gebhart/patrepeval huggingface dataset:
Identification of a Hydrophobic Residue as a Key Determinant of Fructose Transport by the Facilitative Hexose Transporter SLC2A7 (GLUT7) (2005)

Until recently, the only facilitated hexose transporter GLUT proteins (SLC2A) known to transport fructose were GLUTs 2 and 5. However, the recently cloned GLUT7 can also transport fructose as well as glucose. Comparison of sequence alignments indicated that GLUTs 2, 5, and 7 all had an isoleucine residue at position "314" (GLUT7), whereas the non-fructose-transporting isoforms, GLUTs 1, 3, and 4, had a valine at this position. Mutation of Ile-314 to a valine in GLUT7 resulted in a loss of fructose transport, whereas glucose transport remained completely unaffected. Similar results were obtained with GLUTs 2 and 5. Energy minimization modeling of GLUT7 indicated that Ile-314 projects from transmembrane domain 7 (TM7) into the lumen of the aqueous pore, where it could form a hydrophobic interaction with tryptophan 89 from TM2. A valine residue at 314 appeared to produce a narrowing of the vestibule when compared with the isoleucine. It is proposed that this hydrophobic interaction across the pore forms a selectivity filter restricting the access of some hexoses to the substrate binding site(s) within the aqueous channel. The presence of a selectivity filter in the extracellular vestibule of GLUT proteins would allow for subtle changes in substrate specificity without changing the kinetic parameters of the protein.
Disruption of neurofascin and gliomedin at nodes of Ranvier precedes demyelination in experimental allergic neuritis (2008)

High densities of voltage-gated sodium (Nav) channels at nodes of Ranvier enable the rapid regeneration and propagation of the action potentials along myelinated axons. In demyelinating pathologies, myelin alterations lead to conduction slowing and even to conduction block. In order to unravel the mechanisms of conduction failure in inflammatory demyelinating diseases, we have examined two models of Guillain-Barré syndrome: the experimental allergic neuritis induced in the Lewis rat by immunization against peripheral myelin (EAN-PM) and against a neuritogenic P2 peptide (EAN-P2). We found that Nav channel clusters were disrupted at EAN-PM nodes. Neurofascin and gliomedin, two cell adhesion molecules involved with aggregating Nav channels at nodes, were selectively affected prior to demyelination in EAN-PM, indicating that degradation of the axo-glial unit initiated node alteration. This was associated with autoantibodies to neurofascin and gliomedin. Node disruption was, however, independent from complement deposition at nodes, and deposits of the terminal complement complex (C5b-9) were found on the external surface of Schwann cells in EAN-PM. In these animals, the paranodal junctions were also affected and Kv1 channels, which are normally juxtaparanodal, were found dispersed at nodes and paranodes. Altogether, these alterations were associated with conduction deficits in EAN-PM ventral spinal roots. EAN-P2 animals also exhibited inflammatory demyelination, but did not show alteration in nodal clusters or autoantibodies. Our results highlighted the complex mechanisms underlying conduction abnormalities in demyelinating disorders, and unraveled neurofascin and gliomedin as two novel immune targets in experimental allergic neuritis.
A low-cost capacitive relative humidity sensor for food moisture monitoring application (2012)

In this paper, a low-cost capacitive relative humidity hygrometer suitable for food moisture monitoring is presented. The variation of dielectric constant of polyimide film to relative humidity enables the sensor's functionality. A fully differential capacitance to digital converter is utilized as the hygrometer digital readout, which is immune to circuit wiring parasitic and enable the sensor's long-term stability. The humidity sensor is implemented using TSMC1P6M 0.18μm technology with thick top metal option. Simulation results indicate that an inaccuracy of +6/-5%RH can be achieved sensing from 10%RH ~ 90%RH, with 5.4μW power consumption for sensing and 21.6mW power consumption for sensor heating.
Two-dimensional granular flow in a small-angle funnel (1996)

We have investigated a granular flow consisting of a single layer of uniform balls in a two dimensional funnel. The qualitative behavior of the flow depends in a sensitive way on the geometry. For a particular configuration in which only the funnel opening angle \ensuremath{\beta} is varied, we find three regimes. When \ensuremath{\beta}>2\ifmmode^\circ\else\textdegree\fi{}, the flow is dense and steady, and the flow rate is determined by the geometry at the outlet. When 0.1\ifmmode^\circ\else\textdegree\fi{}\ensuremath{\lesssim}\ensuremath{\beta}\ensuremath{\lesssim}1\ifmmode^\circ\else\textdegree\fi{}, the flow is intermittent, consisting of quasiperiodic kinematic waves, probably shock waves, propagating against the flow. The flow rate reaches its maximum in this regime. When \ensuremath{\beta}0.05\ifmmode^\circ\else\textdegree\fi{}, the waves become stationary, and the flow rate is now determined by the geometry at the inlet. We also measure the number density fluctuations of the flow and their power spectra. For all flows, the power spectra are white at low frequencies with structures at higher frequencies resulting from the kinematic waves and short-range correlations. \textcopyright{} 1996 The American Physical Society.
LAF-Net: Locally Adaptive Fusion Networks for Stereo Confidence Estimation (2019)

We present a novel method that estimates confidence map of an initial disparity by making full use of tri-modal input, including matching cost, disparity, and color image through deep networks. The proposed network, termed as Locally Adaptive Fusion Networks (LAF-Net), learns locally-varying attention and scale maps to fuse the tri-modal confidence features. The attention inference networks encode the importance of tri-modal confidence features and then concatenate them using the attention maps in an adaptive and dynamic fashion. This enables us to make an optimal fusion of the heterogeneous features, compared to a simple concatenation technique that is commonly used in conventional approaches. In addition, to encode the confidence features with locally-varying receptive fields, the scale inference networks learn the scale map and warp the fused confidence features through convolutional spatial transformer networks. Finally, the confidence map is progressively estimated in the recursive refinement networks to enforce a spatial context and local consistency. Experimental results show that this model outperforms the state-of-the-art methods on various benchmarks.
Molecular Requirements for Targeting the Polyamine Transport System. Synthesis and Biological Evaluation of Polyamine−Anthracene Conjugates (2003)

A series of nine N(1)-(9-anthracenylmethyl)tetraamines (e.g., Ant-4,4,4-tetraamine) were synthesized and evaluated for cytotoxicity in L1210, alpha-difluoromethylornithine (DFMO)-treated L1210, Chinese hamster ovary (CHO), and CHO-MG cell lines. Surprisingly, the 3,3,4- and 3,4,3-tetraamine motifs had the same or decreased cytotoxicity in DFMO-treated L1210 cells, whereas the rest of the tetraamine systems were usually more cytotoxic and gave lower IC(50) values in this treated cell line. The most sensitive derivatives to DFMO treatment were the Ant-4,4,3- and Ant-4,4,4-tetraamine analogues, which were 7 and 5 times more cytotoxic in DFMO-treated L1210 cells, respectively. K(i) values for each of the anthracenylmethyl(Ant)-polyamine conjugates were determined in L1210 cells and revealed that these systems are high-affinity ligands for the polyamine transporter (PAT). Mixed results were observed in the CHO and CHO-MG assays. The 4,4,4- and 5,4,4-tetraamine motifs were 3 times more toxic to CHO cells with active polyamine transporters. For example, the Ant-4,4,4-tetraamine conjugate displayed IC(50) values of 11 microM in CHO cells and 33 microM in CHO-MG cells, a PAT-deficient cell line. This suggested that these derivatives used the PAT in part to access cells. However, most of the other tetraamine derivatives had similar potencies in both the CHO and CHO-MG cell lines. In terms of vector design, higher affinity for the PAT (lower K(i) values) did not translate into higher potency for the tetraamine conjugate. In contrast, the related triamine systems, which had micromolar K(i) values in L1210 cells, were more efficacious and selective. In one case, the 4,4-triamine motif imparted 150-fold higher potency in CHO cells than the CHO-MG mutant. A deconvolution microscopy study in A375 melanoma cells revealed a rapid internalization of the Ant-4,4-triamine as fluorescent vesicles, whereas the Ant-4,4,4-tetraamine remained mostly at the cell surface. These findings help define the key characteristics required for selective delivery of polyamine-drug conjugates into cell types with active polyamine transporters.
Export of Cytochrome P450 105D1 to the Periplasmic Space of <i>Escherichia coli</i> (2001)

CYP105D1, a cytochrome P450 from Streptomyces griseus, was appended at its amino terminus to the secretory signal of Escherichia coli alkaline phosphatase and placed under the transcriptional control of the native phoA promoter. Heterologous expression in E. coli phosphate-limited medium resulted in abundant synthesis of recombinant CYP105D1 that was translocated across the bacterial inner membrane and processed to yield authentic, heme-incorporated P450 within the periplasmic space. Cell extract and whole-cell activity studies showed that the periplasmically located CYP105D1 competently catalyzed NADH-dependent oxidation of the xenobiotic compounds benzo[a]pyrene and erythromycin, further revealing the presence in the E. coli periplasm of endogenous functional redox partners. This system offers substantial advantages for the application of P450 enzymes to whole-cell biotransformation strategies, where the ability of cells to take up substrates or discard products may be limited.
BMP-2/4 and BMP-6/7 Differentially Utilize Cell Surface Receptors to Induce Osteoblastic Differentiation of Human Bone Marrow-derived Mesenchymal Stem Cells (2008)

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor-beta superfamily of growth factors and are used clinically to induce new bone formation. The purpose of this study was to evaluate receptor utilization by BMP-2, BMP-4, BMP-6, and BMP-7 in primary human mesenchymal stem cells (hMSC), a physiologically relevant cell type that probably mediates the in vivo effects of BMPs. RNA interference-mediated gene knockdown revealed that osteoinductive BMP activities in hMSC are elicited through the type I receptors ACVR1A and BMPR1A and the type II receptors ACVR2A and BMPR2. BMPR1B and ACVR2B were expressed at low levels and were not found to play a significant role in signaling by any of the BMPs evaluated in this study. Type II receptor utilization differed significantly between BMP-2/4 and BMP-6/7. A greater reliance on BMPR2 was observed for BMP-2/4 relative to BMP-6/7, whereas ACVR2A was more critical to signaling by BMP-6/7 than BMP-2/4. Significant differences were also observed for the type I receptors. Although BMP-2/4 used predominantly BMPR1A for signaling, ACVR1A was the preferred type I receptor for BMP-6/7. Signaling by both BMP-2/4 and BMP-6/7 was mediated by homodimers of ACVR1A or BMPR1A. A portion of BMP-2/4 signaling also required concurrent BMPR1A and ACVR1A expression, suggesting that BMP-2/4 signal in part through ACVR1A/BMPR1A heterodimers. The capacity of ACVR1A and BMPR1A to form homodimers and heterodimers was confirmed by bioluminescence resonance energy transfer analyses. These results suggest different mechanisms for BMP-2/4- and BMP-6/7-induced osteoblastic differentiation in primary hMSC.
Diffusible iodine‐based contrast‐enhanced computed tomography (diceCT): an emerging tool for rapid, high‐resolution, 3‐D imaging of metazoan soft tissues (2016)

Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.
Design criteria for a self-actuated shutdown system to ensure limitation of core damage. [LMFBR] (1981)

Safety-based functional requirements and design criteria for a self-actuated shutdown system (SASS) are derived in accordance with LOA-2 success criteria and reliability goals. The design basis transients have been defined and evaluated for the CDS Phase II design, which is a 2550 MWt mixed oxide heterogeneous core reactor. A partial set of reactor responses for selected transients is provided as a function of SASS characteristics such as reactivity worth, trip points, and insertion times.
Curcumin‐induced fibroblast apoptosis and <i>in vitro</i> wound contraction are regulated by antioxidants and heme oxygenase: implications for scar formation (2008)

Fibroblast apoptosis plays a crucial role in normal and pathological scar formation and therefore we studied whether the putative apoptosis-inducing factor curcumin affects fibroblast apoptosis and may function as a novel therapeutic. We show that 25-microM curcumin causes fibroblast apoptosis and that this could be inhibited by co-administration of antioxidants N-acetyl-l-cysteine (NAC), biliverdin or bilirubin, suggesting that reactive oxygen species (ROS) are involved. This is supported by our observation that 25-microM curcumin caused the generation of ROS, which could be completely blocked by addition of NAC or bilirubin. Since biliverdin and bilirubin are downstream products of heme degradation by heme oxygenase (HO), it has been suggested that HO-activity protects against curcumin-induced apoptosis. Interestingly, exposure to curcumin maximally induced HO-1 protein and HO-activity at 10-15 microM, whereas, at a concentration of >20-microM curcumin HO-1-expression and HO-activity was negligible. NAC-mediated inhibition of 25-microM curcumin-induced apoptosis was demonstrated to act in part via restored HO-1-induction, since the rescuing effect of NAC could be reduced by inhibiting HO-activity. Moreover pre-induction of HO-1 using 5-microM curcumin protected fibroblasts against 25-microM curcumin-induced apoptosis. On a functional level, fibroblast-mediated collagen gel contraction, an in vitro wound contraction model, was completely prevented by 25-microM curcumin, while this could be reversed by co-incubation with NAC, an effect that was also partially HO-mediated. In conclusion, curcumin treatment in high doses (>25 microM) may provide a novel way to modulate pathological scar formation through the induction of fibroblast apoptosis, while antioxidants, HO-activity and its effector molecules act as a possible fine-tuning regulator.
Total synthesis of three eudesman-12,8-olides, (±)-isoalantolactone, (±)-dihydrocallitrisin and (±)-septuplinolide; structure revision of septuplinolide (1993)

Four eudesman-12,8-olides, (±)-isoalantolactone, (±)-dihydrocallitrisin, (±)-septuplinolide and its epimeric eudesmanolide at C-4 were synthesized stereoselectively via the route involving alkylation annulation of 2-methyl-3-furoic acid and oxidation of the furan ring. It was found that the structure of septuplinolide is the C-4 epimer of the reported structure.
Real-time volumetric lighting using polygonal light volume (2014)

In this paper, we present a novel method to simulate single scattering in homogeneous participating media, which can greatly enhance the immersion of environment simulation. We construct a light volume with a polygonal mesh based on shadow map to restrict the ray-marching segments, place samples at discontinuities along the epipolar lines of the final image to speed up the ray-marching process, and add support for textured light. Our method is implemented on GPUs, and can render a complex scene with participating media in real time.
Electrophoresis of viral proteins in formic acid 1. General aspects (1981)

Abstract The excellent solublizing properties of high concentrations of formic acid solutions for polypeptides and proteins, including those with high hydrophobicity, are used in polyacrylamide gel electrophoresis. The technical handling of the system is described in detail. The structural polypeptide of poliovirus type1, VP1, VP2, VP3 an dVP4, until now separable in polyacrylamide gel rods containing 70% formic acid. By two‐dimensional analysis, namely formic acid electrophoresis in the first dimension and SDS electrophoresis in the second, we have shown that the electrophoretic mobility in formic acid is of the order VP2‐VP1‐VP3‐VP4. with several marker proteins we have also demonstrated that the migration velocity depends not only on the molecular weights but also on the secondary structure of the proteins, especially on disulfide cross‐links. High concentrations of salts (3 MCsCI or 6 m Guanidine hydrochloride) in the protein sample do not change the separation pattern, which, however, is strongly affected by 6 m urea.
Elevated Oxidative Stress in Patients with Ataxia Telangiectasia (2002)

Ataxia telangiectasia (AT) is a pleiotropic genetic disorder characterized by progressive neurodegeneration, especially of cerebellar Purkinje cells, immunodeficiency, increased incidence of cancer, and premature aging. The disease is caused by functional inactivation of the ATM (AT-mutated) gene product, which is thought to act as a sensor of reactive oxygen species and oxidative damage of cellular macromolecules and DNA. The compound phenotype of AT might thus be linked to a continuous state of oxidative stress leading to an increase of programmed cell death (apoptosis). To assess this hypothesis, we analyzed lipid peroxidation products and the oxidative stress associated DNA base damage 8-hydroxy-2-deoxyguanosine in patients with AT. Oxidative damage to lipids and DNA was found to be markedly increased in AT patients. These results indicate that ATM might play an important role in the maintenance of cell homeostasis in response to oxidative damage. In this context, a better control of levels of reactive oxygen species could be a rational foundation of therapeutic intervention to help alleviate some of the symptoms associated with AT.
Structure Effects on Resistive Switching of $ \hbox{Al/TiO}_{x}/\hbox{Al}$ Devices for RRAM Applications (2008)

Resistive switching characteristics are investigated for Al/TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /Al devices, particularly for the structural effects in crossbar and via-hole-type devices. The via-hole structure shows more reliable switching characteristics than the crossbar structure, owing to the elimination of possible edge effects. The asymmetric switching behavior is analyzed with top Al/TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> , and bottom Al/TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> interfaces. A trap-controlled space-charge- limited-current model is proposed as a possible switching mechanism, and it is verified that switching mainly occurs on the top electrode/TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> , interface side.
ROLE OF ENDOGENOUS INTERLEUKIN-10 IN LOCAL AND DISTANT ORGAN INJURY AFTER VISCERAL ISCHEMIA-REPERFUSION (2003)

The anti-inflammatory cytokine interleukin (IL)-10 has been detected in serum after visceral ischemia-reperfusion injury and exogenous IL-10 administration has been shown to attenuate the associated distant organ injury. This study was designed to examine the role that endogenous IL-10 production plays on both local and distant organ injury after visceral ischemia-reperfusion injury. Wild-type and IL-10(-/-)-null C57BL/6 mice were subjected to 20 min of supraceliac aortic occlusion or sham laparotomy. Serum and lung tissue cytokine levels (tumor necrosis factor alpha, IL-1beta, IL-6, KC/GRO, and IL-10) were measured after reperfusion (1, 2, and/or 4 h) using either enzyme-linked immunoassay or bioassay. Lung neutrophil infiltration and injury were quantified after reperfusion injury using myeloperoxidase concentration (2 h) and mean capillary permeability (4 h), respectively, whereas the direct liver injury was quantified with serum aspartate aminotransferase levels (1, 2, and 4 h). A subset of IL-10(-/-)-null animals was administered human recombinant IL-10 before the visceral ischemia and lung MPO was measured after reperfusion (2 h). Visceral ischemia-reperfusion in the wild-type and IL-10(-/-)-null mice was associated with in an increase in both serum (IL-1beta, KC/GRO, IL-6) and lung tissue (IL-1beta, KC/GRO) cytokine levels and resulted in lung neutrophil infiltration (myeloperoxidase), lung injury (mean capillary permeability) and liver injury (aspartate aminotransferase). The magnitude of the lung tissue cytokine response (IL-1beta, KC/GRO), neutrophil infiltration, and injury were greater in the IL-10(-/-)-null mice. Exogenous IL-10 resulted in a decrease in the lung neutrophil infiltration in the IL-10(-/-)-null mice. The endogenous IL-10 response to visceral ischemia-reperfusion attenuates the associated lung neutrophil infiltration and injury but has no effect upon either the hepatic injury or the magnitude of the systemic inflammatory response. The beneficial effects of IL-10 may be mediated by the inhibition of IL-1beta and KC/GRO through an endocrine rather than paracrine signal.
Demonstration of a linear optics controlled-NOT gate (2004)

We experimentally demonstrate an all-optical quantum gate that, with high fidelity, reproduces the entanglement and truth table of a controlled-NOT. We completely characterize it using quantum process tomography, obtaining an average process fidelity of 0.81.