gebhart/patrepeval huggingface dataset:
Platelet Lysate Therapy Attenuates Hypoxia Induced Apoptosis in Human Uroepithelial SV-HUC-1 Cells through Regulating the Oxidative Stress and Mitochondrial-Mediated Intrinsic Apoptotic Pathway (2023)

(1) Background: Ischemia/hypoxia plays an important role in interstitial cystitis/bladder pain syndrome (IC/BPS). Platelet-rich plasma (PRP) has been shown to relieve symptoms of IC/BPS by regulating new inflammatory processes and promoting tissue repair. However, the mechanism of action of PRP on the IC/BPS bladder remains unclear. We hypothesize that PRP might protect the urothelium during ischemia/hypoxia by decreasing apoptosis. (2) Methods: SV-HUC-1 cells were cultured under hypoxia for 3 h and treated with or without 2% PLTGold<sup>®</sup> human platelet lysate (PL). Cell viability assays using trypan blue cell counts were examined. Molecules involved in the mitochondrial-mediated intrinsic apoptosis pathway, HIF1α, and PCNA were assessed by Western blot analysis. The detection of apoptotic cells and CM-H2DCFDA, an indicator of reactive oxygen species (ROS) in cells, was analyzed by flow cytometry. (3) Results: After 3 h of hypoxia, the viability of SV-HUC-1 cells and expression of PCNA were significantly decreased, and the expression of ROS, HIF1α, Bax, cytochrome c, caspase 3, and early apoptosis rate were significantly increased, all of which were attenuated by PL treatment. The addition of the antioxidant N-acetyl-L-cysteine (NAC) suppressed the levels of ROS induced by hypoxia, leading to inhibition of late apoptosis. (4) Conclusions: PL treatment could potentially protect the urothelium from apoptosis during ischemia/hypoxia by a mechanism that modulates the expression of HIF1α, the mitochondria-mediated intrinsic apoptotic pathway, and reduces ROS.
Multiple channel hybrid active noise control systems (1998)

This paper introduces a multiple-channel hybrid filtered-X least mean square (MHFLMS) active noise control (ANC) algorithm. The algorithm is capable of cancelling both narrow-band and broadband noises in complicated noise environments. The algorithm structure is discussed under a very general active noise cancelling condition. The MHFLMS algorithm is an integration of a multiple-channel filtered-X least mean square algorithm and a multiple-channel feedback filtered-X least mean square algorithm. The MHFLMS algorithm performance is analyzed for its steady-state noise cancelling behavior. Extensive computer simulations verify that the MHFLMS algorithm outperforms several existing ANC algorithms under various noise cancelling conditions. Analysis results of the actual noise from a large plant for which a real-time ANC system is being developed also demonstrate the performance advantages of the MHFLMS algorithm over the other ANC algorithms.
Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target (2021)

With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran <b>1</b> was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against <i>Mycobacterium tuberculosis</i>, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.
Angle-resolved photoemission study of the Kitaev candidateα−RuCl3 (2016)

$\ensuremath{\alpha}\ensuremath{-}{\mathrm{RuCl}}_{3}$ has been hinted to be a spin-orbital-assisted Mott insulator in proximity to a Kitaev spin liquid state. Here we present angle-resolved photoemission measurements on single-crystal $\ensuremath{\alpha}\ensuremath{-}{\mathrm{RuCl}}_{3}$ in both the pristine and electron-doped states, and combine them with Local Density Approximation (LDA)+Spin Orbital Coupling (SOC)+U calculations performed for several low-energy competing magnetically ordered states as well as the paramagnetic state. A large Mott gap is found in the measured band structure of the pristine compound that persists to more than 30 times beyond the magnetic ordering temperature, though the paramagnetic calculation shows almost no gap. Upon electron doping, spectral weight is transferred into the gap but the new states still maintain a sizable gap from the Fermi edge. These findings are most consistent with a Mott insulator with a somewhat exotic evolution out of the Mott state with both temperature and doping, likely related to unusually strong spin fluctuations.
Synthesizing Physical Character-Scene Interactions (2023)

Movement is how people interact with and affect their environment. For realistic character animation, it is necessary to synthesize such interactions between virtual characters and their surroundings. Despite recent progress in character animation using machine learning, most systems focus on controlling an agent's movements in fairly simple and homogeneous environments, with limited interactions with other objects. Furthermore, many previous approaches that synthesize human-scene interactions require significant manual labeling of the training data. In contrast, we present a system that uses adversarial imitation learning and reinforcement learning to train physically-simulated characters that perform scene interaction tasks in a natural and life-like manner. Our method learns scene interaction behaviors from large unstructured motion datasets, without manual annotation of the motion data. These scene interactions are learned using an adversarial discriminator that evaluates the realism of a motion within the context of a scene. The key novelty involves conditioning both the discriminator and the policy networks on scene context. We demonstrate the effectiveness of our approach through three challenging scene interaction tasks: carrying, sitting, and lying down, which require coordination of a character's movements in relation to objects in the environment. Our policies learn to seamlessly transition between different behaviors like idling, walking, and sitting. By randomizing the properties of the objects and their placements during training, our method is able to generalize beyond the objects and scenarios depicted in the training dataset, producing natural character-scene interactions for a wide variety of object shapes and placements. The approach takes physics-based character motion generation a step closer to broad applicability.
Ultrafast and broadband frequency chirp signal generation using a high-extinction-ratio optical modulator (2010)

We successfully demonstrate ultrafast frequency sweep signal generation using the double-sideband suppressed carrier modulation technique with a high-extinction-ratio optical modulator that helps realize clear signals with no filters. The resultant sweep rate was achieved at 3.67 × 10(16) Hz/s with an extinction ratio above 25 dB, which corresponds to a bandwidth of 11 GHz with a pulse duration of 300 ns.
Synthesis of Bi-Te-X (X=Sn, Sb) Tertiary Thermoelectric Alloy Nano Particles by Precise Control of Metal Complexes Structures (2011)

Abstract not Available.
TPMS-based membrane lung with locally-modified permeabilities for optimal flow distribution (2022)

Membrane lungs consist of thousands of hollow fiber membranes packed together as a bundle. The devices often suffer from complications because of non-uniform flow through the membrane bundle, including regions of both excessively high flow and stagnant flow. Here, we present a proof-of-concept design for a membrane lung containing a membrane module based on triply periodic minimal surfaces (TPMS). By warping the original TPMS geometries, the local permeability within any region of the module could be raised or lowered, allowing for the tailoring of the blood flow distribution through the device. By creating an iterative optimization scheme for determining the distribution of streamwise permeability inside a computational porous domain, the desired form of a lattice of TPMS elements was determined via simulation. This desired form was translated into a computer-aided design (CAD) model for a prototype device. The device was then produced via additive manufacturing in order to test the novel design against an industry-standard predicate device. Flow distribution was verifiably homogenized and residence time reduced, promising a more efficient performance and increased resistance to thrombosis. This work shows the promising extent to which TPMS can serve as a new building block for exchange processes in medical devices.
ChemInform Abstract: SELEKTIVE EINFUEHRUNG VON WASSERSTOFF‐ISOTOPEN DURCH ELEKTROLYTISCHE RED. VON KOHLENSTOFF‐HALOGEN‐BINDUNGEN (1972)

Abstract 3‐H‐Pentachlorcyclobuten (I) reagiert mit Butyllithium und Isobutylen (II) zu den beiden Addukten (III) und (IV), mit 2‐Butin (V) zu (VI).
Functional mapping of sensorimotor activation in the human thalamus at 9.4 Tesla (2023)

Although the thalamus is perceived as a passive relay station for almost all sensory signals, the function of individual thalamic nuclei remains unresolved. In the present study, we aimed to identify the sensorimotor nuclei of the thalamus in humans using task-based fMRI at a field strength of 9.4T by assessing the individual subject-specific sensorimotor BOLD response during a combined active motor (finger-tapping) and passive sensory (tactile-finger) stimulation. We demonstrate that both tasks increase BOLD signal response in the lateral nuclei group (VPL, VA, VLa, and VLp), and in the pulvinar nuclei group (PuA, PuM, and PuL). Finger-tapping stimuli evokes a stronger BOLD response compared to the tactile stimuli, and additionally engages the intralaminar nuclei group (CM and Pf). In addition, our results demonstrate reproducible thalamic nuclei activation during motor and tactile stimuli. This work provides important insight into understanding the function of individual thalamic nuclei in processing various input signals and corroborates the benefits of using ultra-high-field MR scanners for functional imaging of fine-scale deeply located brain structures.
The Distribution of Fox Squirrel (Sciurus niger) Leaf Nests within Forest Fragments in Central Indiana (2004)

We examined the abundance and placement of leaf nests by fox squirrels in six urban woodlots in central Indiana ranging in size from 1.06 to 8.28 ha. Four of the woodlots were disturbed, or subject to extensive human impact, whereas the remaining two were nature preserves. We counted all leaf nests present in each woodlot and recorded nest tree characteristics. We then conducted a quantitative vegetation analysis of trees present and estimated percentages of herbaceous and shrub cover along a minimum of two 100 m transects at each site. Fox squirrels showed a preference to build nests in certain species of trees. However, preference for nest tree species was not consistent across sites. Fox squirrels preferred to build nests in large trees with vines in the canopy at all sites. Characteristics of nests and nest trees did not differ among sites, but nest density was greater in the disturbed sites compared to the nature preserve sites. The nature preserve sites differed from the disturbed sites only with regard to the amount of shrub and herbaceous cover; shrub cover was greater and herbaceous cover was less at the disturbed sites. Results of this study suggest that fox squirrels are flexible with regard to nest tree species used and that the choice of a nest tree is dependent, in part, on tree size and the presence of vines. Further, a higher density of leaf nests in disturbed woodlots suggests that habitat disturbance and fragmentation due to urbanization may not have detrimental effects on the abundance and persistence of fox squirrels.
Table S1 from USP9X Downregulation Renders Breast Cancer Cells Resistant to Tamoxifen (2023)

&lt;p&gt;ChIP-seq read counts, aligned reads and peak numbers&lt;/p&gt;
Germline mutations in the von Hippel-Lindau disease tumor suppressor gene: Correlations with phenotype (1995)

von Hippel-Lindau disease (VHL) is an inherited neoplastic disease characterized by a predisposition to develop retinal angiomas, central nervous system hemangioblastomas, renal cell carcinomas, pancreatic cysts, and pheochromocytomas. The VHL gene was recently isolated by positional cloning. The cDNA encodes 852 nucleotides in 3 exons. The VHL gene is unrelated to any known gene families. We identified germline mutations in 85/114 (75%) of VHL families. Clinical heterogeneity is a well-known feature of VHL. VHL families were classified into 2 types based on the presence or absence of pheochromocytoma. The types of mutations responsible for VHL without pheochromocytoma (VHL type 1) differed from those responsible for VHL with pheochromocytoma (VHL type 2). Fifty-six % of the mutations responsible for VHL type 1 were microdeletions/insertions, nonsense mutations, or deletions; 96% of the mutations responsible for VHL type 2 were missense mutations. Specific mutations in codon 238 accounted for 43% of the mutations responsible for VHL type 2. The mutations identified in these families will be useful in presymptomatic diagnosis. The identification of mutations associated with phenotypes contributes to the understanding of fundamental genetic mechanisms of VHL disease.
Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling (2023)

Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used MERFISH to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations; charted their spatial organization; and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.
[A tolerability study of A cremophor-free albumin bound nanoparticle paclitaxel intravenously administered in patients with advanced solid tumor]. (2004)

This phase I trial has demonstrated that Capxol has several advantages on clinical application, which include non-premedication required, shorter infusion time,higher paclitaxel MTD and safer toxicity. The results support for that a phase II clinical trial to further evaluate the antitumor activity of this drug in Chinese patients is worthy. The recommended dose for phase II clinical trial is 260 mg/m(2), I.V. over 30 minutes,and treatment repeats at every 3 weeks.
Repurposing a novel anti-cancer RXR agonist to attenuate murine acute GVHD and maintain graft-versus-leukemia responses (2020)

The nuclear receptor (NR) subclass, retinoid X receptors (RXRs), exert immunomodulatory functions that control inflammation and metabolism via homodimers and heterodimers, with several other NRs, including retinoic acid receptors. IRX4204 is a novel, highly specific RXR agonist in clinical trials that potently and selectively activates RXR homodimers, but not heterodimers. In this study, in vivo IRX4204 compared favorably with FK506 in abrogating acute graft-versus-host disease (GVHD), which was associated with inhibiting allogeneic donor T-cell proliferation, reducing T-helper 1 differentiation, and promoting regulatory T-cell (Treg) generation. Recipient IRX4204 treatment reduced intestinal injury and decreased IFN-γ and TNF-α serum levels. Transcriptional analysis of donor T cells isolated from intestines of GVHD mice treated with IRX4204 revealed significant decreases in transcripts regulating proinflammatory pathways. In vitro, inducible Treg differentiation from naive CD4+ T cells was enhanced by IRX4204. In vivo, IRX4204 increased the conversion of donor Foxp3- T cells into peripheral Foxp3+ Tregs in GVHD mice. Using Foxp3 lineage-tracer mice in which both the origin and current FoxP3 expression of Tregs can be tracked, we demonstrated that IRX4204 supports Treg stability. Despite favoring Tregs and reducing Th1 differentiation, IRX4204-treated recipients maintained graft-versus-leukemia responses against both leukemia and lymphoma cells. Notably, IRX4204 reduced in vitro human T-cell proliferation and enhanced Treg generation in mixed lymphocyte reaction cultures. Collectively, these beneficial effects indicate that targeting RXRs with IRX4204 could be a novel approach to preventing acute GVHD in the clinic.
Precursor Concentration Affects Grain Size, Crystal Orientation, and Local Performance in Mixed-Ion Lead Perovskite Solar Cells (2018)

A key debate involving mixed-cation lead mixed-halide perovskite thin-films relates to the effects of process conditions on film morphology and local performance of perovskite solar cells. In this contribution, we investigate the influence of precursor concentration on the film thickness, grain size, and orientation of these polycrystalline thin-films. We vary the molar concentration of the perovskite precursor containing Rb, Cs, MA, FA, Pb, I, and Br from 0.4 to 1.2 M. We use optical and electrical probes to measure local properties and correlate the effect of crystallographic orientation on the inter- and intragrain charge-carrier transport. We find that, with increasing precursor concentration, the grain size of the polycrystalline thin-films becomes larger and more faceted. Films with small grains show mostly random grain orientation angles, whereas films with large grains are oriented with {100} planes around an angle of 20° relative to the surface normal. These films with oriented large grains also show longer-lived charge-carrier lifetimes and an improved charge-carrier extraction at the surface. Our results provide new insights into the role of process conditions (precursor concentration) on film morphology (grain size and orientation), and consequently on the homogeneity of local performance, which could bring perovskite solar cells beyond the state-of-the-art.
Development of an Automated High Throughput LCP-FRAP Assay to Guide Membrane Protein Crystallization in Lipid Mesophases (2011)

Crystallization in lipidic mesophases (in meso) has been successfully used to obtain a number of high-resolution membrane protein structures including challenging members of the human G protein-coupled receptor (GPCR) family. Crystallogenesis in arguably the most successful mesophase, lipidic cubic phase (LCP), critically depends on the ability of protein to diffuse in the LCP matrix and to form specific protein-protein contacts to support crystal nucleation and growth. The ability of an integral membrane protein to diffuse in LCP is strongly affected by the protein aggregation state, the structural parameters of LCP, and the chemical environment. In order to satisfy both requirements of diffusion and specific interactions, one must balance multiple parameters, such as identity of LCP host lipid, composition of precipitant solution, identity of ligand, and protein modifications. Screening within such multi-dimensional crystallization space presents a significant bottleneck in obtaining initial crystal leads. To reduce this combinatorial challenge, we developed a pre-crystallization screening assay to measure the diffusion characteristics of a protein target in LCP. Utilizing the Fluorescence Recovery After Photobleaching (FRAP) technique in an automated and high throughput manner, we were able to map conditions that support adequate diffusion in LCP using a minimal amount of protein. Data collection and processing protocols were validated using two model GPCR targets: the β(2)-adrenergic receptor and the A(2A) adenosine receptor.
Photonic encryption : modeling and functional analysis of all optical logic. (2004)

With the build-out of large transport networks utilizing optical technologies, more and more capacity is being made available. Innovations in Dense Wave Division Multiplexing (DWDM) and the elimination of optical-electrical-optical conversions have brought on advances in communication speeds as we move into 10 Gigabit Ethernet and above. Of course, there is a need to encrypt data on these optical links as the data traverses public and private network backbones. Unfortunately, as the communications infrastructure becomes increasingly optical, advances in encryption (done electronically) have failed to keep up. This project examines the use of optical logic for implementing encryption in the photonic domain to achieve the requisite encryption rates. This paper documents the innovations and advances of work first detailed in 'Photonic Encryption using All Optical Logic,' [1]. A discussion of underlying concepts can be found in SAND2003-4474. In order to realize photonic encryption designs, technology developed for electrical logic circuits must be translated to the photonic regime. This paper examines S-SEED devices and how discrete logic elements can be interconnected and cascaded to form an optical circuit. Because there is no known software that can model these devices at a circuit level, the functionality of S-SEED devices in an optical circuit was modeled in PSpice. PSpice allows modeling of the macro characteristics of the devices in context of a logic element as opposed to device level computational modeling. By representing light intensity as voltage, 'black box' models are generated that accurately represent the intensity response and logic levels in both technologies. By modeling the behavior at the systems level, one can incorporate systems design tools and a simulation environment to aid in the overall functional design. Each black box model takes certain parameters (reflectance, intensity, input response), and models the optical ripple and time delay characteristics. These 'black box' models are interconnected and cascaded in an encrypting/scrambling algorithm based on a study of candidate encryption algorithms. Demonstration circuits show how these logic elements can be used to form NAND, NOR, and XOR functions. This paper also presents functional analysis of a serial, low gate count demonstration algorithm suitable for scrambling/encryption using S-SEED devices.
Three-dimensional patterning using fine step motion in synchrotron radiation lithography (2006)

A simple method of fabricating blazed diffraction gratings using synchrotron radiation lithography was developed that employs an ordinary binary mask with a line-and-space pattern, a step-and-expose procedure that provides a linear cumulative-dose distribution, and a thick resist with a linear sensitivity curve. This method enables the fabrication of blazed gratings with a grating pitch of 1μm and a blaze angle of 15°–40°. The angle and pitch can be changed by changing the dose from step to step and/or by using mask spaces of different widths.