gebhart/patrepeval huggingface dataset:
Antibacterial Activity Observed in the Seeds of Some Coprophilous Plants (1997)

Seeds of 40 plant species, which were frequently observed growing on cattle dung heaps were screened for their antibacterial properties against Bacillus subtilis, Escherichia coli, Pseudomonas cichorii and Salmonella typhimurium. Antibacterial activities were observed in the seeds of 36 species. The seeds of a large majority of these antibacterial positive plant species were active against P. cichorii (97%), B. subtilis (83%), S. typhimurium (69%) and E. coli (55%). The seeds of Citrullus vulgaris, Cajanus cajan, Sida acuta, Boerhaavia diffusa, Eclipta alba, Echinochloa crusgalli and Achyranthes aspera showed relatively large inhibition zones.
Practical byzantine fault tolerance and proactive recovery (2002)

Our growing reliance on online services accessible on the Internet demands highly available systems that provide correct service without interruptions. Software bugs, operator mistakes, and malicious attacks are a major cause of service interruptions and they can cause arbitrary behavior, that is, Byzantine faults. This article describes a new replication algorithm, BFT, that can be used to build highly available systems that tolerate Byzantine faults. BFT can be used in practice to implement real services: it performs well, it is safe in asynchronous environments such as the Internet, it incorporates mechanisms to defend against Byzantine-faulty clients, and it recovers replicas proactively. The recovery mechanism allows the algorithm to tolerate any number of faults over the lifetime of the system provided fewer than 1/3 of the replicas become faulty within a small window of vulnerability. BFT has been implemented as a generic program library with a simple interface. We used the library to implement the first Byzantine-fault-tolerant NFS file system, BFS. The BFT library and BFS perform well because the library incorporates several important optimizations, the most important of which is the use of symmetric cryptography to authenticate messages. The performance results show that BFS performs 2% faster to 24% slower than production implementations of the NFS protocol that are not replicated. This supports our claim that the BFT library can be used to build practical systems that tolerate Byzantine faults.
Drivers of i-DNA Formation in a Variety of Environments Revealed by Four-Dimensional UV Melting and Annealing (2021)

i-DNA is a four-stranded, pH-sensitive structure formed by cytosine-rich DNA sequences. Previous reports have addressed the conditions for formation of this motif in DNA <i>in vitro</i> and validated its existence in human cells. Unfortunately, these <i>in vitro</i> studies have often been performed under different experimental conditions, making comparisons difficult. To overcome this, we developed a four-dimensional UV melting and annealing (4DUVMA) approach to analyze i-DNA formation under a variety of conditions (e.g., pH, temperature, salt, crowding). Analysis of 25 sequences provided a global understanding of i-DNA formation under disparate conditions, which should ultimately allow the design of accurate prediction tools. For example, we found reliable linear correlations between the midpoint of pH transition and temperature (-0.04 ± 0.003 pH unit per 1.0 °C temperature increment) and between the melting temperature and pH (-23.8 ± 1.1 °C per pH unit increment). In addition, by analyzing the hysteresis between denaturing and renaturing profiles in both pH and thermal transitions, we found that loop length, nature of the C-tracts, pH, temperature, and crowding agents all play roles in i-DNA folding kinetics. Interestingly, our data indicate which conformer is more favorable for the sequences with an odd number of cytosine base pairs. Then the thermal and pH stabilities of "native" i-DNAs from human promoter genes were measured under near physiological conditions (pH 7.0, 37 °C). The 4DUVMA method can become a universal resource to analyze the properties of any i-DNA-prone sequence.
Laboratory Evaluation of H2S Bioscavenging in Produced Water at 60°C (2013)

Abstract Nitrate can control biogenic souring by lowering sulfate reducing bacteria (SRB) metabolic activity and shifting the microbial community such that nitrate-reducing bacteria (NRB) out-compete SRB for nutrients. Nitrate was applied in a laboratory study using a 20-cc packed bed upflow reactor to determine kinetic rate of H2S removal. The objectives of the testing were to (1) enrich for nitrate-reducing, sulfide-oxidizing microorganisms derived from produced water and (2) determine the kinetic rate of H2S removal at 60˚C in a synthetic medium with an H2S:nitrate molar ratio of 2, and (3) describe the microbial community involved in nitrate-mediated souring control in this system. Sulfide was measured at the face and at the discharge of the column to determine the sulfide oxidation rate. Residence time in the reactor was varied by changing flow rate but a removal rate of nearly 50% H2S was achieved across the column in one hour residence time. This paper provides a description of the microbial community cultivated at high temperature using 16S rRNA to profile the population dynamics resulting from nitrate treatment. Phospholipid fatty acid analysis was also used for taxonomic evaluation and quantifying physiological changes in the biomass due to nitrate treatment.
How the Double Spherules of Infectious Bronchitis Virus Impact Our Understanding of RNA Virus Replicative Organelles (2013)

Powered by advances in electron tomography, recent studies have extended our understanding of how viruses construct "replication factories" inside infected cells. Their function, however, remains an area of speculation with important implications for human health. It is clear from these studies that whatever their purpose, organelle structure is dynamic (M. Ulasli, M. H. Verheije, C. A. de Haan, and F. Reggiori, Cell. Microbiol. 12:844-861, 2010) and intricate (K. Knoops, M. Kikkert, S. H. Worm, J. C. Zevenhoven-Dobbe, Y. van der Meer, et al., PLOS Biol. 6:e226, 2008). But by concentrating on medically important viruses, these studies have failed to take advantage of the genetic variation inherent in a family of viruses that is as diverse as the archaea, bacteria, and eukaryotes combined (C. Lauber, J. J. Goeman, M. del Carmen Parquet, P. T. Nga, E. J. Snijder, et al., PLOS Pathog. 9:e1003500, 2013). In this climate, Maier et al. (H. J. Maier, P. C. Hawes, E. M. Cottam, J. Mantell, P. Verkade, et al., mBio 4:e00801-13, 2013) explored the replicative structures formed by an avian coronavirus that appears to have diverged at an early point in coronavirus evolution and shed light on controversial aspects of viral biology.
The Second Intracellular Loop of the Calcitonin Gene-related Peptide Receptor Provides Molecular Determinants for Signal Transduction and Cell Surface Expression (2005)

The calcitonin gene-related peptide (CGRP) receptor is a heterodimer of a family B G-protein-coupled receptor, calcitonin receptor-like receptor (CLR), and the accessory protein receptor activity modifying protein 1. It couples to G(s), but it is not known which intracellular loops mediate this. We have identified the boundaries of this loop based on the relative position and length of the juxtamembrane transmembrane regions 3 and 4. The loop has been analyzed by systematic mutagenesis of all residues to alanine, measuring cAMP accumulation, CGRP affinity, and receptor expression. Unlike rhodopsin, ICL2 of the CGRP receptor plays a part in the conformational switch after agonist interaction. His-216 and Lys-227 were essential for a functional CGRP-induced cAMP response. The effect of (H216A)CLR is due to a disruption to the cell surface transport or surface stability of the mutant receptor. In contrast, (K227A)CLR had wild-type expression and agonist affinity, suggesting a direct disruption to the downstream signal transduction mechanism of the CGRP receptor. Modeling suggests that the loop undergoes a significant shift in position during receptor activation, exposing a potential G-protein binding pocket. Lys-227 changes position to point into the pocket, potentially allowing it to interact with bound G-proteins. His-216 occupies a position similar to that of Tyr-136 in bovine rhodopsin, part of the DRY motif of the latter receptor. This is the first comprehensive analysis of an entire intracellular loop within the calcitonin family of G-protein-coupled receptor. These data help to define the structural and functional characteristics of the CGRP-receptor and of family B G-protein-coupled receptors in general.
Polymeric structure of a coproporphyrin I ruthenium(II) complex: a powder diffraction study (2016)

Porphyrin complexes of ruthenium are widely used as models for the heme protein system, for modelling naturally occurring iron-porphyrin systems and as catalysts in epoxidation reactions. The structural diversity of ruthenium complexes offers an opportunity to use them in the design of multifunctional supramolecular assemblies. Coproporphyrins and metallocoproporphyrins are used as sensors in bioassay and the potential use of derivatives as multiparametric sensors for oxygen and H<sup>+</sup> is one of the main factors driving a growing interest in the synthesis of new porphyrin derivatives. In the coproporphyrin I Ru<sup>II</sup> complex catena-poly[[carbonylruthenium(II)]-μ-2,7,12,17-tetrakis[2-(ethoxycarbonyl)ethyl]-3,8,13,18-tetramethylporphyrinato-κ<sup>5</sup>N,N',N'',N''':O], [Ru(C<sub>44</sub>H<sub>52</sub>N<sub>4</sub>O<sub>8</sub>)(CO)]<sub>n</sub>, the Ru<sup>II</sup> centre is coordinated by four N atoms in the basal plane, and by axial C (carbonyl ligand) and O (ethoxycarbonylethyl arm from a neighbouring complex) atoms. The complex adopts a distorted octahedral geometry. Self-assembly of the molecules during crystallization from a methylene chloride-ethanol (1:10 v/v) solution at room temperature gives one-dimensional polymeric chains.
MAPPING THE FUNDAMENTAL NICHE: PHYSIOLOGY, CLIMATE, AND THE DISTRIBUTION OF A NOCTURNAL LIZARD (2004)

The fundamental niche can be viewed as the set of conditions and resources that allow a given organism to survive and reproduce in the absence of biotic interactions. Quantitative descriptions of the environmental variables with which organisms are associated are becoming common with the advent of geographic information systems (GIS). Although such descriptive approaches to the niche are useful for interpolating species distributions, they implicitly incorporate biotic interactions and therefore do not represent the fundamental niche. A mechanistic understanding of the fundamental niche, when combined with GIS data, can provide us with greater insight into the causes of distribution and abundance, a solid foundation for exploring the role of biotic interactions, and greater confidence in extrapolating to novel circumstances such as climate change and species introductions. We apply such a mechanistic approach to study the climatic component of the fundamental niche of a nocturnal lizard, Heteronotia binoei, across an entire continent. We combine physiological measurements of this species (thermal requirements for egg development, thermal preferences and tolerances, metabolic and evaporative water loss rates), and high-resolution climatic data for the Australian continent (air temperature, cloud cover, wind speed, humidity, and radiation), with biophysical models to calculate the climatic component of the fundamental niche of this lizard and map it onto the Australian landscape at high resolution. We also use this approach to predict the effects of a mild global warming on the degree-days in the soil for egg development and the potential for aboveground activity of the study organism.
Artificial pinning centers using the barrier layer of ordered nanoporous alumina templates (2009)

The barrier layer of self-ordered anodized aluminium oxide, which is grown from an aluminium foil, has been revealed by a selective chemical etching of the remaining aluminium. The surface obtained in this way consists of a triangular lattice of bumps with 100 nm spacing, and heights of approximately 50 nm. Using this surface as a template for controlling the pinning in thin superconducting films, superconducting Nb was deposited with different thicknesses and under different deposition angles. The evaporation under a 30 degrees angle shows an asymmetric pinning potential composed of two triangular lattices having different pinning strengths. Matching effects are observed up to 1T. Matching effects are also maintained at relatively low temperature.
GoldenEye: The Clandestine UAV (2003)

GoldenEye is an answer to a DARPA requirement for a small clandestine VTOL UAV with fast cruise capability. Design attributes include a long duct shrouded fan, torsionally free wings, thrust vectoring, active stabilization, and functional autonomy. Discussion of the development, configuration, and test program of GoldenEye is presented with emphasis on design features distinct from traditional aircraft and helicopters.
Therapeutic drug monitoring (1987)

Director Clinical Chemistry Division of Laboratory Medicine Waterbury Hospital Health Center Waterbury, Connecticut Clinical Assistant Professor Department of Laboratory Medicine University of Connecticut School of Medicine Farmington, Connecticut
Artesunate overcomes drug resistance in multiple myeloma by inducing mitochondrial stress and non-caspase apoptosis (2014)

Although novel drugs have contributed immensely to improving outcomes of patients with multiple myeloma (MM), many patients develop drug resistance and ultimately succumb to MM. Here, we show that artesunate, an anti-malarial drug, reliably induces cell death in vitro in naïve as well as drug-resistant MM cells at concentrations shown to be safe in humans. Artesunate induced apoptosis predominantly through the non-caspase mediated pathway by primarily targeting mitochondria and causing outer mitochondrial membrane permeabilization that led to cytosolic and subsequent nuclear translocation of mitochondrial proteins apoptosis inducing factor (AIF) and endonuclease G (EndoG). Nuclear translocation of AIF and EndoG was accompanied by low levels of reactive oxygen species (ROS) and increased mitochondrial production of superoxide. These effects were present before apoptosis was evident and were related to intracellular levels of bivalent iron (Fe+2). Artesunate's unique mechanism probably was at least partially responsible for, its ability to act synergistically with multiple anti-myeloma agents. Our findings suggest that artesunate acts through iron to affect the mitochondria and induce low ROS and non-caspase-mediated apoptosis. Its potency, toxicity profile, and synergism with other drugs make it an intriguing new candidate for MM treatment.
ChemInform Abstract: Straightforward Synthesis of Axially Chiral 1,4‐Naphthodiazepine 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.
Targeted Dual Intervention-Oriented Drug-Encapsulated (DIODE) Nanoformulations for Improved Treatment of Pancreatic Cancer (2020)

Despite recent advancements, effective treatment for pancreatic ductal adenocarcinoma (PDAC) has remained elusive. The overall survival rate in PDAC patients has been dismally low due to resistance to standard therapies. In fact, the failure of monotherapies to provide long-term survival benefits in patients led to ascension of several combination therapies for PDAC treatment. However, these combination therapies provided modest survival improvements while increasing treatment-related adverse side effects. Hence, recent developments in drug delivery methods hold the potential for enhancing therapeutic benefits by offering cocktail drug loading and minimizing chemotherapy-associated side effects. Nanoformulations-aided deliveries of anticancer agents have been a success in recent years. Yet, improving the tumor-targeted delivery of drugs to PDAC remains a major hurdle. In the present paper, we developed several new tumor-targeted dual intervention-oriented drug-encapsulated (DIODE) liposomes. We successfully formulated liposomes loaded with gemcitabine (G), paclitaxel (P), erlotinib (E), XL-184 (c-Met inhibitor, X), and their combinations (GP, GE, and GX) and evaluated their in vitro and in vivo efficacies. Our novel DIODE liposomal formulations improved median survival in comparison with gemcitabine-loaded liposomes or vehicle. Our findings are suggestive of the importance of the targeted delivery for combination therapies in improving pancreatic cancer treatment.
Science data systems (2006)

Digital generation of acceleration voltage for mass spectrometer, and development of low power, nondestructive readout, plated-wire memory
Supplementary Table S3 from Genetic Associations in Classical Hodgkin Lymphoma: A Systematic Review and Insights into Susceptibility Mechanisms (2023)

&lt;p&gt;Overview of genome wide association studies in classical Hodgkin lymphoma.&lt;/p&gt;
HARTMANN-SHACK WAVEFRONT ABERRATIONS IN A KERATOCONIC POPULATION WITH AND WITHOUT CONTACT LENS CORRECTION. (2001)

Cheng, Xu MD, MS; Kollbaum, Peter OD; Riley, Colleen OD, MS; Thibos, Larry PhD; Bradley, Arthur PhD Author Information
Oncovex: A Family of Oncolytic Herpes Simplex Viruses Optimised for Therapeutic Use (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Dendritic Cells and Vaccines
Dynamics and locking of switching waves in a normally dispersive fiber ring resonator (Conference Presentation) (2018)

Switching waves (SWs) are walls that connect two homogeneous stable states of a multistable system. They are typically transient: a single SW will travel until the more stable state invades completely the less stable one. A single SW is only ever stationary at the so-called Maxwell point, a set of parameters where the two states have the same marginal stability. For parameters close to the Maxwell point, two approaching SWs can form a stable stationary structure provided that they have oscillatory tails through which they interlock. Such structures have recently been observed in the normal dispersion regime of microresonators and are known to correspond to dark pulse Kerr frequency combs. However, the small physical size of microresonators means that quantitative study of the transient dynamics that leads to their formation is difficult. In this contribution, we overcome this challenge by performing systematic experiments and simulations in a synchronously-driven macroscopic fiber ring resonator, and report on observations of transient SW dynamics. Our resonator is made of normal dispersion fiber, which allows for the coexistence of two homogeneous steady states and their connection through a SW. We have measured the SW velocities across a wide range of parameters, and close to the identified Maxwell point, observed interlocked SWs persisting for 100’s of resonator photon lifetimes. Our results provide significant experimental insights on the transient dynamics of SWs that have been theoretically predicted to underpin the formation of Kerr frequency combs in normally dispersive microresonators.
Engineering threshold-based selection systems (2021)

Using model organisms to identify novel therapeutic targets is frequently constrained by pre-existing genetic toolkits. To expedite positive selection for identification of novel downstream effectors, we engineered conditional expression of activated CED-10/Rac to disrupt Caenorhabditis elegans embryonic morphogenesis, titrated to 100% lethality. The strategy of engineering thresholds for positive selection using experimental animals was validated with pharmacological and genetic suppression and is generalizable to diverse molecular processes and experimental systems.
Macroscopic Rotator Cuff Tendinopathy and Histopathology Do Not Predict Repair Outcomes of Rotator Cuff Tears (2018)

The degree of tendinopathy did not correlate with morphological appearance of the tendon. Neither of these parameters correlated with healing or patient outcome. This study suggests that the degree of tendinopathy, unlike muscle atrophy, may not be predictive of outcomes and that, on appearance, poor quality tendon has adequate healing capacity. Therefore, abnormal gross tendon appearance should not affect the repair effort or technique.
Is the juice worth the squeeze? Transdisciplinary team science in bladder health (2020)

A diverse group has matured into a productive transdisciplinary team science consortium. Achieving this outcome required dedicated effort for each member to engage in activities that often required more time than single discipline research activities. Provision of the necessary time and tools has fostered a transdisciplinary team science culture and rich research agenda that reflects the complexity of the health issue to be addressed. Our experience may be useful for others embarking on team science projects.
Site-selective immobilization of functionalized DNA origami on nanopatterned Teflon AF (2017)

Teflon AF acts as a negative e-beam resist, here utilized for immobilization of porphyrin-anchored single DNA molecules on nanopillars, and precise determination of individual label positions.
The Observational Scale of Level of Arousal: A brief tool for assessing and monitoring level of arousal in patients with delirium outside the ICU (2020)

This study provides preliminary evidence supporting use of the OSLA as an instrument for identifying abnormal level of arousal associated with delirium and monitoring this longitudinally. Further validation in larger cohorts with blinded raters is required. J Am Geriatr Soc 68:-, 2020.
Effects of Estrogen on Nonverbal Processing Speed and Motor Function in Girls with Turner’s Syndrome1 (1998)

The Turner syndrome (TS) phenotype is characterized by a specific neurocognitive profile of normal verbal skills, impaired visual-spatial and/or visual-perceptual abilities, and difficulty with motor function. In the current study, we investigated motor function and nonverbal processing speed in estrogen- and placebo-treated girls (aged 10-12 years) with TS and in age-matched female controls. The goal of this study was to examine whether estrogen replacement therapy would reverse deficits in motor function and in nonverbal processing speed, a measure of the time required to perform certain disparate nonverbal tasks, in adolescent girls with TS. Children received either estrogen (ethinyl estradiol, 12.5-50 ng/kg.day), or placebo for durations of 1-7 yr (mean, 4.0 +/- 2.1 yr) in this randomized, double blind study. Cognitive and motor tasks administered included the Wechsler Intelligence Scale for Children-Revised; nonspatial, repetitive motor tasks (tapping and three tasks from the Paness); and spatially mediated motor tasks [nongrooved pegboard (Lafayette), pursuit rotor, visual-motor integration, and money street map]. Questionnaires administered included the Self-Concept Scale. The major result of this study was the positive estrogen treatment effect on nonverbal processing speed and speeded motor performance in 12-yr-old TS girls. That motor performance would be slower in estrogen-deficient TS females is consistent with previous studies of the influence of estrogen on motor function. Estrogen replacement is thus the most likely explanation for the improved motor speed and nonverbal processing time in the estrogen-treated TS girls compared to that in the placebo-treated TS girls. Whether these findings will influence the psychoeducational outcome or quality of life of females with TS is not yet known.