gebhart/patrepeval huggingface dataset:
Ischemic injury induces ADF relocalization to the apical domain of rat proximal tubule cells (2001)

Breakdown of proximal tubule cell apical membrane microvilli is an early-occurring hallmark of ischemic acute renal failure. Intracellular mechanisms responsible for these apical membrane changes remain unknown, but it is known that actin cytoskeleton alterations play a critical role in this cellular process. Our laboratory previously demonstrated that ischemia-induced cell injury resulted in dephosphorylation and activation of the actin-binding protein, actin depolymerizing factor [(ADF); Schwartz, N, Hosford M, Sandoval RM, Wagner MC, Atkinson SJ, Bamburg J, and Molitoris BA. Am J Physiol Renal Fluid Electrolyte Physiol 276: F544-F551, 1999]. Therefore, we postulated that ischemia-induced ADF relocalization from the cytoplasm to the apical microvillar microfilament core was an early event occurring before F-actin alterations. To directly investigate this hypothesis, we examined the intracellular localization of ADF in ischemic rat cortical tissues by immunofluorescence and quantified the concentration of ADF in brush-border membrane vesicles prepared from ischemic rat kidneys by using Western blot techniques. Within 5 min of the induction of ischemia, ADF relocalized to the apical membrane region. The length of ischemia correlated with the time-related increase in ADF in isolated brush-border membrane vesicles. Finally, depolymerization of microvillar F-actin to G-actin was documented by using colocalization studies for G- and F-actin. Collectively, these data indicate that ischemia induces ADF activation and relocalization to the apical domain before microvillar destruction. These data further suggest that ADF plays a critical role in microvillar microfilament destruction and apical membrane damage during ischemia.
Menaquinone synthesis is critical for maintaining mycobacterial viability during exponential growth and recovery from non‐replicating persistence (2009)

Understanding the basis of bacterial persistence in latent infections is critical for eradication of tuberculosis. Analysis of Mycobacterium tuberculosis mRNA expression in an in vitro model of non-replicating persistence indicated that the bacilli require electron transport chain components and ATP synthesis for survival. Additionally, low microM concentrations of aminoalkoxydiphenylmethane derivatives inhibited both the aerobic growth and survival of non-replicating, persistent M. tuberculosis. Metabolic labelling studies and quantification of cellular menaquinone levels suggested that menaquinone synthesis, and consequently electron transport, is the target of the aminoalkoxydiphenylmethane derivatives. This hypothesis is strongly supported by the observations that treatment with these compounds inhibits oxygen consumption and that supplementation of growth medium with exogenous menaquinone rescued both growth and oxygen consumption of treated bacilli. In vitro assays indicate that the aminoalkoxydiphenylmethane derivatives specifically inhibit MenA, an enzyme involved in the synthesis of menaquinone. Thus, the results provide insight into the physiology of mycobacterial persistence and a basis for the development of novel drugs that enhance eradication of persistent bacilli and latent tuberculosis.
Future trends in synthetic biology in Asia (2021)

Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest developments in the key enabling technologies of synthetic biology and its application in bio-manufacturing, medicine, food and agriculture in Asia. Asia-centric strengths in synthetic biology to grow the bio-based economy, such as advances in genome editing and the presence of biofoundries combined with the availability of natural resources and vast markets, are also highlighted. The potential barriers to the sustainable development of the field, including inadequate infrastructure and policies, with suggestions to overcome these by building public-private partnerships, more effective multi-lateral collaborations and well-developed governance framework, are presented. Finally, the roles of technology, education and regulation in mitigating potential biosecurity risks are examined. Through these discussions, stakeholders from different groups, including academia, industry and government, are expectantly better positioned to contribute towards the establishment of innovation and bio-economy hubs in Asia.
Doping of Direct Gap Ge1 -y Sn y Alloys to Attain Electroluminescence and Enhanced Photoluminescence (2015)

Low temperature (T &lt; 300°C) in-situ doping protocols were developed for Ge 1- y Sn y alloys with compositions above the indirect-to-direct gap crossover point, which were deposited using CVD. Trisilylphosphine (P(SiH 3 ) 3 ) was used as the n -type dopant source while diborane (B 2 H 6 ) was used for n -type doping. This enabled the fabrication of pin diode structures with compositions up to y = 0.137. These photodiodes exhibit electroluminescence at wavelengths up to 2700 nm. Furthermore, it was demonstrated that n -type doping enhances the photoluminescence obtained from these materials.
Removing Shadows using Flash/Noflash Image Edges (2006)

Flash/noflash pairs have been used for noise-reduction in ambient-light images. But not explicitly studied is the problem of shadows in the ambient images. While shadows are lessened in a flash image, other problems arise, and other shadows are produced. It is known that we can in fact produce a flash-only (no ambient) image by subtracting the two images, but the result is not as pleasant as the ambient image, because of several artifacts due to the flash. Here, we use the pure-flash image to detect the ambient shadows. We argue that first going to a "spectrally sharpened" color space, and then focusing on the difference in a log domain of the flash image minus the ambient image, gives a very simple feature space consisting of two components-one in an illuminant-change 3-vector direction, and one along the gray axis. This space provides excellent separation of the shadow and nonshadow areas. Inserting edges from the flash image within the ambient-shadow region into the ambient image edge map and inverting Poisson's equation fills in the shadow. In this way, we arrive at an image with the advantages of the ambient-only image-warmth, no flash effects such as disturbing illumination dropoff with distance, pixel saturation etc.-but no shadows
ChemInform Abstract: Neutral Sulfur Nucleophiles: Synthesis of Thioethers and Thioesters by Substitution Reactions of N‐Heterocyclic Carbene Boryl Sulfides and Thioamides. (2014)

Abstract Boryl sulfide (I) and N‐borylthioamide (IV) are employed as neutral sources of sulfur nucleophiles in substitution reactions with alkyl‐ and acyl halogenides.
Isolation of the antigen-active components from leptospiral serovar-specific lipopolysaccharide antigen by mild acid hydrolysis. (1982)

The serovar-specific main antigen (TM antigen) from Leptospira interrogans serovar kremastos strain Kyoto was mildly hydrolyzed With 2 N formic acid or 0.5 N sulfuric acid. Both treatments yielded an immunologically actvie component which was able to pass through a Diaflo membrane filter. The compound obtained by formic acid hydrolysis was shown to be more homogeneous by molecular sieve gel chromatography than that obtained by sulfuric acid hydrolysis. The molecular weight of the former compound was estimated to be approximately 3, 000 daltons. The compound consisted mainly of carbohydrates, and it lost almost all of its fatty acids and proteins. The substance lost its immunoprecipitable activity but showed serovar-specific inhibitory potency in a radio-immunoassay system.
High‐Speed Ionic Synaptic Memory Based on 2D Titanium Carbide MXene (2021)

Abstract Synaptic devices with linear high‐speed switching can accelerate learning in artificial neural networks (ANNs) embodied in hardware. Conventional resistive memories however suffer from high write noise and asymmetric conductance tuning, preventing parallel programming of ANN arrays. Electrochemical random‐access memories (ECRAMs), where resistive switching occurs by ion insertion into a redox‐active channel, aim to address these challenges due to their linear switching and low noise. ECRAMs using 2D materials and metal oxides however suffer from slow ion kinetics, whereas organic ECRAMs enable high‐speed operation but face challenges toward on‐chip integration due to poor temperature stability of polymers. Here, ECRAMs using 2D titanium carbide (Ti 3 C 2 T x ) MXene that combine the high speed of organics and the integration compatibility of inorganic materials in a single high‐performance device are demonstrated. These ECRAMs combine the speed, linearity, write noise, switching energy, and endurance metrics essential for parallel acceleration of ANNs, and importantly, they are stable after heat treatment needed for back‐end‐of‐line integration with Si electronics. The high speed and performance of these ECRAMs introduces MXenes, a large family of 2D carbides and nitrides with more than 30 stoichiometric compositions synthesized to date, as promising candidates for devices operating at the nexus of electrochemistry and electronics.
Novel technologies in coater/developer to enhance the CD stability and to improve the defectivity toward N7 and smaller nodes (2019)

EUV lithography has been brought into mass production. To enhance the yield, improvements in critical dimension (CD) stability, and defectivity still remain of utmost importance. In order to enhance the defectivity performance on contact hole pattern, continuous work has been executed.<sup>1</sup> As the result of process optimizations presented at SPIE 2018 for 24 nm contact hole half pitch pattern, single- and multi-closed hole modes as caused by particles included in coating materials, called “in-film particles”, or stochastic failures are the major of defects modes. For defectivity improvement work done this year, optimization of material dispense has been carried out in an attempt to improve the defectivity of single- and multi-closed holes as caused by in-film particles. As the result, totally 19 % of defectivity improvement was obtained as compared with conventional dispense conditions. On the other hand, CD variability is comprised of several components such as wafer to wafer, field to field, within field, and local CD. In addition, not only coater/developer but also scanner, mask, and materials contribute to the variations. In this paper, CD uniformity (CDU) optimization on also contact hole 24 nm half pitch pattern has been executed to improve each component from the standpoint of coater/developer. As a result of the optimization of development process, 13.9 and 6.4 % of field to field and within field CDU improvement have been achieved, respectively.
New Approaches for the Use of Non-conventional Cell Disruption Technologies to Extract Potential Food Additives and Nutraceuticals from Microalgae (2014)

In recent decades, microalgae species have focused the attention of several research groups and food industry as they are a great source of nutritionally valuable compounds. The use of environmentally friendly technologies has led to researchers and food industry to develop new alternative processes that can extract nutritionally valuable compounds from different sources, including microalgae. This note describes the potential use of some non-conventional methods including sub- and supercritical fluid extraction, pulsed electric fields, high-voltage electric discharges, high-pressure homogenization, ultrasound- and microwave-assisted extraction, which involve cell disruption to recover nutritionally valuable compounds from microalgae and can help to comply with criteria of green chemistry concepts and sustainability.
Investigation of Multi-Objective Optimization criteria for RNA design (2016)

RNA design is the inverse of RNA folding and it appears to be NP-hard. In RNA design, a secondary structure is given and the goal is to find a nucleotide sequence that will fold into this structure. To find such sequence(s) involves exploring the exponentially large sequence space. In literature, heuristic algorithms are the standard technique for tackling the RNA design. Heuristic algorithms enable effective and efficient exploration of the high-dimensional sequence-structure space when searching for candidates that fold into a given target structure. The main goal of this paper is to investigate the use of multi-objective criteria in SIMARD and Quality Pre-selection Strategy (QPS). The objectives that we optimize are Hamming distance (between designed structure and target structure) and thermodynamic free energy. We examine the different combinations of optimization criteria, and attempt to draw conclusions about the relationships between them. We find that energy is a poor primary objective but makes an excellent secondary objective. We also find that using multi-objective pre-selection produces viable solutions in far fewer steps than was previously possible with SIMARD.
Behind The Game: Implicit Spatio-Temporal Intervention in Inter-personal Remote Physical Interactions on Playing Air Hockey (2021)

When playing inter-personal sports games remotely, the time lag between user actions and feedback decreases the user’s performance and sense of agency. While computational assistance can improve performance, naive intervention independent of the context also compromises the user’s sense of agency. We propose a context-aware assistance method that retrieves both user performance and sense of agency, and we demonstrate the method using air hockey (a two-dimensional physical game) as a testbed. Our system includes a 2D plotter-like machine that controls the striker on half of the table surface, and a web application interface that enables manipulation of the striker from a remote location. Using our system, a remote player can play against a physical opponent from anywhere through a web browser. We designed the striker control assistance based on the context by computationally predicting the puck’s trajectory using a real-time captured video image. With this assistance, the remote player exhibits an improved performance without compromising their sense of agency, and both players can experience the excitement of the game.
Strain-Induced Transformation of Bulk Alloys to Zinc Nanowires (2021)

One-dimensional metal nanowires (NWs) with high aspect ratios are highly desirable for a wide range of critical applications due to their unique electrical and mechanical characteristics. Unfortunately, such nanomaterials are challenging and expensive to synthesize, and their production is difficult to scale up. Here, we report a rather straightforward strategy to directly convert binary zinc (Zn) alloys into Zn NWs under ambient temperature and pressure conditions without using any catalyst, template, or costly/toxic chemical. The formation of NWs follows the mechanism based on minimization of strain energy at the boundary of a chemical reaction front. We show that micrometer-sized Zn–Li grains gradually evolve and transform into hybrid Zn and zinc-alkoxide NWs during a dealloying reaction. Such NW mixtures can be eventually converted into pure Zn metal NWs after thermal reduction in a H2–Ar atmosphere. We investigate the effect of Zn–Li alloy composition, dealloying, and annealing temperature on the diameter and length of the formed Zn NWs. The approach reported in this study is expected to open new avenues for multiple cost-effective synthesis routes of metal NWs with tunable composition and morphology for their widespread applications.
Abstract 730: Genomic characterization of hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a rare and aggressive kidney cancer (2019)

Abstract Background Hereditary Leiomyomatosis and Renal Cell Carcinoma (HLRCC) is a rare autosomal-dominant syndromic disorder associated with germline FH mutations. Affected individuals have a predisposition to cutaneous and uterine leiomyoma’s, and are at increased risk of developing a renal cell carcinoma (HLRCC- associated RCC) with aggressive clinical outcome. However, aside from FH bi-allelic loss, additional genomic features of HLRCC are currently poorly understood. Method Five cases of HLRCC-associated RCC were characterized using integrated next generation sequencing (NGS) technology. This included an index case where multiple tumor sites (kidney, lung, liver, lymph node, skin, and uterine) from a single patient were characterized. For integrative analysis, in-house data were combined with five RCC cases with FH bi-allelic loss from The Cancer Genome Atlas Study. Single cell sequencing was carried out on normal human kidney to study the cell of origin for HLRCC- associated RCC. Results: Integrative NGS profiling and analysis of HLRCC-associated RCC tumors (n=10) revealed several important observations such as 1) a high frequency loss of whole chromosomes, which is reminiscent of tumors arising from the distal nephron, 2) low mutational burden similar to that observed in other kidney tumors and, 3) a HLRCC specific gene expression signature and discovery of a novel therapeutic candidate (HLRCC-TC1). Importantly, among renal tumors, HLRCC-TC1 was specifically expressed in HLRCC and other RCCs with poor clinical outcome. Application of siRNAs and neutralizing antibodies to HLRCC-TC1 reduced cell proliferation of the HLRCC cell line UOK262, but did not for that of control cell lines. Conclusion: The observed FH bi-allelic mutation along with recurrent chromosome-wide losses and integrative analysis with human kidney single cell sequencing data support a distal nephron origin for HLRCC- associated RCC. In addition, our study provides evidence for nominating HLRCC-TC1 as a novel cancer-specific therapeutic target. Further studies are needed to conduct an in-depth characterization of HLRCC-TC1. Citation Format: Pankaj Vats, Yuping Zhang, Sarvana Mohan Dhanashekaran, Narayanan Sathiya Pandi, Xuhong Cao, Fengyun Su, Sudhanshu Shukla, Rui Wang, Marcin Cieslik, Jincheng Pan, Christopher J. Ricketts, Prem Kumar Kumpati, Ajjai Alva, Marston W. Linehan, Rohit Mehra, Arul M. Chinnaiyan. Genomic characterization of hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a rare and aggressive kidney cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 730.
A Hepatitis C Virus Xenograft Mouse Efficacy Model (2009)

The lack of a robust small-animal model for hepatitis C virus (HCV) has hindered the discovery and development of novel drug treatments for HCV infections. We developed a reproducible and easily accessible xenograft mouse efficacy model in which HCV RNA replication is accurately monitored in vivo by real-time, noninvasive, whole-body imaging of gamma-irradiated SCID mice implanted with a mouse-adapted luciferase replicon-containing Huh-7 cell line. The model has been validated by demonstrating that both a small molecule NS3/4A protease inhibitor (BILN 2061) and human interferon- alpha (IFN-alpha) decreased HCV RNA replication and that treatment withdrawal resulted in a rebound in replication, which paralleled clinical outcomes in humans. The efficacy of protease inhibitor plus IFN-alpha demonstrated the application of the model for testing compounds in combination therapies. This robust mouse efficacy model provides a powerful tool for rapid evaluation of potential anti-HCV compounds in vivo.
Supplementary Figure 1 from α<sub>v</sub>β<sub>3</sub>/α<sub>v</sub>β<sub>5</sub> Integrins-FAK-RhoB: A Novel Pathway for Hypoxia Regulation in Glioblastoma (2023)

Supplementary Figure 1 from α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;3&lt;/sub&gt;/α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;5&lt;/sub&gt; Integrins-FAK-RhoB: A Novel Pathway for Hypoxia Regulation in Glioblastoma
Indirect Solid Freeform Fabrication of an Initiator‐Free Photocrosslinkable Hydrogel Precursor for the Creation of Porous Scaffolds (2016)

In the present work, a photopolymerized urethane-based poly(ethylene glycol) hydrogel is applied as a porous scaffold material using indirect solid freeform fabrication (SFF). This approach combines the benefits of SFF with a large freedom in material selection and applicable concentration ranges. A sacrificial 3D poly(ε-caprolactone) structure is generated using fused deposition modeling and used as template to produce hydrogel scaffolds. By changing the template plotting parameters, the scaffold channel sizes vary from 280 to 360 μm, and the strut diameters from 340 to 400 μm. This enables the production of scaffolds with tunable mechanical properties, characterized by an average hardness ranging from 9 to 43 N and from 1 to 6 N for dry and hydrated scaffolds, respectively. Experiments using mouse calvaria preosteoblasts indicate that a gelatin methacrylamide coating of the scaffolds results in an increased cell adhesion and proliferation with improved cell morphology.
ChemInform Abstract: Remarkably Simple One‐Step Preparation of Hexakis(trimethylsilyl)‐3,3′‐ bicyclopropenyl, a Stable Valence Isomer of Hexakis(trimethylsilyl) benzene. (1994)

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.
DDDR-04. CA-4948 IN COMBINATION WITH BRAF/MEK INHIBITION IN MELANOMA BRAIN METASTASES (2022)

Abstract Melanoma brain metastases (MBM) remain a primary driver of melanoma morbidity and mortality. It is estimated that as many as 60% of all metastatic melanoma patients will develop MBM during the course of their disease. Once found, dual checkpoint inhibitor therapy or BRAF/MEK inhibition in BRAF mutated cancers, are the best options currently available. Even with these treatments, the response to therapy is less than what is seen with disease outside the. In BRAF mutated cancers, which constitute 50% of all patients, initial response to targeted therapy is rapid but resistance to therapy develops 3 months sooner than resistance outside of the brain. Novel strategies to prevent onset of resistance or to work in concert with BRAF/MEK inhibition are needed for this treatment population. The exact mechanism of resistance to targeted therapy in MBM is not known, but mutations in EphA2, PI3K, pAKT, and re-activation of MAPK signaling through secondary mechanisms have all been identified as drivers of resistance. One pathway of MAPK reactivation is through activation of phospho-ERK (eIF2alpha kinase) which also activates the JNK pathway. Our group has previously shown that MBM express high levels of the inflammatory transcription factor IRAK-4, the terminal chaperone of the inflammatory myddosome downstream of TLR and IL1R signally. This increase in IRAK-4 results in constitutive activation of NF-KB, JNK, and MAPK. We have additionally shown the novel oral IRAK-4 inhibitor CA-4948 can reach therapeutically relevant concentrations past the blood brain barrier in both tumor-bearing and naïve mice. We additionally show CA-4948 inhibits MAPK expression in melanoma and suppresses the escape pathways pERK and JNK signaling which can contribute to the prevention of resistance to targeted therapy. This study supports further investigation into the combination potential of CA-4948 with BRAF/MEK inhibitors as triplet therapy to delay intracranial resistance.