gebhart/patrepeval huggingface dataset:
Successful re-initiation of calcineurin inhibitors in patients with posterior reversible encephalopathy syndrome (PRES) (2008)

18014 Background: Posterior Reversible Encephalopathy Syndrome (PRES) is characterized by headache, altered mental status, seizure or visual loss and is associated with white matter vasogenic edema predominantly affecting the posterior occipital and parietal lobes of the brain. It often occurs after abrupt increases in blood pressure in the background of calcineurin inhibitor therapy. Methods: Retrospective study of 10 patients (pts) diagnosed with PRES while receiving cyclosporine (CSA). Results: Six children, (mean age 10.7 y; range 8–14 y), and 4 adults (mean age 28 y, range 20–35 y) were diagnosed with PRES. Seven had severe aplastic anemia as a primary diagnosis while one pt each had MDS, AML- M4 and Pre B-ALL. Seven had undergone an allogeneic stem cell transplant and all 10 pts were on CSA when PRES occurred. Besides CSA use, potential inciting risk factors for PRES include: concomitant infections (7pts), grade 3–4 GVHD (4 pts), use of ATG (5 pts), high dose steroids (5 pts), meropenem (4 pts) and hypomagnesemia (5 pts). Eight pts experienced seizures and 5 had visual disturbances. The average Mean Arterial Pressure (MAP) when PRES was diagnosed (132 mmHg; range 108–169) was significantly higher than baseline (mean rise 36.94 mmHg; range 12–85). MRI findings of increased T2 fluid attenuated inversion recovery signal predominantly involved the posterior brain regions (8 pts), but atypical findings of global involvement with frontal preponderance were seen in 2 pts. Nine pts required anti-epileptic drugs (AED) acutely; the 8 pts who seized continued AED (single agent levetiracetam in 7/8 pts). Continuous infusional antihypertensives were required for acute BP management in 4 pts; 7 pts required maintenance antihypertensives. CSA was never discontinued in 2 pts and restarted in all pts (median 2 days; range 0–79 days, from diagnosis of PRES to reinitiating CSA) without recurrence of PRES. Conclusions: The “typical” characteristics of specific posterior and white matter involvement is not always observed in PRES. Single agent levetiracetam can effectively prevent recurrent PRES-associated seizures. Prompt BP management and seizure prophylaxis can safely allow for continuing or promptly restarting calcineurin inhibitors critical to pt management. No significant financial relationships to disclose.
Transmission spectra of crystals at elevated temperatures for the calculation of internal radiant heat transport during crystal growth – Part 1: The spectrometer and its performance (2003)

Abstract We report the construction, operation and performance of a transmission spectrometer for the visible to the IR (up to 3.5 μm wavelength) to measure crystals up to a temperature of 1400 °C. The spectral resolution is almost comparable to that of a commercial spectrometer. The performance of the spectrometer and some problems are demonstrated by spectra of YAG : Nd at different temperatures. (© 2003 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Displacements induced in piezoelectric structures (1988)

From the knowledge of piezoelectric material tensorial components and using the finite-element method, it is possible to calculate the electrical impedance vs. frequency and simulate the mechanical deformation of piezoelectric bars. To check the validity of the simulation, interferrometric measurements of the mechanical deformation amplitude were performed. It is shown that these measurements can reveal the homogeneity of the materials under study and that a small error in the tensorial parameter absolute values leads to an inconsistent picture of simulated mechanical deformation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identification of functionally active fragments of staphylococcal enterotoxin B (1992)

It has been found that staphylococcal enterotoxin B contains a proteolysis-sensitive sequence in the cysteine loop formed by two half-cystines located in the middle of the toxin polypeptide chain. Fragments of the enterotoxin formed as a result of its digestion in this region have been isolated, their N-terminal sequences have been determined and sites of proteolysis have been identified. It has been demonstrated that the N-terminal fragment of staphylococcal enterotoxin B is capable of activating T cell proliferation in the culture of human mononuclear cells practically to the same degree as the intact enterotoxin. The toxin's C-terminal fragment possesses an ability to activate calmodulin-dependent enzymes and is probably the toxicogenic part of the enterotoxin.
Correlation between Magnetic Resonance Imaging and Clinical Profiles of Periventricular Leukomalacia. (1999)

Magnetic resonance imaging (MRI) findings of 70 children with periventricular leukomalacia (PVL), examined between 1 year 2 months and 8 years of age (mean: 2 years 4 months of age), were analysed. Neurological assessments were made between 1 year 3 months and 15 years (mean: 4 years 9 months). The possible correlations between MRI findings and clinical profiles of PVL were investigated using three parameters of the MRI findings. The grade of ventriculomegaly correlated well with the severity of cerebral palsy (CP) but not with the severity of mental impairment. The grade of reduction of periventricular white matter correlated well with the severity of CP and mental impairment, and is the most reliable parameter for neurological prognosis. The degree of periventricular hyperintensity on T2-weighted images did not correlate well with severity of CP, but correlated to some degree with mental impairment. There was a significantly lower degree of periventricular hyperintensity in children at less than 28 weeks of gestation than at 28 or more weeks of gestation, but no significant difference in other parameters. The periventricular hyperintensity should be evaluated in view of the gestational age.
Heterogeneity of Anti-Phospholipid and Anti-Endothelial Cell Antibodies (1998)

The role of the anti-phospholipid antibodies (APLA) and anti-endothelial cell antibodies (AECA) in the pathogenesis of anti-phospholipid syndrome (APS) is unclear. Differences in the reported involvement of APLA may be due, in part, to the polyclonal nature of these antibodies and the use of serum and serum fractions for analysis. To circumvent this issue, we generated monoclonal antibodies (MAB) from three patients with APS and two healthy controls. We then compared the antigen binding patterns and the heavy chain variable region (VH) DNA sequences of the MAB derived from patients with APS to those from healthy controls. The results of this study indicate that APLA and AECA comprise a highly heterogeneous population of antibodies with respect to the antigens they recognize, as well as VH gene usage. MAB derived from patients with APS do not differ from those derived from normal individuals based on either antigen recognition or VH gene usage. These results suggest the importance of additional predisposing factors in the pathogenesis of APS.
Transcriptome network component analysis with limited microarray data (2006)

The NCA Toolbox for MATLAB is available at http://www.seas.ucla.edu/~liaoj/download.htm.
Modulation of Lysosomal pH in RPE Cells (2006)

Lysosomal enzymes function optimally in an acidic environment. In RPE cells, lysosomal alkalinization is associated with decreased clearance of photoreceptor outer segments and may contribute to the development of macular degeneration. Tamoxifen is known to increase lysosomal pH in other cells, and to decrease the activity of cathespin D in RPE cells. We thus asked whether tamoxifen increased lysosomal pH in RPE cells and slowed clearance of outer segments. Lysosomal pH was measured in ARPE‐19 cells using the ratiometric pH indicator Lysosensor Yellow Blue once optimal loading conditions were determined, with the pH calibrated for each trial. The indicator was localized to late endosomal and lysosomal vesicles, with a pH of 4.5. Tamoxifen elevated lysosomal pH, increasing the pH over a unit at the EC 50 of 30 μM. The response was rapid, and complete within 15 min. 17‐β‐estrodiol did not effect the pH, suggesting estrogen receptors were not involved. Tamoxifen and the lysosmotropic agent chloroquine both slowed clearance of outer segments, consistent with a requirement for acidic lysosomes. Several agonists were able to restore pH. In conclusion, tamoxifen increased lysosomal pH and interfered with the degradation of outer segments. While retinal disorders in association with tamoxifen treatment are rare, they do occur and are consistent with lysosomal enzyme disfunction. Perhaps more importantly, this has identified a model for widespread disorders such as macular degeneration and some lysosomal storage disorders where vesicle alkalinization is thought to be detrimental.
Hypertension and Male Fertility (2017)

As the age of paternity rises in the developed world, issues of chronic disease may affect prospective fathers. Given the high prevalence of hypertension, researchers have begun to explore the relationship between hypertensive disease and male fertility. The current literature suggests an association between hypertension and semen quality. The use of various antihypertensive medications has also been linked to impaired semen parameters, making it difficult to discern whether the association exists with hypertension or its treatment. Further investigation is warranted to determine whether the observed associations are causal.
Engineering a Carboxyl Methyltransferase for the Formation of a Furan‐Based Bioplastic Precursor (2023)

Abstract FtpM from Aspergillus fumigatus was the first carboxyl methyltransferase reported to catalyse the dimethylation of dicarboxylic acids. Here the creation of mutant R166M that can catalyse the quantitative conversion of bio‐derived 2,5‐furandicarboxylic acid (FDCA) to its dimethyl ester (FDME), a bioplastics precursor, was reported. Wild type FtpM gave low conversion due to its reduced catalytic efficiency for the second methylation step. An AlphaFold 2 model revealed a highly electropositive active site, due to the presence of 4 arginine residues, postulated to favour the binding of the dicarboxylic acid over the intermediate monoester. The R166M mutation improved both binding and turnover of the monoester to permit near quantitative conversion to the target dimethyl ester product. The mutant also had improved activity for other diacids and a range of monoacids. R166M was incorporated into 2 multienzyme cascades for the synthesis of the bioplastics precursor FDME from bioderived 5‐hydroxymethylfurfural (HMF) as well as from poly(ethylene furanoate) (PEF) plastic, demonstrating the potential to recycle waste plastic.
Ossicular resonance modes of the human middle ear for bone and air conduction (2009)

The mean resonance frequency of the human middle ear under air conduction (AC) excitation is known to be around 0.8-1.2 kHz. However, studies suggest that the mean resonance frequency under bone conduction (BC) excitation is at a higher frequency around 1.5-2 kHz. To identify the cause for this difference, middle-ear responses to both AC and BC excitations were measured at the umbo and lateral process of the malleus using five human cadaver temporal bones. The resonance modes identified from these measurements, along with finite element analysis results, indicate the presence of two ossicular modes below 2 kHz. The dominant mode under AC excitation is the first mode, which typically occurs around 1.2 kHz and is characterized by a "hinging" ossicular motion, whereas the dominant mode under BC excitation is the second mode, which typically occurs around 1.7 kHz and is characterized by a "pivoting" ossicular motion. The results indicate that this second mode is responsible for the translational component in the malleus handle motion. The finding is also consistent with the hypothesis that a middle-ear structural resonance is responsible for the prominent peak seen at 1.5-2 kHz in BC limit data.
Copper-Filled Through-Silicon Vias With Parylene-HT Liner (2016)

Organic low-k materials have been considered in the literature for satisfying the requirements of lowering the dielectric constant of the dielectric layer to decrease the problem of signal delay, lower power consumption, and to reduce cross talk between the neighboring paths, and lowering the fabrication temperature budget. In this paper, the feasibility of using Parylene-HT as a low-temperature deposition, high-uniformity coverage low-dielectric liner for copper-filled through-silicon vias (TSVs) in 3-D integration is investigated. In particular, the capability of embedding Parylene-HT in via-last fabrication process is validated through the demonstration of 100-μm-depth bottom-up copper-filled TSVs. TSVs with Parylene-HT as a liner were realized through vias etching, parylene vapor deposition, and copper electroplating processes. The Parylene-HT deposition and copper electroplating processes were implemented at room temperature, such that thermal-related issue would be avoided and device reliability would be enhanced. The insulation function of the Parylene-HT liner of the fabricated TSVs was characterized. Capacitance of 0.164 pF/TSV and leakage current density of 22 pA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at a field of 0.25 MV/cm were obtained through the measurement of the TSV arrays. The obtained results reveal the possibility of using such a high potential parylene in low-temperature budget 3-D integration applications.
Secondary cancers after hematopoietic stem cell transplantation in Japan (2004)

6650 Background: Among late complications after hematopoietic stem cell transplantation (HSCT), secondary cancers are a serious determinant of patient's outcome. The incidence and risk factors of secondary cancers, however, have not been thoroughly evaluated in Asian countries. Herein, Japanese consequence was retrospectively analyzed using NBMTG database. Methods: For 809 patients who had received HSCT between 1981 and 2000, the number of person-years at risk was calculated from the date of transplantation until the date of last contact, death, diagnosis of a new cancer, or completion of the study, whichever occurred first. Age-, sex-, year-, and region-specific incidence rates were applied to the appropriate person-years at risk to compute the expected numbers of cancers. Incidence rates for all invasive cancers were obtained from the data from the Research Group for Population-based Cancer Registration in Japan. The relationship between the occurrence of secondary cancer and concomitant variables was calculated by means of the Cox proportional-hazards model. Results: Fifteen newly diagnosed solid cancers after HSCT were observed. The risk for cancer development was 3.3 times as high as expected cases. The cumulative incidence ratio at five years and that of ten years were 1.9% and 4.8%, respectively. The risk was significantly elevated for buccal cavity cancer (standard incidental ratio (SIR), 47.35: 95% confidence interval (CI) 15.37 to 110.50), esophagus cancer (SIR, 18.10: 95% CI 2.19 to 65.38), cervix cancer (SIR, 11.72: 95% CI 1.42 to 42.32), uterus cancer (SIR, 12.93: 95% CI 0.33 to 72.08). In multivariate analyses, chronic graft-versus-host disease (GVHD) and age at the time of transplantation were associated with higher risk for solid cancers. Among 15 patients, 14 patients received therapy for secondary cancers. 10 patients are still alive and 5-year probability of survival is 59.3 %. Conclusions: Patients who underwent HSCT have increased risk for secondary cancers. Chronic GVHD and age are two major risk factors for cancer development. Furthermore, our data strongly suggests that appropriate therapy for secondary cancers could prolong patient over all survival. No significant financial relationships to disclose.
Model Predictive Direct Power Control for Grid-Connected NPC Converters (2015)

This paper presents a model predictive direct power control scheme for high-power grid-connected neutral-point-clamped converters. The controller regulates the instantaneous real and reactive powers, as well as the neutral-point potential of the converter, within a set of symmetrical bounds while, at the same time, minimizing the switching frequency of the converter. The proposed approach is distinct from previous predictive power control strategies in that a long prediction horizon is used, allowing lower device switching frequencies to be achieved. A detailed model of the system is provided, and the control algorithm is discussed. Simulation results validate the applicability of the controller to a 3-kV 6.72-MVA system. Experimental results, which are presented for a 240-V 1.68-kVA prototype, show good agreement with those obtained in simulation and further validate the concept.
Automatic Freeway Incident Detection Based on Fundamental Diagrams of Traffic Flow (2009)

Algorithms for automatic incident detection (AID) detect traffic incidents on the basis of traffic flow measurements. There are two important steps in an AID algorithm: traffic flow feature generation and incident decision making. In the past decade, the research on freeway AID algorithms has been focused on using artificial intelligence to optimize the decision making of AID algorithms. In this paper, the primary focus is on finding a new set of variables for the feature generation. The new variables, uncongested and congested regime shifts (URS and CRS), are generated by conducting coordinate transformation on loop-detected flow and occupancy measurements. A novel AID algorithm, the fundamental diagrams–based automatic incident detection (FD AID) algorithm, is then developed by implementing the incident-related traffic flow knowledge using those variables. Preliminary results show superior performance of the FD algorithm compared with legacy algorithms.
Anti HIV-2 Serological Screening in Portuguese Populations Native from or Having Had Close Contact with Africa (1987)

To gather epidemiologic information on the spread of human immunodeficiency virus (HIV)-2 in Portugal, sera were collected in 1985 from 156 healthy adults currently living in Portugal but natives of Guinea Bissau, Cape Verde Islands, Saint Tome/Prince, Angola, and Mozambique and from 321 native Portuguese men and women who had close contact with local African populations. As a control, sera were collected from 102 health Portuguese with no previous contact with Africa or African natives. The enzyme-linked immunosorbent assay (ELISA) developed by Diagnostic Pasteur was used to screen for antibodies to HIV. No positive reactions were recorded in the control population. In contracts, 9 (6%) of the African natives and 7 (2%) of the contacts of Africans were HIV-positive, 6 of the positive sera were from women and 10 were from men. Significantly, 1 of the HIV-2-positive serum samples was from a native of Mozambique and 3 were from natives of Angola. This suggests that HIV-2 infection may have spread to other former Portuguese colonies, and foreign army soldiers who were at 1 time residents of Mozambique or Angola should be considered a risk group capable of spreading HIV-2 infection to other countries.
Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate (2020)

Abstract Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of Nov 15, 2020 has claimed 1,319,946 lives worldwide. Vaccine development focuses on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralisation. Immunogen integrity is therefore important for glycoprotein-based vaccine candidates. Here we show how site-specific glycosylation differs between virus-derived spikes and spike proteins derived from a viral vectored SARS-CoV-2 vaccine candidate. We show that their distinctive cellular secretion pathways result in different protein glycosylation and secretion patterns, which may have implications for the resulting immune response and future vaccine design.
Towards broadly optimum multi-core fiber designs (2019)

This paper is a postprint of a paper submitted to and accepted for publication in 45th European Conference on Optical Communication (ECOC 2019) and is subject to Institution of Engineering and Technology Copyright. The copy of record is available at IET Digital Library
Tip-induced relaxation and amplitude of cantilever vibration observed on GaAs(110) surface (2005)

Based on topographic images of the GaAs(110) surface obtained by non-contact atomic force microscopy (NC-AFM) with different tip–sample distances, we discuss the tip–sample distance dependence of the cantilever vibration amplitude and the tip-induced surface Ga atom relaxation. In the case of a tip which reveals only As atoms as one kind of protrusion in the NC-AFM image, the damping of the cantilever vibration amplitude is small, and the frequency shift decreases gradually with decreasing tip–sample distance. On the other type of tip with which the bright and darker protrusions corresponding to both As and Ga atoms are observed, a large damping of cantilever vibration amplitude is measured with decreasing tip–sample distance. The frequency shift curve measured with this tip has a singular point. From this frequency shift curve, we conclude that the force acting between this type of tip and the sample surface is a hysteretic force. In this tip case, tip-induced surface relaxation of the topmost Ga atoms occurs. There is a relationship between the damping of the cantilever vibration amplitude and the tip-induced surface atom relaxation; that is, the energy dissipation due to the relaxation becomes remarkable.
Supplementary Materials and Methods from Adipocyte-Derived Fibroblasts Promote Tumor Progression and Contribute to the Desmoplastic Reaction in Breast Cancer (2023)

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MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability (2018)

The c-MYC (MYC) oncoprotein is deregulated in over 50% of cancers, yet regulatory mechanisms controlling MYC remain unclear. To this end, we interrogated the MYC interactome using BioID mass spectrometry (MS) and identified PP1 (protein phosphatase 1) and its regulatory subunit PNUTS (protein phosphatase-1 nuclear-targeting subunit) as MYC interactors. We demonstrate that endogenous MYC and PNUTS interact across multiple cell types and that they co-occupy MYC target gene promoters. Inhibiting PP1 by RNAi or pharmacological inhibition results in MYC hyperphosphorylation at multiple serine and threonine residues, leading to a decrease in MYC protein levels due to proteasomal degradation through the canonical SCF<sup>FBXW7</sup> pathway. MYC hyperphosphorylation can be rescued specifically with exogenous PP1, but not other phosphatases. Hyperphosphorylated MYC retained interaction with its transcriptional partner MAX, but binding to chromatin is significantly compromised. Our work demonstrates that PP1/PNUTS stabilizes chromatin-bound MYC in proliferating cells.