gebhart/patrepeval huggingface dataset:
Cell‐Selective siRNA Delivery Using Glycosylated Dynamic Covalent Polymers Self‐Assembled In Situ by RNA Templating (2020)

Dynamic covalent libraries enable exploring complex chemical systems from which bioactive assemblies can adaptively emerge through template effects. In this work, we studied dynamic covalent libraries made of complementary bifunctional cationic peptides, yielding a diversity of species from macrocycles to polymers. Although polymers are typically expressed only at high concentration, we found that siRNA acts as a template in the formation of dynamic covalent polymers at low concentration in a process guided by electrostatic binding. Using a glycosylated building block, we were able to show that this templated polymerization further translates into the multivalent presentation of carbohydrate ligands, which subsequently promotes cell uptake and even cell-selective siRNA delivery.
Development of Prosthetic Finger with Actuator (2019)

A new prosthetic finger including an actuator in the proximal phalanx has been developed for finger amputees. By designing the prosthetic finger with the actuator inside, the mounting part does not need to include the actuators; this leads to a simple and compact design of the prosthetic finger. Thus, the comfort of wearing and the aesthetics for the user are improved. The proposed prosthetic finger is designed as under-actuated mechanism having four degree-of-freedoms (4-DOFs) with the distal interphalangeal joint (DIP joint) driven directly (1-DOF) and the proximal interphalangeal joint (PIP joint) and the metacarpophalangeal joint (MCP joint) driven indirectly (3-DOFs). The indirect driving is realized using leaf springs. The force from the actuator is transferred to each phalanx by the tendon. The finger enables self-adaptive grasping according to object shapes as well as flexion/extension motions and adduction/ abduction motions. The prototype was manufactured using 3D printing and machining. Experiments show the feasibility of the proposed prosthetic finger.
Effective Spoken Language Labeling with Deep Recurrent Neural Networks (2017)

Understanding spoken language is a highly complex problem, which can be decomposed into several simpler tasks. In this paper, we focus on Spoken Language Understanding (SLU), the module of spoken dialog systems responsible for extracting a semantic interpretation from the user utterance. The task is treated as a labeling problem. In the past, SLU has been performed with a wide variety of probabilistic models. The rise of neural networks, in the last couple of years, has opened new interesting research directions in this domain. Recurrent Neural Networks (RNNs) in particular are able not only to represent several pieces of information as embeddings but also, thanks to their recurrent architecture, to encode as embeddings relatively long contexts. Such long contexts are in general out of reach for models previously used for SLU. In this paper we propose novel RNNs architectures for SLU which outperform previous ones. Starting from a published idea as base block, we design new deep RNNs achieving state-of-the-art results on two widely used corpora for SLU: ATIS (Air Traveling Information System), in English, and MEDIA (Hotel information and reservation in France), in French.
CGA-PoseNet: Camera Pose Regression via a 1D-Up Approach to Conformal Geometric Algebra (2023)

We introduce CGA-PoseNet, which uses the 1D-Up approach to Conformal Geometric Algebra (CGA) to represent rotations and translations with a single mathematical object, the motor, for camera pose regression. We do so starting from PoseNet, which successfully predicts camera poses from small datasets of RGB frames. State-of-the-art methods, however, require expensive tuning to balance the orientational and translational components of the camera pose.This is usually done through complex, ad-hoc loss function to be minimized, and in some cases also requires 3D points as well as images. Our approach has the advantage of unifying the camera position and orientation through the motor. Consequently, the network searches for a single object which lives in a well-behaved 4D space with a Euclidean signature. This means that we can address the case of image-only datasets and work efficiently with a simple loss function, namely the mean squared error (MSE) between the predicted and ground truth motors. We show that it is possible to achieve high accuracy camera pose regression with a significantly simpler problem formulation. This 1D-Up approach to CGA can be employed to overcome the dichotomy between translational and orientational components in camera pose regression in a compact and elegant way.
An experimental and clinical evaluation of immunomodulating potential of ascorbic acid (1998)

Objectives: To find the effects of ascorbic acid on immune system in rabbits and human volunteers.

Methods: In humans, humoral immunity was measured by immunoglobulin estimation (IgG, IgM, IgA) using tripantigen plates and cell mediated immunity by total lymphocyte count and T-cell count. In rabbits, widal agglutination test using typhoid-H antigen and Dinitro chlorobenzene (DNCB) and tuberculin skin sensitivity tests were performed as measurement of humoral and cell-mediated immunity, respectively. 

Result: Administration of ascorbic acid 500 mg thrice daily orally for 21 days increased serum immunoglobulin in human subjects. In rabbits, ascorbic acid administration in the dose of 200 mg/kg/day orally for 21 days caused a rise in antibody titre. No effect on cell mediated immunity was found in human as well as animal models.

Conclusion: Ascorbic acid appears to stimulate humoral immunity through increased antibody synthesis particularly IgG, IgA and IgM types and also by activating the macrophages.
Electronic characterization of silicon doped beyond the solubility limit via femtosecond laser irradiation (2008)

We have performed temperature-dependent resistivity measurements of silicon after doping with sulfur via femtosecond laser irradiation. Results are consistent with a theoretically predicted binding energy for sulfur donors of 100 meV below the conduction-band edge.
Harmonic Testing for Continuous Well and Reservoir Monitoring (2002)

Abstract Harmonic testing for obtaining dynamic reservoir information was first proposed some thirty years ago. Although not much used in the oil industry, interest in the method is revived periodically, mostly for the determination of skin effect and near-wellbore permeability. This paper looks at the practical aspects of using periodic rate variations for testing oil wells. It is shown that such tests can provide the same information as conventional well tests and can be interpreted in the same way. Their main advantage is that they do not require fluids to be brought to surface in exploration or early appraisal testing, or wells to be shut-in in production testing. They also provide data that are less affected by measurement errors and wellbore effects such as multiphase flow or phase redistribution. The main limitation is that, for the same radius of investigation, harmonic tests are significantly longer than conventional tests. Consequently, they cannot be used for reservoir characterization in exploration and appraisal wells. They appear well suited, however, for monitoring reservoir changes from production wells.
Mechanistic Insight into Trimethylamine N -Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3 (2015)

Trimethylamine N-oxide (TMAO) is an important nitrogen source for marine bacteria. The products of TMAO metabolized by bacteria are part of the precursors of the greenhouse gas nitrous oxide. It is unclear how TMAO is recognized and imported by bacteria. TmoX is the substrate-binding protein of a TMAO-specific transporter. Here, the substrate specificity of TmoX of Ruegeria pomeroyi DSS-3 was characterized. The TMAO-binding mechanism of TmoX was studied by biochemical, structural, and mutational analyses. Moreover, our results suggest that the TMAO-binding mechanism may have universal significance in marine bacteria. This study sheds light on how marine microorganisms utilize TMAO and should lead to a better understanding of marine nitrogen cycling.
CONTRAST OPTIMISATION FOR BACKSCATTERED ELECTRON IMAGING OF RESIN EMBEDDED CELLS (1999)

Adhesions between cells and substrates can be observed when the undersurfaces of resin-embedded cells are examined using high emission current backscattered electron (HCBSE) imaging with a Field Emission Scanning Electron Microscope (FESEM). The aim of this study was to find a fixation procedure that would optimise the contrast of cell adhesion areas when observed at low beam energies as well as the nucleus and stress fibres of the cell cytoskeleton viewed at medium beam energies. Balb/c 3T3 and L929 fibroblast cells were cultured on plastic discs, fixed and stained with one of six variant protocols, comprising of a variety of chemical fixatives, mordants and stains. Following dehydration the cells were embedded in acrylic resin. After the plastic discs were removed, the specimens were coated with Au/Pd, and examined in a FESEM using the HCBSE technique, at accelerating voltages of 4, 8 and 15 kV. The application of fixation protocol variants resulted in obtaining different contrast levels of the adhesion areas. The addition of 0.1% OsO 4 to the primary fixative was beneficial to the cells’ contrast, but the best results were obtained from the additional binding of osmium in the OTO method. The different focal adhesion organisation observed in Balb/c 3T3 and L929 cells may have resulted from different effects of the fixatives on the different cell types.
Unsupervised Monocular Depth Estimation Using Attention and Multi-Warp Reconstruction (2021)

Monocular depth estimation has become one of the most studied topics in computer vision. Most approaches treat depth prediction as a fully supervised regression problem requiring vast amounts of corresponding ground-truth depth and image pairs for training. Unsupervised monocular depth estimation has emerged as a promising alternative that eliminates dataset limitations. This paper proposes an end-to-end unsupervised deep learning framework integrating attention blocks and multi-warp loss for monocular depth estimation. In this framework, to explore more general contextual information among the feature volumes, an attention block that sequentially refines the feature maps along the channel and spatial dimensions is inserted after the first and last stages of the network encoder. Additionally, to further utilize the errors in the original disparity estimation from the network, a novel multi-warp reconstruction strategy is designed for the loss function. The experimental results evaluated on the KITTI, CityScapes and Make3D datasets demonstrate the state-of-the-art performance and satisfactory generalization ability of our proposed method.
Quantization effects in metal/a-Si:H/metal devices (1992)

Abstract We present experimental results showing that metal/p+/metal amorphous silicon (a-Si: H) memory structures exhibit room temperature quantized electron transport associated with quantized resistance. The quantization of resistance is observed at values of R = h/2ie2, where i is an integer or a half integer.
Structural Segmentation of Musical Audio by Constrained Clustering (2008)

We describe a method of segmenting musical audio into structural sections based on a hierarchical labeling of spectral features. Frames of audio are first labeled as belonging to one of a number of discrete states using a hidden Markov model trained on the features. Histograms of neighboring frames are then clustered into segment-types representing distinct distributions of states, using a clustering algorithm in which temporal continuity is expressed as a set of constraints modeled by a hidden Markov random field. We give experimental results which show that in many cases the resulting segmentations correspond well to conventional notions of musical form. We show further how the constrained clustering approach can easily be extended to include prior musical knowledge, input from other machine approaches, or semi-supervision.
Towards migrating object-oriented frameworks to enable synthesis of product line members (2015)

For many software engineers, object-oriented frameworks represent the highest level of achievement in extensible design. The framework designers become experts in a specific application domain and design cooperating classes that impose specific responsibilities and collaborations for those seeking to extend the framework. In short, once a framework matures, it has complicated usage patterns that must be followed otherwise nothing works. Turning a framework into a software product line is challenging because of the difficulty in coding these complex behaviors and enabling the configuration of product line members using the framework. We propose to support this migration process by showing how to design a repository of modular units to synthesize member applications compositionally. These units are formalized using combinatory logic synthesis, a type-based approach to component-oriented synthesis. We demonstrate the feasibility of our approach with a Java-based product line for which we can automatically synthesize member applications.
Ciprofloxacin Release from Polymeric Films. Modeling and Pharmaceutical Parameters Determination (2020)

Ciprofloxacin (Cipro) is a broad-spectrum antibiotic used against both Gram (+) and Gram (−) bacteria. Its biological half-life is very short (4–5 h) and its conventional administration forms present a limited absorption efficiency. For this reason, the aim of this work was to study other administration strategies based on topical films. Sodium alginate (SA), a naturally occurring polymer, and a recombinant elastin-like polymer (rELP) produced by advanced genetic engineering techniques were evaluated as potential carrier systems. The films were obtained by the casting technique, adding the Cipro by direct dispersion in the polymer solution using 16.6% w/w rELP or 1.5% w/w SA. The in vitro release assays were performed at 37 °C in physiological solution and with orbital shaking at 90 rpm. Cipro concentration was determined by ultraviolet (UV) spectrophotometry at 276 nm. The release profiles were analyzed and adjusted using the Lumped model developed and validated by our research group. Pharmaceutical interest parameters were calculated and compared for both polymer-Cipro systems: the time required to reach 80% of the drug dissolved (t80%), the dissolution efficiency (DE) and the mean dissolution time (MDT). The SA-Cipro platform released the 80% of the drug in 35 min, while this parameter was 209 min for the rELP-Cipro system. The MDT80% was 8.9 and 53 min for the SA-Cipro and rELP-Cipro, respectively, while the DE, evaluated at 200 min, was 66.6 and 58.8 for each platform, respectively. These parameter values demonstrate that the rELP films were able to modulate the drug release rate and for the SA ones, release can be considered immediate. Therefore, both systems are promising strategies for the topical application of Cipro.
'Superpolyamines'. Macrocyclic polyamines induce highly efficient actin polymerization (1985)

Macrocyclic polyammonium ions induce much more efficient polymerization of actin than the natural polyamines, behaving thus as 'superpolyamines'. The processes observed display large increases in rate, marked structural dependence, macrocyclic and ditopic binding effects and positive cooperativity.
Arginine methylation enhances the RNA chaperone activity of the West Nile virus host factor AUF1 p45 (2016)

A prerequisite for the intracellular replication process of the Flavivirus West Nile virus (WNV) is the cyclization of the viral RNA genome, which enables the viral replicase to initiate RNA synthesis. Our earlier studies indicated that the p45 isoform of the cellular AU-rich element binding protein 1 (AUF1) has an RNA chaperone activity, which supports RNA cyclization and viral RNA synthesis by destabilizing a stem structure at the WNV RNA's 3'-end. Here we show that in mammalian cells, AUF1 p45 is consistently modified by arginine methylation of its C terminus. By a combination of different experimental approaches, we can demonstrate that the methyltransferase PRMT1 is necessary and sufficient for AUF1 p45 methylation and that PRMT1 is required for efficient WNV replication. Interestingly, in comparison to the nonmethylated AUF1 p45, the methylated AUF1 p45(aDMA) exhibits a significantly increased affinity to the WNV RNA termini. Further data also revealed that the RNA chaperone activity of AUF1 p45(aDMA) is improved and the methylated protein stimulates viral RNA synthesis considerably more efficiently than the nonmethylated AUF1 p45. In addition to its destabilizing RNA chaperone activity, we identified an RNA annealing activity of AUF1 p45, which is not affected by methylation. Arginine methylation of AUF1 p45 thus represents a specific determinant of its RNA chaperone activity while functioning as a WNV host factor. Our data suggest that the methylation modifies the conformation of AUF1 p45 and in this way affects its RNA binding and restructuring activities.
Electrical connection using submicron porous gold bumps for wafer-level packaging of mems using anodically-bondable LTCC wafer (2011)

An anodically-bondable low temperature cofired ceramic (LTCC) wafer offers a versatile, clean and reliable wafer-level hermetic packaging for MEMS. This paper reports electrical connection in parallel with anodic bonding between MEMS on a Si wafer and vias in the LTCC wafer using porous Au bump. The Au bump is made of submicron Au particles, and so compliant as it easily absorbs large height difference. The LTCC wafer with the Au bumps and an SOI wafer with Au/Pt/Cr pads and diaphragms were anodically bonded. 100% yield of both electrical connection and hermetic sealing was demonstrated. Heat cycle test confirmed the reliability of both electrical connection and hermeticity. In addition, the transfer of the porous Au bumps from a mother glass wafer to a target LTCC wafer was demonstrated. This method dispenses with the fabrication of the porous Au bumps by users, which includes non-standard processes.
[Myocardial necrosis due to tocolysis with fenoterol (author's transl)]. (1979)

95 women had undergone treatment with beta-adrenergic Fenoterol for periods lasting as long as 9 weeks in order to try to avoid premature labour. Electrocardiographic studies and regular controls of the kinase isoenzymes of creatin which is specific for cardiac muscle were carried out in order to avoid myocardial damage, as was MB creatinkinase. In no case was a pathological rise in the activity of the enzyme shown even after full doses of the substance had been given for a long time.
Supporting scalable activity modeling in simulators (2009)

Simulators have been widely used for recreating conditions for the purpose of testing in different domains. Emerging applications require simulators to support large scale and complex activities, and to support testing and training at multiple levels of abstractions. Modeling such large scale scenarios requires participation of multiple simulators operating toward a common goal, and scalability is a fundamental issue. Modeling such scenarios results in large volumes of queries and updates to the system and is impacted by computationally intensive planning algorithms across large geographical areas. The focus of this thesis is to address scalability challenges across multiple levels in large scale activity simulations. Using evacuation as a driving activity, we will address scalability in both integrated simulations and single simulators. 
The first part of the thesis addresses scalability in a micro simulator that models an activity in micro time slices and on high resolution geographical spaces. In systems where agents drive the activity by programmed behavior, scalability issues become pronounced with the presence of large number of agents, and complex resource intensive operations like path planning. In this thesis we develop an efficient path reuse strategy which aids participating agents in quickly computing evacuation routes to common safe destinations. The techniques proposed in this thesis have been evaluated in the context of an agent based activity simulator (DrillSIM) that we have designed. 
The second part of the thesis deals with scalability at the integrated simulation level. Here activity planning is affected by the presence of multiple simulators which operate on heterogeneous data sources. Specifically, the activities must span several geographical maps, and the heterogeneity and scale of participating geographies contribute to scalability challenges. This thesis will address the multi-geography route planning problem in the context of a large scale evacuation, where different simulators both at micro and macro level participate. The proposed solution involves an efficient algorithm for planning paths across different geographies along with precomputation strategies to speed up planning. We study our strategies in the MetaSIM platform, a web-based platform for the integration of simulation tools developed for disaster response, operating on a campus geography.
The Yin and Yang of Cystic Fibrosis Transmembrane Conductance Regulator Function (2013)

The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) is a cAMP-activated anion channel, primarily expressed in ciliated epithelial cells that have an endoluminal lining of mucus. Genetic mutations in CFTR are known to induce its peripheral and/or endoplasmic reticulum–associated degradation affecting its cell surface expression and/or stability, resulting in the pathological manifestations of CF lung disease, including hypohydration and increased viscosity of mucus, predisposing affected individuals to recurrent infections. Recent studies have identified low levels of CFTR expression in inflammatory cells such as T cells, neutrophils, and macrophages (1–3), suggesting an additional role for CFTR in the pathogenesis of chronic inflammatory CF lung disease. CFTR has also been suggested to mediate internalization and phagocytosis (4, 5) of Pseudomonas aeruginosa (Pa), a common CF pathogen. A recent study suggests that a bacterial toxin, Cif (PA2934) secreted in outer membrane vesicles by Pa, reduces CFTR-mediated chloride secretion by human airway epithelial cells (6). In this issue of the Journal, Le Gars and colleagues (pp. 170–179) describe a novel mechanism for proteolytic cleavage of CFTR that disables the channel function (7).
In vivo assessment of wall shear stress in the atherosclerotic aorta using flow‐sensitive 4D MRI (2010)

Our purpose was to correlate atherogenic low wall shear stress (WSS) and high oscillatory shear index (OSI) with the localization of aortic plaques. Flow-sensitive four-dimensional MRI was used to acquire three-dimensional blood flow in the aorta of 62 patients with proven aortic atherosclerosis and 31 healthy volunteers. Multiplanar data analysis of WSS magnitude and OSI in 12 wall segments was performed in analysis planes distributed along the aorta. Disturbed WSS and OSI were defined as areas exposed to low WSS magnitude and high OSI beyond individual 15% thresholds. Planewise analysis revealed a good correlation (r = 0.85) of individual low WSS magnitude but not of high OSI with plaque distribution. Although plaques occurred only rarely in the ascending aorta, the incidence of low WSS magnitude and high OSI was similar to findings in other aortic segments where plaques occurred more frequently. Case-by-case comparisons of plaque location and critical wall parameters revealed a shift of atherogenic WSS magnitude (78% of all cases) and OSI (91%) to wall segments adjacent to the atheroma. Our results indicate that the predictive value of WSS for plaque existence depends on the aortic segment and that locations of critical wall parameters move to neighboring segments of regions affected by atherosclerosis.