gebhart/patrepeval huggingface dataset:
Six missense mutations associated with type I and type II protein C deficiency and implications obtained from molecular modelling (1994)

The molecular basis of protein C deficiency was studied in three type I and three type II heterozygotes. Three probands showed thrombotic complications. All the exons and intron/exon junctions of the protein C gene were studied using a strategy combining by the polymerase chain reaction (PCR) amplification, single-strand conformational polymorphism (SSCP) analysis, and DNA sequencing of the PCR-amplified fragments. Six missense mutations were identified, including three novel ones. One was located in exon II, in which the initiating translation codon (ATG) encoding for Met at position -42 was replaced by ACG encoding for Thr. The other five were located in exon IX, and included TAC(Tyr399)-->CAC(His), CCG(Pro327)-->CTG(Leu), GAC(Asp359)-->AAC(Asn) in two cases, and GGG(Gly350)-->AGG(Arg). Four of the six missense mutations occurred in CG dinucleotide. Sequence analysis of the other exons excluded additional mutations. By restriction enzyme analysis, co-segregation of the mutation with protein C deficiency was observed in four families. The other two mutations at amino acid positions -42 and 350 were also considered to be associated with protein C deficiency due to the absence of these mutations in 50 normal individuals. A structural model of the protease domain of mutant activated protein C was constructed by the chimeric modelling method, and the resultant model suggested conformational changes due to each missense mutation identified in protein C deficiency. The present data also provide some evidence regarding the genetic heterogeneity of protein C deficiency.
Prediction of residual angina after percutaneous coronary intervention (2015)

Based on a large, multicentre cohort of PCI patients, we created a model of residual angina 6 months after PCI that can provide patients realistic expectations of angina relief, guide follow-up strategies, support the use of residual angina as a means of comparing PCI quality, and enable comparative effectiveness research.
Associations between body shape across the life course and adulthood concentrations of sex hormones in men and pre- and postmenopausal women: a multicohort study (2021)

The objective was to investigate associations between life-course adiposity and sex hormone concentrations: trajectory of adiposity from age 5 to 40 (premenopausal)/60 (postmenopausal women and men) in relation to levels of oestrone (E1), oestradiol (E2), sex hormone-binding globulins (SHBG), testosterone in 4801 premenopausal and 6019 postmenopausal women in the Nurses' Health Study (NHS) and NHS II, and 2431 men in the Health Professionals Follow-up Study. We used group-based trajectory models to identify groups within each cohort based on recalled somatotypes and reported BMI. Multivariate linear regression models were used to compare sex hormone concentration across different trajectory groups. The mean age at blood draw was 64·1 ± 8·1 years for men, 59·4 ± 6·0 for postmenopausal and 44·1 ± 4·6 for premenopausal women. In men, compared with the medium-stable group, lean-marked increase and medium increase groups had lower levels of SHBG (percentage difference: -17 and -9 %) and testosterone (-15 and -13 %). In postmenopausal women, compared with the medium-stable group, lean-marked increase and medium increase groups had higher levels of E1 (21 and 34 %) and E2 (45 and 68 %) but lower level of SHBG (-29 and -35 %). In premenopausal women, compared with the lean-moderate increase group, medium-stable/increase and heavy-stable/increase groups had lower levels of SHBG (-6 and -28 %). Attained adulthood adiposity and middle-life weight gain were associated with lower SHBG and testosterone in men, higher E1 and E2 and lower SHBG in postmenopausal women, and lower SHBG in premenopausal women. The study indicates the importance of maintaining a healthy body weight throughout life course for homoeostasis of sex hormones.
A sensitivity study of ray-tracing based wireless channel simulators using field measurements (2007)

Toward the goal of achieving robust ray tracing based channel models this paper compares simulation results using a 3D ray-tracing tool [F. Aryanfar and S. Safavi-Naeini, 1998] vs. field measurements in different environments. The tool has been validated for many outdoor and indoor scenes at different frequency bands and is capable of accurate prediction of wireless channel parameters. To test model robustness, we also examine the sensitivity of the predicted results on inputs such as angular resolution, material properties and detail of geometry.
mGlu<sub>5</sub>positive allosteric modulation normalizes synaptic plasticity defects and motor phenotypes in a mouse model of Rett syndrome (2016)

Rett syndrome (RS) is a neurodevelopmental disorder that shares many symptomatic and pathological commonalities with idiopathic autism. Alterations in protein synthesis-dependent synaptic plasticity (PSDSP) are a hallmark of a number of syndromic forms of autism; in the present work, we explore the consequences of disruption and rescue of PSDSP in a mouse model of RS. We report that expression of a key regulator of synaptic protein synthesis, the metabotropic glutamate receptor 5 (mGlu<sub>5</sub>) protein, is significantly reduced in both the brains of RS model mice and in the motor cortex of human RS autopsy samples. Furthermore, we demonstrate that reduced mGlu<sub>5</sub> expression correlates with attenuated DHPG-induced long-term depression in the hippocampus of RS model mice, and that administration of a novel mGlu<sub>5</sub> positive allosteric modulator (PAM), termed VU0462807, can rescue synaptic plasticity defects. Additionally, treatment of Mecp2-deficient mice with VU0462807 improves motor performance (open-field behavior and gait dynamics), corrects repetitive clasping behavior, as well as normalizes cued fear-conditioning defects. Importantly, due to the rationale drug discovery approach used in its development, our novel mGlu<sub>5</sub> PAM improves RS phenotypes and synaptic plasticity defects without evoking the overt adverse effects commonly associated with potentiation of mGlu<sub>5</sub> signaling (i.e. seizures), or affecting cardiorespiratory defects in RS model mice. These findings provide strong support for the continued development of mGlu<sub>5</sub> PAMs as potential therapeutic agents for use in RS, and, more broadly, for utility in idiopathic autism.
Laser Frequency Drift Stabilization using an Integrated Dual-Mode Locking Si3N4 Waveguide Reference Cavity (2021)

We demonstrate an integrated Si3N4 waveguide resonator designed as a dual-mode locking (DML) cavity that stabilizes laser frequency to 1.7×10 -10 Allan deviation in a 1000-second average measurement with a temperature sensitivity of 187.56 MHz/K.
Extracting Tritium from Water Using a Protonic Manganese Oxide Spinel (2015)

Extracting tritium of parts-per-trillion-levels from water at room temperature was provided using a protonic manganese oxide with a spinel crystal structure under weakly acidic conditions. Indeed, using 0.48 g of the protonic manganese oxide powder led to the removal of 1.75 × 105 Bq of tritium in 20 min at room temperature from a test water (100 mL) that contained a tritium concentration of 5.6 × 106 Bq/L (i.e., 15.6 ng/L). The extraction capability of tritium significantly depended on the crystal structure of manganese oxides and the proton content in the spinel crystal structure.
Amplitude monopulse pillbox antenna in SIW technology (2016)

A new amplitude monopulse multi-beam antenna is proposed in substrate integrated waveguide (SIW) technology. The antenna system is a dual-layer structure incorporating the monopulse technique along its scanning plane (E-plane). The radiating part, in the upper most layer, is an array of slotted waveguides. In the lower layer the feeding system consists of five horn pairs located in the focal plane of the pillbox transition. The in-phase and out-of-phase operations of each horn pair form the sum (Σ) and difference (Δ) radiation patterns in the antenna scanning plane. This allows enhanced angular resolution in E-plane without mechanical rotation of the antenna structure. The proposed concept has been validated numerically at 24.15 GHz. At the design frequency, very good scanning performance is obtained over an angular sector of ±26° with side lobe level (SLL) lower than -11dB and -6dB respectively, for the Σ and Δ patterns. The null depth is better that -28dB for all Δ patterns.
On Contraction Analysis of Switched Systems With Mixed Contracting-Noncontracting Modes via Mode-Dependent Average Dwell Time (2023)

This article studies contraction analysis of switched systems that are composed of a mixture of contracting and noncontracting modes. The first result pertains to the equivalence of the contraction of a switched system and the uniform global exponential stability of its variational system. Based on this equivalence property, sufficient conditions for a mode-dependent average dwell/leave-time based switching law to be contractive are established. Correspondingly, linear matrix inequality (LMI) conditions are derived that allow for numerical validation of contraction property of nonlinear switched systems, which include those with all noncontracting modes.
Supplementary Material for: Expression of Fucosyltransferase 8 Is Associated with an Unfavorable Clinical Outcome in Non-Small Cell Lung Cancers (2017)

<b><i>Objecitive:</i></b> Fucosyltransferase 8 (FUT8), the only enzyme responsible for the core α1,6-fucosylation of asparagine-linked oligosaccharides of glycoproteins, is a vital enzyme in cancer development and progression. We examined FUT8 expression in non-small cell lung cancers (NSCLCs) to analyze its clinical significance. We also examined the expression of guanosine diphosphate-mannose-4,6-dehydratase (GMD), which is imperative for the synthesis of fucosylated oligosaccharides. <b><i>Methods:</i></b> Using immunohistochemistry, we evaluated the expression of FUT8 and GMD in relation to patient survival and prognosis in potentially curatively resected NSCLCs. <b><i>Results:</i></b> High expression of FUT8 was found in 67 of 129 NSCLCs (51.9%) and was significantly found in non-squamous cell carcinomas (p = 0.008). High expression of FUT8 was associated with poor survival (p = 0.03) and was also a significant and independent unfavorable prognostic factor in patients with potentially curatively resected NSCLCs (p = 0.047). High expression of GMD was significantly associated with high FUT8 expression (p = 0.04). <b><i>Conclusions:</i></b> High expression of FUT8 is associated with an unfavorable clinical outcome in patients with potentially curatively resected NSCLCs, suggesting that FUT8 can be a prognostic factor. The analysis of FUT8 expression and its core fucosylated products may provide new insights for the therapeutic targets of NSCLCs.
Dynamic crystallography reveals spontaneous anisotropy in cubic GeTe (2022)

Cubic energy materials such as thermoelectrics or hybrid perovskite materials are often understood to be highly disordered. In GeTe and related IV-VI compounds, this is thought to provide the low thermal conductivities needed for thermoelectric applications. Since conventional crystallography cannot distinguish between static disorder and atomic motions, we develop the energy-resolved variable-shutter pair distribution function technique. This collects structural snapshots with varying exposure times, on timescales relevant for atomic motions. In disagreement with previous interpretations, we find the time-averaged structure of GeTe to be crystalline at all temperatures, but with anisotropic anharmonic dynamics at higher temperatures that resemble static disorder at fast shutter speeds, with correlated ferroelectric fluctuations along the $&lt;$100$&gt;$c direction. We show that this anisotropy naturally emerges from a Ginzburg-Landau model that couples polarization fluctuations through long-range elastic interactions. By accessing time-dependent atomic correlations in energy materials, we resolve the long-standing disagreement between local and average structure probes, and show that spontaneous anisotropy is ubiquitous in cubic IV-VI materials.
Design, fabrication, and characterization of an electrochemically-based dose tracking system for closed-loop drug delivery (2012)

A real-time integrated electrochemically-based dose tracking system for closed-loop drug delivery is presented. Thin film Pt sensors were integrated in an electrolytic MEMS drug delivery pump to allow dose tracking via electrochemical impedance measurement. Measurement electrode placement and composition were investigated. A bolus resolution of 230 nL was demonstrated. The sensor was calibrated for use with water (low conductivity) and 1 × PBS (high conductivity), the selected model aqueous drugs. The impedance response is dependent on delivered volume and not affected by actuation parameters. A graphical user interface was created for real-time impedance based dose tracking and leakage/blockage detection in the system. Drift in the impedance response of an idle system after perturbation (actuation) were investigated and mitigated through the use of Pt wire electrodes as opposed to thin film electrodes.
Interactive Visualization of Multivariate Statistical Data (2006)

This paper introduces web-based interactive Linked Micromap (LM) plots, a set of dynamic visualization methods that allows readers to interactively select variables and modify the different views to help reveal relationships among the study units. This methodology provided the foundation for web-based micromaps used by the National Cancer Institute (NCI). This illustrates the power of visualization to make statistical summaries involving health and risk factors for millions of people accessible to health planners than may have never had a statistics class. LM plots methodology is in use by the Department of Agriculture and readily extend to other application in other agencies in the United States. The interactive methods can be as useful in such extensions as they were for the National Cancer Institute
Automated Directional Drilling Software and Remote Operations Centers Drive Rig Fleet Well Delivery Improvement (2018)

Abstract Early in 2017, initial discussions began to define an Automated Remote Drilling project that would use a centralized command center and specialized distributed software systems to automate the directional drilling decision-making workflow and the implementation of these decisions at the rigsite. The objective of this de-manning of directional resources at the rigsite was to enable the Operator's in-house directional supervisors to efficiently and safely control a larger number of rigs than was previously possible with legacy work practices and software. In addition to the standard high-speed data links from office to rig, the project was based on an automated directional software guidance system configured to optimize directional motor slide drilling. This integrated directional navigation software suite also communicates directly with the top drive directional control system to ensure slide commands are implemented exactly as calculated. The software suite captures and assesses the effectiveness of slides automatically and uses sophisticated steering logic and steering targeting systems to support directional drilling best practices and geo-steering adjustments in the production zone. The paper presents aggregated feedback from directional drillers on the automated systems' decisions and the results of following system directives in the low angle and nudge sections, in the curve, and in the lateral wellbore. Case studies are presented, along with summaries of the workflow changes implemented in town and at the rigsite. Several current lateral Bakken wells are presented as evidence of the effectiveness of the Automated Remote Drilling project approach and the benefits of this level of collaboration between a forward-looking Operator and drilling contractor. The combination of the directional navigation software, the automated implementation, the geo-steering support, and a new Automation Assisted Workflow presents a new approach to an industry-wide challenge in the current market of how to do more with less without compromising efficiency, safety, or intervention capabilities.
An embedded coder for multispectral image compression based on vector lifting structures (2005)

In the context of satellite image compression, we are interested in simultaneously exploiting the spatial and spectral activity of multispectral data by using improved lifting structures. The novelty of our approach lies in two aspects. Firstly, we employ nonseparable vector lifting structures that extend the conventional separable lifting scheme. Secondly, the problem of coding the resulting coefficients is addressed. More precisely, we propose an extension to the vector and nonseparable case of Shapiro's embedded zerotrees of wavelet coefficients which achieves further saving in the bitrate. Experimental results carried out on natural remote sensing images show the good performance of the proposed compression procedure.
“Tall Oil”–Derived Phytosterols Reduce Atherosclerosis in ApoE-Deficient Mice (1997)

We investigated the effects of a "tall oil"-derived phytosterol mixture (TODPM) on the formation of atherosclerotic lesions in apoE-deficient mice. TODPM was added at 2% (wt/wt) to the chow of nine mice; the control group had six animals. The diet of all animals contained 9% (wt/wt) fat and 0.15% (wt/wt) cholesterol. After 4 weeks, plasma total cholesterol levels were significantly reduced in the TODPM-treated mice (26.6 versus 42.0 mmol/L, P < .0001). The mean body weight of the TODPM-supplemented group was significantly higher at week 5 and throughout the study (29.4 versus 27.7 g, P < .05). The experiment was terminated at 18 weeks. Histological examination showed mature atherosclerotic lesions composed of foam cells underlying the endothelium, a mosaic of extracellular glycosaminoglycans, numerous apparently proliferative smooth muscle cells, and foci of cholesterol clefts in the control animals. By contrast, the TODPM-treated mice showed only early lesions containing mainly superficial foam cells. As assessed by morphometry, the lesion area in the aortic sinuses of TODPM-treated animals was less than half that of control animals (P < .0001). This reduced lesion area was accompanied by a substantial reduction in all lesional components, reflecting a delay in progression of atheromatous changes. A strong positive correlation (r = .69, P < .01) was found between plasma total cholesterol levels and lesion area in the aortic sinuses. TODPM also prevented the occurrence of xanthomatosis. We conclude that supplementation of a cholesterol-enriched diet with TODPM significantly lowers plasma cholesterol and retards development of atherosclerosis in apoE-deficient mice, suggesting a therapeutic potential for the mixture of phytosterols studied.
Structure factor of a relaxor ferroelectric (2015)

We study a minimal model for a relaxor ferroelectric including dipolar interactions and short-range harmonic and anharmonic forces for the critical modes as in the theory of pure ferroelectrics together with quenched disorder coupled linearly to the critical modes. We present the simplest approximate solution of the model necessary to obtain the principal features of the correlation functions. Specifically, we calculate and compare the structure factor measured by neutron scattering in different characteristic regimes of temperature in the relaxor $\mathrm{Pb}({\mathrm{Mg}}_{1/3}{\mathrm{Nb}}_{2/3}){\mathrm{O}}_{3}$.
In vitro plant regeneration and Agrobacterium-mediated genetic transformation of a carnivorous plant, Nepenthes mirabilis (2020)

In nutrient-poor habitats, carnivorous plants have developed novel feeding strategies based on the capture and digestion of prey and the assimilation of prey-derived nutrients by specialized traps. The Nepenthes genus, comprising nearly 160 species, presents a remarkable pitcher-shaped trap, leading to great interest among biologists, but the species of this genus are listed as threatened. In this work, we developed a protocol for reproducing Nepenthes mirabilis through shoot regeneration from calli. The cultivation of stem segments of N. mirabilis on MS medium containing thidiazuron induced organogenic calli after 10 weeks. Subcultured calli exposed to 6-benzylaminopurine showed shoot regeneration in 3 weeks with considerable yields (143 shoots/g of calli). Excised shoots transferred to medium with indole-3-butyric acid allowed rooting in 4 weeks, and rooted plantlets had a 100% survival rate. Based on this method, we also developed an Agrobacterium-mediated genetic transformation protocol using calli as explants and ipt as a positive method of selection. Twelve weeks post infection, regenerated shoots were observed at the surface of calli. Their transgenic status was confirmed by PCR and RT-PCR. In conclusion, this study provides an efficient method for regenerating Nepenthes and the first protocol for its stable genetic transformation, a new tool for studying carnivory.
Stereoselective Total Synthesis of (–)‐Batzellasides A, B, and C (2013)

Abstract Total synthesis of (–)‐ L ‐batzellasides A, B, and C has been achieved in 13 steps from known lactone 2 in 12.6, 13.2, and 13.8 % overall yields, respectively. The key steps in this synthesis were the stereoselective introduction of an allyl group at the C1 position by acyliminium chemistry and Brown's asymmetric allylation of the corresponding aldehydes to construct a stereocenter on the side chain.
Coronavirus Disease-2019: Implication for the care and management of patients with systemic lupus erythematosus (2020)

Systemic lupus erythematosus is a chronic remitting-relapsing autoimmune disease that affects multiple organ systems. In this article we discuss aspects in the management of lupus patients that are particularly relevant during the current SARS-CoV-2 pandemic. We speculate that lupus patients might be more susceptible for a more severe COVID-19 disease course and emphasize the importance of maintaining remission in lupus patients. We discuss the critical role hydroxychloroquine plays in the management of lupus patients and suggest considering the psychosocial implications of the current pandemic on lupus care.