gebhart/patrepeval huggingface dataset:
G-protein Pathway Suppressor 2 (GPS2) Interacts with the Regulatory Factor X4 Variant 3 (RFX4_v3) and Functions as a Transcriptional Co-activator (2008)

RFX4_v3 (regulatory factor X4 variant 3) is a brain-specific isoform of the transcription factor RFX4. Insertional mutagenesis in mice demonstrates that Rfx4_v3 is crucial for normal brain development. Many genes involved in critical processes during brain morphogenesis are dysregulated in Rfx4_v3 mutant brains. For example, Cx3cl1 is a CX3C-type chemokine that is abundant in brain and is a direct transcriptional target of RFX4_v3 through a specific promoter X-box (X-box 1), the responsive element for RFX proteins. To identify potential interacting partners for RFX4_v3, we performed yeast two-hybrid analysis. Nine candidate interactors were identified, including GPS2 (G-protein pathway suppressor 2). Indirect immunofluorescence demonstrated that GPS2 and RFX4_v3 co-localized to the nucleus. Both GPS2 and RFX4_v3 mRNAs were also present in most portions of the adult mouse brain as well as in brains at different ages, suggesting that the two proteins could bind to each other. Co-immunoprecipitation assays indicated that physical interactions between GPS2 and RFX4_v3 did indeed occur. Furthermore, GPS2 was recruited to the Cx3cl1 promoter by RFX4_v3 and potentiated RFX4_v3 transactivation on this promoter through X-box 1, suggesting that the protein-protein interaction was functionally relevant. GPS2 bound to both the carboxyl-terminal region (amino acids 575-735) and the middle region (amino acids 250-574) of the RFX4_v3 protein. RFX4_v3 amino acids 1-574 stimulated the Cx3cl1 promoter to a similar extent as the full-length RFX4_v3 protein; however, deletion of the carboxyl-terminal region of RFX4_v3 impaired the co-activating abilities of GPS2. Based on these data, we conclude that GPS2 interacts with RFX4_v3 to modulate transactivation of genes involved in brain morphogenesis, including Cx3Cl1.
Convergence of Kohonen's learning vector quantization (1990)

It is shown that the learning vector quantization (LVQ) algorithm (T. Kohonen, 1986), converges to locally asymptotic stable equilibria of an ordinary differential equation. It is shown that the learning algorithm performs stochastic approximation. Convergence of the vectors is guaranteed under the appropriate conditions on the underlying statistics of the classification problem. Also presented is a modification to the learning algorithm which results in more robust convergence. With this modification, it is possible to show that as the appropriate parameters go to infinity, the decision regions associated with the modified LVQ algorithm approach the Bayesian optimal
Heat Transfer of Springs in Oblique Crossflows (2017)

An experimental program is presented of heated tension springs in an external crossflow over a range of laminar Reynolds numbers, spring stretch ratios, and angles of attack. Extensive measurements of the forced convection heat transfer of helical wire within a wind tunnel reveal an interesting nonmonotonic dependence on angle of attack. Computational fluid dynamics (CFD) simulations, showing good agreement with the experimental data, are used to explore the behavior and gain a better understanding of the observed trends. A dimensionless correlation is developed that well captures the experimental and CFD data and can be used as an efficient computational tool in broader applications.
Non-bladder centric interstitial cystitis/bladder pain syndrome phenotype is significantly associated with co-occurring endometriosis. (2020)

Patients with IC/BPS and co-occurring endometriosis were significantly more likely to carry a non-bladder centric IC/BPS phenotype as well as several comorbid, systemic pain diagnoses. This study characterizes features of a target IC/BPS phenotype that could potentially benefit from endometriosis and systemic pain syndrome screening.
Water Oxidation Catalysis using Amorphous Manganese Oxides, Octahedral Molecular Sieves (OMS-2), and Octahedral Layered (OL-1) Manganese Oxide Structures (2012)

Water oxidation is the bottleneck in artificial photosynthetic systems that aim to split water into hydrogen and oxygen. However, water oxidation occurs readily in plants, catalyzed by the Mn4O4Ca manganese cluster. In addition to this, manganese minerals are ubiquitous in nature displaying layered and tunnel structures. In this study, mixed valent porous amorphous manganese oxides (AMO), along with cryptomelane type tunnel manganese oxides (OMS-2) and layered birnessite (OL-1) have been used as water oxidation catalysts. Significantly higher turnovers were obtained with AMO (290 mmol O2/mol Mn) compared to tunnel structure OMS-2 (110 mmol O2/mol Mn) and layered structure OL-1 (27 mmol O2/mol Mn) in water oxidation tests with Ce4+. Oxygen evolution was also confirmed under photochemical conditions using Ru(bpy)3 2+ as a photosensitizer and persulfate as a sacrificial agent. The differences in catalytic activity among these catalysts have been probed using X-ray diffraction, transmission electron microscopy, Raman and Fourier transform infrared (FTIR) spectroscopy, average oxidation state, and compositional analyses. Comparison of AMO against prominent manganese catalysts described in literature shows AMO provided the highest turnover numbers. AMO catalyst was also reusable after regeneration. O-18 labeling studies proved that water was the source of dioxygen and IR proved the structural stability of AMO after reaction. AMO is related to hexagonal birnessites such as layered biogenic manganese oxides or H+-birnessite that have cation vacancies in the MnO2 sheets rather than completely filled Mn3+/Mn4+ sheets, and this is influential in catalytic activity.
9.6-mm diameter femtosecond laser microsurgery probe (2012)

We present a 9.6-mm fiber-coupled probe for femtosecond laser microsurgery and nonlinear imaging. Towards enabling clinical use, we successfully reduced the volume of our earlier 18-mm surgery probe by 5 times, while improving optical performance.
EFFECT OF PROPRANOLOL ON CENTRAL NEUROTRANSMITTER RELEASE IN WISTAR RATS ANALYSED BY BRAIN MICRODIALYSIS (1999)

1. The effect of propranolol on amino acid neurotransmitter release in the rostral ventrolateral medulla (RVLM) was examined in urethane-anaesthetized male Wistar rats. 2. Amino acids released in the RVLM in response to intravenous administration of propranolol (0.4 mg/kg per min; n = 6) or nitroglycerin (0.02 mg/kg per min; n = 5) were determined by the brain microdialysis method. 3. Amino acids in dialysates were analysed by high-performance liquid chromatography and were quantified by ultraviolet absorbance. 4. Administration of both intravenous propranolol and nitroglycerin significantly decreased arterial blood pressure. Heart rate was decreased only by propranolol. 5. The reduction in arterial blood pressure produced by intravenous propranolol was accompanied by a decrease in the release of the excitatory amino acid glutamate in the RVLM. 6. The reduction in arterial blood pressure following intravenous nitroglycerin was not accompanied by a release of glutamate. 7. There were no significant changes in the levels of other amino acids (glycine, taurine, GABA) following either propranolol or nitroglycerin. 8. The decrease in glutamate release in the RVLM may account, in part, for the central depressor mechanism of propranolol.
Regulation of WNT Signaling by VSX2 During Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells (2016)

Few gene targets of Visual System Homeobox 2 (VSX2) have been identified despite its broad and critical role in the maintenance of neural retina (NR) fate during early retinogenesis. We performed VSX2 ChIP-seq and ChIP-PCR assays on early stage optic vesicle-like structures (OVs) derived from human iPS cells (hiPSCs), which highlighted WNT pathway genes as direct regulatory targets of VSX2. Examination of early NR patterning in hiPSC-OVs from a patient with a functional null mutation in VSX2 revealed mis-expression and upregulation of WNT pathway components and retinal pigmented epithelium (RPE) markers in comparison to control hiPSC-OVs. Furthermore, pharmacological inhibition of WNT signaling rescued the early mutant phenotype, whereas augmentation of WNT signaling in control hiPSC-OVs phenocopied the mutant. These findings reveal an important role for VSX2 as a regulator of WNT signaling and suggest that VSX2 may act to maintain NR identity at the expense of RPE in part by direct repression of WNT pathway constituents. Stem Cells 2016;34:2625-2634.
Two-dimensional light confinement in periodic InGaN/GaN nanocolumn arrays and optically pumped blue stimulated emission (2009)

Two-dimensional (2D) light diffraction in a uniform array of GaN nanocolumns arranged in a rectangular lattice dramatically enhanced the light intensity at a specific wavelength, indicating the function of 2D distributed feedback (DFB). Here a GaN rectangular-lattice nanocolumn array, which integrated InGaN/GaN multiple quantum wells (MQWs) in the top region of the nanocolumns, was grown by rf-plasma-assisted molecular beam epitaxy (rf-MBE). At a specific wavelength of 471.1 nm, the first observation of stimulated emission from 2D-DFB in an InGaN-based nanocolumn array was obtained. The specific wavelength is calculated by the 2D finite-difference time domain (2D-FDTD) method on the assumption of a refractive index dispersion of GaN; a simple expression for specific wavelength, which is a function of the array period L and the hexagon side length S of each nanocolumn, is proposed, which is convenient for producing a simple design of a GaN nanocolumn array structure in a square lattice.
Tumor-Promoting Desmoplasia Is Disrupted by Depleting FAP-Expressing Stromal Cells (2015)

Malignant cells drive the generation of a desmoplastic and immunosuppressive tumor microenvironment. Cancer-associated stromal cells (CASC) are a heterogeneous population that provides both negative and positive signals for tumor cell growth and metastasis. Fibroblast activation protein (FAP) is a marker of a major subset of CASCs in virtually all carcinomas. Clinically, FAP expression serves as an independent negative prognostic factor for multiple types of human malignancies. Prior studies established that depletion of FAP(+) cells inhibits tumor growth by augmenting antitumor immunity. However, the potential for immune-independent effects on tumor growth have not been defined. Herein, we demonstrate that FAP(+) CASCs are required for maintenance of the provisional tumor stroma because depletion of these cells, by adoptive transfer of FAP-targeted chimeric antigen receptor (CAR) T cells, reduced extracellular matrix proteins and glycosaminoglycans. Adoptive transfer of FAP-CAR T cells also decreased tumor vascular density and restrained growth of desmoplastic human lung cancer xenografts and syngeneic murine pancreatic cancers in an immune-independent fashion. Adoptive transfer of FAP-CAR T cells also restrained autochthonous pancreatic cancer growth. These data distinguish the function of FAP(+) CASCs from other CASC subsets and provide support for further development of FAP(+) stromal cell-targeted therapies for the treatment of solid tumors.
Contribution of Factor VIII A2 Domain Residues 400–409 to a Factor X-Interactive Site in the Factor Xase Complex (2018)

The link between factor (F)VIII and FX is essential for optimum activity of the tenase complex. The interactive site(s) in FVIII for FX remains to be completely clarified, however. We investigated the FVIII A2 domain-FX association that was speculated from inhibitory mechanism(s) by an anti-A2 autoantibody. SDS-PAGE demonstrated that the purified inhibitor IgG recognizing residues 373-562 blocked FXa cleavage at Arg372 in FVIII, and surface-plasmon resonance (SPR)-based assays showed that intact A2 subunit directly bound to FX (<i>K</i><sub>d</sub>; 63 nM). The FVIII structure model indicated possible FX-binding site(s) in residues 400-429 in A2. One peptide corresponding to residues 400-409 competitively inhibited both the A2-FX binding and FVIIIa/FIXa-dependent FXa generation. Covalent cross-linking was observed between this peptide and FX following reaction with EDC (1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide) using SDS-PAGE. K408 and S409 were not evident in N-terminal sequence analysis of the cross-linked product, suggesting that two residues participated in cross-link formation. SPR-based assays using recombinant FVIII mutants with one or both residues substituted to alanine demonstrated that K408A and K408A/S409A had approximately fourfold high <i>K</i><sub>d</sub> values of wild-type (WT-)FVIII. FXa cleavages at Arg372 in both mutants were significantly delayed, suggesting a contribution of K408 for FXa cleavage at Arg372. Furthermore, FXa generation assays with these mutants demonstrated that the <i>K</i><sub>m</sub> values were 1.4- to 1.7-fold greater, and overall catalytic efficiency (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub>) was 0.49- to 0.89-fold lower than with WT-FVIII, suggesting a significant contribution of K408 for FVIII-FX interaction in tenase assembly. We concluded that the K408 in the A2 domain provided an interactive-site for FX.
Internal Transport and Metabolism of Cobalamin in Spirometra mansonoides (Cestoda) Spargana (1982)

Paul A. Friedman, Paul P. Weinstein, Justus F. Mueller, Robert H. Allen, Internal Transport and Metabolism of Cobalamin in Spirometra mansonoides (Cestoda) Spargana, The Journal of Parasitology, Vol. 68, No. 6 (Dec., 1982), pp. 983-992
Structure and Sodium Channel Activity of an Excitatory I1-Superfamily Conotoxin, (2007)

Conotoxin iota-RXIA, from the fish-hunting species Conus radiatus, is a member of the recently characterized I1-superfamily, which contains eight cysteine residues arranged in a -C-C-CC-CC-C-C- pattern. iota-RXIA (formerly designated r11a) is one of three characterized I1 peptides in which the third last residue is posttranslationally isomerized to the d configuration. Naturally occurring iota-RXIA with d-Phe44 is significantly more active as an excitotoxin than the l-Phe analogue both in vitro and in vivo. We have determined the solution structures of both forms by NMR spectroscopy, the first for an I1-superfamily member. The disulfide connectivities were determined from structure calculations and confirmed chemically as 5-19, 12-22, 18-27, and 21-38, suggesting that iota-RXIA has an ICK structural motif with one additional disulfide (21-38). Indeed, apart from the first few residues, the structure is well defined up to around residue 35 and does adopt an ICK structure. The C-terminal region, including Phe44, is disordered. Comparison of the d-Phe44 and l-Phe44 forms indicates that the switch from one enantiomer to the other has very little effect on the structure, even though it is clearly important for receptor interaction based on activity data. Finally, we identify the target of iota-RXIA as a voltage-gated sodium channel; iota-RXIA is an agonist, shifting the voltage dependence of activation of mouse NaV1.6 expressed in Xenopus oocytes to more hyperpolarized potentials. Thus, there is a convergence of structure and function in iota-RXIA, as its disulfide pairing and structure resemble those of funnel web spider toxins that also target sodium channels.
High efficiency Inverted Metamorphic (IMM) solar cells (2013)

High efficiency Inverted Metamorphic (IMM) multi-junction solar cells have been under development at Spectrolab for use in space and near space applications This paper reviews the present state-of-the-art of this technology at Spectrolab with an emphasis on performance characterization data at in-flight operating conditions. Large area IMM3J and IMM4J solar cells with 1X AM0 efficiency greater than 32% at 28 °C have been fabricated and characterized. Degradation factors after exposure to 1 MeV electron irradiation for both IMM3J and IMM4J technologies is presented. A coupon utilizing large area, IMM solar cells has been assembled and subjected to thermal cycling. Pre-and post thermal cycling data have been collected. Preliminary temperature cycling data indicate that a small coupon populated with strings of these cells suffered no degradation.
CD8+ T cells inhibit HIV replication in naturally infected CD4+ T cells. Evidence for a soluble inhibitor. (1990)

This study describes the inhibitory effect exerted by activated CD8+ T cells on the replication of HIV in naturally infected CD4+ T cells. Highly purified CD4+ T cells from asymptomatic HIV seropositive individuals were stimulated with anti-TCR mAb-coated beads in the presence of IL-2. HIV was subsequently reproducibly isolated in cell supernatants from all study participants (53 cultures from 42 individuals). Both autologous and allogeneic CD8+ T cells from asymptomatic HIV seropositive and healthy HIV seronegative individuals inhibited the replication of HIV in these cultures in a dose-dependent manner. CD8+ T cells from patients with AIDS showed reduced or no such inhibitory activity. The inhibitory effect was not dependent on direct cell-cell contact: an inhibitory effect was exerted by CD8+ T cells across a semipermeable membrane, and an inhibitory activity was also exerted by the cell-free supernatants from activated CD8+ T cells. These results suggest that activated CD8+ T cells secrete a soluble inhibitor of HIV replication.
Microorganism image classification with circle-based Multi-Region Binarization and mutual-information-based feature selection (2021)

An important part of water quality control is waterborne pathogen detection. Conventional microorganism detections are done by costly and complicated biochemical approaches, which leave chemical pollutions and require professional laboratories, technicians, and much time. Recently, machine-learning-based image classification algorithms are developed for faster, cheaper, simpler, and more environmentally friendly microorganism detection. Most of them are designed for conventional microscopic images. On the other hand, the optofluidic system is a smaller and cheaper alternative to conventional microscopes, so we aim to propose a microorganism classification algorithm for optofluidic images. In our previous study, the Binarized-Greyscale-Hybrid Algorithm with Multi-Region Binarization (BiGHAM) algorithm was developed for our optofluidic image dataset. In this paper, a new circle-based region partition method for the Multi-Region Binarization and a new mutual-information-based feature selection method were proposed to improve the BiGHAM method. Additionally, an implementation example of how to adapt and apply our method on an open dataset was presented. With the circle-based region partition method and the new feature combination selected based on mutual information, the improved-BiGHAM algorithm achieved higher classification accuracies, and the algorithm is simpler than the previous BiGHAM method during training. For our optofluidic image dataset, the accuracy improvement for the 1000-image-per-class case was from 94.8 to 96.3%, and for the 30-image-per-class case was from 77.8 to 85.6% with the support vector machine as the classifier. The adapted algorithm also works well on the open dataset, showing the potential to be extended to applications on different microorganism images.
Gradual AutoML using Lale (2022)

Lale is a sklearn-compatible library for automated machine learning (AutoML). It is open-source (https://github.com/ibm/lale) and addresses the need for gradual automation of machine learning as opposed to offering a black-box AutoML tool. Black-box AutoML tools are difficult to customize and thus restrict data scientists in leveraging their knowledge and intuition in the automation process. Lale is built on three principles: progressive disclosure, orthogonality, and least surprise. These enable a gradual approach offering a spectrum of usage patterns starting from total automation to controlling almost every aspect of AutoML. Lale provides compositional constructs that let data scientists control some aspects of their pipelines while leaving other aspects free to be searched automatically. This tutorial demonstrates the use of Lale for various machine-learning tasks, showing how to progressively exercise more customization. It also covers AutoML for advanced scenarios such as class imbalance correction, bias detection and mitigation, multi-objective optimization, and working with multi-table datasets. While Lale comes with hyperparameter specifications for 216 operators out-of-the-box, users can also add more operators of their own, and this tutorial covers how to do that. Overall, this tutorial teaches you how you can exercise fine-grained control over AutoML without having to be an AutoML expert.
Solvent effects on the dynamics of (dG‐dC)3 (1983)

Abstract The kinetics of the coil‐to‐helix transition of (dG‐dC) 3 in M NaCl, 45 m M sodium cacodylate, pH 7, were measured in H 2 O, D 2 O, 10 mol % ethanol, 10 mol % urea, and 10 mol % glycerol. At 43°C in H 2 O the recombination rate is 1.3 ± 0.2 × 10 7 M −1 s −1 ; the dissociation rate is 68 ± 10 s −1 . The destabilization of the helix in 10 mol % ethanol and 10 mol % urea relative to water is primarily due to a large increase in the helix‐dissociation rate. In 10 mol % glycerol, the destabilization of the helix is due to a decrease in the recombination rate and an increase in the dissociation rate. Above 20°C, two exponential decays longer than 1 μs are observed after a temperature jump. The slower relaxation time is 4–10 times faster than the bimolecular component and is independent of oligomer concentration. We attribute this relaxation to a rapid equilibrium between two helical states. At low temperatures and oligomer concentrations of 1 m M or greater, the helices aggregate in 1 M NaCl. Experimental data are presented under conditions where aggregation is unimportant and evidence is given that the Δ H ‐determined spectroscopically is unaffected by aggregation.
ChemInform Abstract: Synthesis and Properties of Redox‐Active Dendrimers Containing Phenothiazines. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
High-Performance Self-Aligned SiGeC HBT with Selectively Grown Si Ge C Base by (2003)

Si Ge C selective epitaxial growth (SEG) was performed by cold-wall, ultrahigh-vacuum chemical vapor deposition, and the effects of incorporating C on the crystallinity of Si Ge C layers and the performance of a self-aligned SiGeC heterojunction bipolar transistor (HBT) were evaluated. AS i Ge C layer with good crystallinity was obtained by optimizing the growth conditions. Device performance was significantly improved by incorporating C, as a result of applying Si Ge C SEG to form the base of a self-aligned HBT. Fluctuations in device performance were suppressed by alleviating the lattice strain. Furthermore, since the B out diffusion could be suppressed by incorporating C, the cutoff frequency was able to be increased with almost the same base resistance. A maximum oscillation frequency of 174 GHz and an emitter coupled logic gate-delay time of 5.65 ps were obtained at a C content of 0.4%, which shows promise for future ultrahigh-speed communication systems. Index Terms—Crystallinity, cutoff frequency, emitter coupled logic (ECL), heterojunction bipolar transistor (HBT), max- imum oscillation frequency, selective epitaxial growth (SEG), Si Ge C.