gebhart/patrepeval huggingface dataset:
Microangiopathy in primary familial brain calcification: Evidence from skin biopsies (2017)

Autosomal dominant primary familial brain calcification (PFBC) is a rare cerebral microvascular calcifying disorder defined by the presence of calcifications affecting at least the basal ganglia with no secondary cause. It is associated with diverse symptoms including movement disorders, psychiatric disturbances, and cognitive impairment.1 PFBC is caused by loss-of-function mutations in 2 groups of genes: (1) PDGFB , which encodes the platelet-derived growth factor B2 and PDGFRB , which encodes its main receptor platelet-derived growth factor receptor–beta (PDGFR-β)3 and (2) SLC20A2 and XPR1 encoding inorganic phosphate transporters.4,5 Mice carrying Pdgfb hypomorphic alleles exhibit lower pericyte coverage in cerebral microvessels, blood-brain barrier (BBB) impairment, and cerebral microvascular calcifications.2 Recently, a novel PDGFB mutation was reported in an Italian family with PFBC and white-matter hyperintensities (WMH).6 Although brain calcification is a mandatory criterion for diagnosing PFBC, WMH were also reported as a major neuroimaging feature in the first described families with a PDGFRB or a PDGFB mutation2,3 (table e-1 at [Neurology.org/ng][1]). To date, the precise nature of WMH remains unknown but may be regarded as resulting from microangiopathy. This led to the hypothesis that in mice, alterations of the microvessels leading to BBB impairment may be a causal mechanism between microangiopathy and vascular calcifications.2 Transmission electron microscopy analysis of a skin biopsy from a patient belonging to the above-mentioned PDGFB family revealed thickened and fragmented areas in the basal lamina, consistent with microangiopathy.6 We report here the results of skin biopsies performed in 2 patients carrying a PDGFRB and an XPR1 mutation, respectively. [1]: /lookup/doi/10.1212/NXG.0000000000000134
Regenerative Cells for Transplantation in Hepatic Failure (2012)

Human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells have an enormous potential; however, their potential clinical application is being arrested due to various limitations such as teratoma formation followed by tumorigenesis, emergent usage, and the quality control of cells, as well as safety issues regarding long-term culture are also delaying their clinical application. In addition, human ES cells have two crucial issues: immunogenicity and ethical issues associated with their clinical application. The efficient generation of human iPS cells requires gene transfer, yet the mechanism underlying pluripotent stem cell induction has not yet been fully elucidated. Otherwise, although human adult regenerative cells including mesenchymal stem cells have a limited capacity for differentiation, they are nevertheless promising candidates for tissue regeneration in a clinical setting. This review highlights the use of regenerative cells for transplantation in hepatic failure.
Plane-wave excited lens/reflector antennas made of uniaxially anisotropic metamaterials (2010)

The dispersion relations of uniaxially anisotropic metamaterials (UAM) have been numerically investigated extensively, but their applications are still scarce. In this paper, a lens and a meta-reflector antenna made of the UAM are proposed and formulated, and design parameters versus different thickness or different incident/ deflected angles are given in details. Compared to the lens, the meta-reflector antenna presents only a half thickness or a half variation of permittivity or permeability. Simulated results of near-field distributions prove the validity of the two proposed antennas.
Photon-mediated interactions between quantum emitters in a diamond nanocavity (2018)

Photon-mediated interactions between quantum systems are essential for realizing quantum networks and scalable quantum information processing. We demonstrate such interactions between pairs of silicon-vacancy (SiV) color centers coupled to a diamond nanophotonic cavity. When the optical transitions of the two color centers are tuned into resonance, the coupling to the common cavity mode results in a coherent interaction between them, leading to spectrally resolved superradiant and subradiant states. We use the electronic spin degrees of freedom of the SiV centers to control these optically mediated interactions. Such controlled interactions will be crucial in developing cavity-mediated quantum gates between spin qubits and for realizing scalable quantum network nodes.
A Comparative Study between Etiological Factors of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate Urolithiasis (1996)

A comparative study between different etiological factors of calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD) is presented. The most frequent alteration in COD urolithiasis was associated with hypercalciuria, whereas in COM urolithiasis was associated with urinary pH. A comparison between COM and COD groups of stone formers that exhibited 1, 2 or 3 alterations was performed. Thus, in individuals with two simultaneous alterations, the association between altered urinary pH and hypomagnesiuria was the most frequent in the COM group, whereas the association between hypercalciuria and altered urinary pH was most frequent in the COD group. In individuals with three simultaneous alterations, the association between hypercalciuria, hyperphosphaturia and hyperuricuria was most frequent in both COM and COD stone formers.
Effects of Pitavastatin-NP on RISK pathway. (2015)

&lt;p&gt;&lt;b&gt;(A)&lt;/b&gt;, Western blot analysis of phosphorylated Akt (Ser 473) in IR myocardium 3 hours after reperfusion. N = 6 per group. Data are compared using one-way ANOVA followed by Dunnett’s multiple comparison tests. &lt;b&gt;(B)&lt;/b&gt;, Western blot analysis of phosphorylated Akt in IR myocardium from animals treated with WM or with WM plus pitavastatin-NP, 3 hours after reperfusion. Data are mean±SEM (n = 6 per group) &lt;b&gt;(C)&lt;/b&gt; Western blot analysis of phosphorylated Akt in IR myocardium from animals treated with FITC-NP or with pitavastatin-NP, 15 and 30 minutes after reperfusion. &lt;b&gt;(D)&lt;/b&gt;, Representative photomicrographs of IR areas of hearts treated with FITC-NP (left) and Pitavastatin-NP (middle and right) stained immunohistochemically with antibody against phospho-Akt, and an expanded view of the boxed area of the middle panel (right). Scale bar: 100 μm. &lt;b&gt;(E)&lt;/b&gt;, Western blot analysis of phosphorylated GSK3β (S9A) in IR myocardium 3 hours after reperfusion. N = 6 per group. Data are compared using one-way ANOVA followed by Dunnett’s multiple comparison tests.&lt;/p&gt;
Privacy, Personalization, and the Web: A Utility-Theoretic Approach (2007)

Online offerings such as web search face the challenge of providing high-quality service to a large, heterogeneous user base. Recent efforts have highighted the potential to improve performance by introducing methods to personalize services based on special knowledge about users. For example, a user’s location, demographics, and past search and browsing may be useful in enhancing the efficiency and accuracy of web search. However, reasonable concerns about privacy by both users and providers limit access by services to such information. We explore the rich space of possibility where people can opt to share, in a standing or a real-time manner, personal information in return for expected enhancements in the quality of an online service. We present methods and studies on addressing such tradeoffs between privacy and utility in online services. We introduce concrete and realistic objective functions for efficacy and privacy and demonstrate how we can efficiently find a provably near-optimal optimization of the utility-privacy tradeoff. We evaluate our methodology on data drawn from a large-scale web search log of people who volunteered to have their logs explored so as to contribute to enhancing search performance. In order to incorporate personal preferences about privacy and utility, and the willingness to trade off revealing some quantity of personal data to a search system in returns for gains in efficiency, we performed a user study with 1400 participants. Employing utility and preferences estimated from the real-world data, we show that a significant level of personalization can be achieved using only a small amount of information about users. 1
Enhanced Heterologous Production of Desosaminyl Macrolides and Their Hydroxylated Derivatives by Overexpression of the pikD Regulatory Gene in Streptomyces venezuelae (2008)

To elevate the production level of heterologous polyketide in Streptomyces venezuelae, an additional copy of the positive regulatory gene pikD was introduced into the pikromycin (Pik) polyketide synthase (PKS) deletion mutant of S. venezuelae ATCC 15439 expressing tylosin PKS genes. The resulting mutant strain showed enhanced production of both tylactone (TL) and desosaminyl tylactone (DesTL) of 2.7- and 17.1-fold, respectively. The notable increase in DesTL production strongly suggested that PikD upregulates the expression of the desosamine (des) biosynthetic gene cluster. In addition, two hydroxylated forms of DesTL were newly detected from the extract of this mutant. These hydroxylated forms presumably resulted from a PikD-dependent increase in expression of the pikC gene that encodes P450 hydroxylase. Gene expression analysis by reverse transcriptase PCR and bioconversion experiments of 10-deoxymethynolide, narbonolide, and TL into the corresponding desosaminyl macrolides indicated that PikD is a positive regulator of the des and pikC genes, as well as the Pik PKS genes. These results demonstrate the role of PikD as a pathway-specific positive regulator of the entire Pik biosynthetic pathway and its usefulness in the development of a host-vector system for efficient heterologous production of desosaminyl macrolides and novel hydroxylated compounds.
Calculation of Relative Differences in the Binding Free Energies of HIV1 Protease Inhibitors: A Thermodynamic Cycle Perturbation Approach (1994)

An iterative computer-assisted drug design (CADD) method that combines molecular mechanics, dynamics, thermodynamic cycle perturbation (TCP) calculations, molecular design, synthesis, and biochemical testing of peptidomimetic inhibitors and crystallographic structure determination of the protein-inhibitor complexes has been successfully applied to the design of novel inhibitors for the HIV1 protease. The first "designer" compound in this series (I) was designed by replacing the C-terminal Val-Val methyl ester of a known hydroxyethylene inhibitor with a diphenhydramine amide derivative in which two phenyl groups fill the p2' and p3' side-chain binding pockets in the HIV1 protease. Subsequent testing showed modest inhibition (Ki = 1.67 microM). Concurrently, molecular mechanics calculations on designed analogs indicated the feasibility of replacement of a phenyl ring with an indole ring (II). Synthesis and biochemical testing resulted in better inhibition potency for II. X-ray crystal structure determination of HIV1 protease complexed with I and II provided structural information for subsequent design and TCP calculations. A TCP protocol was established and validated for the mutation of I-->II. TCP results showed a net gain of 2.1 (+/- 0.9) kcal/mol in replacing II with I, which agreed with experimental result within an error margin of 0.8 kcal/mol. TCP calculations for six other mutations (I-->III, II-->III, IV, V, VI, and VII) were performed prior to synthesis and testing. These results allowed for the prioritization of design ideas for synthesis. In all cases where experimental results are available, TCP calculations showed good agreement. These results demonstrate that the TCP approach can be used with medicinal chemistry and crystallography for screening the proposed derivatives of a lead compound prior to synthesis, thus potentially reducing the time for the discovery of new drugs.
Development of Femtocell Simulator Based on LTE Systems for Interference and Performance Evaluation (2011)

최근 가정 또는 사무실과 같은 실내 환경에서 음영지역을 해소하고 고품질의 서비스 제공을 위한 방안으로 초소형 기지국인 펨토셀(Femtocell)이 많은 관심을 받고 있다. 펨토셀은 사업자 및 사용자에게 다양한 이점을 제공하지만 펨토셀의 도입을 위해 서는 채널 선택에 따른 간섭제어, 네트워크 동기화, 자기 최적화 등 다양한 기술적 문제점이 해결되어야 한다. 이를 위해 본 연구에서는 펨토셀의 도입으로 인하여 발생 가능한 다양한 신호간섭 문제들에 대한 분석을 용이하게 하기 위한 LTE(Long Term Evolution) 시스템 기반 펨토셀 시뮬레이터를 개발하였다. 개발된 시뮬레이터는 단말 이동성, 스케줄러, 호 수락 제어, 트래픽 생성, MCS(Modulation and Coding Scheme) 결정의 5개의 블록과 이를 연결하고 관리하는 메인 모듈로 구성되어 있다. 또한 사용자의 편의성을 도모하기 위하여 시뮬레이션 결과를 실시간으로 관측할 수 있는 GUI(Graphical User Interface)를 적용하였다. 본 시뮬레이터는 실제와 유사한 환경에서 매크로셀과 펨토셀 사이의 간섭영향을 면밀히 분석하고 이동통신 시스템의 성능을 효과적으로 평가할 수 있도록 지원하며, 다양한 펨토셀 시스템을 개발하는데 크게 기여할 수 있을 것으로 예상된다. Recently, femtocell has been concerned as one of effective solutions to relieve shadow region and provide high quality services to users in indoor environments. Even though femtocell offers various benefits to cellular operators and users, many technical issues, such as interference coordination, network synchronization, self-configuration, self-optimization, and so on, should be solved to deploy the femtocell in current network. In this paper, we develop a simulator for evaluating performance of long term evolution (LTE) femtocell systems under various interference scenarios. The simulator consists of a main-module and five sub-modules. The main-module connects and manages five sub-modules which have the functionality managing user mobility, packet scheduling, call admission control, traffic generation, and modulation and coding scheme (MCS). To provide user convenience, the simulator adopts graphical user interface (GUI) which can observes simulation results in real time. We expect that this simulator can contribute to developing effective femtocell systems by supporting a tool for analyzing the effect of interference between macrocell and femtocell.
Hereditary Paragangliomas (2011)

Paragangliomas (PGL) and pheochromocytomas (PCC) are rare, usually benign tumors that originate from the neuroendocrine tissue along the paravertebral axis. Up to 35% of these tumors may be hereditary; they are associated with germline mutations in genes encoding subunits of the succinate dehydrogenase (SDH) enzyme complex in the context of the familial PGL syndromes, PGL1, 3 and 4 caused by mutations in the SDHD,SDHC and SDHB genes, respectively. Another familial PGL syndrome, PGL2, is caused by mutations in SDHAF2/SDH5, which encodes for a molecule that is an accessory to the function of the SDH enzyme and its SDHA subunit. Less frequently, mutations in the genes responsible for Von Hippel Lindau disease (VHL), multiple endocrine neoplasia type 2 (MEN2), and neurofibromatosis type 1 (NF1) are also found in patients with hereditary PGL and PCC. Recently mutations were found in the SDHA subunit in a limited number of patients with PGL and/or PCC. The SDHB, SDHC and SDHD gene mutations (but not SDHA) can also be found in patients with PGL and/or PCC and gastrointestinal stromal tumors (GISTs), also known as the Carney-Stratakis syndrome; SDHB mutations, in particular, may also predispose to thyroid and renal cancer, and possibly other tumors. A new gene was recently found to predispose to PGL and/or PCC when mutated is TMEM127. In this text, we provide an overview of the genetics of PGLs and related conditions with an emphasis on genetic risk assessment, prevention, and prognosis.
Template-Free Preparation of Metal Nanowires by Two-Phase Electrolysis Using Cells Composed of Water and Oil Phases (2021)

Sn nanowires were prepared by template-free electrodeposition by two-phase electrolysis using a cell composed of water and oil phases. Prior to the electrodeposition, the water phase containing SnO 4 , NaCl, H 2 SO 4 , and C 2 H 3 N was mixed with the oil phase, methyl isobutyl ketone, to extract Sn species from the water phase to the oil phase. Sn nanowires were formed continuously on the surface of the electrode placed in the oil phase during electrodeposition. By using the water phase containing CuSO 4 , Cu nanowires were also obtained by two-phase electrolysis. The present process allows the high-throughput preparation of metal nanowires because the metal nanowires can be obtained continuously without the need for templates. The obtained metal nanowires are expected to be used in various applications, such as batteries, catalysts, and sensors.
Computer-aided design/engineering of bearing systems using the Dempster-Shafer theory (1995)

Abstract Research in computer-aided design/engineering (CAD/E) has focused on enhancing the capability of computer systems in a design environment, and this work has continued in this trend by illustrating the use of the Dempster-Shafer theory to expand the computer’s role in a CAD/E environment. An expert system was created using Dempster-Shafer methods that effectively modeled the professional judgment of a skilled tribologist in the selection of rolling element bearings. A qualitative and symbolic approach was used, but access to simple quantitative models was provided to the expert system shell. Although there has been significant discussion in the literature regarding modification/improvement of the Dempster-Shafer theory, Shafer’s theories were found adequate in all respects for replicating the expert’s judgment. However, an understanding of the basic theory is required for interpreting the results.
Cell type‐specific responses to salinity – the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum (2015)

Mesembryanthemum crystallinum (ice plant) exhibits extreme tolerance to salt. Epidermal bladder cells (EBCs), developing on the surface of aerial tissues and specialized in sodium sequestration and other protective functions, are critical for the plant's stress adaptation. We present the first transcriptome analysis of EBCs isolated from intact plants, to investigate cell type-specific responses during plant salt adaptation. We developed a de novo assembled, nonredundant EBC reference transcriptome. Using RNAseq, we compared the expression patterns of the EBC-specific transcriptome between control and salt-treated plants. The EBC reference transcriptome consists of 37 341 transcript-contigs, of which 7% showed significantly different expression between salt-treated and control samples. We identified significant changes in ion transport, metabolism related to energy generation and osmolyte accumulation, stress signalling, and organelle functions, as well as a number of lineage-specific genes of unknown function, in response to salt treatment. The salinity-induced EBC transcriptome includes active transcript clusters, refuting the view of EBCs as passive storage compartments in the whole-plant stress response. EBC transcriptomes, differing from those of whole plants or leaf tissue, exemplify the importance of cell type-specific resolution in understanding stress adaptive mechanisms.
A method for estimating the risk of drug-induced phototoxicity and its application to smoothened inhibitors (2011)

The energy difference between the frontier-orbital HOMO–LUMO gaps calculated for the ground state of marketed oral drugs correlated with their observed phototoxicity. This molecular descriptor, together with their maximal molar absorptivity for UV light above 290 nm, can be used to predict phototoxicity risks. This is demonstrated for the phototoxicity mitigation of 1-piperazinyl phthalazines, a class of smoothened inhibitors.
Effects of Temperature, Environment, and Orientation on the Fracture Toughness of Single‐Crystal YAG (1997)

The fracture toughness of single‐crystal YAG was measured as a function of temperature in air and under vacuum using the SENB technique up to 1600°C. The measured KIC was 2.2 MPa·m 1/2 at room temperature and it increased with temperature above 1200°C, reaching a value of 4.5 MPa·m 1/2 at 1600°C in air. The effects of crystallo‐graphic orientation and oxygen partial pressure on tough‐ness were studied at 1600°C. The toughness increased further to 5.5 MPa·m 1/2 when tested under vacuum (10 ‐5 torr)at 1600°C. Both temperature and testing environments were found to influence the fracture toughness, but there was no significant effect of crystallographic orientation.
MO-E-332-01: DXS a Diagnostic X-Ray Spectra Generator (2008)

Purpose: To numerically generate radiographic x-ray spectra that can be conveniently employed in radiation transport simulations or other radiation detection applications. Method and Materials: Based initially on the Tucker, et al model, we developed and evaluated a new code, DXS (Diagnostic X-Ray Spectra), to numerically generate spectra for tungsten-target x-ray tubes spanning the radiographic energy range. The model parameters in our code were adjusted by comparison with corresponding MCNP5 simulated spectra; we modified the semi-analytical formulation for the characteristic x-ray production, a caveat of Tucker's model, by incorporating a factor that better accounts for the dependence of the K-peaks on the tube potential. Parametric fitting functions are used to model the self-attenuation in the target and attenuation due to inherent and added filtration (aluminum, beryllium, copper, tantalum are the options implemented in the code), as well as for the tungsten mass stopping power and the Thomson-Whiddington constant. Comparison with Monte Carlo simulated and published measured spectra were used to validate the new code. Results: Normalized to unit area DXS code-generated spectra for several tube potentials from 50 to 140 kVp agree well, less than 2% relative difference in nearly all energy bins (2 keV), with corresponding MCNP5 simulated spectra for similar tube parameters. Few exceptions are noted and may be attributed to either poorer statistics in the low and high energy tails of the spectrum, or to insufficient accuracy of the numerical computations for the steepest part of the spectra at high accelerating potentials. Good agreement is seen between the DXS and Bhat et al measured spectra. Conclusion: The DXS code generates the spectra, according to user specified input parameters (tube potential, anode angle, filtratation) and energy intervals, and augments them into any discretized energy group structure. Hence, the code can be of great benefit in radiation transport simulations.
Experimental investigation and comparison of different equalizers for four level pulse amplitude modulation (2015)

Numerical and experimental investigations are undertaken to analyze and compare the performance of different equalizers for four-level pulse amplitude modulation, which is considered a promising candidate for the next generation of data center interconnects. Numerical and experimental investigations are undertaken to analyze and compare the performance of different equalizers for four-level pulse amplitude modulation, which is considered a promising candidate for the next generation of data center interconnects.