gebhart/patrepeval huggingface dataset:
Structure Elucidation of Roselipins, Inhibitors of Diacylglycerol Acyltransferase Produced by Gliocladium roseum KF-1040. (1999)

The structures of roselipins 1A, 1B, 2A and 2B were elucidated by spectroscopic studies including 1H-1H COSY, 13C-1H COSY, 13C-1H HMQC and 13C-1H HMBC NMR experiments, and degradation experiments. They have the common skeleton of 2,4,6,8,10,12,14,16,18-nonamethyl-5,9,13-trihydroxy-2E,6E, 10E-icosenoic acid modified with a D-mannose and a D-arabinitol. Roselipin A and B groups were stereoisomers at the arabinitol moiety, which esterified the fatty acid from the different terminal hydroxy residue. Roselipin 2 group was 6"-O-acetyl roselipin 1 group.
Characterization of Organosilicon‐Infiltrated Porous Reaction‐Sintered Si <sub>3</sub> N <sub>4</sub> (1978)

Polymeric organosilicon compounds such as hexaphenylcyclo‐trisilazane and methylphenyl polysilane were used to infiltrate porous reaction‐sintered silicon nitride. The in situ thermal decomposition of the infiltrated body under controlled atmosphere and temperature resulted in pronounced changes in the microstructure, increased densities, and significantly improved room‐temperature strength. The silicon oxynitride phase present in some as‐received materials is eliminated and the ratio of α ‐ to β ‐phase silicon nitride increases during infiltration processing
Transcription factor E2F binds DNA as a heterodimer. (1993)

E2F is a mammalian transcription factor that appears to play an important role in cell cycle control. DNA affinity column-purified E2F from HeLa cells reproducibly exhibits multiple protein bands when analyzed by SDS/PAGE. After electrophoretic purification, electroelution, and refolding of the individual protein components, the E2F DNA binding activity of the individual proteins was poor. However, upon mixing the individual components together, a dramatic (100- to 1000-fold) increase in specific DNA binding activity was observed. The five protein bands isolated can be separated into two groups based on apparent molecular mass. Optimal reconstitution of activity requires one of the two proteins found in the group of larger molecular mass (approximately 60 kDa) and one of the three proteins in the smaller-sized group (approximately 50 kDa). The reconstituted heterodimer is identical to authentic affinity-purified E2F by three criteria: DNA-binding specificity, DNA pattern, and binding to the retinoblastoma gene product. A recently cloned protein with E2F-like activity, RBP3/E2F-1, is related to the protein components of the group of larger molecular mass, as determined by Western blot analysis and reconstitution experiments. These data suggest that E2F, like many other transcription factors, binds DNA as an oligomeric complex composed of at least two distinct proteins.
Design of Lubricant Infused Surfaces (2017)

Lubricant infused surfaces (LIS) are a recently developed and promising approach to fluid repellency for applications in biology, microfluidics, thermal management, lab-on-a-chip, and beyond. The design of LIS has been explored in past work in terms of surface energies, which need to be determined empirically for each interface in a given system. Here, we developed an approach that predicts a priori whether an arbitrary combination of solid and lubricant will repel a given impinging fluid. This model was validated with experiments performed in our work as well as in literature and was subsequently used to develop a new framework for LIS with distinct design guidelines. Furthermore, insights gained from the model led to the experimental demonstration of LIS using uncoated high-surface-energy solids, thereby eliminating the need for unreliable low-surface-energy coatings and resulting in LIS repelling the lowest surface tension impinging fluid (butane, γ ≈ 13 mN/m) reported to date.
A fast-transient-response hybrid buck converter with automatic and nearly-seamless loop transition for portable applications (2012)

This paper presents a fast-transient-response hybrid buck converter (HBC) which consists of a voltage mode PWM switching converter with Type III compensation and two auxiliary linear regulators for portable applications. With techniques of hysteretic load transient detection and adaptive duty ratio compensation, the proposed HBC achieves automatic and nearly-seamless loop transition during load transient to achieve small voltage dip and short recovery time. The auxiliary linear regulators can be automatically deactivated in the steady state such that the power efficiency of the switching converter is not compromised. Experimental results of a 0.13-μm CMOS prototype with 10 MHz switching frequency show that, compared with the conventional design, the proposed HBC reduces the voltage dip from 145mV to 55mV and the recovery time from 7.0μs to 1.5μs for a 300mA load current step-up within 20ns.
Affordable emerging computer hardware for neuromorphic computing applications (2010)

We are pursuing an investigation of neuromorphic computational models and architectures in order to leverage present understanding of how the estimated 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sup> neurons and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</sup> neuron connections in the mammalian brain are able to do some of the things a human does, and as quickly as it does it, using slow base components, while consuming very little power on affordable synthetic non-biological computing hardware. Understanding and harvesting neurologically based methods is a promising approach with great potential that may help us achieve massively parallel computation far beyond the scope of traditional computing.
Aluminophosphate Molecular Sieves: A New Class of Microporous Crystalline Inorganic Solids (1983)

A novel class of crystalline, microporous aluminophosphate phases has been discovered. It represents the first class of molecular sieves with framework oxide compositions free of silica. The new class of materials encompasses some fourteen reported three-dimensional microporous framework structures, and six two-dimensional layer-type structures. The three-dimensional structures include structural analogues of the zeolites sodalite and erionite-offretite. The novel phases can be synthesized hydrothermally in the presence of organic amines and quaternary ammonium templates. The template is entrapped or clathrated within the crystallizing aluminophosphate network. After thermal decomposition of the template the three-dimensional molecular sieves have the general composition of Al2O3·1.0± 0.2 P2O5. The various structures exhibit intracrystalline adsorption pore volumes from 0.04 to 0.35 cm3/g, and pore sizes from 0.3 to 0.8nm. The aluminophosphate frameworks are hydrophilic.
Frailty status can be accurately assessed using inertial sensors and the TUG test (2013)

results suggest that a simple protocol involving assessment using a well-known mobility test (Timed Up and Go (TUG)) and inertial sensors can be a fast and effective means of automatic, non-expert assessment of frailty.
ChemInform Abstract: Bipyridine‐ and Phenanthroline‐Based Metal—Organic Frameworks for Highly Efficient and Tandem Catalytic Organic Transformations via Directed C—H Activation. (2015)

Abstract A series of robust and porous bipyridyl‐ and phenanthryl‐based metal—organic frameworks (MOFs) of UiO topology is prepared and metalated with [Ir(cod)(OMe)] 2 to provide Ir—MOF complexes which are highly active catalysts for tandem hydrosilylation of aryl ketones and aldehydes followed by dehydrogenative ortho‐silylation as well as C—H boration of arenes.
Abstract 141: Histone Methyltransferase Setdb2 is important for miRNA mediated cardiac reprogramming (2013)

Rationale: Regeneration of damaged cardiac tissue after injury presents a daunting challenge in cardiovascular medicine. Recent developments in reprogramming of somatic cells directly to cells of other lineages have raised the possibility of using this approach for cardiac regenerative therapy. Our group recently demonstrated successful miRNA mediated cardiac reprogramming in vitro and in vivo using a combination of miRNAs 1, 133, 206 and 499. Although, the molecular mechanisms underlying miRNA mediated fibroblast reprogramming to cardiomyocytes are yet unknown, accumulating evidence suggest that reprogramming acts through distinct phases and that histone modifications play an important role in these processes. Objective: Identify key genes involved in initiating miRNA mediated reprogramming via histone modifications. Methods and Results: For this, we analyzed the expression levels of 81 different genes involved in chromatin modification 4 days after miRNA transfection using PCR arrays. This analysis revealed that 6 of the 81 tested genes showed differential gene expression (≤-1.5-fold and p <0.02). JAK inhibitor-1 treatment, known for increasing reprogramming efficiency, further enhanced gene expression changes in 5 of these 6 genes. Setdb2, an H3K9 methyltransferase, was one of the most down-regulated targets 4 days after miRNA transfection (-1.4 fold, p<0.001). This effect was enhanced further when miRNAs were combined with the JAK inhibitor-1 (-2.6 fold, p<0.001). Silencing of Setdb2 using siRNAs further accentuated miRNA cardiac reprogramming as measured by cardiac transcription factor expression at 3 days and 6 days post treatment. Similar trends were observed by FACS analysis detecting increased percentage of αMHC-positive cells in siRNA treated fibroblasts compared to control treated only with the miRNA combination. Interestingly, our data showed that Setdb2 silencing alone was sufficient to initiate cardiac reprogramming, suggesting that Setdb2 might play a crucial role in defining cardiac cell fate. Conclusion: In conclusion our results indicate that Setdb2 down-regulation plays an important role in the direct reprogramming of fibroblasts to cardiomyocyte-like cells.
Secreted frizzled related protein 2 (Sfrp2) is the key Akt-mesenchymal stem cell-released paracrine factor mediating myocardial survival and repair (2007)

Stem cell therapy has emerged as a promising tool for the treatment of a variety of diseases. Previously, we have shown that Akt-modified mesenchymal stem cells mediate tissue repair through paracrine mechanisms. Using a comprehensive functional genomic strategy, we show that secreted frizzled related protein 2 (Sfrp2) is the key stem cell paracrine factor that mediates myocardial survival and repair after ischemic injury. Sfrp2 is known to modulate Wnt signaling, and we demonstrate that cardiomyocytes treated with secreted frizzled related protein increase cellular beta-catenin and up-regulate expression of antiapoptotic genes. These findings reveal the key role played by Sfrp2 in mediating the paracrine effects of Akt-mesenchymal stem cells on tissue repair and identify modulation of Wnt signaling as a therapeutic target for heart disease.
XPlainer: Explaining XPath within Eclipse (2006)

The popularity of XML has motivated the development of novel XML processing tools many of which embed the XPath language for XML querying, transformation, constraint specification, etc. XPath developers (as well as less technical users) have access to commercial tools to help them use the language effectively. Example tools include debuggers that return the result of XPath subexpressions visualized in the context of the input XML document. This paper describes XPlainer-Eclipse, a novel kind of query understanding and debugging tool that provides visual explanations of why XPath expressions return a specific answer. XPlainer-Eclipse combines editors for visualizing both XML documents and XPath expressions as trees together with the explanation of the answers.
Volumetric tomography of fluorescent proteins through small animals <i>in vivo</i> (2005)

Volumetric detection and accurate quantification of fluorescent proteins in entire animals would greatly enhance our ability to monitor biological processes in vivo. Here we present a quantitative tomographic technique for visualization of superficial and deep-seated (>2-3 mm) fluorescent protein activity in vivo. We demonstrate noninvasive imaging of lung tumor progression in a murine model, as well as imaging of gene delivery using a herpes virus vector. This technology can significantly improve imaging capacity over the current state of the art and should find wide in vivo imaging applications in drug discovery, immunology, and cancer research.
The ‘endo-blue method’ for direct cloning of restriction endonuclease genes in<i>E.coli</i> (1994)

A new E. coli strain has been constructed that contains the dinD1::LacZ+ fusion and is deficient in methylation-dependent restriction systems (McrA-, McrBC-, Mrr-). This strain has been used to clone restriction endonuclease genes directly into E. coli. When E. coli cells are not fully protected by the cognate methylase, the restriction enzyme damages the DNA in vivo and induces the SOS response. The SOS-induced cells form blue colonies on indicator plates containing X-gal. Using this method the genes coding for the thermostable restriction enzymes Taql (5'TCGA3') and Tth111l (5'GACNNNGTC3') have been successfully cloned in E. coli. The new strain will be useful to clone other genes involved in DNA metabolism.
An improved region growing algorithm for phase correction in MRI (2015)

The improved region-growing algorithm can be used for reliable and robust phase correction even when regions of high noise, artifacts, or spatially isolated objects are present in an image. Magn Reson Med 76:519-529, 2016. © 2015 Wiley Periodicals, Inc.
Numerical design of three-dimensional gradient refractive index structures for beam shaping (2020)

A numerical design method is demonstrated for gradient refractive index (GRIN) beam shapers embedded in a medium. The three-dimensional refractive index profile Δn(x, y, z) gradually changes the spatial characteristics of a beam during propagation. Diffraction effects such as beam expansion are controlled and compensated by the refractive index profile, resulting in efficient field transformations with no coherent artifacts. The solution is found using phase retrieval and a paraxial scalar wave beam propagation model. An example design is shown in which small changes in refractive index (Δn < 10<sup>-3</sup>) are used to transform a beam over a device length of 10 mm.
Expression Analyses of β-tubulin Isotype Genes in Rice (2003)

Microtubules play important roles in many cellular processes, such as cell division and cell elongation in plants. beta-tubulins, which are the basic components of microtubules, are encoded by multigene family in eukaryotes and their nucleotide sequences are highly conserved in protein coding regions. A homology search within the rice expressed sequence tag database identified at least eight beta-tubulin (OsTUB) isotypes including three novel OsTUB genes. Northern analysis using specific probes to 3'-UTR of OsTUB isotypes showed differential and tissue-specific expression. Seven out of eight OsTUB genes dominantly expressed in leaf sheath, while OsTUB8 was preferentially expressed in anther including mature pollens. The existence of anther-specific beta-tubulin suggests its unique role in the formation of microtubules during the anther and pollen development or pollen tube growth. Furthermore, transcripts of OsTUB5, 6 and 7 genes were significantly enhanced by gibberellin but all eight OsTUB genes were repressed by abscisic acid. Our results imply that OsTUB genes are differentially regulated by developmental and hormonal signals and different OsTUB isotypes might play special role in the growth and development of specific organs in rice.
Liver Expression of a MiniATP7B Gene Results in Long‐Term Restoration of Copper Homeostasis in a Wilson Disease Model in Mice (2019)

Gene therapy with an adeno-associated vector (AAV) serotype 8 encoding the human ATPase copper-transporting beta polypeptide (ATP7B) complementary DNA (cDNA; AAV8-ATP7B) is able to provide long-term copper metabolism correction in 6-week-old male Wilson disease (WD) mice. However, the size of the genome (5.2 kilobases [kb]) surpasses the optimal packaging capacity of the vector, which resulted in low-yield production; in addition, further analyses in WD female mice and in animals with a more advanced disease revealed reduced therapeutic efficacy, as compared to younger males. To improve efficacy of the treatment, an optimized shorter AAV vector was generated, in which four out of six metal-binding domains (MBDs) were deleted from the ATP7B coding sequence, giving rise to the miniATP7B protein (Δ57-486-ATP7B). In contrast to AAV8-ATP7B, AAV8-miniATP7B could be produced at high titers and was able to restore copper homeostasis in 6- and 12-week-old male and female WD mice. In addition, a recently developed synthetic AAV vector, AAVAnc80, carrying the miniATP7B gene was similarly effective at preventing liver damage, restoring copper homeostasis, and improving survival 1 year after treatment. Transduction of approximately 20% of hepatocytes was sufficient to normalize copper homeostasis, suggesting that corrected hepatocytes are acting as a sink to eliminate excess of copper. Importantly, administration of AAVAnc80-miniATP7B was safe in healthy mice and did not result in copper deficiency. Conclusion: In summary, gene therapy using an optimized therapeutic cassette in different AAV systems provides long-term correction of copper metabolism regardless of sex or stage of disease in a clinically relevant WD mouse model. These results pave the way for the implementation of gene therapy in WD patients.
Practical and Secure IoT Device Authentication Using Physical Unclonable Functions (2016)

Devices in the internet of things (IoT) are frequently (i) resource-constrained, and (ii) deployed in unmonitored, physically unsecured environments. Securing these devices requires tractable cryptographic protocols, as well as cost effective tamper resistance solutions. We propose and evaluate cryptographic protocols that leverage physical unclonable functions (PUFs): circuits whose input to output mapping depends on the unique characteristics of the physical hardware on which it is executed. PUF-based protocols have the benefit of minimizing private key exposure, as well as providing cost-effective tamper resistance. We present and experimentally evaluate an elliptic curve based variant of a theoretical PUF-based authentication protocol proposed previously in the literature. Our work improves over an existing proof-of-concept implementation, which relied on the discrete logarithm problem as proposed in the original work. In contrast, our construction uses elliptic curve cryptography, which substantially reduces the computational and storage burden on the device. We describe PUF-based algorithms for device enrollment, authentication, decryption, and digital signature generation. The performance of each construction is experimentally evaluated on a resource-constrained device to demonstrate tractability in the IoT domain. We demonstrate that our implementation achieves practical performance results, while also providing realistic security. Our work demonstrates that PUF-based protocols may be practically and securely deployed on low-cost resource-constrained IoT devices.
Tricyclic Benzimidazoles as Potent Poly(ADP-ribose) Polymerase-1 Inhibitors (2002)

Novel tricyclic benzimidazole carboxamide poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors have been synthesized. Several compounds were found to be powerful chemopotentiators of temozolomide and topotecan in both A549 and LoVo cell lines. In vitro inhibition of PARP-1 was confirmed by direct measurement of NAD+ depletion and ADP-ribose polymer formation caused by chemically induced DNA damage.
Surface functionalization of biomaterials with tissue-inductive artificial extracellular matrices (2013)

Bone tissue engineering includes a broad range of strategies and approaches to improve osteoinductive and osteoconductive properties of biomaterials. One approach is applying components of the native extracellular matrix (ECM) to mimic a favorable environment for bone forming cells like osteoblasts and their progenitors. The development of such artificial extracellular matrices (aECMs) is based on collagen, which can be modified by glycoproteins, proteoglycans and glycosaminoglycans. This article reviews the preparation, immobilization and the biochemical characteristics of these coatings for scaffolds and implants. In addition, the influence of aECM coating on cells, bone-implant contact and new bone formation in small and large animals is discussed.
Achievements and Challenges in Understanding Plant Abiotic Stress Responses and Tolerance (2011)

Intensive research over the last decade has gradually unraveled the mechanisms that underlie how plants react to environmental adversity. Genes involved in many of the essential steps of the stress response have been identified and characterized. In particular, the recent discovery of ABA receptors, progress in understanding the transcriptional and post-transcriptional regulation of stress-responsive gene expression, and studies on hormone interactions under stress have facilitated addressing the molecular basis of how plant cells respond to abiotic stress. Here, we summarize recent research progress on these issues, especially focusing on progress related to the essential and classically important signaling pathways and genes. Despite this wealth of achievements, many challenges remain not only for the further elucidation of stress response mechanisms but also for evaluation of the natural genetic variations and associating them with specific gene functions. Finally, the proper application of this knowledge to benefit humans and agriculture is another important issue that lies ahead. Collaborative wisdom and efforts are needed to confront these challenges.
Synthesis of a New Class of Pyridine Herbicides (1991)

A new class of fluoroalkyled pyridine herbicides has been synthesized from ethyl 4,4,4-trifluoroacetoacetate. The synthetic route involves formation of dihydropyridine intermediate which upon oxidation or dehydrofluorination produces the desired pyridine compounds. Hydrolysis of the ester groups followed by derivatization of the resulting acids yields a variety of herbicidally active pyridine compounds.
High‐order high‐frequency solutions of rough surface scattering problems (2002)

A new method is introduced for the solution of problems of scattering by rough surfaces in the high‐frequency regime. It is shown that high‐order summations of expansions in inverse powers of the wave number can be used within an integral equation framework to produce highly accurate results for surfaces and wavelengths of interest in applications. Our algorithm is based on systematic use and manipulation of certain Taylor‐Fourier series representations and explicit asymptotic expansions of oscillatory integrals. Results with machine precision accuracy are presented which were obtained from computations involving expansions of order as high as 20.
A new fermented milk using capsular polysaccharide-producing <i>Lactobacillus kefiranofaciens</i> isolated from kefir grains (1991)

Summary A new fermented milk was prepared by using capsular polysaccharide-producing Lactobacillus kefiranofaciens K 1 isolated from kefir grains. Fermentation was carried out at 30°C for 18 h, when pH 4·5 was attained. The product had a ropy consistency and was resistant to syneresis. However, the product was given lower scores for acceptability by a consumer panel than a similar product made with Lb. delbrueckii subsp. bulgaricus .