gebhart/patrepeval huggingface dataset:
Quality Assurance for Biomolecular Simulations (2006)

Contemporary structural biology has an increased emphasis on high-throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality of biomolecular simulation data. In this Letter, we suggest suitable measures for the quality assurance of molecular dynamics simulations of biomolecules. These measures are designed to be simple, fast, and general. Reporting of these measures in simulation papers should become an expected practice, analogous to the reporting of comparable quality measures in protein crystallography. We wish to solicit views and suggestions from the simulation community on methods to obtain reliability measures from molecular-dynamics trajectories. In a database which provides access to previously obtained simulations [Formula: see text] for example BioSimGrid ( http://www.biosimgrid.org/ ) [Formula: see text] the user needs to be confident that the simulation trajectory is suitable for further investigation. This can be provided by the simulation quality measures which a user would examine prior to more extensive analyses.
An Open‐Label Comparison of Nabilone and Gabapentin as Adjuvant Therapy or Monotherapy in the Management of Neuropathic Pain in Patients with Peripheral Neuropathy (2010)

Neuropathic pain (NeP) is prevalent in patients with peripheral neuropathy (PN), regardless of etiology. We sought to compare the efficacy of the cannabinoid nabilone as either monotherapy or adjuvant therapy with a first-line medication for NeP, gabapentin, in a patient population with PN-NeP. Patients diagnosed with PN-NeP were permitted to initiate monotherapy (nabilone or gabapentin) or add one of these two medications (adjuvant therapy) to their existing NeP treatment regimen in a non-randomized open-label nature. Baseline data collected included a primary outcome (visual analog scores [VAS] of pain) and secondary outcomes (quality of life [EuroQol 5 Domains and Short-Form 36] assessments and assessments of sleep [Medical Outcomes Sleep Study Scale {MOSSS}], anxiety and depression [Hospital Anxiety and Depression Scale], and pain [Brief Pain Inventory]). Reassessment and modulation of dosing and/or medications occurred at 3- and 6-month intervals. Medication adverse effects and drug efficacy, as well as questionnaires, were assessed at 6 months. Matched analysis of variance testing was performed to compare 3- and 6-month scores with baseline, as well as to compare therapies at equal time points. Significant improvements in pain VAS were seen in all treatment groups at 6 months. Numerous sleep parameters within MOSSS, Brief Pain Inventory, and Short-Form 36 improved in patients receiving nabilone or gabapentin either as monotherapy or adjuvant treatment. Hospital Anxiety and Depression Scale-A scores were significantly improved in all treatment groups. Sleep adequacy and the sleep problems index within the MOSSS improved in nabilone monotherapy patients in particular. The benefits of monotherapy or adjuvant therapy with nabilone appear comparable to gabapentin for management of NeP. We advocate for head-to-head randomized, double-blind studies for current therapies for NeP in order to determine potential advantages beneficial in this patient population.
A practical method for predicting frequent use of emergency department care using routinely available electronic registration data (2016)

We demonstrate a strong association between predictor variables present in registration data and frequent ED use. The algorithm's performance characteristics suggest that it is technically feasible to use routinely collected registration data to predict future frequent ED use.
An Efficient Total Synthesis of (−)-Epothilone B (2012)

An efficient total synthesis of (-)-epothilone B has been achieved in ca. 8% yield over 11 steps from 9 (or 10 steps from 7/8), which features a bissiloxane-tethered ring closing metathesis reaction to approach the trisubstituted (Z) double bond and forms a new basis for further development of an industrial process for epothilone B and ixabepilone.
Microstrip Ridge Gap Waveguide Hybrid Coupler at 60 GHz (2018)

A 3dB hybrid coupler is designed to cover the 60 GHz band (57-64GHz) using the Microstrip Ridge-Gap-Waveguide (MRGW) technology. The hybrid coupler has magnitude variation less than 0.6 dB and a 90 ±2.5° phase variation between the output ports.
Determination of Viscosity Coefficents of a Nematic Liqid Crystal Using A Shear Waves Relectance Technique (1971)

Abstract Dispersion equations for shear waves propagating in a nematic liqid crystal are derived from the Ericksen and Leslie's hydrodynamic equations. The complex refection coefficient of a shear wave at a solid-nematic liquid crystal interface is related to effective viscosity coefficients depeding on the orientation of the molecules with respect to the polarization of the wave. Some experimental results relative to paramethoxybenzilidene-butylanilin are presented.
Phase Synchronization and invariant measures in sinusoidally perturbed chaotic systems (2005)

We show that, in periodically perturbed chaotic systems, Phase Synchronization appears, associated to a special type of stroboscopic map, in which not only averages quantities are equal to invariants of the perturbation, the angular frequency, but also it exists a very large number of non-transient transformations, possibly infinity. In cases where there is not phase synchronization there is either only transitive transformations on the attractor, or a finite number of non-transitive transformations. We base our statements in experimental and numerical results from the sinusoidally perturbed Chua's circuit.
CyAnno : a semi-automated approach for cell type annotation of mass cytometry datasets (2021)

Supplementary data are available at Bioinformatics online.
Leukotriene C4 binds to human glomerular epithelial cells and promotes their proliferation in vitro. (1985)

In human and experimental glomerulonephritis, glomerular hypercellularity results both from accumulation of macrophages and proliferation of resident glomerular cells. The recent identification of macrophage-derived factors that stimulate mesangial and epithelial cell proliferation suggests that these factors might contribute to the hypercellularity. To determine the identity of such macrophage-derived growth factors, we studied the effect of leukotrienes (LTs), products that are released from macrophages and leukocytes, on proliferation of human glomerular epithelial cells in culture. Dose-dependent (1-100 nM) stimulation of [3H]thymidine incorporation, an index of cell proliferation, was observed in cells incubated with the sulfidopeptide LTs, LTC4 and LTD4, but not with LTB4. The response was 248 and 172% of control values at 100 nM LTC4 and LTD4, respectively. This effect of LTC4 was abolished by FPL 55712. Subsequent binding studies demonstrated that glomerular epithelial cells possess specific receptors for LTC4. [3H]LTC4 bound rapidly at 8 degrees C to the cells. There was a plateau after 40 min incubation. Maximum specific binding was 70-90% of total binding. Specific binding was totally reversible with addition of an excess of unlabeled LTC4. Analysis of time-course association slopes at two concentrations of [3H]LTC4 and of the competition between a single concentration of [3H]LTC4 and increasing concentrations of unlabelled LTC4 allowed calculation of dissociation constants (Kd) of 220 and 217 nM, respectively. Both LTD4 and LTE4 exhibited ED50 values that were at least one order of magnitude higher than for LTC4. Thus, our findings suggest that LTC4 binds to specific receptors of glomerular epithelial cells, promotes proliferation of these cells, and could contribute to epithelial hypercellularity found in glomerulonephritis.
Tumor necrosis factor receptor‐associated factor 5 is an essential mediator of ischemic brain infarction (2013)

Tumor necrosis factor receptor-associated factor 5 (TRAF5) is an adaptor protein of the tumor necrosis factor (TNF) receptor superfamily and the interleukin-1 receptor/Toll-like receptor superfamily and plays important roles in regulating multiple signaling pathways. This study was conducted to investigate the role of TRAF5 in the context of brain ischemia/reperfusion (I/R) injury. Transient occlusion of the middle cerebral artery was performed on TRAF5 knockout mice (KO), neuron-specific TRAF5 transgene (TG), and the appropriate controls. Compared with the WT mice, the TRAF5 KO mice showed lower infarct volumes and better outcomes in the neurological tests. A low neuronal apoptosis level, an attenuated blood-brain barrier (BBB) disruption and an inhibited inflammatory response were exhibited in TRAF5 KO mice. TRAF5 TG mice exhibited an opposite phenotype. Moreover, the Akt/FoxO1 signaling pathway was enhanced in the ischemic brains of the TRAF5 KO mice. These results provide the first demonstration that TRAF5 is a critical mediator of I/R injury in an experimental stroke model. The Akt /FoxO1 signaling pathway probably plays an important role in the biological function of TRAF5 in this model.
Movement‐related cortical potentials preceding repetitive and random‐choice hand movements in parkinson's disease (1995)

The movement-related cortical electroencephalographic potential was recorded from scalp electrodes in 8 patients with idiopathic Parkinson's disease studied at least 12 hours after withdrawal of their normal drug therapy, and compared with the results from a group of 8 age-matched control subjects. Two types of self-paced voluntary arm movements were examined: repetitive forward movement of a joystick, and random-choice movements of the same joystick in which subjects had to choose freely the direction in which they were to move the stick (forward, backward, left, or right). In normal subjects, the movement-related cortical potential was larger prior to random-choice movements, whereas in the patients, the amplitude was the same in both tasks. The implication is that processes involved in self-selection of movement are abnormal in Parkinson's disease. This may contribute to the difficulty that patients have in initiating voluntary movement in the absence of any external cues.
Perspective: Developing a Nutrient-Based Framework for Protein Quality (2023)

The future of precision nutrition requires treating amino acids as essential nutrients. Currently, recognition of essential amino acid requirements is embedded within a generalized measure of protein quality known as the PDCAAS (Protein Digestibility-Corrected Amino Acid Score). Calculating the PDCAAS includes the FAO/WHO/UNU amino acid score, which is based on the limiting amino acid in a food, that is, the single amino acid with the lowest concentration compared to the reference standard. That "limiting" amino acid score is then multiplied by a bioavailability factor to obtain the PDCAAS, which ranks proteins from 0.0 (poor quality) to 1.0 (high quality). However, the PDCAAS has multiple limitations: it only allows for direct protein quality comparison between 2 proteins, and it is not scalable, transparent, or additive. We therefore propose that shifting the protein quality evaluation paradigm from the current generalized perspective to a precision nutrition focus treating amino acids as unique, metabolically active nutrients will be valuable for multiple areas of science and public health. We report the development and validation of the Essential Amino Acid 9 (EAA-9) score, an innovative, nutrient-based protein quality scoring framework. EAA-9 scores can be used to ensure that dietary recommendations for each essential amino acid are met. The EAA-9 scoring framework also offers the advantages of being additive and, perhaps most importantly, allows for personalization of essential amino acid needs based on age or metabolic conditions. Comparisons of the EAA-9 score with PDCAAS demonstrated the validity of the EAA-9 framework, and practical applications demonstrated that the EAA-9 framework is a powerful tool for precision nutrition applications.
Optical pumping and negative luminescence polarization in charged GaAs quantum dots (2009)

Optical pumping of electron spins and negative photoluminescence polarization are observed when interface quantum dots in a GaAs quantum well are excited nonresonantly by circularly polarized light. Both observations can be explained by the formation of long-lived dark excitons through hole spin relaxation in the GaAs quantum well prior to exciton capture. In this model, optical pumping of resident electron spins is caused by capture of dark excitons and recombination in charged quantum dots. Negative polarization results from accumulation of dark excitons in the quantum well and is enhanced by optical pumping. The dark exciton model describes the experimental results very well, including intensity and bias dependence of the photoluminescence polarization and the Hanle effect.
Hyperexcitability and brain morphological differences in mice lacking the cystine/glutamate antiporter, system x c − (2021)

System x<sub>c</sub><sup>-</sup> (Sx<sub>c</sub><sup>-</sup> ) is a heteromeric antiporter (L-cystine/L-glutamate exchanger) expressed predominately on astrocytes in the central nervous system. Its activity contributes importantly to the maintenance of the ambient extracellular glutamate levels, as well as, to cellular redox homeostasis. Since alterations in glutamate levels and redox modifications could cause structural changes, we analyzed gross regional morphology of thionin-stained brain sections and cellular and subcellular morphology of Golgi-Cox stained layer V pyramidal neurons in the primary motor cortex (PM1) of mice naturally null for SLC7A11 (SLC7A11<sup>sut/sut</sup> )-the gene that encodes the substrate specific light chain (xCT) for Sx<sub>c</sub><sup>-</sup> . Intriguingly, in comparison to age- and sex-matched wild-type (SLC7A11<sup>+/+</sup> ) littermate controls, we found morphologic changes-including increased dendritic complexity and mushroom spine area in males and reduced corpus callosum and soma size in females-that have previously been described, in each case, as morphological correlates of excitability. Consistent with this, we found that both male and female SLC7A11<sup>sut/sut</sup> mice had lower convulsive seizure thresholds and greater seizure severity than their sex-matched wild-type (SLC7A11<sup>+/+</sup> ) littermates after acute challenge with two pharmacologically distinct chemoconvulsants: the Glu receptor agonist, kainic acid (KA), or the GABA<sub>A</sub> receptor antagonist, pentylenetetrazole (PTZ). These results suggest that the loss of Sx<sub>c</sub><sup>-</sup> signaling in males and females perturbs excitatory/inhibitory (E/I) balance in vivo, potentially through its regulation of cellular and subcellular morphology.
Profile Control And Stringer Removal During Plasma Etch Of Submicrometer Polysilicon Lines (1990)

Polysilicon etch profile is examined as a function of process variation for submicrometer-patterned polysilicon on gate oxide. A Lam Research Rainbow 4400 single-wafer etcher was used to etch polysilicon wafers for a variety of bulk etch and overetch process combinations in order to establish trends for polysilicon etch profile using photoresist and oxide masks. Scanning electron microscope analysis was completed to determine the resulting polysilicon profile for each combination, and process trends for profile were established. A process which demonstrated profile control, critical dimension control and high oxide selectivity after extended overetch was then used to etch polysilicon lines on gate oxide over underlying topography. Scanning electron microscope analysis was completed to determine the effectiveness of the process in removing the polysilicon stringer while maintaining a vertical profile, critical dimension loss of less than 0.1 um, and gate oxide loss of less than 50 A.
Effects of explant source, culture medium: Strength and growth regulators on the in‐vitro propagation of three Jamaican yams: (Dioscorea cayenensis, D trifida and d rotundata) (1995)

Abstract Explants of tuber, meristem and vines from three widely cultivated yam species in Jamaica— D cayenensis, D rotundata and D trifida —were examined for their responses to mineral media strength, inorganic ammonium and growth regulator supplements. Tuber pieces (5mm 3 ) showed some positive growth responses but did not produce in‐vitro plantlets on all the media tested. Meristem tips of D trifida grew rapidly on basal media (BM) supplemented with either 0.1 mglitre −1 6‐benzylamino purine (BAP) and 0.01 mg litre −1 indole butyric acid or 0.2 mg litre −1 BAP and 1.0 mg litre −1 naphthalene acetic acid (NAA) producing plantlets by 28 weeks. The nodal explants grew rapidly with plantlets obtained from all the cultivars within 4 weeks. Use of young, vigorously growing vines of 8 weeks or less, as explant source, gave low contamination levels (16–25%) in culture when sterilised for 30 min in 200 g litre −1 NaOCl in the case of D trifida and 300 g litre −1 NaOCl in the case of D cayenesis prior to culturing. Initiation of growth was optimal when explants were taken from monopodial vines grown in October or January and placed on BM supplemented with 0.5 mg litre −1 BAP (BM0.5BAP). Addition of 0.5 mg litre −1 kinetin to the BM or 0.05 mg litre −1 NAA to BM0.5BAP depressed shoot production, while 5.0 mg litre −1 kinetin increased swelling of the nodal region in explants from sympodial shoots and from vines grown in March. The results suggest that nodal segments excised from young, fast growing vines of these species are the best explant source for the purpose of commercial micropropagation.
The Active Interface of Ta-Doped Li7La3Zr2O12 for Li Plating/Stripping Revealed by Acid Aqueous Etching (2019)

All-solid-state lithium batteries incorporating oxide-based solid electrolytes have attracted much attention as a promising battery system for enabling highly reversible Li metal anodes. However, the cycling stability of Li plating/stripping reactions at higher charging/discharging rates on garnet-type solid-state electrolytes must be improved to realize a practical Li metal anode for solid-state batteries. Here, we report that a short acid etching procedure performed in ambient air significantly activates the Ta-doped Li7La3Zr2O12 (LLZT) surface compared to polishing under inert gas atmosphere such as dry Ar. It has been believed that Li7La3Zr2O12 (LLZ) and related doped LLZ solid electrolyte surfaces need to be mechanically polished in dry Ar before the cell fabrication to remove Li2CO3 and LiOH that are present on the surface. However, a commonly used mechanical polishing procedure is found to form a thin electrochemically inactive layer on the LLZT surface, whereas a short acid etching procedure (e.g., HCl) removes the inactive layer, and the acid-etched LLZT exhibits excellent cycling stability.
Nix and Nip3 Form a Subfamily of Pro-apoptotic Mitochondrial Proteins (1999)

We have identified Nix, a homolog of the E1B 19K/Bcl-2 binding and pro-apoptotic protein Nip3. Human and murine Nix have a 56 and 53% amino acid identity to human and murine Nip3, respectively. The carboxyl terminus of Nix, including a transmembrane domain, is highly homologous to Nip3 but it bears a longer and distinct asparagine/proline-rich N terminus. Human Nip3 maps to chromosome 14q11.2-q12, whereas Nix/BNip3L was found on 8q21. Nix encodes a 23. 8-kDa protein but it is expressed as a 48-kDa protein, suggesting that it homodimerizes similarly to Nip3. Following transfection, Nix protein undergoes progressive proteolysis to an 11-kDa C-terminal fragment, which is blocked by the proteasome inhibitor lactacystin. Nix colocalizes with the mitochondrial matrix protein HSP60, and removal of the putative transmembrane domain (TM) results in general cytoplasmic and nuclear expression. When transiently expressed, Nix and Nip3 but not TM deletion mutants rapidly activate apoptosis. Nix can overcome the suppressers Bcl-2 and Bcl-XL, although high levels of Bcl-XL expression will inhibit apoptosis. We propose that Nix and Nip3 form a new subfamily of pro-apoptotic mitochondrial proteins.
An integrated, underwater optical /acoustic communications system (2010)

Communication underwater is severely limited when compared to communications in air because water is essentially opaque to electromagnetic radiation except in the visible band. Even in the visible band, light penetrates only a few hundred meters in the clearest waters and much less in waters made turbid by suspended sediment or high concentrations of marine life. Consequently, acoustic techniques have been developed for underwater communication systems and now represent a relatively mature and robust technology. Acoustic systems are capable of long range communication, but offer limited data rates and significant latency (due to the speed of sound in water). We are developing an optical communication system that complements and integrates with existing acoustic systems resulting in an underwater communications capability offering high data rates and low latency when within optical range combined with long range and robustness of acoustics when outside of optical range. Amongst a wide array of applications, this combination of capabilities will make it possible to operate self-powered ROVs from support vessels or platforms without requiring a physical connection to the ROV. Such a capability will help simplify operations and potentially reduce costs through the use of less capable surface vessels. New deployment strategies may offer game-changing opportunities within all areas of undersea activities. For example, rapid event response will be enhanced and repair and maintenance of the emerging ocean observatory infrastructure will become more cost effective. Such through-water communications will likewise enable exchange of large data files from fixed sensors using AUVs (or ROVs) as data mules, shuttling real-time video from untethered vehicles for inspection, identification, and other related operations. Interconnectivity for dense arrays of underwater sensors without the need for expensive and difficult to install undersea cables is also possible. An unmanned battery operated vehicle, dedicated to a subsea node, that can be wirelessly operated though a combination of acoustic and optical communications, will be an important asset for both scientific exploration and commercial applications. We have demonstrated robust multi-point, low power omnidirectional optical communications over ranges of 100 meters at data rates up to 10 mega bits per second using a few tens of Watts of battery power with small, inexpensive transmitters and receivers. During the next few years, we will be exploring applications of this new technology directly in support of ongoing science and engineering programs. High-speed underwater optical communication is an enabling technology that has many potential applications in a range of environments from the deep sea to coastal waters. This development effort will enhance infrastructure for scientific research and commercial use by providing technology to efficiently communicate between surface vessels, underwater vehicles and seafloor infrastructure.