gebhart/patrepeval huggingface dataset:
Time-Dependent Changes in Protein Composition of Medial Prefrontal Cortex in Rats with Neuropathic Pain (2022)

Chronic pain is associated with time-dependent structural and functional reorganization of the prefrontal cortex that may reflect adaptive pain compensatory and/or maladaptive pain-promoting mechanisms. However, the molecular underpinnings of these changes and whether there are time-dependent relationships to pain progression are not well characterized. In this study, we analyzed protein composition in the medial prefrontal cortex (mPFC) of rats at two timepoints after spinal nerve ligation (SNL) using two-dimensional gel electrophoresis (2D-ELFO) and liquid chromatography with tandem mass spectrometry (LC-MS/MS). SNL, but not sham-operated, rats developed persistent tactile allodynia and thermal hyperalgesia, confirming the presence of experimental neuropathic pain. Two weeks after SNL (early timepoint), we identified 11 proteins involved in signal transduction, protein transport, cell homeostasis, metabolism, and apoptosis, as well as heat-shock proteins and chaperones that were upregulated by more than 1.5-fold compared to the sham-operated rats. Interestingly, there were only four significantly altered proteins identified at 8 weeks after SNL (late timepoint). These findings demonstrate extensive time-dependent modifications of protein expression in the rat mPFC under a chronic neuropathic pain state that might underlie the evolution of chronic pain characterized by early pain-compensatory and later aberrant mechanisms.
The real-time operating system of MARS (1989)

This paper gives a short overview of the architecture of the distributed real-time system MARS ( MA intainable R eal-Time S ystem) and describes the design and implementation of its operating system. The main purpose of the MARS kernel is to achieve a timely execution of hard real-time tasks and to provide an efficient communication mechanism suitable for distributed real-time systems.
Stability Impact of IEEE 1547 Operational Mode Changes Under High DER Penetration in the Presence of Cyber Adversary (2021)

The IEEE 1547 standard addresses the integration of Distributed Energy Resources (DER) into Area Electric Power Systems (AEPS). The updated standard, released in 2018 with revisions ongoing, specifies the need for more flexible settings, requiring the DER to remain connected during certain disturbances and provide voltage support via active and reactive power modes. With these increased capabilities comes increased risks, and our analysis of the standard has produced potential settings combinations, which, while allowable under the standard, may actually create instability. This contradicts the main purpose of the revised standard. Since the DER must support a communication interface through which the AEPS operator can change settings, adversarial mode changes are possible via a cyberattack. This concern is heightened as DER penetration increases, where under a reasonable threat model, an attacker could affect multiple DER simultaneously. We have conducted a simulation analysis of potentially adverse combinations of mode change and ride-through parameters on a hypothetical AEPS with varying degrees of DER penetration. We conclude that certain adverse mode changes, whether through error or cyberattack, can lead to unstable conditions with DER penetrations as low as 24% of the AEPS system capacity.
Comparison of CKD-EPI Cystatin C and Creatinine Glomerular Filtration Rate Estimation Equations in Asian Indians (2014)

Background. Chronic kidney disease (CKD) is identified in the general population using estimated glomerular filtration rates (eGFR) calculated from a serum creatinine-based equation, the chronic kidney disease-epidemiology collaboration (CKD-EPI) equation. Using serum cystatin C in combination may improve eGFR accuracy. We evaluated the new CKD-EPI equations incorporating cystatin C in a population of Asian Indians in classifying CKD across body mass index, diabetes, and hypertension status. Methods. We retrieved standardized serum creatinine and serum cystatin C data from a cohort of 2877 Asian Indians aged 40-80 years from the Singapore Indian Eye Study and calculated eGFR (in mL/min/1.73 m(2)) with the new CKD-EPI equations and serum creatinine only equation. Results. The creatinine only equation mean eGFR (88 ± 17) was similar to using spline Log cystatin C (88 ± 22). The lowest mean eGFR (81 ± 21) was obtained with the spline Log cystatin C-age, sex, and weight equation. The creatinine only equation had the fewest participants (7.1%) with eGFR <60 and spline Log cystatin C-age, sex, and weight equation had the most (16.1%). Conclusions. Using serum cystatin C resulted in widely varying eGFR which significantly affected the classification of chronic kidney disease.
The orphan nuclear receptor SHP regulates ER stress response by inhibiting XBP1s degradation (2019)

The orphan nuclear receptor SHP (small heterodimer partner) is a well-known transcriptional corepressor of bile acid and lipid metabolism in the liver; however, its function in other tissues is poorly understood. Here, we report an unexpected role for SHP in the exocrine pancreas as a modulator of the endoplasmic reticulum (ER) stress response. SHP expression is induced in acinar cells in response to ER stress and regulates the protein stability of the spliced form of X-box-binding protein 1 (XBP1s), a key mediator of ER stress response. Loss of SHP reduces XBP1s protein level and transcriptional activity, which in turn attenuates the ER stress response during the fasting-feeding cycle. Consequently, SHP-deficient mice also are more susceptible to cerulein-induced pancreatitis. Mechanistically, we show that SHP physically interacts with the transactivation domain of XBP1s, thereby inhibiting the polyubiquitination and degradation of XBP1s by the Cullin3-SPOP (speckle-type POZ protein) E3 ligase complex. Together, our data implicate SHP in governing ER homeostasis and identify a novel posttranslational regulatory mechanism for the key ER stress response effector XBP1.
Atmospheric Influence upon Crystallization and Electronic Disorder and Its Impact on the Photophysical Properties of Organic–Inorganic Perovskite Solar Cells (2015)

Recently, solution-processable organic-inorganic metal halide perovskites have come to the fore as a result of their high power-conversion efficiencies (PCE) in photovoltaics, exceeding 17%. To attain reproducibility in the performance, one of the critical factors is the processing conditions of the perovskite film, which directly influences the photophysical properties and hence the device performance. Here we study the effect of annealing parameters on the crystal structure of the perovskite films and correlate these changes with its photophysical properties. We find that the crystal formation is kinetically driven by the annealing atmosphere, time and temperature. Annealing in air produces an improved crystallinity and large grain domains as compared to nitrogen. Lower photoluminescence quantum efficiency (PLQE) and shorter photoluminescence (PL) lifetimes are observed for nitrogen annealed perovskite films as compared to the air-annealed counterparts. We note that the limiting nonradiative pathways (i.e., maximizing PLQE) is important for obtaining the highest device efficiency. This indicates a critical impact of the atmosphere upon crystallization and the ultimate device performance.
GENOMIC ANALYSIS OF AVIAN INFLUENZA VIRUSES FROM WATERFOWL IN WESTERN ALASKA, USA (2013)

The Yukon-Kuskokwim Delta (Y-K Delta) in western Alaska is an immense and important breeding ground for waterfowl. Migratory birds from the Pacific Americas, Central Pacific, and East Asian-Australasian flyways converge in this region, providing opportunities for intermixing of North American- and Eurasian-origin hosts and infectious agents, such as avian influenza virus (AIV). We characterized the genomes of 90 low pathogenic (LP) AIV isolates from 11 species of waterfowl sampled on the Y-K Delta between 2006 and 2009 as part of an interagency surveillance program for the detection of the H5N1 highly pathogenic (HP) strain of AIV. We found evidence for subtype and genetic differences between viruses from swans and geese, dabbling ducks, and sea ducks. At least one gene segment in 39% of all isolates was Eurasian in origin. Target species (those ranked as having a relatively high potential to introduce HP H5N1 AIV to North America) were no more likely than nontarget species to carry viruses with genes of Eurasian origin. These findings provide evidence that the frequency at which viral gene segments of Eurasian origin are detected does not result from a strong species effect, but rather we suspect it is linked to the geographic location of the Y-K Delta in western Alaska where flyways from different continents overlap. This study provides support for retaining the Y-K Delta as a high priority region for the surveillance of Asian avian pathogens such as HP H5N1 AIV.
Discrete-Time H-Infinity Synthesis of Frequency-Shaped Sliding Mode Control for Suppression of Vibration With Multiple Peak Frequencies (2016)

Vibration with multiple large peaks at high frequencies may cause significant performance degradation and have become a major concern in modern high precision control systems. To deal with such high-frequency peaks, it is proposed to design a frequency-shaped sliding mode controller based on H∞ synthesis. It obtains an ‘optimal’ filter to shape the sliding surface, and thus provides frequency-dependent control allocation. The proposed frequency-shaping method assures the stability in the presence of multiple-peak vibration sources, and minimizes the weighted H∞ norm of the sliding surface dynamics. The evaluation is performed on a simulated hard disk drive with actual vibration sources from experiments, and the effectiveness of large vibration peak suppression is demonstrated.
Identification of genes expressed in cultures of E. coli lysogens carrying the Shiga toxin-encoding prophage Φ24B (2012)

Propagation of a lysogen culture in which no cells at all are undergoing spontaneous lysis is impossible. To overcome this, RT-qPCR was used to determine gene expression profiles associated with the growth phase of lysogens. This enabled the definitive identification of three lambdoid Stx phage genes that are expressed in the lysogen and seven that are expressed during lysis. Conservation of these genes in this phage genome, and other Stx phages where they have been identified as present, indicates their importance in the phage/lysogen life cycle, with possible implications for the biology and pathogenicity of the bacterial host.
Equine infectious anemia virus Tat is a predominantly helical protein (1993)

Nuclear magnetic resonance (NMR) spectroscopy revealed features of the secondary structure of the equine infectious anemia virus (EIAV) Tat protein in solution. We could show that this protein, which is required in the replication cycle of lentiviruses, forms a predominantly helical structure in trifluoroethanol/water (40% by vol.) solution. In particular, the basic RNA-binding region and the adjacent core domain, which are highly conserved among lentiviral Tat proteins, show helix-type secondary structure under these conditions. Our observations, in concert with recent biochemical data from other laboratories, suggest that the core sequence region and the basic sequence region form interdependent structural domains, both possibly necessary for correct RNA binding.
Effects of nintedanib on markers of epithelial damage in subjects with IPF: data from the INMARK trial (2020)

<b>Introduction:</b> The INMARK trial investigated effects of nintedanib on blood biomarkers in subjects with IPF. <b>Aim:</b> To investigate the effect of nintedanib on markers of epithelial damage. <b>Methods:</b> Subjects (n=346) with IPF and FVC ≥80% predicted were randomised 1:2 to receive nintedanib 150 mg bid or placebo double-blind for 12 weeks, followed by open-label nintedanib for 40 weeks. Blood samples were taken at weeks 4, 8, 12, 16, 20, 24, 36, and 52. We assessed the rate of change (slope) in log<sub>10</sub>-transformed CA-125 and CA19-9 (two markers of epithelial damage) from baseline to week 12 using random coefficient regression and changes in log<sub>10</sub>-transformed CA-125 and CA19-9 over 52 weeks using a mixed model for repeated measures. <b>Results:</b> The adjusted rate of change in CA-125 levels from baseline to week 12 was significantly different for nintedanib vs placebo (difference -0.046 U/mL/month [95% CI ‑0.056, -0.035]; p&lt;0.001). Adjusted mean CA-125 levels decreased with nintedanib vs placebo from week 4; after week 12 CA-125 levels were similar between groups (Figure). There was no significant difference between nintedanib and placebo in the adjusted rate of change in CA19-9 levels from baseline to week 12 (difference -0.023 U/mL/month [95% CI -0.055, 0.009]; p=0.17). Adjusted mean CA19-9 levels over 52 weeks were similar in both groups. <b>Conclusion:</b> CA-125 may be a biomarker of response to nintedanib in patients with IPF.
Salt inducible kinases 2 and 3 are required for thymic T cell development (2021)

Abstract Salt Inducible Kinases (SIKs), of which there are 3 isoforms, are established to play roles in innate immunity, metabolic control and neuronal function, but their role in adaptive immunity is unknown. To address this gap, we used a combination of SIK knockout and kinase-inactive knock-in mice. The combined loss of SIK1 and SIK2 activity did not block T cell development. Conditional knockout of SIK3 in haemopoietic cells, driven by a Vav-iCre transgene, resulted in a moderate reduction in the numbers of peripheral T cells, but normal B cell numbers. Constitutive knockout of SIK2 combined with conditional knockout of SIK3 in the haemopoietic cells resulted in a severe reduction in peripheral T cells without reducing B cell number. A similar effect was seen when SIK3 deletion was driven via CD4-Cre transgene to delete at the DP stage of T cell development. Analysis of the SIK2/3 Vav-iCre mice showed that thymocyte number was greatly reduced, but development was not blocked completely as indicated by the presence of low numbers CD4 and CD8 single positive cells. SIK2 and SIK3 were not required for rearrangement of the TCRβ locus, or for low level cell surface expression of the TCR complex on the surface of CD4/CD8 double positive thymocytes. In the absence of both SIK2 and SIK3, progression to mature single positive cells was greatly reduced, suggesting a defect in negative and/or positive selection in the thymus. In agreement with an effect on negative selection, increased apoptosis was seen in thymic TCRbeta high/CD5 positive cells from SIK2/3 knockout mice. Together, these results show an important role for SIK2 and SIK3 in thymic T cell development.
Domain-Driven Data Mining for IT Infrastructure Support (2010)

Support analytics (i.e., statistical analysis, modeling and mining of customer/operations support tickets data) is important in service industries. In this paper, we adopt a domain-driven data mining approach to support analytics with a focus on IT infrastructure Support (ITIS) services. We identify specific business questions and then propose algorithms for answering them. The questions are: (1) How to reduce the overall workload? (2) How to improve efforts spent in ticket processing? (3) How to improve compliance to service level agreements? We propose novel formalizations of these notions and propose rigorous statistics-based algorithms for these questions. The approach is domain-driven in the sense that the results produced are directly usable by and easy to understand for end-users having no expertise in data-mining, do not require any experimentation and often discover novel and non-obvious answers. All this helps in better acceptance among end-users and more active use of the results produced. The algorithms have been implemented and have produced satisfactory results on more than 25 real-life ITIS datasets, one of which we use for illustration.
LATE COMPLICATIONS VS. METHOD OF TREATMENT IN A LARGE SERIES OF MID-FACIAL FRACTURES (1978)

Reference process models capture common practices in a given domain and variations thereof. Such models are intended to be configured in a specific setting, leading to individualized process models. Although the advantages of reference process models are widely accepted, their configuration still requires a high degree of modeling expertise. Thus users not only need to be domain experts, but also need to master the notation in which the reference process model is captured. In this paper we propose a framework for reference process modeling wherein the domain variability is represented separately from the actual process model. Domain variability is captured as a questionnaire that reflects the decisions that need to be made during configuration and their interrelationships. This questionnaire allows subject matter experts to configure the process model without requiring them to understand the process modeling notation. The approach guarantees that the resulting process models are correct according to certain constraints. To demonstrate the applicability of the proposal, we have implemented a questionnaire toolset that guides users through the configuration of reference process models captured in two different notations.
The 157-nm Good/Bad News from Intel (2003)

The <i>Journal of Micro/Nanopatterning, Materials, and Metrology</i> (JM3) publishes peer-reviewed papers on the core enabling technologies that address the patterning needs of the electronics industry.
Optical Control of MicroRNA Function in Zebrafish Embryos (2022)

MicroRNAs play crucial and dynamic roles in vertebrate development and diseases. Some, like miR-430, are highly expressed during early embryo development and regulate hundreds of transcripts, which can make it difficult to study their role in the timing and location of specific developmental processes using conventional morpholino oligonucleotide (MO) knockdown or genetic deletion approaches. We demonstrate that light-activated circular morpholino oligonucleotides (cMOs) can be applied to the conditional control of microRNA function. We targeted miR-430 in zebrafish embryos to study its role in the development of the embryo body and the heart. Using 405 nm irradiation, precise spatial and temporal control over miR-430 function was demonstrated, offering insight into the cell populations and developmental timepoints involved in each process.
Two-dimensional exciton dynamics in InGaAs/GaAs quantum wells (1992)

We have investigated the exciton dynamics in InGaAs/GaAs single quantum wells using time-resolved photoluminescence spectroscopy. The temperature dependence of the decay time shows that the scattering rate of two-dimensional excitons is reduced in the narrower wells compared with that of AlGaAs/GaAs quantum wells. The results suggest the dominant contribution of the alloy disorder scattering to the exciton scattering processes over the interface roughness scattering.
High-Amplitude and Long-Burst Pulse Transmission Array Probe for Phase-Change Molecular Imaging (2009)

Analysis of the breakdown of a conventional imaging probe based on experiments and numerical simulations is described. Both results of simulation and measurements of the electric impedances and round-trip responses of imaging arrays during the breakdown show that the breakdown was caused by peeling of the adhesive between the piezoelectric material and the matching layer. Since the peeling was suppressed by cooling, it was considered to be caused by thermal stress due to the difference in thermal expansion coefficient between these two layers. To increase the maximum transmission ultrasonic power by overcoming this problem, we proposed an imaging array structure with an optimized heat-conductive backing layer connected to a water-cooling bath. Simulation results show that the combination of heat-conductive backing and water cooling can reduce the temperature rise to 1/42 that of the conventional structure. The thickness of the heat-conductive backing layer, consisting of epoxy resin containing graphite fibers, was optimized for heat conductance and pulse response. This proposed structure may be useful for ultrasound molecular imaging using phase-change nanodroplets.
ARTHROSCOPIC TREATMENT OF CALCIFIED TENDINOPATHY OF THE SHOULDER: SHOULD THE GLENOHUMERAL JOINT BE EXPLORED? (2002)

Purpose: Arthroscopic treatment of calcified tendinopathy is classically performed in two times: exploration of the glenohumeral joint followed by subacromial arthroscopy to evacuate the calcification. In our experience, glenohumeral arthroscopy has only exceptionally provided a diagnostic element. In addition, the principal complication of this procedure is retractile capsulitis which may be a secondary effect of glenohumeral aggression. We conducted a retrospective analysis to assess the effect of systematic exploration of the glenohumeral joint. Material and methods: Two homogeneous groups of patients were identified. Group 1 included 32 patients who had had glenohumeral arthroscopy then resection of the calcifications using a bursoscope. Group 2 included 32 patients whose treatment was limited to subacromial arthroscopy for resection. The preoperative Constant score (52 in group 1 and 54 in group 2), disease duration (34 and 40 months respectively), and localisation of the calcification were comparable for the two groups. Acromioplasty was not performed in these patients. All were reviewed at minimal follow-up of 6 months for assessment of the Constant score and a radiography study. Results: At last follow-up the mean Constant score was 70 in group 1; calcifications had disappeared in 84% of the cases and delay to recovery (total pain relief and return to work) was 11 months. There were 4 cases of postoperative capsulitis (12.5%). The mean Constant score was 79 in group 2; calcifications had disappeared in 78% of the cases and delay to recovery was 6.5 weeks (p = 0.0001). There was one case of retractile capsulitis (3%). In group 1, glenohu-meral arthroscopy did not lead to the discovery of specific elements except in two cases where it identified partial tear of the deep aspect of the supraspinatus. Acromioplasty was never performed. Discussion-Conclusion: Systematic glenohumeral arthros-copy is not warranted in patients undergoing treatment for calcified tendinopathy. The fact that glenohumeral exploration did not disclose any particular element and had no effect on healing and capsulitis rates favours the use of a subacromial approach alone.
Laser assisted works for pulsed ion sources: Plasma productions, diagnostics and related computations (1994)

Recent laser assisted works for pulsed ion beam drivers are described in this paper. The first one is a plasma production by a KrF laser light which may be applicable to an ion source. The second item is a transverse‐mode‐diagnostic of a discharge‐pumped laser. The third one is a one‐dimensional computation of the latter laser.
Metabolomics as a tool for Personalizing Medicine: 2012 Update (2013)

Numerous factors in conjunction with an individual's genetic make up will determine predisposition to disease, adverse or beneficial effects of drug treatment or therapy, and disease progression. A major limitation of current clinical measures is that the disease phenotype, which is comprised of the genotype and other environmental factors, is underestimated. Rather, each disease is treated similarly even though the disease process is highly complex. Methods that evaluate the interaction of genotype and environmental factors would likely be a better indicator of patients' response to medical treatments. The omics technologies, specifically metabolomics, will play a major role in the movement towards personalized medicine. Metabolomics is phenotype driven and should provide better clinical biomarkers. Furthermore, recent studies have shown that associations between genetic variants and downstream metabolite changes can provide a unique description of an individual's genotype and phenotype, which will further enhance the movement towards personalized medicine.