gebhart/patrepeval huggingface dataset:
In Vitro Comparison of a Novel Single Probe Dual-Energy Lithotripter to Current Devices (2018)

Single probe dual-energy devices, such as Trilogy and ShockPulse, represent the next generation of lithotripters. Trilogy more efficiently cleared stone than currently available devices, which could be explained by its larger probe diameter and greater downward tip displacement during both US and impactor functions.
Correction of the Exon 2 Duplication in DMD Myoblasts by a Single CRISPR/Cas9 System (2017)

Exonic duplications account for 10%-15% of all mutations in Duchenne muscular dystrophy (DMD), a severe hereditary neuromuscular disorder. We report a CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-based strategy to correct the most frequent (exon 2) duplication in the DMD gene by targeted deletion, and tested the efficacy of such an approach in patient-derived myogenic cells. We demonstrate restoration of wild-type dystrophin expression at transcriptional and protein level in myotubes derived from genome-edited myoblasts in the absence of selection. Removal of the duplicated exon was achieved by the use of only one guide RNA (gRNA) directed against an intronic duplicated region, thereby increasing editing efficiency and reducing the risk of off-target effects. This study opens a novel therapeutic perspective for patients carrying disease-causing duplications.
Subpopulation Data Poisoning Attacks (2021)

Machine learning systems are deployed in critical settings, but they might fail in unexpected ways, impacting the accuracy of their predictions. Poisoning attacks against machine learning induce adversarial modification of data used by a machine learning algorithm to selectively change its output when it is deployed. In this work, we introduce a novel data poisoning attack called a \emph{subpopulation attack}, which is particularly relevant when datasets are large and diverse. We design a modular framework for subpopulation attacks, instantiate it with different building blocks, and show that the attacks are effective for a variety of datasets and machine learning models. We further optimize the attacks in continuous domains using influence functions and gradient optimization methods. Compared to existing backdoor poisoning attacks, subpopulation attacks have the advantage of inducing misclassification in naturally distributed data points at inference time, making the attacks extremely stealthy. We also show that our attack strategy can be used to improve upon existing targeted attacks. We prove that, under some assumptions, subpopulation attacks are impossible to defend against, and empirically demonstrate the limitations of existing defenses against our attacks, highlighting the difficulty of protecting machine learning against this threat.
Binding of a Benzoate Dye-Molecule Analogue to Rutile Titanium Dioxide Surfaces (2011)

Scanning tunneling microscopy (STM) has been used to investigate the adsorption of benzoic acid on the rutile TiO2(110)(1 × 1) and the reconstructed TiO2(110)(1 × 2) surfaces. Benzoic acid binds to both surfaces dissociatively via a bridging geometry to two Ti5c sites. At a slightly elevated sample temperature during deposition onto the (110) (1 × 1) surface, a well-ordered (2 × 1) overlayer was formed at saturated benzoate coverage. On the reconstructed (110) (1 × 2) surface, benzoate was observed to adsorb between the (1 × 2) strands leading to a (2 × 2) superstructure at higher coverage. Elongation along the [11̅0] direction in the STM images indicates a rotation of the benzene ring of 90° relative to the carboxylate group, which is reasonably explained by hydrogen bond interactions between terminating O-atoms on the surface and H-atoms of the ring.
Crystallization and preliminary X-ray crystallographic analysis of a putative agmatinase fromDeinococcus radiodurans (2004)

Agmatine, which results from the decarboxylation of arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines. The enzyme agmatinase catalyses the hydrolysis of agmatine to putresine and urea. Recent studies indicate that agmatinase plays important roles in mammals. Human mitochondrial agmatinase shows a considerable level of sequence similarity to bacterial agmatinases, including a putative agmatinase from Deinococcus radiodurans. The putative agmatinase from D. radiodurans has been overexpressed in Escherichia coli and crystallized at 297 K using polyethylene glycol 3000 as a precipitant. X-ray diffraction data were collected to 1.80 A from a crystal grown in the presence of Mn2+ and 1,6-hexanediamine. The crystals are orthorhombic, belonging to the space group P2(1)2(1)2(1), with unit-cell parameters a = 81.77, b = 131.44, c = 168.85 A, alpha = beta = gamma = 90 degrees. A hexameric molecule is likely to be present in the asymmetric unit, giving a crystal volume per protein weight (VM) of 2.15 A3 Da(-1) and a solvent content of 41.8%.
TUPM 7.3 A Remote Electronic Object Emulation Applications (1994)

The design and implementation of a hardware emulation system for CEBw objects is described. The emulator is accessed remotely from a PC-based GUI. It may be easily programmed to combme several CAL objects to emulate common CEBw devices.
A Method for Analyzing Influence of Emotions of Posts in SNS Conversations (2013)

We devised a method for analyzing communication, which focuses on influences between two sequential posts in a conversation on a social-network service (SNS). Posts expressed on an SNS are classified into three emotions: positive, negative, or neutral. Two influences were analyzed: the emotion of a person's preceding post on the emotion of a post from another person, and the emotion of a person's post on the emotion of a subsequent post from the same person. To analyze these influences, the basis of the frequency of emotional transitions of two sequential posts in actual conversational data is evaluated by probability and information entropy analysis. Three tendencies were found: first, a person who posted positively before is likely to post positively again, second, a neutral emotion of a person's post is more likely to be induced when both that person and another person expressed a neutral emotion in the past, third, negative posts do not have a strong influence on the emotion of subsequent posts of that person and other persons. These findings may be useful, for example, in promoting positive conversations.
Efficient Implementation Of The Time-Recursive Capon And Apes Spectral Estimators (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Sleep spindles changes in people with previous COVID-19 infection (2022)

Stage 2 sleep spindles are considered useful biomarkers for the integrity of the central nervous system and for cognitive and memory skills. We investigated sleep spindles patterns in subjects after 12 months of their hospitalization in the intensive care unit (ICU) of the Padova Teaching Hospital due to COVID-19 between March and November 2020. Before the nap, participants (13 hospitalized in ICU - ICU; 9 hospitalized who received noninvasive ventilation - nonlCU; 9 age and sex-matched healthy controls - CTRL, i.e., not infected by COVID-19) underwent a cognitive and psychological as-sessment. During the nap, high-density electroencephalography (EEG) recordings were acquired. Slow (i.e., [9]-[12] Hz) and fast (i.e.,]12-16] Hz) spindles were automatically detected. Spindle density and spindle source reconstruction in brain grey matter were extracted. The psychological assessment revealed a statistical difference comparing CTRL and nonlCU in Beck Depression Inventory score and in the Physical Quality of Life index (p<sub>value</sub> = 0.03). The cognitive assessment revealed a trend of worsening results in executive functions in COVID-19 survivors. Slow spindle density significantly decreased comparing CTRL to COVID-19 survivors (p<sub>value</sub>= 0.001). There were statistically significant differences in EEG source-waveforms fast spindle amplitude onset among the three groups, mainly between CTRL and nonlCU. Clinical Relevance- Our results suggest that nonlCU were more susceptible to the hospitalization experience than ICU participants with a slight effect on cognitive tests. This impacted the spindle generation revealing a decreased density of slow spindles and affecting the generators of fast spindles in COVID-19 survivors especially in nonlCU.
Nutrient sensing anabolic pathway is increased in the elderly following chronic dietary leucine supplementation (2010)

Leucine has been shown to act as a key regulator of the nutrient sensing anabolic pathway. Acute administration of leucine affects the phosphorylation status of several proteins involved in translation initiation that are regulated by the mTOR pathway. We conducted a 14 day pilot study in which we supplemented regular daily meals of community dwelling elders (n=8, 63–76 yrs) with a small amount of leucine (4 g per meal; 3 meals per day; days 2–13). On days 1 and 14, muscle biopsies were obtained in the post‐absorptive state to determine leucine‐induced modulation of the mTOR signaling pathway. After 14 days of leucine supplementation, there was a trend toward increased phosphorylation of mTOR (P=0.06). In addition, the phosphorylation of the downstream effectors 4E‐BP1 (P=0.03) and p70 S6K (P=0.08) were increased. These data suggest that a provision of leucine supplementation facilitates an adaptive change in components of the mTOR signaling pathway in aging human muscle. Grant Funding Source: UTMB Claude D. Pepper Older Americans Independence Center # P30 AG024832 (to D. Paddon‐Jones) and NIH/NCI grant 5R01 CA127971 (to M. Sheffield‐Moore).
Hybrid and mixed‐penalty finite elements for 3‐D analysis of soft hydrated tissue (1993)

Abstract Solution of biomechanics problems involving three‐dimensional (3‐D) behaviour of soft tissue on geometries representative of such tissue in vivo will require the use of numerical methods. Toward this end, a pair of tetrahedral finite elements has been developed. The equations which are used to model the tissue behaviour for both elements are those commonly known as the linear biphasic equations. This model assumes that hydrated soft tissue is a mixture of two incompressible, immiscible phases, and employs mixture theory to derive governing equations for its mechanical behaviour. The finite element techniques applied to these equations for the two elements are the mixed‐penalty method and the hybrid method. Both elements are described here, and the special requirements for 3‐D analysis are discussed. Results obtained by solving canonical problems in two and three dimensions using both elements are presented and compared. Both elements are found to produce excellent results. The hybrid element is also noted to have advantages for non‐linear analyses involving finite deformation which will require solution in the future.
Enhanced efficiency of ultrathin (∼500 nm)-film microcrystalline silicon photonic crystal solar cells (2016)

Abstract Enhancing the absorption of thin-film microcrystalline silicon solar cells at 600–1000 nm wavelengths is very important to the improvement of the energy conversion efficiency. This can be achieved by creating a large number of resonant modes utilizing two-dimensional photonic crystal band edges, which exceeds the Lambertian limit of absorption in random textures. We focus on suppressing the parasitic absorption of back-reflector metal and doped layers in photonic crystal microcrystalline silicon solar cells. We achieve a high active-area current density of 22.6 mA cm −2 for an ultrathin (∼500 nm)-film silicon layer and obtain an active-area efficiency of ∼9.1%, as independently confirmed by the CSMT of AIST.
P2‐076: Development of DNA aptamers that bind to amyloid oligomers (2011)

In this study, we screened DNA aptamers that specifically bind to a-synuclein oligomers. Aptamers are target-binding oligonucleotide molecules that are screened in vitro. Aptamers can have high affinity and specificity against target molecules that are comparable to those of antibodies. Recent research into neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD) have focused on amyloid protein oligomers as the most important targets since their toxicities are higher than those of fibrils. We also focused on the observation that the quantities of amyloid protein oligomers are elevated in the cerebrospinal fluid of AD and PD patients. Detection of soluble oligomers may enable the early diagnosis of neurodegenerative diseases caused by amyloid proteins. First, two rounds of screening by gel-shift assay were carried out to isolate DNA aptamers having high binding affinity against a-synuclein oligomer. We then selected DNA aptamers that specifically bound to a-synuclein oligomer by a competitive aptamer blotting method that we previously developed. The DNA library was incubated with a nitrocellulose membrane onto which was spotted each of three a-synuclein species: monomer, oligomer, and fibril. We extracted the DNA from the oligomer-immobilized spot and amplified it by PCR. This step was repeated three times and the resulting DNA aptamers were sequenced. Screening the library resulted in eight oligomer-specific aptamers that bound strongly to a-synuclein oligomer but showed little or no binding to monomer and fibril. Moreover, we demonstrated that these aptamers bound to a-synuclein oligomers with greater specificity than a commercial anti-oligomer antibody by using beta-sheet rich proteins as competitors. Surprisingly, we found that these aptamers also bound to amyloid ß oligomer, but not its monomer and fibril. We succeeded in developing amyloid oligomer-specific aptamers. Interestingly, these aptamers not only bound to a-synuclein oligomer, which was used as the target molecule, but also to amyloid ß oligomers. The specificity of these aptamers for oligomers was higher than that of a commercial antibody. We believe these aptamers will be useful for the detection of toxic oligomers and our investigation will lead to the development of new diagnostic and therapeutic tools for AD and PD.
Phase Tracking Sequences for 5G NR in 52.6-71 GHz Band: Design and Analysis (2021)

This paper presents a novel approach to the phase tracking reference signal (PTRS) design for phase noise impact compensation in the 5G NR communication systems intended to work in a new 52.6 GHz to 71 GHz frequency band. For detailed problem illustration, the phase noise compensation algorithms are discussed and explained, from the basic common phase error (CPE) compensation to the MMSE-base inter-carrier interference (ICI) filtering. Performance of the different phase noise compensation algorithms is investigated for the baseline PTRS accepted in the current 5G NR specification and compared with the newly proposed approach to the PTRS design. This approach is based on nulling the subcarriers adjacent to the reference signals to minimize influence of the ICI on the estimation process. It was shown that new nulling PTRS design outperforms currently used distributed PTRS structure. In addition, numerical results represent a trade-off between the filter size and the amount of the allocated training resources to achieve better performance. It was shown that proposed PTRS structures and processing algorithms give ICI compensation level very close to optimal scheme and thus, different approaches (such as time domain compensation) may be required for further progress.
Substrate specificity to maintain cellular ATP along the mouse nephron (1988)

To evaluate substrate utilization along the mouse nephron, cellular ATP content was measured under various conditions by the luciferin-luciferase technique. Individual micro-dissected nephron segments were incubated in a modified Hanks' solution (pH 7.4) with or without each of the following substrates: D-glucose, DL-lactate, beta-hydroxybutyrate (HBA), and L-glutamine. ATP production from glucose was minimal in the early proximal tubule (S1), but was substantial in the late proximal tubule (S3). Glutamine and lactate were the preferred substrates in proximal tubules. In contrast, ATP production from glutamine was less than that from the other substrates in distal nephron segments, including medullary and cortical thick ascending limbs of Henle's loop (MTAL and CTAL), distal tubule including the connecting tubule (DT), and cortical and medullary collecting tubules (CCT and MCT). Lactate and HBA were preferred substrates for ATP maintenance in CTAL, MTAL, and DT. Glucose was the best substrate in CCT. In addition, the specific contribution of anaerobic metabolism to maintaining cellular ATP was low in MTAL and CTAL. On the other hand, the glycolytic capacity of CCT and MCT was high. The above results demonstrate the substrate requirements for maintaining cellular ATP content within specific nephron segments.
A compact physically-based bipolar transistor model (2003)

A comprehensive bipolar transistor model for circuit simulation is discussed. The model is physically based and includes new models for the base region, base-collector depletion region, and epitaxial collector region that account for high-current effects. The model has been implemented in the circuit simulator SLICE and shown to model high current densities accurately. The increase in simulation time compared to the Gummel-Poon model is minimized by not requiring iterations within the model code.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Formation of the Conducting Filament in TaOx-Resistive Switching Devices by Thermal-Gradient-Induced Cation Accumulation (2018)

The distribution of tantalum and oxygen ions in electroformed and/or switched TaO <sub>x</sub>-based resistive switching devices has been assessed by high-angle annular dark-field microscopy, X-ray energy-dispersive spectroscopy, and electron energy-loss spectroscopy. The experiments have been performed in the plan-view geometry on the cross-bar devices producing elemental distribution maps in the direction perpendicular to the electric field. The maps revealed an accumulation of +20% Ta in the inner part of the filament with a 3.5% Ta-depleted ring around it. The diameter of the entire structure was approximately 100 nm. The distribution of oxygen was uniform with changes, if any, below the detection limit of 5%. We interpret the elemental segregation as due to diffusion driven by the temperature gradient, which in turn is induced by the spontaneous current constriction associated with the negative differential resistance-type I- V characteristics of the as-fabricated metal/oxide/metal structures. A finite-element model was used to evaluate the distribution of temperature in the devices and correlated with the elemental maps. In addition, a fine-scale (∼5 nm) intensity contrast was observed within the filament and interpreted as due phase separation of the functional oxide in the two-phase composition region. Understanding the temperature-gradient-induced phenomena is central to the engineering of oxide memory cells.
User-Entity Differential Privacy in Learning Natural Language Models (2022)

In this paper, we introduce a novel concept of user-entity differential privacy (UeDP) to provide formal privacy protection simultaneously to both sensitive entities in textual data and data owners in learning natural language models (NLMs). To preserve UeDP, we developed a novel algorithm, called UeDP-Alg, optimizing the trade-off between privacy loss and model utility with a tight sensitivity bound derived from seamlessly combining user and sensitive entity sampling processes. An extensive theoretical analysis and evaluation show that our UeDP-Alg outperforms baseline approaches in model utility under the same privacy budget consumption on several NLM tasks, using benchmark datasets.
Hydrodynamics of bubble columns operated in the heterogeneous regime: new experimental data and up-scaling rules (2016)

International audience
SU‐DD‐A3‐05: Experimental Investigation of a Monoscopic Real‐Time Tumor Tracking Method Combining Occasional X‐Ray Imaging and Continuous External Respiratory Monitoring (2008)

Purpose: To demonstrate the feasibility of a monoscopic method for real‐time tumour tracking, combining occasional x‐ray imaging and continuous external respiratory monitoring, which incorporates two correlations; (1) the correlation between the two projected components of 3D tumour positions on the imager plane ( x p , y p ) and the external respiratory signal ( R ), (2) the correlation between ( x p , y p ) and the unresolved component ( z ∥ ) along the monoscopic view direction using a prior 3D tumour trajectory that can be obtained by either MV/kV imaging or 4DCBCT. Method and Materials: A lung tumor trajectory acquired by a CyberKnife system was fed into 3D motion platform with a marker‐embedded phantom. The associated external respiratory signal was also fed into a separate 1D motion platform. The moving phantom was imaged by MV and kV imagers simultaneously. The 1D motion was also monitored by RPM system. The marker positions from images were extracted by Varian RPM‐Fluoro application. The performance of the proposed method was compared with stereoscopic estimation under various imaging frequencies. Results: The overall estimation error for continuous kV/MV imaging was 0.1±0.3 mm, which reflects the mechanical uncertainty of imaging systems and the marker extraction uncertainty. The error was 0.2±0.7 mm for stereoscopic estimation with 10‐s interval imaging and 0.6±0.7mm for monoscopic estimation with the same update interval. Conclusion: The proposed method can effectively estimate target position and thus be used for tumor tracking with gantry‐mounted single x‐ray imagers that major linac manufacturers offer. Conflict of Interest: Research supported by Varian Medical Systems.
Detection of eight novel palmitoyl protein thioesterase (PPT) mutations underlying infantile neuronal ceroid lipofuscinosis (INCL;CLN1) (2000)

The infantile form of neuronal ceroid lipofuscinosis (INCL; CLN1) is the earliest onset form of the neuronal ceroid lipofuscinoses (NCL), a group of progressive encephalopathies of children. INCL is caused by mutations in the palmitoyl protein thioesterase (PPT) gene, and we report here eight novel INCL mutations in PPT. Five of the mutations, c.456C>A, c.162-163insA, c.174-175delG, c.774-775insA, and a splice acceptor mutation IVS1-2A>G in intron 1, caused the generation of a premature STOP codon either directly or after a frameshift. One mutation was a three-bp insertion in exon 2 (c. 132-133insTGT) leading to insertion of one extra cysteine (Ser44-insCys-Cys45), and another mutation, a 3-bp deletion in exon 3 (c.249-251delCTT), led to deletion of Phe84 in PPT. A splice acceptor mutation IVS6-1G>T in intron 6 can be predicted to cause skipping of exon 7 in PPT. All of these novel mutations were associated with the classical phenotype of INCL, with the first symptoms starting around 12 months of age. The severe phenotypes could be explained by the nature of the novel mutations: five are predicted to lead to premature translational termination, thus abolishing the active site of PPT, and three will probably cause a misfolding of the nascent polypeptide. Thirty-five percent (7/20) of the disease alleles in these 11 families contained the most prevalent c.451C>T missense mutation outside Finland [Das et al., 1998]. Consequently, 31 different mutations underlying INCL have been found so far, the majority leading to classical INCL.