gebhart/patrepeval huggingface dataset:
Ricin A Chain Fused to a Chloroplast-targeting Signal Is Unfolded on the Chloroplast Surface Prior to Import across the Envelope Membranes (1996)

The initial stages of chloroplast protein import involve the binding of precursor proteins to surface-bound receptors prior to translocation across the envelope membranes in a partially folded conformation. We have analyzed the unfolding process by examining the conformation of a construct, comprising the presequence of a chloroplast protein linked to ricin A chain, before and after binding to the chloroplast surface. We show that the presequence is highly susceptible to proteolysis in solution, probably reflecting a lack of tertiary structure, whereas the A chain passenger protein is resistant to extremely high concentrations of protease, unless deliberately unfolded using denaturant. The A chain moiety is furthermore active, indicating that the presence of the presequence does not prevent formation of a tightly folded, native state. In contrast, receptor-bound p33KRA (fusion protein comprising the 33-kDa presequence plus 22 residues of mature protein, linked to the A chain of ricin) is quantitatively digested by protease concentrations that have little effect on the A chain in solution. We conclude that protein unfolding can take place on the chloroplast surface in the absence of translocation and without the aid of soluble factors. The initial stages of chloroplast protein import involve the binding of precursor proteins to surface-bound receptors prior to translocation across the envelope membranes in a partially folded conformation. We have analyzed the unfolding process by examining the conformation of a construct, comprising the presequence of a chloroplast protein linked to ricin A chain, before and after binding to the chloroplast surface. We show that the presequence is highly susceptible to proteolysis in solution, probably reflecting a lack of tertiary structure, whereas the A chain passenger protein is resistant to extremely high concentrations of protease, unless deliberately unfolded using denaturant. The A chain moiety is furthermore active, indicating that the presence of the presequence does not prevent formation of a tightly folded, native state. In contrast, receptor-bound p33KRA (fusion protein comprising the 33-kDa presequence plus 22 residues of mature protein, linked to the A chain of ricin) is quantitatively digested by protease concentrations that have little effect on the A chain in solution. We conclude that protein unfolding can take place on the chloroplast surface in the absence of translocation and without the aid of soluble factors.
Polytopic TSK fuzzy systems: analysis and synthesis (2002)

In this paper we discuss the problem of analysis and synthesis of Takagi-Sugeno-Kang (TSK) systems by using a polytopic representation of the TSK fuzzy model. This allows us to derive the necessary and sufficient conditions for synthesis of polytopic TSK compensators. The closed loop TSK system under a polytopic TSK compensator is characterized with a stable characteristic polynomial that is not dependent on the firing levels of the rules. Procedures for calculation of the compensators are also presented.
Molecular Scanning of the Gene for Programmed Cell Death‐1 (PDCD‐1) as a Candidate for Type 1 Diabetes Susceptibility (2006)

Multiple genes are involved in the susceptibility to autoimmune type 1 diabetes. The immunoreceptor programmed cell death-1 (PDCD-1), an inhibitory costimulatory molecule regulating peripheral tolerance, was reported to play a role in the development of type 1 diabetes, making the human PDCD-1 gene, PDCD1, as a candidate for disease susceptibility. In this article, we sequenced all 5 exons and exon-intron junctions of PDCD1 in Japanese subjects, and found 10 sequence variants. Preliminary data suggested no association of these polymorphisms with type 1 diabetes. These sequence variants are valuable for further studies to clarify contribution of PDCD1 to susceptibility to type 1 diabetes.
ChemInform Abstract: SELECTIVE HYDROLYSIS‐DECARBOXYLATION OF ETHYL 1,4‐DIMETHYL‐3‐ETHOXYCARBONYL‐1H‐PYRROLE‐2‐ACETATE (1984)

Abstract In Gegenwart von Ethanol und Wasser stehen die beiden Dicarbonsäuremonoester (I) und (II) im Gleichgewicht miteinander.
Bearing current prevention of converter-fed AC machines with a conductive shielding in stator slots (2003)

The paper analyses a shielding method against circulating-type bearing currents in converter-fed AC machines. These currents are induced by the high-frequency flux components that are generated by the common-mode current penetrating the stator core. A conductive shield is placed in the stator slots between the winding and the core, providing a low-impedance path for high-frequency common-mode currents. The shielding effectiveness is analysed using a circuit model, and the fundamental-frequency losses in the shield are analysed by a two-dimensional finite element method and an analytical formulation. The analysis shows that the current penetrating the stator core is attenuated very effectively. The losses in the shield can be reduced to an acceptable level by proper shield thickness selection or by splitting the shield into axial strips.
Computational Method for Estimating DNA Copy Numbers in Normal Samples, Cancer Cell Lines, and Solid Tumors Using Array Comparative Genomic Hybridization (2010)

Genomic copy number variations are a typical feature of cancer. These variations may influence cancer outcomes as well as effectiveness of treatment. There are many computational methods developed to detect regions with deletions and amplifications without estimating actual copy numbers (CN) in these regions. We have developed a computational method capable of detecting regions with deletions and amplifications as well as estimating actual copy numbers in these regions. The method is based on determining how signal intensity from different probes is related to CN, taking into account changes in the total genome size, and incorporating into analysis contamination of the solid tumors with benign tissue. Hidden Markov Model is used to obtain the most likely CN solution. The method has been implemented for Affymetrix 500K GeneChip arrays and Agilent 244K oligonucleotide arrays. The results of CN analysis for normal cell lines, cancer cell lines, and tumor samples are presented. The method is capable of detecting copy number alterations in tumor samples with up to 80% contamination with benign tissue. Analysis of 178 cancer cell lines reveals multiple regions of common homozygous deletions and strong amplifications encompassing known tumor suppressor genes and oncogenes as well as novel cancer related genes.
Multi variation mapping for Dynamic Laser Stimulation analysis (2011)

Dynamic Laser Stimulation is now widely used for soft defect issues and is generally based on the study of device under test functionality (pass or fail). Automatic Test Equipments (ATE) are able to collect a lot of electrical parameters about device under test status but actually only the pass/fail is exploited and mapped has function of the laser beam position. Multi variation mapping (MVM) for Dynamic Laser Stimulation analysis gives the possibility to get all the data in same time than pass/fail and is able in one acquisition to give one mapping per data. Therefore MVM for Dynamic Laser Stimulation analysis offers the unique opportunity of collecting in one scan all the data necessary for a deep integrated circuit analysis.
Composition-Defined Optical Properties and the Direct-to-Indirect Transition in Core–Shell In1–xGaxP/ZnS Colloidal Quantum Dots (2023)

Semiconductors are commonly divided into materials with direct or indirect band gaps based on the relative positions of the top of the valence band and the bottom of the conduction band in crystal momentum (<b>k</b>) space. It has, however, been debated if <b>k</b> is a useful quantum number to describe the band structure in quantum-confined nanocrystalline systems, which blur the distinction between direct and indirect gap semiconductors. In bulk III-V semiconductor alloys like In<sub>1-<i>x</i></sub>Ga<i><sub>x</sub></i>P, the band structure can be tuned continuously from the direct- to indirect-gap by changing the value of <i>x</i>. The effect of strong quantum confinement on the direct-to-indirect transition in this system has yet to be established because high-quality colloidal nanocrystal samples have remained inaccessible. Herein, we report one of the first systematic studies of ternary III-V nanocrystals by utilizing an optimized molten-salt In-to-Ga cation exchange protocol to yield bright In<sub>1-<i>x</i></sub>Ga<i><sub>x</sub></i>P/ZnS core-shell particles with photoluminescence quantum yields exceeding 80%. We performed two-dimensional solid-state NMR studies to assess the alloy homogeneity and the extent of surface oxidation in In<sub>1-<i>x</i></sub>Ga<i><sub>x</sub></i>P cores. The radiative decay lifetime for In<sub>1-<i>x</i></sub>Ga<i><sub>x</sub></i>P/ZnS monotonically increases with higher gallium content. Transient absorption studies on In<sub>1-<i>x</i></sub>Ga<i><sub>x</sub></i>P/ZnS nanocrystals demonstrate signatures of direct- and indirect-like behavior based on the presence or absence, respectively, of excitonic bleach features. Atomistic electronic structure calculations based on the semi-empirical pseudopotential model are used to calculate absorption spectra and radiative lifetimes and evaluate band-edge degeneracy; the resulting calculated electronic properties are consistent with experimental observations. By studying photoluminescence characteristics at elevated temperatures, we demonstrate that a reduced lattice mismatch at the III-V/II-VI core-shell interface can enhance the thermal stability of emission. These insights establish cation exchange in molten inorganic salts as a viable synthetic route to nontoxic, high-quality In<sub>1-<i>x</i></sub>Ga<i><sub>x</sub></i>P/ZnS QD emitters with desirable optoelectronic properties.
Androgen receptor (AR) amplification in patients (pts) with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi) and enzalutamide (Enz): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). (2015)

5068 Background: Mechanisms of resistance to Abi or Enz in mCRPC pts are poorly understood. AR amplification (AR amp) is observed in Abi/Enz naive mCRPC pts, but its role in mCRPC pts who develop resistance to Abi/Enz is not known. As part of the WCDT project, which aims to identify genetic pathways underlying resistance to Abi and Enz, AR amp status was assessed in metastatic tumor biopsies from mCRPC pts. Methods: Eligible mCRPC pts underwent biopsy (bx) at one of 5 WCDT sites, using a uniform bx and clinical follow-up protocol. Formalin fixed, paraffin-embedded tissue underwent pathologic review and fluorescence in situ hybridization (FISH) for assessment of AR amp in a CLIA laboratory. AR amp by FISH was corroborated with array comparative genomic hybridization (aCGH) in select cases. Results: 150 mCRPC pts have undergone bx to date. To date, 92 have been evaluated by FISH for AR amp, including 36 from bone, 35 from lymph nodes, 16 from liver, and 5 from other soft tissues. Overall, 64% of mCRPC tumors were AR amplified by FISH and were corroborated by aCGH in 16/21 cases (76%). AR amp was seen in similar proportions in liver, bone, or nodal bx, and was present in > 50% of tumors with small cell histology. AR amp was observed in 16/19 pts (84%) naïve to both Abi + Enz compared to 17/36 pts (47%) who were resistant to Abi (p = 0.008). 4/6 (67%) of Enz resistant tumor biopsies were AR amplified. In pts that received Abi or Enz post-bx, the PSA response rate (PCWG2 criteria) was 9/17 (53%) in AR amp and 5/12 (42%) in AR non-amplified tumors respectively. Conclusions: AR amplification status can be assessed by FISH from mCRPC biopsies. AR amplification was common in Abi/Enz-naïve tumors including those with small cell histology. AR amp was less frequent in pts with Abi resistance, suggesting that Abi may select for non-AR amplified cells. Sequential (paired) biopsies from the same pts are being evaluated to test this hypothesis. Preliminary data suggest higher rates of AR amp in pts who are resistant to Enz. The predictive utility of AR amp status and AR splice variants is currently being evaluated.
Neuromodulation to improve gait and balance function using a sensory neuroprosthesis in people who report insensate feet – A randomized control cross-over study (2019)

Peripheral neuropathy may cause loss of sensory information from plantar cutaneous mechanoreceptors that is important for balance control and falls management. The current study investigated short-term effects of using Walkasins, an external lower-limb sensory neuroprosthesis, on clinical outcomes of balance and gait in persons who reported peripheral neuropathy and balance problems. The device replaces lost plantar sensation with tactile balance information that modulates cutaneous mechanoreceptors above the ankle where sensation is intact. Thirty-one male community-dwelling Veterans, 56-84 years old with insensate feet and balance problems participated. Initial Functional Gait Assessment, gait speed, and 4-Stage Balance Test outcomes were assessed. After initial assessment, subjects were randomly assigned to either wearing Walkasins turned ON, or OFF, and outcomes were re-assessed following a set of standardized balance exercises. Following a one-hour rest and washout period, treatments were crossed-over between groups and a third outcomes assessment was performed. Before cross-over, 10 of 15 subjects in the ON-then-OFF group improved their Functional Gait Assessment score by at least four points, the Minimal Clinically Important Difference, compared to 5 of 16 in the OFF-then-ON group. After cross-over, 7 of 16 subjects in the OFF-then-ON group improved by at least four points versus 2 of 15 in the ON-then-OFF group. ON treatment was associated with a Functional Gait Assessment improvement of 4.4 ± 3.7 points versus 1.5 ± 1.2 for the OFF treatment (p<0.01). Overall, Functional Gait Assessment scores changed from 15.2 ± 4.8 at initial assessment to 21.1 ± 5.2 after final assessment (p<0.001). At the end of the two treatment sessions, 16 of the 31 individuals had improved their Functional Gait Assessment score beyond 23, indicating normal fall-risk status. Future studies should investigate long-term benefits of the device to reduce fall risk and actual falls in patients with peripheral neuropathy and balance problems.
Partial characterization of retroviruses from boid snakes with inclusion body disease (2001)

A retrovirus was isolated from boid snakes with IBD or exposed to IBD. Western blot analysis of viral proteins indicated that viruses isolated from the different snakes were similar. Whether this virus represents the causative agent of IBD is yet to be determined. The isolation of retroviruses from boid snakes with IBD is an important step n the process of identifying the causative agent of this disease.
Wavelet Based Multigrid Reconstruction Algorithm for Optical Tomography (1996)

In this paper, we present a wavelet based multigrid approach to solve the perturbation encountered in optical tomography. The wavelet based multigrid representation has been applied to obtain regularized least squares (RLS) and total least squares (TLS) solutions. The unknown image, the data, as well as the weight matrix are all represented by wavelet expansions, thus yielding a multi-resolution representation of the perturbation Then, the transformed perturbation is solved by either the RLS or TLS method, using a multigrid scheme, by which an increasing portion of wavelet coefficients of the unknown image are solved in successive approximations. The experimental results show that the multigrid method can achieve similar reconstruction quality with a significantly reduced amount of time than the one-grid algorithm.
Simultaneous and independent processing of multiple input WDM data signals using a tunable optical tapped delay line (2013)

We demonstrate a tunable optical tapped delay line that can simultaneously and independently operate on multiple wavelength-division multiplexed (WDM) data signals. The system utilizes the wavelength-dependent speed of light, together with nonlinear wavelength conversion stages. A phase-preserving scheme enables coherent addition of the weighted taps. We reconfigured the system to perform separate simultaneous correlation (data pattern recognition), equalization, and modulation format conversion on four and eight WDM binary/quadrate phase-shift keyed channels at 26 and 20 Gbaud, respectively. The aggregate throughput of 416 Gb/s is achieved.
Stereoselective Synthesis of 2,6‐Disubstituted 3‐Piperidinols: Application to the Expedient Synthesis of (+)‐Julifloridine. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Front Cover: Low‐Temperature H2 Reduction of Copper Oxide Subnanoparticles (Chem. Eur. J. 33/2021) (2021)

Copper oxide subnanoparticles with sizes of ∼1 nm, which were prepared using a dendritic phenylazomethine template, exhibit the lowest CuII→CuI reduction temperature directly observed by in situ XAFS measurements during temperature-programmed reduction (TPR) with H2. The CuO particles with low atomicity easily release oxygen atoms because of their surface-strained structure and the unprecedented elongation of their Cu−O bonds. More information can be found in the Communication by M. Tanabe, K. Yamamoto et al. (DOI: 10.1002/chem.202100508).
Effect of vitamin D on serum markers of bone turnover in SLE in a randomised controlled trial (2019)

Vitamin D supplementation did not affect the 12-week change in bone turnover markers among SLE subjects in this trial.
The intensity reflection coefficient: a complementary method for investigating blood backscattering properties with ultrasound. (2008)

Parametric imaging of backscatter indices is an active field of research in ultrasound (US) tissue characterization. The US intensity reflection coefficient (IRC) is introduced to characterize porcine blood in a Couette shear flow system. US properties of red blood cells (RBCs) were investigated at shear rates of 5 s(-1) and 500 s(-1) for hematocrits ranging from 0 to 54%. The IRC was determined and compared to the integrated backscatter power (IBP) calculated between 8 MHz and 12 MHz. The frequency dependence of both parameters was also explored using their spectral slopes determined in the same frequency bandwidth. The experimental results showed that the IRC is a mirror function of the IBP and their spectral slopes had similar behavior. At a shear rate of 500 s(-1), selected to disaggregate RBCs, the IRC exhibited a bi-modal variation with a minimum at 23% hematocrit. The minimum was less pronounced and moved down to 13-17% hematocrits in the case of a shear rate of 5 s(-1) that promoted aggregation. The IBP presented a sharp peak at 25% hematocrit for the high shear-rate value, while a plateau appeared after 13% hematocrit in the case of the low shear rate. Furthermore, the transition from lower to higher shear rate was accompanied by a diminution in the level of both indices. In the frequency domain, the spectral slope of the backscatter power presented a Rayleigh scattering behavior (value around 4) for all hematocrits at a shear rate of 500 s(-1). It dropped to a value of 2 beyond 13% hematocrit when the shear rate was decreased to 5 s(-1). At a shear rate of 500 s(-1), the spectral slope of the IRC was constant and close to 3.8 below 28% hematocrit and decreased at higher hematocrits. At 5 s(-1), it was constant (between 3.7 and 3.9) for hematocrits lower than 17% and then decreased. This study showed the potential of the intensity reflection coefficient to investigate the RBC aggregation phenomenon. An advantage of IRC is its easy computation.
1083 nm ytterbium doped fibre amplifier for optical pumping of helium (1997)

International audience
TCP performance over HS-DSCH (2003)

Both the performance of transmission control protocol (TCP) based applications and the effect of TCP on system capacity in a WCDMA system using high speed downlink shared channel (HS-DSCH) are evaluated. It is found that the HS-DSCH improves both the application performance and the system capacity. The effect of TCP on application performance is much stronger than the effect on the system capacity.
Electron-beam activated thermal sputtering of thermoelectric materials (2011)

Thermoelectricity and Seebeck effect have long been observed and validated in bulk materials. With the development of advanced tools of materials characterization, here we report the first observation of such an effect in the nanometer scale: in situ directional sputtering of several thermoelectric materials inside electron microscopes. The temperature gradient introduced by the electron beam creates a voltage-drop across the samples, which enhances spontaneous sputtering of specimen ions. The sputtering occurs along a preferential direction determined by the direction of the temperature gradient. A large number of nanoparticles form and accumulate away from the beam location as a result. The sputtering and re-crystallization are found to occur at temperatures far below the melting points of bulk materials. The sputtering occurs even when a liquid nitrogen cooling holder is used to keep the overall temperature at −170 °C. This unique phenomenon that occurred in the nanometer scale may provide useful clues to understanding the mechanism of thermoelectric effect.
Acoustic streaming induced by MHz-frequency ultrasound extends the volume limit of cell suspension culture (2021)

Large-scale cell suspension culture technology opens up opportunities for numerous medical and bioengineering applications. For these purposes, scale-up of the culture system is paramount. For initial small-scale culture, a simple static suspension culture (SSC) is generally employed. However, cell sedimentation due to the lack of agitation limits the culture volume feasible for SSC. Thus, when scaling up, cell suspensions must be manually transferred from the culture flask to another vessel suitable for agitation, which increases the risk of contamination and human error. Ideally, the number of culture transfer steps should be kept to a minimum. The present study describes the fabrication of an ultrasonic suspension culture system that stirs cell suspensions with the use of acoustic streaming generated by ultrasound irradiation at a MHz frequency. This system was applied to 100-mL suspension cultures of Chinese hamster ovary cells-a volume ten-fold larger than that generally used. The cell proliferation rate in this system was 1.88/day when applying an input voltage of 40 V to the ultrasonic transducer, while that of the SSC was 1.14/day. Hence, the proposed method can extend the volume limit of static cell suspension cultures, thereby reducing the number of cell culture transfer steps.
The Adaptor Protein CD2AP Is a Coordinator of Neurotrophin Signaling-Mediated Axon Arbor Plasticity (2016)

Growth of noninjured axons in the adult nervous system contributes to adaptive and maladaptive plasticity, and dysfunction of this process may contribute to neurologic pathologies. Functional screening of genes regulated during growth of noninjured axons revealed CD2AP as a positive regulator of axon outgrowth. A novel association of CD2AP with TrkA and p85 suggests a distinct intracellular signaling pathway regulating growth of noninjured axons. This may also represent a novel mechanism of generating specificity in multifunctional NGF signaling. Divergent regulation of CD2AP in different axon growth conditions suggests that separate mechanisms exist for different modes of axon growth. CD2AP is the first signaling molecule associated with adult sensory axonal collateral sprouting, and this association may offer new insights for NGF/TrkA-related Alzheimer's disease mechanisms.