gebhart/patrepeval huggingface dataset:
Complex Glycerol Kinase Deficiency and Adrenocortical Insufficiency in Two Neonates (2016)

Contiguous gene deletions of chromosome Xp21 can lead to glycerol kinase deficiency and severe adrenocortical insufficiency (AI) in a male newborn among other problems. We describe our experience with two such patients who presented with dysmorphic facies, AI, and pseudo-hypertriglyceridemia. Both infants had normal serum 17-hidroxyprogesterone levels, and adrenal glands could not be observed with ultrasonography. Creatine kinase and triglyceride levels were measured to elucidate the etiology of adrenal hypoplasia and were above normal limits in both cases. Both patients required steroid and salt supplementation. They were both found to have Xp21.2 deletions (DMD, NR0B1, GK, IL1RAPL1). We conclude that AI in the context of other genetic abnormalities should prompt chromosomal investigations in the absence of another unifying explanation.
Tightly bound ligands for hafnium nanoparticle EUV resists (2012)

Relative ligand binding energies were determined for a series of common ligand types with hafnium oxide nanoparticles, and from these results a series of novel strong binding ligands were developed. The relative equilibrium concentrations of two competing ligands bound to the nanoparticles were measured using nuclear magnetic resonance spectroscopy (NMR). For each ligand type, equilibrium constants and relative binding energies were then calculated and compared. Methane sulfonic acid was found to have the strongest binding energy, 2.0 Kcal/mol stronger than acetic acid. A group of three sulfonate ligands capable of freeradical crosslinking were made, along with three sulfonate ligands capable of creating aqueous developable nanoparticles. One of these ligands resulted in insoluble nanoparticles, however, the other two ligands resulted in nanoparticles that coated well on a silicon substrate and had dissolution rates greater than 100 nm per second.
Ionic transport in K2Ti6O13 (2022)

Abstract The increasing demand for batteries forced the development of energy storage systems that rely on materials consisting of abundant elements in the Earth’s crust. Switching from Li + to K + as the main ionic charge carrier needs highly conducting potassium-bearing electrolytes to realize K + ion batteries (PIBs). The knowledge gained from the design of Li-ion batteries (LIBs) and Na-ion batteries (NIBs) may conceptually inspire also the establishment of PIBs. Considering, for instance, the hexatitanates Na 2 Ti 6 O 13 , Li 2 Ti 6 O 13 , and H 2 Ti 6 O 13 , which were previously investigated as components for LIBs and NIBs, here we investigated ion dynamics in the K-analog K 2 Ti 6 O 13 . Ionic transport in polycrystalline samples of K 2 Ti 6 O 13 was studied in a moisture-free atmosphere by broadband impedance spectroscopy in a temperature range from 20 °C to 450 °C. The current study aims at establishing a correlation between structural features of K 2 Ti 6 O 13 and long-range ionic transport. As expected for K + transport in K 2 Ti 6 O 13 with its geometrically obstructed structure, the overall activation energy of ion transport in the ternary oxide takes a rather high value of 0.97(2) eV. Almost the same result (0.95(3) eV) is obtained for the migration activation energy, which we extracted from the analysis of crossover frequencies of the corresponding conductivity isotherms. By comparing our results with those of Na 2 Ti 6 O 13 (0.82 eV), Li 2 Ti 6 O 13 (0.65 eV), and H 2 Ti 6 O 13 , we clearly see how the size of the mobile cation correlates with both specific conductivities and activation energies. This comparison points to K + being the main charge carrier in K 2 Ti 6 O 13 . It also helps in laying the foundations to derive the relevant structure-property relationships in this class of materials.
Linking Local Environments and Hyperfine Shifts: A Combined Experimental and Theoretical31P and7Li Solid-State NMR Study of Paramagnetic Fe(III) Phosphates (2010)

Iron phosphates (FePO(4)) are among the most promising candidate materials for advanced Li-ion battery cathodes. This work reports upon a combined nuclear magnetic resonance (NMR) experimental and periodic density functional theory (DFT) computational study of the environments and electronic structures occurring in a range of paramagnetic Fe(III) phosphates comprising FePO(4) (heterosite), monoclinic Li(3)Fe(2)(PO(4))(3) (anti-NASICON A type), rhombohedral Li(3)Fe(2)(PO(4))(3) (NASICON B type), LiFeP(2)O(7), orthorhombic FePO(4)·2H(2)O (strengite), monoclinic FePO(4)·2H(2)O (phosphosiderite), and the dehydrated forms of the latter two phases. Many of these materials serve as model compounds relevant to battery chemistry. The (31)P spin-echo mapping and (7)Li magic angle spinning NMR techniques yield the hyperfine shifts of the species of interest, complemented by periodic hybrid functional DFT calculations of the respective hyperfine and quadrupolar tensors. A Curie-Weiss-based magnetic model scaling the DFT-calculated hyperfine parameters from the ferromagnetic into the experimentally relevant paramagnetic state is derived and applied, providing quantitative finite temperature values for each phase. The sensitivity of the hyperfine parameters to the composition of the DFT exchange functional is characterized by the application of hybrid Hamiltonians containing admixtures 0%, 20%, and 35% of Fock exchange. Good agreement between experimental and calculated values is obtained, provided that the residual magnetic couplings persisting in the paramagnetic state are included. The potential applications of a similar combined experimental and theoretical NMR approach to a wider range of cathode materials are discussed.
High Sensitivity Liver Vasculature Visualization Using a Real-Time Coherent Flow Power Doppler (CFPD) Imaging System: A Pilot Clinical Study (2018)

Power Doppler (PD) imaging is a widely used technique for flow detection and vessel visualization in clinics. Despite its wide use, its capability is limited by multiple noise sources, including thermal noise, clutter, and tissue motion. These noise sources lead to deterioration of detection sensitivity to small vessels and slow flow, and a trade-off between acquisition time and PD image signal-to-noise ratio (SNR), particularly in deep body vessel detection among patients with high body-mass-indices (BMI). To improve the sensitivity of slow flow and small vessel detection, and alleviate the trade-off between acquisition time and image SNR, we have proposed the coherent flow power Doppler (CFPD) imaging technique, and shown its performance in flow phantom and porcine models. Here, we report on a pilot clinical study of CFPD on 15 healthy human volunteers to evaluate the clinical feasibility of CFPD in liver vasculature detection and visualization. For the study, we built a real-time CFPD (rtCFPD) imaging system based on a Verasonics Vantage 256 scanner. The real-time processing performed by a GPU-based software beamformer and Doppler processing software. Using the rtCFPD imaging system, the liver Doppler data of 15 healthy volunteers were acquired. PD and CFPD images were produced. The SNR of the images were measured to provide a quantitative comparison of image quality. CFPD images provide an improvement of 8.6 dB in SNR compared to PD produced with the same data. Examples are provided to show that the improvement in SNR leads to subjective improvement of liver vessel visualization.
ROBOTIC-ASSISTANCE ENABLES INEXPERIENCED SURGEONS TO PERFORM UNICOMPARTMENTAL KNEE ARTHROPLASTIES ACCURATELY ON THEIR FIRST ATTEMPT (2013)

Barriers to the adoption of unicompartmental knee arthroplasty (UKA) by new consultants could be explained by its higher revision rate, to which mal-positioned components contribute. The aim of this study was to determine whether robotic technology enables inexperienced surgeons to perform accurate UKAs when compared to current conventional methods After randomisation, sixteen trainees who had never performed UKAs performed three medial UKAs (Corin Uniglide), one per week, on dry-bone simulators by either robotic (Sculptor RGA) or conventional methods. They were instructed to match a universal 3D-CT based pre-operative plan that would result from a UKA based on the conventional jigs and operating guide. The knees were laser scanned and software used to compare the planned and actual implant positions. Feedback was given to trainees between attempts. Translational and rotational positioning errors were measured in all six degrees of freedom for both components At all attempts robotic medial UKAs were more accurate in both translational and rotational alignments for both components reaching statistical significance (p Robotic technology allows inexperienced surgeons to perform medial UKAs on dry bone models with acceptable accuracy and precision on their first attempt. Conventional jigs do not. The adoption of robotic technology might provide new consultants with the confidence to offer UKAs to their patients by limiting the inaccuracies inherent in conventional equipment.
A convenient procedure for the synthesis of nonsymmetrical bivalent selective serotonin reuptake inhibitors using polymer-supported reagents (2000)

A convenient synthesis of nonsymmetrical bivalent inhibitors of the serotonin transporter is described. The synthesis utilizes polymer-supported reagents that allow for rapid access to novel bivalent ligands without the need for isolation or purification of synthetic intermediates.
Navigating Between Right, Wrong, and Relevant: The Use of Mathematical Modeling in Preclinical Decision Making (2022)

The goal of this mini-review is to summarize the collective experience of the authors for how modeling and simulation approaches have been used to inform various decision points from discovery to First-In-Human clinical trials. The article is divided into a high-level overview of the types of problems that are being aided by modeling and simulation approaches, followed by detailed case studies around drug design (Nektar Therapeutics, Genentech), feasibility analysis (Novartis Pharmaceuticals), improvement of preclinical drug design (Pfizer), and preclinical to clinical extrapolation (Merck, Takeda, and Amgen).
Control and Control Theory for Flexible Robots (1993)

As the requirements for robot performance increase, the dynamics of the manipulator become more dominated by flexibility. These flexible effects generate model uncertainty which reduces the end-point positioning accuracy of the manipulator. Residual vibration or tip deflection due to uncertain payloads may contribute to the error in tip position. This paper addresses several control strategies currently used by researchers to account for flexibility in robots and their ability to perform tasks despite the flexibility. The demands for increased robot accuracy coupled with high speed and large workspace requirements necessitate the evaluation of robot flexibility. The influence of flexibilityon modelling and controller design must be better understood to achieve these requirements. This paper presents a review of current research in the control .of flexible robots and reports on algorithms with specific experimental and theoretical results. Other researchers have conducted such surveys regarding modelling, design and control of flexible robot arms. Desoyer, Kopacek, Lugner and Troch (24) compare various modelling methods for I ightweight robots and discuss the effects of flexibi lity on possible control strategies. They examine the kinetostatic method, the vibrational mode approach and the finite element method as a means of modelling flexible systems. Troch and Kopacek (60) discuss control strategies for flexible robots, designs based on model simplification and the effects of actuator dynamics. Peng and Liou (43) survey experimental studies involving flexible mechanisms from a designer's point of view. They examine the identification of damping and mode shapes, vibration reduction and various means of measuring flexible mechanism responses. Book (11) describes the modelling of flexibility, the large motion equations used and the design of flexible arms. He also presents trajectory planning and trajectory tracking strategies for the control of flexible robot arms. . This paper begins with a short discussion of modelling the behavior of a flexible beam. The mathematical expression forthe beam deflection is given as a function of mode shapes and generalized coordinates. The difficulty in choosing appropriate mode shapes and representing the correct boundary conditions is then presented. Once an expression for t~e beam deflection is established, it can be incorporated into a recursive Lagrangian approach for modelling the dynamics of a serial chain of flexible links. The dependence of several control algorithms on model information is then investigated. The control methods surveyed involve end-point tracking, trajectory planning, modal damping and vibration suppression. Several model identification algorithms are also presented to demonstrate adaptive control for flexible systems with_variable payload.
Exploring the role of ferroptosis in C. elegans proteostasis models. (2021)

Motivation: Ferroptosis is a form of regulated cell death involved in degenerative and neoplastic diseases, therefore, understanding the mechanism is very important to treat these diseases. Ferroptosis is caused by an iron-dependent increase in lipid peroxidation of polyunsaturated fatty acid (PUFA)-containing phospholipids, but this peroxidation can be eliminated by a glutathione dependent peroxidase. Therefore, the biosynthesis of glutathione, which is limited by cysteine availability, becomes essential for ferroptosis protection. Interestingly, recent work has found that ferroptosis occurs through an osmotic mechanism. The objective of this research is to characterize the ferroptosis pathway in Caenorhabditis elegans, by genetically impairing the cysteine synthesis pathways and to determine if C.elegans ferroptosis is also altered by increased osmotic pressure in a worm model of Huntington´s Disease. 
Methods: We have used different deletion mutants of cysteine biosynthesis: cbs-1 in the transsulfuration pathway, cysl-1 in cyanide assimilation pathway and trp-14, which is assumed to reduced L-cystine to cysteine. We also used gpdh-1 and gpdh-2 mutants, two genes encoding glycerol-3-phosphate dehydrogenases, involved in osmotic pressure resistance. The mutants above were crossed with Q40 worms in which polyQ aggregates accumulate in muscle cells, wich were quantified in a fluorescence microscope. Moreover, we used diethyl maleate (DEM) to deplete glutathione and measure the size of animals to study the impact of glutathione homeostasis in these worms. 
Results: The Q40; gpdh-1 and Q40; gpdh-1; gpdh-2 strains have more aggregates than the other strains. Intriguingly, the Q40; gpdh-2 and Q40; gpdh-1; gpdh-2 animals display a development delay in comparison with the other strains. Q40 worms are resistant up to 1.5 mM DEM, while Q40; gpdh-1 are up to 1.25 mM DEM and Q40; gpdh-2 and Q40; gpdh-1; gpdh-2 are already sick at 1 mM DEM. Finally, cysl-1 and cysl-1; trp-14 strains show developmental delay when cbs-1 is downregulated by RNAi, while trp-14 mutants development is not affected. 
Conclusions: The lack of trp-14 or gpdh-2 does not seem to affect the number of Q40 aggregates in worm muscle cells while gpdh-1 mutants have increased the number of aggregates, regardless of the presence of the gpdh-2 mutation. The gpdh-2 mutation appears to affect the development of Q40 worms. Finally, cysl-1 mutants seem to be more sensitive to cbs-1 downregulation than trp-14
Alignment-independent technique for 3D QSAR analysis (2016)

Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test (2) = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test (2) = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test (2) = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.
Performance of TDMA and SDMA based Opportunistic Beamforming (2008)

In this work, we analyze opportunistic beamforming with finite number of single-antenna users under the constraint that the feedback overhead from the mobiles to the base is constant. First, we characterize the impact of the fading variances of the users and the spatial correlation on the sum rate of TDMA based opportunistic beamforming using majorization theory. Further, we describe quantitatively the high-SNR behavior in terms of throughput slope and power offset. Next, the impact of the fading variances of the users on an upper bound of the sum rate for space division multiple access (SDMA) based opportunistic beamforming is derived which is tight for high SNR. We propose to adapt the number of active beams to the SNR and the number of active users in a cell and illustrate the corresponding optimization problem by simulations.
Development of a Nanoparticle-Embedded Chitosan Sponge for Topical and Local Administration of Chemotherapeutic Agents (2014)

The following work describes the development of a novel noninvasive transmucosal drug delivery system, the chitosan sponge matrix (CSM). It is composed of cationic chitosan (CS) nanoparticles (NPs) that encapsulate cisplatin (CDDP) embedded within a polymeric mucoadhesive CS matrix. CSM is designed to swell up when exposed to moisture, facilitating release of the NPs via diffusion across the matrix. CSM is intended to be administered topically and locally to mucosal tissues, with its initial indication being oral cancer (OC). Currently, intravenous (IV) administered CDDP is the gold standard chemotherapeutic agent used in the treatment of OC. However, its clinical use has been limited by its renal and hemotoxicity profile. We aim to locally administer CDDP via encapsulation in CS NPs and deliver them directly to the oral cavity with CSM. It is hypothesized that such a delivery device will greatly reduce any systemic toxicity and increase antitumor efficacy. This paper describes the methods for developing CSM and maintaining the integrity of CDDP NPs embedded in the CSM.
Towards lipophilic derivatives of S‐adenosyl‐L‐methionine (1998)

Abstract Two different strategies for the synthesis of S‐Adenosyl‐L‐methionine liphophilic derivatives have been attempted. The first chemical direct modification performed on S‐adenosyl‐L‐methionine is described.
Pi: a parallel architecture interface (2003)

The authors define Pi, a parallel architecture interface that separates model and machine issues, allowing them to be addressed independently. This provides greater flexibility for both the model and machine builder. Pi addresses a set of common parallel model requirements, including low-latency communication, fast task switching, low-cost synchronization, efficient storage management, the ability to exploit locality, and efficiency support for sequential code. Since Pi provides generic parallel operations, it can efficiently support many parallel programming models, including hybrids of existing models. Pi also forms a basis of comparison for architectural components. The authors present an overview of Pi, and a description of several model examples which have been constructed and evaluated on the interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Figures 1 - 5, Tables 1 - 2 from Integrative Analysis of 1q23.3 Copy-Number Gain in Metastatic Urothelial Carcinoma (2023)

&lt;p&gt;PDF file - 423KB, Figure S1: Broad copy numbers at the p- and q-arms in the Spanish cohort; Figure S2: Broad copy numbers at the p- and q-arms in the DFCI cohort. (see Figure S1 for an explanation of this plot); Figure S3: These GISTIC output files show the correlation between gene number and frequency of armlevel events in the (a) Spanish cohort and the (b) DFCI cohort; Figure S4: Recurrent copy number gains in the (a) Spanish and (b) DFCI cohort. Figure S5: Recurrent deletions in the (a) Spanish and (b) DFCI cohorts (see Figure S4 for an explanation of this plot); Table S1: Significant (q-value &lt; 0.25) GISTIC broad aberrations and their association with overall survival after start of chemotherapy (Spanish cohort); Table S2: Significant (q-value &lt; 0.25) GISTIC broad aberrations and their association with overall survival after recurrence (DFCI cohort).&lt;/p&gt;
Addition of a Heparin binding site to a chimeric toxin confers heparin modulation and improves its cytotoxicity to tumor and proliferating vascular smooth muscle cells (1993)

Addition of a Heparin binding site to a chimeric toxin confers heparin modulation and improves its cytotoxicity to tumor and proliferating vascular smooth muscle cells Get access Enrique A. Mesri, Enrique A. Mesri 1Laboratory of Molecular Biology, DCBDC, NCI Search for other works by this author on: Oxford Academic PubMed Google Scholar Ya-min Fu, Ya-min Fu 2Cardiology Branch, NHLBI, NIH, Bethesda MD 20892. Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert J. Kreitman, Robert J. Kreitman 1Laboratory of Molecular Biology, DCBDC, NCI Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen E. Epstein, Stephen E. Epstein 2Cardiology Branch, NHLBI, NIH, Bethesda MD 20892. Search for other works by this author on: Oxford Academic PubMed Google Scholar Ira Pastan Ira Pastan 1Laboratory of Molecular Biology, DCBDC, NCI Search for other works by this author on: Oxford Academic PubMed Google Scholar Protein Engineering, Design and Selection, Volume 6, Issue Supplement, 1993, Page 67, https://doi.org/10.1093/protein/6.Supplement.67-b Published: 01 January 1993
Electron Dynamics of Silicon Surface States: Second-Harmonic Hole Burning onSi(111)−(7×7) (2006)

We report the first all-optical study of homogeneous linewidths of surface excitations by the spectral-hole-burning technique with surface-specific second-harmonic generation as a probe. Measurement of transient spectral holes induced by a 100 fs pump pulse in excitations of the surface dangling-bond states of Si(111)-(7 x 7) led to a pump-fluence-dependent homogeneous linewidth as broad as approximately 100 meV or a dephasing time as short as 15 fs. The hole-burning spectra also revealed a strong coupling between the localized dangling-bond states and the associated surface phonon mode at 570 cm(-1). Carrier-carrier scattering was responsible for the linear dependence of the dephasing rate on pump fluence, and the carrier screening effect appeared to be weak.