importance, since users must be confident that the objects in the changed environment are authentic. We present a novel model for managing authenticity in long term digital preservation systems and a supporting archival storage component. The model and archival storage build on OAIS, the leading standard in the area of long-term digital preservation. The preservation aware storage layer handles provenance data, and documents the relevant events. It collocates provenance data (and other metadata) together with the preserved data in a secure environment, thus enhancing the chances of their co-survival. Handling authenticity and provenance at the storage layer reduces both threats to authenticity and computation times. This work addresses core issues in long-term digital preservation in a novel and practical manner. We present an example of managing authenticity of data objects during data transformation at the storage component.1 1.
Cover Picture: Making the True “CP” Ligand (Angew. Chem. Int. Ed. 37/2006) (2006)

The quest for cyaphide , the phosphorus equivalent of cyanide, has been a challenge for many years. In their Communication on page 6159 ff., H. Grützmacher and co‐workers describe their approach to prepare the first stable terminal cyaphide complex [RuH(CP)(dppe) 2 ] (dppe=bis(1,2‐diphenylphosphinoethane)). In an initial silyl‐protected complex, the Ru center was P‐coordinated by the CP ligand. Removal of the silyl group yielded the C‐coordinated Ru complex, whose structure is shown on the cover picture.
Highly Active and Stable DNAzyme−Carbon Nanotube Hybrids (2005)

We report herein the generation and characterization of DNAzyme-carbon nanotube conjugates. Biotinylated DNAzyme was attached to streptavidin-functionalized MWNTs. The resultant DNAzyme-MWNT conjugates exhibited Michaelis-Menten kinetics and multiple catalytic turnovers. The specific activity of the nanoscale conjugates was approximately 1/3 of that for freely soluble DNAzyme. Such high activity may allow myriad applications ranging from the directed assembly of nanomaterials to nanoscale cellular therapeutics that rely on the RNA cleaving ability of DNAzymes.
Real-Time Relative Positioning with WSN (2008)

This paper addresses a scenario where a wireless sensor network (WSN) is used to implement a real-time relative positioning system. Its goal is to obtain relative coordinates of objects (the WSN nodes) in which the nodes are generally moving relatively to each other. To accomplish this, the distance among nodes is measured and its relative position is computed allowing the representation of their spatial distribution. The test platform uses Crossbow's motes to which special ultrasound (US) boards have been adapted. The US is thus the process used to measure distances in this system. Some of the issues addressed by this work are: precise time-synchronization between nodes, distance measurement procedure, positioning algorithms and its implementation on the TinyOS, operating system used in the Crossbow's motes. Test shave shown that object positioning could be obtained with errors below 2% and using a computing time of about 1s per network node, on average.
Deoxygenation recruitment patterns of abdominal and neck muscles during four bed exercises (2020)

Abdominal muscles are often weak in critically ill patients and in several respiratory conditions. Strengthening these muscles can optimize the appositional action of the diaphragm and active expiration. We aimed to compare deoxygenation recruitment patterns of two abdominal muscles, the rectus abdominis (RA) and external oblique (EO), and of the sternomastoid (SM) during 4 bed exercises. <b>Methods:</b> Eighteen adults performed 30 repetitions of 4 exercises: expiratory threshold loading (ETL), isometric trunk flexion, isometric neck flexion, and neuromuscular electrical stimulation of the abdominal muscles (NMES). ETL, trunk flexion and neck flexion were performed at 50+5% of the maximal expiratory pressure/maximal voluntary effort and NMES was applied at the highest intensity tolerated. Near infrared spectroscopy was used to measure muscle oxygen saturation (SmO2), and changes deoxygenated hemoglobin (HHb) in the RA, EO, and SM. Greater muscle recruitment can increase HHb and decrease SmO2. <b>Results:</b> The greatest increase in deoxy-Hb and the greatest decrease in SmO2 occurred during trunk flexion for the abdominal muscles, and during neck flexion for the SM. <b>Conclusions:</b> Trunk flexion and neck flexion were most effective for recruiting abdominal and neck muscles, respectively. NMES and ETL induced varied or lesser responses compared to trunk flexion. These exercises should be explored in patients with respiratory compromise.
New preparation method for organic–inorganic layered compounds by organo derivatization reaction of Zn(OH)2 with carboxylic acids (2000)

A new preparation method for organic–inorganic nanohybrids has been developed by the reaction of Zn(OH)2 with various carboxylic acids. The resulting layered structures are similar to the reaction products of Zn(OH)2 or layered double hydroxides (LDHs) with acyl chlorides. The interlayer spacings of the reaction products of Zn(OH)2 with straight chain monocarboxylic acids were in the range 1.19–4.33 nm, and with dicarboxylic acids were 0.71–1.48 nm. These values depended on the length of the organic compounds and the number of carboxyl groups. IR spectra showed new peaks due to the RCOO–Zn vibration at ca. 1400 and 1550 cm−1 indicating that the hydroxy groups had reacted with the carboxylic acids. SEM images of the reaction products of Zn(OH)2 with carboxylic acids showed that they were of plate-like morphology similar to the LDHs. On the other hand, the morphology of the reaction products of Zn(OH)2 with bulky carboxylic acids were fibrous, although they also had layered structures.