gebhart/patrepeval huggingface dataset:
Role of calcium oxalate monohydrate crystal interactions with renal epithelial cells in the pathogenesis of nephrolithiasis: a review. (1996)

Renal tubular fluid in the distal nephron is supersaturated with calcium and oxalate ions that nucleate to form crystals of calcium oxalate monohydrate (COM), the most common crystal in renal stones. How these nascent crystals are retained in the nephron to form calculi in certain individuals is not known. Recent studies from this laboratory have demonstrated that COM crystals can bind within seconds to the apical surface of renal epithelial cells, suggesting one mechanism whereby crystals could be retained in the tubule. Adherence of crystals to cells along the nephron may be opposed by specific urinary anions such as glycosaminoglycans, uropontin, nephrocalcin, and citrate. In culture, adherent crystals are quickly internalized by renal cells, and reorganization of the cytoskeleton, alterations in gene expression, and initiation of proliferation can ensue. Each of these cellular events appears to be regulated by extracellular factors. Identification of molecules in tubular fluid and on the cell surface that determine whether a crystal-cell interaction results in retention of the crystal or its passage out of the nephron appears critical for understanding the pathogenesis of nephrolithiasis.
6‐2: Novel Liquid Crystal Display Mode “UV<sup>2</sup>A II” with Photo Alignment Technology for a Large‐Screen 8K Display (2019)

We have developed a new liquid crystal display mode UV 2 A II which is suitable for a large screen 8K display and commercialized as the 80” 8K TV. UV 2 A II has brought large superiority that are 1.3 times higher transmittance, 35% faster response, and wider viewing angle property to compare with UV 2 A.
Development of a novel human adrenomedullin derivative: human serum albumin-conjugated adrenomedullin (2021)

Adrenomedullin is a biologically active peptide with multiple functions. Here, we have developed a novel human serum albumin-adrenomedullin (HSA-AM) conjugate, which was synthesized by the covalent attachment of a maleimide derivative of adrenomedullin to the 34th cysteine residue of HSA via a linker. Denaturing gel electrophoresis and western blotting for HSA-AM yielded a single band with adrenomedullin immunoreactivity at the position corresponding to a molecular weight (MW) of 73 kDa. Following gel-filtration chromatography, the purified HSA-AM showed a single main peak corresponding with an MW of 73 kDa, indicating that HSA-AM is a monomer. Both adrenomedullin and HSA-AM stimulated the intracellular accumulation of cyclic AMP (cAMP) in HEK-293 cells stably expressing the adrenomedullin 1 receptor. The pEC50 values for adrenomedullin and HSA-AM were 8.660 and 7.208 (equivalent to 2.19 and 61.9 nM as EC50), respectively. The bioavailability of HSA-AM compared with that of adrenomedullin was much improved after subcutaneous administration in the rat, which was probably due to the superior resistance of HSA-AM towards endogenous proteases and its reduced clearance from the blood. HSA-AM may be a promising drug candidate for clinical application.
Discovery of a Novel, Orally Active, Small Molecule Gonadotropin-Releasing Hormone (GnRH) Receptor Antagonist (2006)

Gonadotropin releasing hormone (GnRH) plays an important role in the biology of reproduction. The use of GnRH receptor antagonists has been reported in the literature for the treatment of breast, ovarian, and prostate cancers. In this article, we report the synthesis, in vitro characterization, pharmacokinetics, and pharmacodynamics of an orally bioavailable, potent, small molecule GnRH receptor antagonist N-{4,6-dimethoxy-2-[(3-morpholin-4-ylpropyl)amino]pyrimidin-5-yl}-5-[3,3,6-trimthyl-2,3-dihydro-1H-inden-5-yl)oxy]-2-furamide (compound 1).
Chemistry and Applications of Porous Metal–Organic Frameworks (2008)

Abstract The sections in this article are Introduction Terminology and Structure Synthesis Characterization Emerging Applications Adsorption Properties Diffusional Properties Gas Purification Gas Separation Gas Storage Catalysis Conclusions
Abstract 3172: Methylation portraits discriminate between hepatocellular carcinoma cases and controls (2011)

Abstract Background: Most genome-wide methylation studies have focused on technology to profile and identify therapeutic biomarkers in HCC. However, attempts to integrate these technologies to clinical and population based studies are still lacking. Objective: Our aim was to identify existing methylation profiling technologies that can be used in translational epigenomic efforts. Methods: We examined Quantitative Methylation specific PCR, oligonucleotide methylation tiling arrays (MeDIP-chip), and Methylation BeadChip arrays and their ability to distinguish between HHC cases and controls, a key goal in Phase I biomarker development trials. Scatterplots, histograms and heat maps of genome-wide DNA methylation array data were used to provide a snapshot of the differences in methylation patterns between tumor and normal samples. Results: The representative tumor sample had a lower methylation score median and less significant genome-wide methylated probes (1,503) than either normal liver tissue samples (2,585 and 2,2887 respectively). RASSF1A and B4GALT1 had a sensitivity of 52%, a specificity of 100% and an AUC of 0.73 (RASSF1A) and 0.75 (B4GALT1). SSBP2 had a sensitivity of 38%, a specificity of 100% and an AUC of 0.58. A panel combining these genes with HCC risk factors had a sensitivity of 87%, a specificity of 100% and an AUC of 0.91. Conclusions: We have shown that genome-wide and gene-specific methylation platforms, which interrogate gene promoter regions, can be used to examine novel biomarkers and differentiate HCC from normal liver tissue. Additional studies will confirm the value of using methylation-profiling technologies to evaluate these new markers as we move forward. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3172. doi:10.1158/1538-7445.AM2011-3172
Broadband optical frequency comb generation with a phase-modulated parametric oscillator (1999)

We introduce a novel broadband optical frequency comb generator consisting of a parametric oscillator with an intracavity electro-optic phase modulator. The parametric oscillator is pumped by 532-nm light and produces near-degenerate signal and idler fields. The modulator generates a comb structure about both the signal and the idler. Coupling between the two families of modes results in a dispersion-limited comb that spans 20 nm (5.3 THz). A signal-to-noise ratio of >30 dB in a 300-kHz bandwidth is observed in the beat frequency between individual comb elements and a reference laser.
Distributed Storage Allocation for High Reliability (2010)

We consider the problem of optimally allocating a given total storage budget in a distributed storage system. A source has a data object which it can code and store over a set of storage nodes; it is allowed to store any amount of data in each storage node, subject to a given total storage budget constraint. A data collector subsequently attempts to recover the original data object by accessing a random fixed-size subset of these storage nodes. Successful recovery of the data object occurs when the total amount of coded data in this subset of storage nodes is at least the size of the original data object. The goal is to determine the amount of data to store in each storage node so that the probability of successful recovery is maximized. We solve this problem in the high recovery probability regime. Our results can be applied to a variety of distributed storage systems, including delay tolerant networks (DTNs), content delivery networks (CDNs), and sensor networks.
Current status on plant molecular farming via chloroplast transformation (2010)

고등식물의 엽록체 형질전환은 핵 형질전환에서 기대 할 수 없는 여러 가지 이점을 가진다. 외래 단백질의 발현율을 획기적으로 높일 수 있고, 여러 유전자를 동시에 발현시킬 수 있으며, 상동재조합에 의한 부위-특이적 유전자 삽입으로 인해 유전자 침묵 및 위치효과가 없다. 더욱이, 대부분 작물은 화분을 통한 도입된 유전자의 전이가 불가능한 모계 유전을 하기 때문에 엽록체 형질전환은 환경 친화적이다. 엽록체 형질전환 시스템은 핵 형질 전환과 달리 작물에서의 성공에 제한적이었으나 지난 10년 동안 이런 한계가 극복되어 콩, 당근, 상추 및 유채 등의 작물에서도 성공하게 되었다. 그러므로 이제 작물의 엽록체 형질전환은 농업적 형질의 개선뿐 만 아니라, 고부가가치 백신과 의료용 단백질 생산을 통한 의약품 산업의 성장에 활용될 수 있을 것이다. Chloroplast transformation in higher plants offers many attractive advantages over nuclear transformation, including a high-level accumulation of foreign proteins, multi-gene expression in single transformation event via transgene stacking in operons and no position effect due to site-specific integration of transgenes by homologous recombination. Most importantly, chloroplast transgenic plants are eco-friendly because their transgenes are maternally inheritance in most crop plants. However, chloroplast transformation system has limited success in crops alike nuclear transformation. In the past two decades, great progress has been made to overcome the limitations of chloroplast transformation, thus expending chloroplast bioreactor to several important crops including soybean, carrot, lettuce, and oilseed. Therefore, it has become possible that chloroplast transformation of crops can be used not only for the improvement of agronomic traits, but also for the production of vaccines and high valuable therapeutic proteins in pharmaceutical industry.
Sound separation by humming. (2010)

We present a novel interface for selecting and isolating sounds from complex audio mixtures. Traditional interfaces in audio editors provide graphical representations of sounds through which a user might be able to visually identify elements of sounds in a mixture; they do not, however, facilitate object-specific editing (e.g., selecting only the voice of a singer in a song). The proposed interface uses audio guidance from a user in order to specify a target sound within a mixture. The user is asked to vocalize the desired target sound, and an automated process identifies and isolates the elements of the mixture that best relate to the user’s input. Such a tool makes the extraction of complex sources an easier process than using graphical tools or statistical source separation models.
Development of sunflower germplasm with high delta-tocopherol content (2004)

Tocopherols are the main compounds with antioxidant activity in oilseeds Sunflower seeds contain predominantly alpha-tocopherol, which accounts for more than 90% of the total tocopherols in the seeds. This tocopherol derivative possesses a maximum vitamin E or in vivo antioxidant activity, but it exerts a minimum in vitro protective action in oils and food containing them. Other tocopherol derivatives such as beta-, gamma-, and delta-tocopherol are more powerful antioxidants than alpha-tocopherol. Accordingly, a partial replacement of alpha-tocopherol in sunflower seeds is an important breeding objective. So far, variants with high gamma tocopherol content (>85%), medium beta-tocopherol content (30% to 50%), and medium delta-tocopherol content (<25%) have been developed. The objective of the present research was to develop sunflower germplasm with novel tocopherol profiles. Seed of four Peredovik accessions of different origins were used for chemical mutagenesis with ethyl methane sulfonate (EMS). Single-seed screening in the M2 generation resulted in the identification of an M2 seed with 19% gamma-tocopherol. M3 seeds exhibited wide segregation for gamma-tocopherol content, from zero to about 85%. Such a wide segregation has not been observed in previously developed high gamma-tocopherol germplasms which segregate for low and high but not for intermediate levels of gamma-tocopherol. Selection for high gamma-tocopherol content within this mutant produced an M4:5 line with stable high concentration of gamma-tocopherol, above 90% of the total tocopherols. The line was designated IAST-1. Crosses between IAST-1 and the line T589, with medium beta-tocopherol content, produced segregants with increased levels of up to 68% delta-tocopherol.
A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter (2012)

High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydrated via vapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryo-cooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.
Complex structure of a maize Myb gene promoter: functional analysis in transgenic plants (2000)

The maize P gene encodes a Myb-like transcription factor that regulates synthesis of red flavonoid pigments in floral organs. To study the transcriptional regulation of the P gene, candidate regulatory sequences of the P1-rr gene promoter were identified by Ac insertional mutagenesis and subjected to functional testing in transgenic maize plants. The results indicate that a 561 bp fragment (Pb) encompassing the transcription start site (-235 to +326) supports weak expression of a GUS reporter gene in floral organs, including husk, silk, kernel pericarp, cob and male inflorescence. Two other fragments, located approximately 1 and 5 kb 5' of the transcription start site, increased the levels of GUS activity in floral tissues and thus appear to contain enhancer elements. All of the tested constructs gave similar patterns of GUS expression, suggesting that the 561 bp Pb fragment that is common among the transgene constructs contains regulatory elements that promote activation in floral organs. The basal promoter and proximal enhancer fragments contain putative binding sites for bZip regulatory factors, and a complex arrangement of palindromes including a large inverted repeat of two tRNA-like genes. Possibly, interconversions between linear and cruciform conformations of the palindromes may affect protein/DNA interactions and thereby modulate P1-rr expression.
Mechanistic Study of Charge Separation in a Nonfullerene Organic Donor–Acceptor Blend Using Multispectral Multidimensional Spectroscopy (2021)

Organic photovoltaics (OPVs) based on nonfullerene acceptors are now approaching commercially viable efficiencies. One key to their success is efficient charge separation with low potential loss at the donor-acceptor heterojunction. Due to the lack of spectroscopic probes, open questions remain about the mechanisms of charge separation. Here, we study charge separation of a model system composed of the donor, poly[(2,6-(4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)-benzo[1,2-b:4,5-b']dithiophene))-<i>alt</i>-(5,5-(1',3'-di-2-thienyl-5',7'-bis(2-ethylhexyl)benzo[1',2'-c:4',5'-c']dithiophene-4,8-dione) (PBDB-T), and the nonfullerene acceptor, 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC), using multidimensional spectroscopy spanning the visible to the mid-infrared. We find that bound polaron pairs (BPPs) generated within ITIC domains play a dominant role in efficient hole transfer, transitioning to delocalized polarons within 100 fs. The weak electron-hole binding within the BPPs and the resulting polaron delocalization are key factors for efficient charge separation at nearly zero driving force. Our work provides useful insight into how to further improve the power conversion efficiency in OPVs.
Abstract 18124: An Irx4+ Ventricular Progenitor Isolated by Spherical Nucleic Acid Nanoparticles (2015)

While human pluripotent stem cell-derived cardiomyocytes have shown promise in engrafting and maturing in animals following myocardial infarction, transplanted cells largely exist as histologically self-contained blocks of cells with moderate or undetectable functional benefit. We therefore sought to develop methods to isolate a proliferative progenitor capable of differentiating both to functional ventricular cardiomyocytes and supportive cardiac mesenchymal cells, as these cells may hold promise for regenerative medicine. To isolate a ventricular progenitor, fluorescent spherical DNA nanoparticles (nanoflares) were synthesized to target RNA of the ventricular transcription factor Irx4 at an intermediate stage in cardiac differentiation of human pluripotent stem cells using small molecule, defined conditions without genetic modification or transfection. The synthesized nanoflare was nontoxic by Annexin V/7AAD flow cytometry and did not affect differentiation or expression of cardiac genes in RT-qPCR, including Irx4. Upon differentiation, nanoflare-FACS-separated Irx4+ cells were found to give rise to 50% cTnT+ cardiomyocytes and 46% Thy1+ mesenchymal cells. In sorted cells, we used sensitive droplet digital RT-PCR to detect early upregulation of lineage-specific genes. Relative to Irx4 -/Low cells, Irx4+ cells had significant upregulation of ventricular-specific mlc2v but not atrial genes (Hey1, CoupTF2, SLN). In characterizing their mesenchymal potency, Irx4+ cells had significant enrichment in smooth muscle actin and N-cadherin. Intriguingly, during monolayer differentiation of Irx4+ cells, a marked aggregation occurs in which Thy1+ mesenchymal cells surround and embed large assemblies of beating cTnT+ cardiomyocytes. Consistent with a matrix remodeling phenotype, both protease inbitior expression (TIMP1) and protease activity by zymography were increased in sorted Irx4+ compared to negative cells. Conclusions: We have here isolated early ventricular progenitor cells using novel, non-invasive methods. Their remodeling activity may allow more seamless myocardial integration than differentiated cardiomyocytes and provide insights into the role of cell-cell interactions during human cardiac development.
Alkaline cellulases for laundry detergents: Production by alkalophilic strains of Bacillus and some properties of the crude enzymes. (1990)

Three strains of alkalophilic Bacillus, KSM-19, KSM-64 and KSM-520, were isolated which produced alkaline cellulases suitable as additives for improving the efficiency of detergent products. Their activities were not inhibited at all by metal ions or various components of laundry products, such as surfactants, chelating agents and proteinases. The enzyme preparations showed strong activities toward carboxv methyl cellulose, the optimum pHs being 8.5-9.5 and the optimum temperatures about 50°C. Maximum growth of the isolates was observed at an initial pH of 8.5-9.5; slight growth occurred at neutral pH. Production of the alkaline cellulases required the presence of carboxymethyl cellulose, and it was controlled by a mechanism involving catabolite repression and induction. Two strains, KSM19 and KSM-64, produced alkaline lichenan-hydrolyzing enzymes.
Fundamentals of Controlled/Living Radical Polymerization (2012)

Abstract Principles and special features of controlled/living radical polymerization (CRP) processes such as nitroxide‐mediated polymerization (NMP), organometallic radical polymerization (OMRP), and atom transfer radical polymerization (ATRP) and degenerative transfer (DT) processes such as reversible addition‐fragmentation transfer (RAFT) systems are discussed. CRP is critically compared with conventional radical polymerization. Proportion of terminated chains in CRP as a function of polymerization rate, conversion, targeted degree of polymerization, and monomer concentration is described and compared for ATRP and DT processes. Concept of persistent radical effect is introduced and its application to determine equilibrium constants in NMP and ATRP is presented. Current challenges and future perspectives are briefly discussed.
Study of a Potent Small‐Molecule Benzosuberene Anti‐Cancer Agent (2012)

The discovery of a benzosuberene‐based, small‐molecule anti‐cancer agent (KGP18) with remarkable cytotoxicity against selected human cancer cell lines (BMC 2008 16, 8161–8171) provided the inspiration for a collaborative research program to investigate the mechanism of action of this compound and related benzosuberene analogues. The structure of KGP18 and its ability to inhibit tubulin polymerization into microtubules in vitro suggests that it may act as a vascular disrupting agent (VDA). An adequate blood supply is required for tumor growth and metastasis. VDAs represent a promising new class of anti‐cancer agents that function by selectively disrupting the tumor vasculature, thus starving the tumor of nutrients and oxygen via an adequate blood supply. Tubulin‐binding VDAs inhibit microtubule assembly in the activated endothelial cells, lining the tumor vasculature, leading to cytoskeletal reorganization, activation of RhoA and RhoA kinase, increased vascular permeability, cell rounding and detachment, and vessel occlusion. The lead benzosuberene analogue (KGP18) binds to tubulin at the colchicine binding site as determined by a competitive radiometric assay. Flow cytometry indicates that MDA‐MB‐231 cells treated with KGP18 are arrested at the G2/M phase of the cell cycle. (Supported by Oxigene Inc., the NIH, and CPRIT).
Catheter Ablation of Supraventricular Arrhythmias: (2004)

Peer Reviewed
Deep Stereo: Learning to Predict New Views from the World's Imagery (2016)

Deep networks have recently enjoyed enormous success when applied to recognition and classification problems in computer vision [22, 33], but their use in graphics problems has been limited ([23, 7] are notable recent exceptions). In this work, we present a novel deep architecture that performs new view synthesis directly from pixels, trained from a large number of posed image sets. In contrast to traditional approaches, which consist of multiple complex stages of processing, each of which requires careful tuning and can fail in unexpected ways, our system is trained end-to-end. The pixels from neighboring views of a scene are presented to the network, which then directly produces the pixels of the unseen view. The benefits of our approach include generality (we only require posed image sets and can easily apply our method to different domains), and high quality results on traditionally difficult scenes. We believe this is due to the end-to-end nature of our system, which is able to plausibly generate pixels according to color, depth, and texture priors learnt automatically from the training data. We show view interpolation results on imagery from the KITTI dataset [12], from data from [1] as well as on Google Street View images. To our knowledge, our work is the first to apply deep learning to the problem of new view synthesis from sets of real-world, natural imagery.