gebhart/patrepeval huggingface dataset:
Precursor-Directed Biosynthesis and Fluorescence Labeling of Clickable Microcystins (2020)

Microcystins, cyclic nonribosomal heptapeptides, are the most well-known cyanobacterial toxins. They are exceptionally well studied, but open questions remain concerning their physiological role for the producing microorganism or their suitability as lead compounds for anticancer drug development. One means to study specialized metabolites in more detail is the introduction of functional groups that make a compound amenable for bioorthogonal, so-called click reactions. Although it was reported that microcystins cannot be derivatized by precursor-directed biosynthesis, we successfully used this approach to prepare clickable microcystins. Supplementing different azide- or terminal alkyne containing amino acid analogues into the cultivation medium of microcystin-producing cyanobacteria strains, we found that these strains differ strongly in their substrate acceptance. Exploiting this flexibility, we generated more than 40 different clickable microcystins. We conjugated one of these derivatives with a fluorogenic dye and showed that neither incorporation of the unnatural amino acid analogue nor attachment of the fluorescent label significantly affects the cytotoxicity against cell lines expressing the human organic anion transporting polypeptides 1B1 or 1B3. Using time-lapse microscopy, we observed that the fluorescent microcystin is rapidly taken up into eukaryotic cells expressing these transporters.
Synthesis of vertically aligned carbon nanotubes on a large area using thermal chemical vapor deposition (2001)

Vertically well-aligned carbon nanotubes (CNTs) were homogeneously grown on iron deposited silicon oxide substrate by thermal chemical vapor deposition of acetylene. The CNTs have an uniform length of 100 μm and a diameter in the range from 100 to 200 nm. The CNTs reveal closed tip and very clean surface without any carbonaceous particles. The CNTs have no encapsulated iron particles at the closed tip and a bamboo structure in which the curvature of compartment layers is directed to the tip.
Self-Assembly of Liquid Crystalline Complexes Having Angular Structures through Intermolecular Hydrogen Bonding (1992)

Abstract Novel liquid crystalline materials having angular structures with mesogens pointing in two directions have been prepared by complexation of phthalic or isophthalic acid and two molecules of a stilbazole through intermolecular hydrogen bonding.
Sparstolonin B, a Novel Plant Derived Compound, Arrests Cell Cycle and Induces Apoptosis in N-Myc Amplified and N-Myc Nonamplified Neuroblastoma Cells (2014)

Neuroblastoma is one of the most common solid tumors and accounts for ∼ 15% of all the cancer related deaths in the children. Despite the standard therapy for advanced disease including chemotherapy, surgery, and radiation, the mortality rate remains high for these patients. Hence, novel therapeutic agents are desperately needed. Here we examined the anticancer activity of a novel plant-derived compound, sparstolonin B (SsnB; 8,5'-dihydroxy-4-phenyl-5,2'-oxidoisocoumarin) using neuroblastoma cell lines of different genetics. SsnB was recently isolated from an aquatic Chinese herb, Sparganium stoloniferum, and tubers of this herb have been used in traditional Chinese medicine for the treatment of several inflammatory diseases and cancers. Our cell viability and morphological analysis indicated that SsnB at 10 µM concentration significantly inhibited the growth of both N-myc amplified (SK-N-BE(2), NGP, and IMR-32 cells) and N-myc nonamplified (SH-SY5Y and SKNF-1 cells) neuroblastoma cells. The flow cytometric analyses suggested that SsnB arrests the cell cycle progression at G2-M phase in all neuroblastoma cell lines tested. Exposure of SsnB inhibited the compact spheroid formation and reduced the tumorigenicity of SH-SY5Y cells and SK-N-BE(2) cells in in vitro 3-D cell culture assays (anchorage-independent colony formation assay and hanging drop assay). SsnB lowers the cellular level of glutathione (GSH), increases generation of reactive oxygen species and activates the cleavage of caspase-3 whereas co-incubation of a GSH precursor, N-acetylcysteine, along with SsnB attenuates the inhibitory effects of SsnB and increases the neuroblastoma cell viability. Our results for the first time demonstrate that SsnB possesses anticancer activity indicating that SsnB-induced reactive oxygen species generation promotes apoptotic cell death in neuroblastoma cells of different genetic background. Thus these data suggest that SsnB can be a promising drug candidate in neuroblastoma therapy.
BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis (2018)

Our results identify and validate a BAL signature that predicts mortality in IPF and improves the accuracy of outcome prediction based on clinical parameters. The BAL signature associated with mortality unmasks a potential role for airway basal cells in IPF.
A new approach for allocating buffers and bandwidth to heterogeneous, regulated traffic in an ATM node (1995)

A new approach to determining the admissibility of variable bit rate (VBR) traffic in buffered digital networks is developed. In this approach all traffic presented to the network is assumed to have been subjected to leaky-bucket regulation, and extremal, periodic, on-off regulated traffic is considered; the analysis is based on fluid models. Each regulated traffic stream is allocated bandwidth and buffer resources which are independent of other traffic. Bandwidth and buffer allocations are traded off in a manner optimal for an adversarial situation involving minimal knowledge of other traffic. This leads to a single-resource statistical-multiplexing problem which is solved using techniques previously used for unbuffered traffic. VBR traffic is found to be divisible into two classes, one for which statistical multiplexing is effective and one for which statistical multiplexing is ineffective in the sense that accepting small losses provides no advantage over lossless performance. The boundary of the set of admissible traffic sources is examined, and is found to be sufficiently linear that an effective bandwidth can be meaningfully assigned to each VBR source, so long as only statistically-multiplexable sources are considered, or only nonstatistically-multiplexable sources are considered. If these two types of sources are intermixed, then nonlinear interactions occur and fewer sources can be admitted than a linear theory would predict. A qualitative characterization of the nonlinearities is presented. The complete analysis involves conservative approximations; however, admission decisions based on this work are expected to be less overly conservative than decisions based on alternative approaches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Expression, purification and characterization of BGERII: a novel pan-TGF  inhibitor (2008)

Transforming growth factor beta (TGFbeta) isoforms are known to be upregulated during the progression of some diseases. They have been shown to stimulate invasion and metastasis during carcinogenesis and promote many pathological fibrotic diseases when overstimulated. This involvement in late-stage carcinoma and pathological fibrosis makes TGFbeta isoforms prime targets for therapeutic intervention. Although soluble ectodomains of TGFbeta type II (RII) and betaglycan (BG) have been utilized as TGFbeta inhibitors, their antagonistic potency against different TGFbeta isoforms varies considerably because RII does not appreciably bind to TGFbeta2 whereas BG binds weakly to TGFbeta1 and TGFbeta3. In this study, we have successfully constructed and expressed a recombinant fusion protein containing the endoglin domain of BG (BG(E)) and the extracellular domain of RII. The fusion protein (named BG(E)RII) was purified from bacterial inclusion bodies by immobilized metal ion chromatography, refolded and characterized. It bound with higher affinity to TGFbeta1 and TGFbeta3 than a commercially available soluble RII and to TGFbeta2 than a commercially available soluble BG. More significantly, whereas BG(E) or RII alone showed no antagonistic activity towards TGFbeta2, BG(E)RII inhibited the signaling of both TGFbeta1 and TGFbeta2 in cell-based assays including TGFbeta-induced phosphorylation of Smad2 and Smad3, and transcription from a TGFbeta-responsive promoter more effectively than equimolar concentrations of either RII or BG. After further purification by gel filtration chromatography, BG(E)RII was found to have greater activity than other potent TGFbeta inhibitors in blocking the signaling of TGFbeta1 and TGFbeta3. Thus, BG(E)RII is a potent pan-TGFbeta inhibitor in vitro and has potential for blocking TGFbeta-induced pathogenesis in vivo.
Unburned Carbon from Fly Ash for Mercury Adsorption: II. Adsorption Isotherms and Mechanisms (2002)

Adsorption behavior of unburned carbons from fly ash has been investigated in this study. Batch tests and column test were carried out for several unburned carbon samples from various ash sources and processing schemes. Adsorption isotherms have been obtained from these tests. Results show that the unburned carbons have equal or better adsorption capacity for elemental mercury comparing with some general purpose commercial activated carbons at low gas phase mercury concentration that is in the range of power plant emissions. Also it has been found that heat treatment of unburned carbon in the presence of air at 400 o C enhanced the adsorption capacity, and the adsorption capacity decreased with the increase of the adsorption temperature. The mechanism of mercury adsorption on the unburned carbon was explained by the physical and chemical interaction between mercury and primary sites on the carbon surface.
PLEXIN-B1 MUTATIONS AND PROSTATE CANCER (2008)

You have accessJournal of Urology1 Apr 2008PLEXIN-B1 MUTATIONS AND PROSTATE CANCER Tharani Nitkunan, Oscar GW Wong, Chun Zhou, Joseph Nariculam, Phillipa Munson, Jason Constantinou, Alex Freeman, John R Masters, and Magali Williamson Tharani NitkunanTharani Nitkunan More articles by this author , Oscar GW WongOscar GW Wong More articles by this author , Chun ZhouChun Zhou More articles by this author , Joseph NariculamJoseph Nariculam More articles by this author , Phillipa MunsonPhillipa Munson More articles by this author , Jason ConstantinouJason Constantinou More articles by this author , Alex FreemanAlex Freeman More articles by this author , John R MastersJohn R Masters More articles by this author , and Magali WilliamsonMagali Williamson More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)61144-1AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "PLEXIN-B1 MUTATIONS AND PROSTATE CANCER." The Journal of Urology, 179(4S), p. 391 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 391 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information Tharani Nitkunan More articles by this author Oscar GW Wong More articles by this author Chun Zhou More articles by this author Joseph Nariculam More articles by this author Phillipa Munson More articles by this author Jason Constantinou More articles by this author Alex Freeman More articles by this author John R Masters More articles by this author Magali Williamson More articles by this author Expand All Advertisement PDF downloadLoading ...
A pipeline-based approach for maximal-sized matching scheduling in input-buffered switches (2001)

This letter proposes an innovative pipeline-based maximal-sized matching scheduling approach, called PMM, for input-buffered switches. It dramatically relaxes the timing constraint for arbitration with a maximal matching scheme. In the PMM approach, arbitration operates in a pipelined manner. Each subscheduler is allowed to take more than one time slot for its matching. Every time slot, one of them provides the matching result. The subscheduler can adopt a pre-existing efficient round-robin-based maximal matching algorithm. We show that PMM provides 100% throughput under uniform traffic since it preserves a desynchronization effect of the round-robin pointers as in the preexisting algorithm. In addition, PMM maintains fairness for best-effort traffic due to the round-robin-based arbitration.
Probiotics: on-going research on atopic individuals (2002)

The challenge for the modern health care system is to fight against the increasing prevalence of atopic disease. The introduction of scientifically composed probiotic functional foods for prophylactic or therapeutic purposes could be one solution. Probiotics are live microbial food supplements or components of bacteria which have beneficial effects on human health. Specific strains have been demonstrated to exert powerful anti-pathogenic, anti-inflammatory and anti-allergic effects. The hygiene hypothesis suggests that atopic disease may arise from a lack of counterbalancing microbial exposure at an early age. The initial compositional development of the gut microflora is considered a key determinant of the development of both the immune responder phenotype and normal gut barrier functions. The regulatory role of probiotics in human allergic disease was first emphasised in the demonstration of a suppressive effect on lymphocyte proliferation and interleukin-4 generation in vitro. Subsequently, a significant improvement in the clinical course of atopic eczema was reported in infants given a probiotic-supplemented diet. The potential of probiotics to reduce the risk of atopic disease has recently been demonstrated in a double-blind, placebo-controlled study: probiotics administered pre- and postnatally for 6 months to at-risk subjects reduced the prevalence of atopic eczema to half of that observed in infants receiving placebo. Ongoing research is directed towards the development of novel techniques to characterise the gut microflora. Future research will clarify the mechanisms to control specific physiological processes in the evolution of atopic disease in at-risk populations or in the management of allergic diseases.
ESD protection for the deep sub micron regime - a challenge for design methodology (2004)

ESD protection has been an inevitable component of integrated circuits since the invention of semiconductor devices. A huge number of concepts and protection devices have been designed and optimized for this purpose by ESD engineers. Even it seems to be a simple functionality just to shunt a discharge current during an ESD event, almost each step in the shrinking path needs new adjustment of the protection circuits and sometimes even implementation of totally new concepts. Entering the sub 100 nm regime the protection development goes much beyond the development of a specific optimized protection element. A sophisticated protection network has to be designed which covers both the IO circuit and the core region, where low oxides thickness and low junction breakdown voltages lead to hard constraints on the maximum voltage overshoot during ESD. In especially designs with multiple power supply domains will complicate the ESD supply protection concept extremely. To achieve a good ESD robustness it will be necessary to consider the ESD protection as integral part of the IC development starting from the concept phase. To support this and to extract the necessary data for an ESD optimization an IC level ESD simulation approach is presented which analyses the critical discharge paths across the chip.
Reply to Chakrabarti et al.: Corneal angiogenesis in patients with null <i>FOXC1</i> variants (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Detecting Backdoor Attacks on Deep Neural Networks by Activation\n Clustering (2018)

While machine learning (ML) models are being increasingly trusted to make\ndecisions in different and varying areas, the safety of systems using such\nmodels has become an increasing concern. In particular, ML models are often\ntrained on data from potentially untrustworthy sources, providing adversaries\nwith the opportunity to manipulate them by inserting carefully crafted samples\ninto the training set. Recent work has shown that this type of attack, called a\npoisoning attack, allows adversaries to insert backdoors or trojans into the\nmodel, enabling malicious behavior with simple external backdoor triggers at\ninference time and only a blackbox perspective of the model itself. Detecting\nthis type of attack is challenging because the unexpected behavior occurs only\nwhen a backdoor trigger, which is known only to the adversary, is present.\nModel users, either direct users of training data or users of pre-trained model\nfrom a catalog, may not guarantee the safe operation of their ML-based system.\nIn this paper, we propose a novel approach to backdoor detection and removal\nfor neural networks. Through extensive experimental results, we demonstrate its\neffectiveness for neural networks classifying text and images. To the best of\nour knowledge, this is the first methodology capable of detecting poisonous\ndata crafted to insert backdoors and repairing the model that does not require\na verified and trusted dataset.\n
Design and Synthesis of Cannabinoid Receptor 1 Antagonists for Peripheral Selectivity (2012)

Antagonists of cannabinoid receptor 1 (CB1) have potential for the treatment of several diseases such as obesity, liver disease, and diabetes. Recently, development of several CB1 antagonists was halted because of adverse central nervous system (CNS) related side effects observed with rimonabant, the first clinically approved CB1 inverse agonist. However, recent studies indicate that regulation of peripherally expressed CB1 with CNS-sparing compounds is a viable strategy to treat several important disorders. Our efforts aimed at rationally designing peripherally restricted CB1 antagonists have resulted in compounds that have limited blood-brain barrier (BBB) permeability and CNS exposure in preclinical in vitro and in vivo models. Typically, compounds with high topological polar surface areas (TPSAs) do not cross the BBB passively. Compounds with TPSAs higher than that for rimonabant (rimonabant TPSA = 50) and excellent functional activity with limited CNS penetration were identified. These compounds will serve as templates for further optimization.
An image-guided tool to prevent hospital acquired infections (2011)

Hospital Acquired Infections (HAI) represent the fourth leading cause of death in the United States, and claims hundreds of thousands of lives annually in the rest of the world. This paper presents a novel low-cost mobile device|called Stery-Hand|that helps to avoid HAI by improving hand hygiene control through providing an objective evaluation of the quality of hand washing. The use of the system is intuitive: having performed hand washing with a soap mixed with UV re ective powder, the skin appears brighter in UV illumination on the disinfected surfaces. Washed hands are inserted into the Stery-Hand box, where a digital image is taken under UV lighting. Automated image processing algorithms are employed in three steps to evaluate the quality of hand washing. First, the contour of the hand is extracted in order to distinguish the hand from the background. Next, a semi-supervised clustering algorithm classies the pixels of the hand into three groups, corresponding to clean, partially clean and dirty areas. The clustering algorithm is derived from the histogram-based quick fuzzy c-means approach, using a priori information extracted from reference images, evaluated by experts. Finally, the identied areas are adjusted to suppress shading eects, and quantied in order to give a verdict on hand disinfection quality. The proposed methodology was validated through tests using hundreds of images recorded in our laboratory. The proposed system was found robust and accurate, producing correct estimation for over 98% of the test cases. Stery-Hand may be employed in general practice, and it may also serve educational purposes.
Angle-Insensitive Structural Colours based on Metallic Nanocavities and Coloured Pixels beyond the Diffraction Limit (2013)

To move beyond colorant-based pigmentation display technologies, a variety of photonic and plasmonic crystal based structures have been designed and applied as colour filters. Nanostructure based colour filtering offers increased efficiencies, low power consumption, slim dimensions, and enhanced resolution. However, incident angle tolerance still needs to be improved. In this work, we propose a new scheme through localized resonance in metallic nanoslits by light funneling. Angle insensitive colour filters up to ±80 degrees have been achieved, capable of wide colour tunability across the entire visible band with pixel size beyond the diffraction limit (~λ/2). This work opens the door to angle insensitive manipulation of light with structural filtering.
Catalytic Use of a Boron Source for Boron Enolate Mediated Stereoselective Aldol Reactions in Water (2001)

Use of boron enolates in water! Boron enolates can be generated and used for aldol reactions in water by using a catalytic amount of Ph<sub>2</sub> BOH. This is the first example of a catalytic use of a boron source in stereoselective aldol reactions mediated by boron enolates. The mechanism of the reaction is discussed.
Delivery quality score model for Internet video (2014)

The vast majority of today's internet video services are consumed over-the-top (OTT) via reliable streaming (HTTP via TCP), where the primary noticeable delivery-related impairments are startup delay and stalling. In this paper we introduce an objective model called the delivery quality score (DQS) model, to predict user's QoE in the presence of such impairments. We describe a large subjective study that we carried out to tune and validate this model. Our experiments demonstrate that the DQS model correlates highly with the subjective data and that it outperforms other emerging models.
Scheduling and rescheduling with iterative repair (1993)

The GERRY scheduling and rescheduling system being applied to coordinate Space Shuttle ground processing is described. The system uses constraint-based iterative repair, a technique that starts with a complete but possibly flawed schedule and iteratively improves it by using constraint knowledge within repair heuristics. The tradeoff between the informedness and the computational cost of several repair heuristics is explored. It is shown empirically that some knowledge can greatly improve the convergence speed of a repair-based system, but that too much knowledge can overwhelm a system and result in degraded performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Analysis of Nearest Neighbor Interactions in the Pyrimidine Triple Helix Motif by Affinity Cleaving (1991)

Abstract : Oligonucleotide-directed sequence specific recognition of double helical DNA is length and sequence composition dependent. In order to dissect the relative importance of nearest neighbor interactions on triplet stabilities, binding by oligonucleotides of different sequence composition has been characterized by affinity cleaving. Several groups of target duplexes were synthesized with a central base triplet held constant and the adjacent 3' and 5' triplets systematically varied. By incorporating a thymidine residue with the Deovy Ribonucleic acids DNA-cleaving moiety EDTA in the third strand, the relative stabilities of Hoogsteen base triplets T.AT and C+GC as well as the newly discovered base triplets G.TA, Z.TA, and D3.CG were assessed in the context of different sequences.