gebhart/patrepeval huggingface dataset:
Mass distribution on clusters at the percolation threshold (1995)

Monte Carlo simulations and a scaling hypothesis are used to study the distribution of blob masses on two-dimensional finite-mass clusters at the percolation threshold. The exponents associated with this distribution function are a combination of backbone and percolation exponents. This work offers insights into the structure and fragmentation properties of percolation clusters in particular, and provides methods applicable to other fractal distribution problems in general.
Artificial tertiary motifs stabilize <i>trans</i>-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures (2004)

Tertiary stabilizing motifs (TSMs) between terminal loops or internal bulges facilitate folding of natural hammerhead ribozymes (hRz) under physiological conditions. However, both substrate and enzyme strands contribute nucleotides to the TSMs of trans -cleaving hRz, complicating the design of hRz that exploit TSMs to target specific mRNA. To overcome this limitation, we used SELEX to identify new, artificial TSMs that are less sensitive to sequence context. Nucleotides in loop II or in a bulge within the ribozyme strand of stem I were randomized, while the interaction partner was held constant. All nucleotides of the substrate pair with the ribozyme, minimizing their possible recruitment into the TSM, as such recruitment could constrain choice of candidate target sequences. Six cycles of selection identified cis -acting ribozymes that were active in 100 μM MgCl 2 . The selected motifs partially recapitulate TSMs found in natural hRz, suggesting that the natural motifs are close to optimal for their respective contexts. Ribozyme “RzB” showed enhanced thermal stability by retaining trans -cleavage activity at 80°C in 10 mM MgCl 2 and at 70°C in 2 mM MgCl 2 . A variant of ribozyme “RzB” with a continuously paired stem 1 rapidly lost activity as temperature was increased. The selected motifs are modular, in that they permit trans -cleavage of several substrates in submillimolar MgCl 2 , including two substrates derived from the U5 genomic region of HIV-1. The new, artificial tertiary stabilized hRz are thus nearly independent of sequence context and enable for the first time the use of highly active hRz targeting almost any mRNA at physiologically relevant magnesium concentrations.
Caspase-mediated cleavage converts Livin from an antiapoptotic to a proapoptotic factor: implications for drug-resistant melanoma. (2003)

Inhibitor of apoptosis protein (IAP) is a family of intracellular proteins that plays an essential role in the regulation of apoptosis. Recently, we and others discovered a new member of this family, termed Livin. Many studies have focused on the inhibitory effect of IAPs on caspases. Here, we describe a novel regulatory mechanism by which Livin is cleaved by the caspases. Strikingly, the cleaved Livin, although containing intact baculovirus IAP repeat and RING domains, does not only lose its antiapoptotic function but also gains a proapoptotic effect. The cleavage is site specific at Asp-52 and is restricted to effector caspase-3 and -7. Most importantly, we demonstrate the role of Livin and this regulatory mechanism in the drug resistance of melanoma patients. Using primary cultures derived from melanoma patients, we found a correlation between Livin overexpression, in vitro drug resistance, and the patient's clinical response.
Cdk5/p25-Induced Cytosolic PLA2-Mediated Lysophosphatidylcholine Production Regulates Neuroinflammation and Triggers Neurodegeneration (2012)

The deregulation of cyclin-dependent kinase 5 (Cdk5) by p25 has been shown to contribute to the pathogenesis in a number of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD) and Alzheimer's disease (AD). In particular, p25/Cdk5 has been shown to produce hyperphosphorylated tau, neurofibrillary tangles as well as aberrant amyloid precursor protein processing found in AD. Neuroinflammation has been observed alongside the pathogenic process in these neurodegenerative diseases, however the precise mechanism behind the induction of neuroinflammation and the significance in the AD pathogenesis has not been fully elucidated. In this report, we uncover a novel pathway for p25-induced neuroinflammation where p25 expression induces an early trigger of neuroinflammation in vivo in mice. Lipidomic mass spectrometry, in vitro coculture and conditioned media transfer experiments show that the soluble lipid mediator lysophosphatidylcholine (LPC) is released by p25 overexpressing neurons to initiate astrogliosis, neuroinflammation and subsequent neurodegeneration. Reverse transcriptase PCR and gene silencing experiments show that cytosolic phospholipase 2 (cPLA2) is the key enzyme mediating the p25-induced LPC production and cPLA2 upregulation is critical in triggering the p25-mediated inflammatory and neurodegenerative process. Together, our findings delineate a potential therapeutic target for the reduction of neuroinflammation in neurodegenerative diseases including AD.
Structural comparison of Cu<sup>I</sup>and Cu<sup>II</sup>complexes displaying analogous N<sub>2</sub>S<sub>2</sub>co-ordination; X-ray analysis of tetraco-ordinate [Cu(pma)]BPh<sub>4</sub>and pentaco-ordinate [Cu(pma)SO<sub>4</sub>][pma2-pyridylmethylbis-(2-ethylthioethyl)amine] (1980)

The synthesis and X-ray structural characterization of the CuI and CuII complexes [Cu(pma)]BPh4 and [Cu(pma)SO4][pma2-pyridylmethylbis-(2-ethylthioethyl)amine] are reported; both display N2S2 co-ordination with the CuI complex exhibiting trigonal pyramidal geometry while the CuII derivative shows a distorted trigonal bipyramidal geometry which includes a co-ordinated sulphate group.
Electrochemical Capacitors Employing Zeolite Templated Carbons: Temperature Effects in a Variety of Electrolytes (2012)

Abstract not Available.
Personalized medicine for brain metastases (BrMets) through patient-derived organoid (PDO) drug testing. (2023)

11 Background: Therapeutic development for BrMets remains a critical need. Our previous work on functional precision medicine using patient-derived xenografts (PDXs) from BrMets suggested that drug sensitivity testing may help prioritize drug selection. However, the time needed to establish PDXs makes the PDX platform less desirable for translation into the clinic. Thus, we examined the feasibility of PDOs from BrMets to evaluate the drug sensitivities in a clinically meaningful time frame. Methods: BrMets were prospectively collected from clinically indicated neurosurgery. We collected DNA and RNA and cultured tumors as 3D organoids. Drugs were curated for each case based on clinical characteristics and molecular profiles when known a priori. The drugs included standard of care and investigational drugs. Rapid Nanostring PanCancer profiling was conducted to examine if contemporary source tumor profiling would inform additional drug selection. Results: 21 patients with breast cancer were consented to the biobanking program. 3 patients had no tissues collected. 17 PDOs were established from 20 cases: 3 without PDO were necrosis without viable tumors or primary brain tumors. 2 patients had multiple collections (recurrence and synchronous lesions). Clinical subtypes included HR+/- HER2+ (N=7), HR+HER2- (N=2), HR-HER2- (N=8). The median number of drugs tested was 19.5 (range:7-32). The median time for drug testing was 12.5 days (range: 9-32). Nanostring profiling was conducted at the time of drug testing in 12/17 PDOs, and pathway analysis indicated potential targeted drugs. The most common alteration was TP53 mutation with additional NGS. The potentially targetable alterations included mutation to PIK3CA, EGFR, FGFR, CDK2NA, and CDK4. The pair of initial and recurrent lesions was molecularly similar but demonstrated differential response to select chemotherapies following patient exposure to radiation. On the other hand, the pair of synchronous lesions showed discordance in PIK3CA status and discordant sensitivity to Pi3K inhibitors. Conclusions: Predictive drug testing with BrMet PDOs in a clinically meaningful time frame is feasible. The use of real-time PDO drug testing along with molecular profiling could be potentially leveraged to further personalize therapy and discover novel therapy options for patients with BrMets. We are currently conducting clinical correlations and working toward clinical validation of our proposed drug testing platform.
Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein (2016)

Uropathogenic E. coli (UPEC) is the primary cause of urinary tract infection (UTI), a disease of major significance to human health. Globally, the incidence of UPEC-mediated UTI is strongly associated with increasing antibiotic resistance, making this extremely common infection a major public health concern. In this report, we describe the regulatory, structural, functional, and immunogenic properties of a candidate UPEC vaccine antigen, IrmA. We demonstrate that IrmA is a small UPEC protein that forms a unique domain-swapped dimer with structural mimicry to several human cytokine receptors. We also show that IrmA binds to IL-2, IL-4, and IL-10, is strongly immunogenic in urosepsis patients, and is coexpressed with factors associated with biofilm formation. Overall, this work suggests a potential novel contribution for IrmA in UPEC infection.
Structural investigation of interface and defects in epitaxial Bi3.25La0.75Ti3O12 film on SrRuO3/SrTiO3 (111) and (100) (2013)

The structure of La-doped bismuth titanate (BLT), Bi3.25La0.75Ti3O12, is investigated with atomic resolution high-angle annular dark field (HAADF) scanning transmission electron microscopy. The images reveal evidence of the tilting of TiO6 octahedra within the perovskite-like layers of the BLT unit cell. The tendency of La ions to substitute Bi ions and occupy the top part of the (Bi2O2)2+ layer, previously observed from electron energy loss spectroscopy (EELS) mapping experiments, is explained based on the tolerance factors and stress relief mechanism. The atomic resolution HAADF images also reveal the presence of the out-of-phase boundaries (OPBs). The role of OPBs in BLT is discussed in terms of its fatigue resistance as the OPBs provide extra nucleation sites for ferroelectric domains during polarization reversals. Further, we show evidence that the first deposited atomic layer at the interface also governs the subsequent film growth, resulting in the modulation of the “defect-free” and the “defected” regions throughout the BLT film in the lateral direction, parallel to the film-substrate interface. As demonstrated from atomic-resolved elemental mapping with EELS, the generation of the defect-free and regions with defect in the BLT film are likely to be induced by the presence of surface steps and dislocations at the film-substrate interface. These effects are discussed in terms of the large remanent polarization and enhanced fatigue resistance in BLT.
Hydroxyethoxy phenyl butanone, a new cosmetic preservative, does not cause bacterial cross-resistance to antimicrobials (2020)

<b>Introduction.</b> Biocide-induced cross-resistance to antimicrobials in bacteria has been described and is a concern for regulators. We have recently reported on a new protocol to predict the propensity of biocide to induce phenotypic resistance in bacteria.<b>Aim.</b> To measure bacterial propensity to develop antimicrobial resistance following exposure to a new cosmetic preservative developed by L'Oréal R and I.<b>Methodology.</b> Well-established antimicrobials including triclosan (TRI) and benzalkonium chloride (BZC) and a new molecule hydroxyethoxy phenyl butanone (HEPB) were investigated for their antimicrobial efficacy, effect on bacterial growth, and their potential to induce resistance to chemotherapeutic antibiotics using a new predictive protocol.<b>Results.</b> The use of this predictive protocol with <i>Staphylococcus aureus</i>, <i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i> showed that TRI and BZC significantly affected bacterial growth, MICs and minimum bactericidal concentrations (MBCs). There was no change in antibiotic susceptibility profile following exposure to BZC, but <i>E. coli</i> became intermediate resistant to tobramycin following treatment with TRI (0.00002 % w/v). HEPB did not change the antimicrobial susceptibility profile in <i>P. aeruginosa</i> and <i>S. aureus</i> but <i>E. coli</i> became susceptible to gentamicin. TRI exposure resulted in bacterial susceptibility profile alteration consistent with the literature and confirmed the use of TRI as a positive control in such a test.<b>Conclusion.</b> Data produced on the propensity of a molecule to induce bacterial resistance is useful and appropriate when launching a new preservative.
An Integrated Face–Body Representation in the Fusiform Gyrus but Not the Lateral Occipital Cortex (2014)

Faces and bodies are processed by distinct category-selective brain areas. Neuroimaging studies have so far presented isolated faces and headless bodies, and therefore little is known on whether and where faces and headless bodies are grouped together to one object, as they appear in the real world. The current study examined whether a face presented above a body are represented as two separate images or as an integrated face-body representation in face and body-selective brain areas by employing a fMRI competition paradigm. This paradigm has been shown to reveal higher fMRI response to sequential than simultaneous presentation of multiple stimuli (i.e., the competition effect), indicating competitive interactions among simultaneously presented multiple stimuli. We therefore hypothesized that if a face above a body is integrated to an image of a person whereas a body above a face is represented as two separate objects, the competition effect will be larger for the latter than the former. Consistent with our hypothesis, our findings reveal a competition effect when a body is presented above a face, but not when a face is presented above a body, suggesting that a body above a face is represented as two separate objects whereas a face above a body is represented as an integrated image of a person. Interestingly, this integration of a face and a body to an image of a person was found in the fusiform, but not the lateral-occipital face and body areas. We conclude that faces and bodies are processed separately at early stages and are integrated to a unified image of a person at mid-level stages of object processing.
Preliminary Study on the Application of Temperature Swing Adsorption in Aqueous Phase for Pesticide Removal (2018)

Temperature swing adsorption (TSA) is a well-established process for gas purification. In this work, the feasibility of TSA in aqueous phase was studied. This concept could enable in situ adsorbent regeneration and thus fostering sustainable decentralized adsorption processes applied to water treatment. The adsorption processes with the use of granular activated carbon (GAC) have been widely applied to remove the residual amounts of pesticides in water treatment. Amitrole was chosen as a typical pesticide in this study, GAC was selected as the main adsorbent for amitrole removal. Adsorption isotherm experiments were conducted at different temperatures of 20°C, 57°C and 94°C to identify the most appropriate sorptive – sorbent system for dynamic adsorption and TSA research. Once the isotherm experiments were accomplished, breakthrough curve experiments were subsequently investigated. Finally, TSA process was conducted with the activated carbon regeneration at the elevated temperature of 125°C. Consequently, initial obtained results proved the feasibility of the proposed TSA technique for pesticide removal in aqueous phase.
Novel Denitrifying Bacterium <i>Ochrobactrum anthropi</i> YD50.2 Tolerates High Levels of Reactive Nitrogen Oxides (2009)

ABSTRACT Most studies of bacterial denitrification have used nitrate (NO 3 − ) as the first electron acceptor, whereas relatively less is understood about nitrite (NO 2 − ) denitrification. We isolated novel bacteria that proliferated in the presence of high levels of NO 2 − (72 mM). Strain YD50.2, among several isolates, was taxonomically positioned within the α subclass of Proteobacteria and identified as Ochrobactrum anthropi YD50.2. This strain denitrified NO 2 − , as well as NO 3 − . The gene clusters for denitrification ( nar , nir , nor , and nos ) were cloned from O. anthropi YD50.2, in which the nir and nor operons were linked. We confirmed that nirK in the nir - nor operon produced a functional NO 2 − reductase containing copper that was involved in bacterial NO 2 − reduction. The strain denitrified up to 40 mM NO 2 − to dinitrogen under anaerobic conditions in which other denitrifiers or NO 3 − reducers such as Pseudomonas aeruginosa and Ralstonia eutropha and nitrate-respiring Escherichia coli neither proliferated nor reduced NO 2 − . Under nondenitrifying aerobic conditions, O. anthropi YD50.2 and its type strain ATCC 49188 T proliferated even in the presence of higher levels of NO 2 − (100 mM), and both were considerably more resistant to acidic NO 2 − than were the other strains noted above. These results indicated that O. anthropi YD50.2 is a novel denitrifier that has evolved reactive nitrogen oxide tolerance mechanisms.
Processing Big Data in Motion (2016)

Summary form only given. Streaming analytics is about identifying and responding to events happening in your business, in your service or application, and with your customers in near real-time. Sensors, mobile and IoT devices, social networks, and online transactions are all generating data that can be monitored constantly to enable a business to detect and then act on events and insights before they lose their value. The need for large scale, real-time stream processing of big data in motion is more evident than ever before but the potential remains largely untapped by most firms. It's not the size but rather the speed at which this data must be processed that presents the greatest technical challenges. Streaming analytics systems can enable business to inspect, correlate and analyze data in real-time to extract insights in the same manner that traditional analytics tools have allowed them to do with data at rest. In this talk I will draw upon our experience with Amazon Kinesis data streaming services to highlight use cases, discuss technical challenges and approaches, and look ahead to the future of stream data processing and role of cloud computing.
Crystal structure of hematopoietic prostaglandin D synthase complexed of HQL-79 (2005)

layer with oxygen and La/Ba atoms is stacked by two types. One is cubic ABCABC stacking for perovskite layer and hexagonal ABAB stacking for junction slabs which is composed three octahedral with face contact. There are three positions for Ba/La ions as follows: A1 position with La and Ba is located near vacant octahedron, A2 position is located next stacking layer, and A3 position is occupied the center of perovskite layer. Structures of BaLa 4 Ti 4 O 15 substituted Ca and Sr for Ba are also analyzed. And relationship between structure and properties of them are presented.
Distributed multi-robot formation control among obstacles: A geometric and optimization approach with consensus (2016)

This paper presents a distributed method for navigating a team of robots in formation in 2D and 3D environments with static and dynamic obstacles. The robots are assumed to have a reduced communication and visibility radius and share information with their neighbors. Via distributed consensus the robots compute (a) the convex hull of the robot positions and (b) the largest convex region within free space. The robots then compute, via sequential convex programming, the locally optimal parameters for the formation within this convex neighborhood of the robots. Reconfiguration is allowed, when required, by considering a set of target formations. The robots navigate towards the target collision-free formation with individual local planners that account for their dynamics. The approach is efficient and scalable with the number of robots and performs well in simulations with up to sixteen quadrotors.
A Comparison Study of Functional Groups (Amine vs. Thiol) for Immobilizing AuNPs on Zeolite Surface (2019)

Immobilization of gold nanoparticles (AuNPs) on the surface of zeolite has received a great interest due to Au@zeolite's unique characteristics and high performance for catalysis. In this work we studied the grafting of two different functional molecules; one having an amine group (3-aminopropyl)triethoxysilane (APTES) and the second having a thiol group (3-mercaptopropyl)trimethoxysilane (MPTES) on the surface of zeolite using the same wet chemistry method. The modified zeolite surfaces were characterized using zeta potential measurements; diffuse reflectance infrared fourier transform (DRIFT) and X-ray photoelectron spectroscopy (XPS). The results confirmed a successful deposition of both functional groups at the topmost surface of the zeolite. Furthermore; transmission electron microscopy (TEM), ultraviolet-visible (UV-Vis) spectroscopy and XPS results clearly evidenced that APTES provided a better AuNPs immobilization than MPTES as a result of; (1) less active functions obtained after MPTES deposition, and (2) the better attaching ability of thiol to the gold surface.
ChemInform Abstract: Synthesis of Substituted Oxazolo[4,5‐b]pyridine Derivatives. (2001)

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.
ChemInform Abstract: Suzuki—Miyaura Reactions of Homo gem‐Dihalovinyl Systems (2011)

Abstract Review: 130 refs.
Ecology of Porcine Astrovirus Type 3 in a Herd with Associated Neurologic Disease (2020)

Astroviruses (AstVs) cause disease in a wide variety of species. Porcine AstVs are highly genetically diverse and conventionally assigned to five genetic lineages (PoAstV1-5). Due to the increasing evidence that porcine astrovirus type 3 (PoAstV3) is a cause of encephalomyelitis in swine and to elucidate important ecologic characteristics, the infection dynamics and environmental distribution of PoAstV3 were investigated in a herd with PoAstV3-associated neurologic disease. Over a 22 week period, the frequency of PoAstV3 fecal shedding varied by pig and age. The peak detection by RT-qPCR of PoAstV3 on fecal swabs (95%; 61 of 64) occurred at 3 weeks of age. The lowest frequency of detection was at 21 weeks of age (4%; 2 of 47); however, the frequency increased to 41% (19 of 46) at the final sampling time point (25 weeks of age). Viremia was rare (0.9%: 4 of 433). Detection in oral fluid was consistent with 75% to 100% of samples positive at each time point. Pens and feeders also had a high rate of detection with a majority of samples positive at a majority of sampling time points. Based on the data presented, PoAstV3 can be consistently detected in the environment with a majority of pigs being infected and a subset intermittently shedding the virus in feces out to 25 weeks of age. These findings suggest the importance of as-yet unidentified risk factors associated with the development of PoAstV3-associated polioencephalomyelitis.