gebhart/patrepeval huggingface dataset:
Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods (2018)

RNA sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30-day-old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at -80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.
Ion/Ion Proton Transfer Reactions for Protein Mixture Analysis (1996)

Ion/ion proton transfer reactions are shown to be an effective means to facilitate the resolution of ions in electrospray mass spectrometry that differ in mass and charge but are similar in mass-to-charge ratio. Examples are shown in which a minor contaminant protein in a ribonuclease B solution is clearly apparent after ion/ion proton transfer but not in the conventional electrospray mass spectrum. A further example involving a mixture of bovine serum albumin and bovine transferrin also showed the identification of previously unnoticed "contaminant" polymer. The latter mixture also illustrated important issues in the use of the quadrupole ion trap as a reaction vessel and mass analyzer for high mass-to-charge ratio ions. The results suggest that the use of ion trap operating parameters specifically tailored for storage, ejection, detection, and mass-to-charge analysis of high mass-to-charge ratio ions can have attractive analytical figures of merit for determining mixtures of relatively high-mass proteins and, by extension, other types of high-mass biopolymers.
Interaction of intense laser pulses with overdense plasmas. (2009)

This thesis is devoted to theoretical studies of the interaction of intense laser pulses with solid-state targets. This area of laser physics is very active and fast growing as it might possess a number of useful applications in material science, physics, biology and medicine. The main part of the thesis is devoted to the generation of high-order harmonics on the vacuum-plasma interface due to the longitudinal oscillatory motion of the reflecting surface. This has a prospect of generation of trains or even single attosecond pulses that have much more intensity than those generated in atomic media. Before making this source an instrument for studying electron dynamics in condensed matter or for laser-vacuum interactions, one has to know how to control the important properties of the harmonic beam, namely its temporal and spatial structure. To pursue the answering of the question of control, analytical and numerical studies were performed. Most of the ideas are based on the shaping of the laser pulse (both in temporal and spatial domains) and of the target. The second part of the thesis is devoted to the studies of the generation of energetic ion beams. These beams can be used, for example, in cancer therapy, plasma radiography and isotope production. The studies of the influence of laser pulse ellipticity and target thickness on ion beam monoenergetic features and energy allows one to use the results of this thesis for optimization of future experiments.
Microneedle-based drug delivery systems: Microfabrication, drug delivery, and safety (2010)

Many promising therapeutic agents are limited by their inability to reach the systemic circulation, due to the excellent barrier properties of biological membranes, such as the stratum corneum (SC) of the skin or the sclera/cornea of the eye and others. The outermost layer of the skin, the SC, is the principal barrier to topically-applied medications. The intact SC thus provides the main barrier to exogenous substances, including drugs. Only drugs with very specific physicochemical properties (molecular weight < 500 Da, adequate lipophilicity, and low melting point) can be successfully administered transdermally. Transdermal delivery of hydrophilic drugs and macromolecular agents of interest, including peptides, DNA, and small interfering RNA is problematic. Therefore, facilitation of drug penetration through the SC may involve by-pass or reversible disruption of SC molecular architecture. Microneedles (MNs), when used to puncture skin, will by-pass the SC and create transient aqueous transport pathways of micron dimensions and enhance the transdermal permeability. These micropores are orders of magnitude larger than molecular dimensions, and, therefore, should readily permit the transport of hydrophilic macromolecules. Various strategies have been employed by many research groups and pharmaceutical companies worldwide, for the fabrication of MNs. This review details various types of MNs, fabrication methods and, importantly, investigations of clinical safety of MN.
Optimization, Constraint, and History in the Evolution of Eyes (1990)

Several features of the evolution of eyes and photoreceptors are examined in an effort to explore the relative roles of adaptation and historical and developmental constraints. Optical design shows clear evidence of adaptation, which in some respects approaches optima predictable from physics. The primate fovea, on the other hand, illustrates how adaptation can be channeled by developmental heritage. The primary structures of opsins reveal multiple evolutionary lineages within both Drosophila and humans. The pigments of vertebrae rods comprise a subset of opsins whose evolutionary relationships map onto the phylogeny of the parent species. The evolutionary reasons for why most rod pigments absorb maximally at 500 +/- 10 nm are obscure, as there is no convincing explanation based on adaptation alone. Rods are appropriately distinguished from cones on the basis of which opsin gene is expressed. This criterion is likely to be in conflict with other definitions in phyletic lines (e.g., geckos, snakes) that have long diurnal or nocturnal histories accompanied by loss of one or more opsin genes, followed by a secondary adaptation to life in a different photic environment. Color vision--a generalizable perception associated with the spectral composition of light--is usefully distinguished from wavelength-specific behaviors. The latter are also based on multiple visual pigments and more than one spectral class of receptors but cannot be altered by learning. The distinction is particularly forceful in bees, which exhibit both kinds of behavior. The evolution of primate color vision has been shaped by historical factors involving an extensive period of early mammalian nocturnality. Birds, by contrast, have more elaborate cones and a richer set of visual pigments. Avian color space can be represented in a tetrahedron.
TRANSLUMBAR AORTIC PUNCTURE AND RETROGRADE CATHETERIZATION OF THE AORTA IN AORTOGRAPHY AND RENAL ARTERIOGRAPHY (1950)

Goodwin, Willard E. M.D.; Scardino, Peter L. M.D.; Scott, W. W. M.D.; Baltimore, MD. Author Information
Probabilistic Forecasting of Wind Power at the Minute Time-Scale with Markov-Switching Autoregressive Models (2008)

bstract-Better modelling and forecasting of very short-term power fluctuations at large offshore wind farms may significantly enhance control and management strategies of their power output.The paper introduces a new methodology for modelling and forecasting such very short-term fluctuations.The proposed methodology is based on a Markov-switching autoregressive model with time-varying coefficients.An advantage of the method is that one can easily derive full predictive densities.The quality of this methodology is demonstrated from the test case of 2 large offshore wind farms in Denmark.The exercise consists in 1step ahead forecasting exercise on time-series of wind generation with a time resolution of 10 minute.The quality of the introduced forecasting methodology and its interest for better understanding power fluctuations are finally discussed.
An immunochemical study of Neurospora nucleases (1986)

Nucleases derived from Neurospora crassa mycelia with neutral single-strand (ss) endodeoxyribonuclease activity have been examined by immunochemical techniques and by sodium dodecyl sulfate - DNA gel electrophoresis. All of the intracellular nucleases, which have different divalent metal ion requirements, different strand specificities with single- and double-strand DNA, different modes of action on DNA and RNA, and other distinguishing characteristics, are immunochemically related to Neurospora endo-exonuclease. The evidence indicates that these enzymes are derived from one or more related large, inactive (precursor?) polypeptides that are first converted to 75- to 80-kdalton active polypeptide(s) which are very protease sensitive. Further limited proteolysis results in the production of the various active forms of nuclease studied here. Some proteolytic conversions may occur in a controlled manner in vivo in different cell compartments, but others are very likely artifacts resulting from uncontrolled proteolysis during extraction and isolation. The intracellular forms of Neurospora endo-exonuclease are immunologically cross-active with ss-DNA-binding nucleases isolated from Aspergillus nidulans and Saccharomyces cerevisiae. They are not immunochemically related to two extracellular Neurospora nucleases, the pancreatic DNase-I-like DNase A and a ss-specific exonuclease, and they are also not related to other fungal and plant nucleases with ss-specific endonuclease activity such as the S1 nuclease of Aspergillus oryzae, the P1 nuclease of Penicillium citrinum, and mung bean nuclease.
Chronic softening spinal cord stimulation arrays (2018)

Softening SCS arrays meet the needs for research-grade devices in rats and could be developed into human devices in the future.
Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices (2003)

The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.
Partial Agonists for A3 Adenosine Receptors (2004)

Selective agonists for A(3) adenosine receptors (ARs) could potentially be therapeutic agents for a variety of disorders, including brain and heart ischemic conditions, while partial agonists may have advantages over full agonists as a result of an increased selectivity of action. A number of structural determinants for A(3)AR activation have recently been identified, including the N(6)-benzyl group, methanocarba substitution of ribose, 2-chloro and 2-fluoro substituents, various 2'- and 3'-substitutions and 4'-thio substitution of oxygen. The 2-chloro substitution of CPA and R-PIA led to A(3) antagonism (CCPA) and partial agonism (Cl-R-PIA). 2-Chloroadenosine was a full agonist, while 2-fluoroadenosine was a partial agonist. Both 2'- and 3'- substitutions have a pronounced effect on its efficacy, although the effect of 2'-substitution was more dramatic. The 4-thio substitution of oxygen may also diminish efficacy, depending on other substitutions. Both N(6)-methyl and N(6)-benzyl groups may contribute to the A(3) affinity and selectivity; however, an N(6)-benzyl group but not an N(6)-methyl group diminishes A(3)AR efficacy. N(6)-benzyl substituted adenosine derivatives have similar potency for human and rat A(3)ARs while N(6)-methyl substitution was preferable for the human A(3)AR. The combination of 2-chloro and N(6)-benzyl substitutions appeared to reduce efficacy further than either modification alone. The A(2A)AR agonist DPMA was shown to be an antagonist for the human A(3)AR. Thus, the efficacy of adenosine derivatives at the A(3)AR appears to be more sensitive to small structural changes than at other subtypes. Potent and selective partial agonists for the A(3)AR could be identified by screening known adenosine derivatives and by modifying adenosine and the adenosine derivatives.
Genetic control of pungency in C. chinense via the Pun1 locus (2007)

Capsaicin, the pungent principle in hot peppers, acts to deter mammals from consuming pungent pepper pods. Capsaicinoid biosynthesis is restricted to the genus Capsicum and results from the acylation of the aromatic compound, vanillylamine, with a branched-chain fatty acid. The presence of capsaicinoids is controlled by the Pun1 locus, which encodes a putative acyltransferase. In its homozygous recessive state, pun1/pun1, capsaicinoids are not produced by the pepper plant. HPLC analysis confirmed that capsaicinoids are only found in the interlocular septa of pungent pepper fruits. Immunolocalization studies showed that capsaicinoid biosynthesis is uniformly distributed across the epidermal cells of the interlocular septum. Capsaicinoids are secreted from glandular epidermal cells into subcuticular cavities that swell to form blisters along the epidermis. Blister development is positively associated with capsaicinoid accumulation and blisters are not present in non-pungent fruit. A genetic study was used to determine if the absence of blisters in non-pungent fruit acts independently of Pun1 to control pungency. Screening of non-pungent germplasm and genetic complementation tests identified a previously unknown recessive allele of Pun1, named pun1(2). Sequence analysis of pun1(2) revealed that a four base pair deletion results in a frameshift mutation and the predicted production of a truncated protein. Genetic analysis revealed that pun1(2) co-segregated exactly with the absence of blisters, non-pungency, and a reduced transcript accumulation of several genes involved in capsaicinoid biosynthesis. Collectively, these results establish that blister formation requires the Pun1 allele and that pun1(2) is a recessive allele from C. chinense that results in non-pungency.
Maraviroc Attenuates Trauma-Hemorrhage-Induced Hepatic Injury through PPAR Gamma-Dependent Pathway in Rats (2013)

Maraviroc is a CC-chemokine receptor 5 (CCR5) antagonist with potent antiviral and cancer preventive effects. Recent evidence suggests that the co-existence of CCR5 in various cell types is involved in inflammation. However, the effects that CCR5 antagonists produce in trauma-hemorrhage remain unknown. The peroxisome proliferator-activated receptor gamma (PPAR(γ)) pathway exerts anti-inflammatory effects in injury. In this study, we hypothesized that maraviroc administration in male rats, after trauma-hemorrhage, decreases cytokine production and protects against hepatic injury through a PPAR(γ)-dependent pathway. Male Sprague-Dawley rats underwent trauma-hemorrhage (mean blood pressure maintained at approximately 35-40 mmHg for 90 minutes), followed by fluid resuscitation. During resuscitation, a single dose of maraviroc (3 mg/kg, intravenously) with and without a PPAR(γ) antagonist GW9662 (1 mg/kg, intravenously), GW9662 or vehicle was administered. Plasma alanine aminotransferase (ALT) with aspartate aminotransferase (AST) concentrations and various hepatic parameters were measured (n=8 rats/group) at 24 hours after resuscitation. The results showed that trauma-hemorrhage increased hepatic myeloperoxidase activity, intercellular adhesion molecule-1 and interleukin-6 levels, and plasma ALT and AST concentrations. These parameters were significantly improved in the maraviroc-treated rats subjected to trauma-hemorrhage. Maraviroc treatment also increased hepatic PPAR(γ) expression compared with vehicle-treated trauma-hemorrhaged rats. Co-administration of GW9662 with maraviroc abolished the maraviroc-induced beneficial effects on the above parameters and hepatic injury. These results suggest that the protective effect of maraviroc administration on alleviation of hepatic injury after trauma-hemorrhage, which is, at least in part, through PPAR(γ)-dependent pathway.
On‐line calibration of a computerized biosensor system for continuous measurements of glucose and lactate (1995)

An on-line calibration procedure for application in continuous monitoring systems has been developed. Control of the calibration value and recalibration on-line during monitoring is possible without having to disrupt the sample withdrawal. The calibration procedure has been applied and evaluated in a continuous biosensor system based on the detection of oxygen depletion during enzymatic substrate conversion by immobilized oxidases. Evaluation included on-line calibration during continuous measurements of glucose and lactate in bovine blood samples. Calibration of the complete system consisting of a sampling device, a sample handling step, a biocatalytic step, a detection step, and a data processing unit is performed by the on-line addition of a calibration solution to a blank sample which is fed through the system. The calibration cycle is completed within 5.5 min. When recalibration is carried out during monitoring, the calibration solution is added to the sample, instead of to a blank sample, and the increase in outlet singl is registered. The major advantage of this internal standard principle is that the calibration solution is fed through the whole system according to the same path as the sample solution and thus takes into account all parameters influencing the sample. (c) 1995 John Wiley & Sons, Inc.
[Vegetation change in Shenzhen City based on NDVI change classification]. (2008)

Based on the TM images of 1988 and 2003 as well as the land-use change survey data in 2004, the vegetation change in Shenzhen City was assessed by a NDVI (normalized difference vegetation index) change classification method, and the impacts from natural and social constraining factors were analyzed. The results showed that as a whole, the rapid urbanization in 1988-2003 had less impact on the vegetation cover in the City, but in its plain areas with low altitude, the vegetation cover degraded more obviously. The main causes of the localized ecological degradation were the invasion of built-ups to woods and orchards, land transformation from woods to orchards at the altitude of above 100 m, and low percentage of green land in some built-ups areas. In the future, the protection and construction of vegetation in Shenzhen should focus on strengthening the protection and restoration of remnant woods, trying to avoid the built-ups' expansion to woods and orchards where are better vegetation-covered, rectifying the unreasonable orchard constructions at the altitude of above 100 m, and consolidating the greenbelt construction inside the built-ups. It was considered that the NDVI change classification method could work well in efficiently uncovering the trend of macroscale vegetation change, and avoiding the effect of random noise in data.
Graphene, a promising transparent conductor (2010)

New electronic devices such as touch screens, flexible displays, printable electronics, solid-state lighting and thin film photovoltaics have led to a rapidly growing market for flexible transparent conductors. Standard indium tin oxide films are unlikely to satisfy future needs due to losses in conductivity on bending and the escalating cost of indium which is in limited supply. Recent advances in the synthesis and characterization of graphene indicate that it may be suitable for many electronic applications including as a transparent conductor. Graphene hybrids with, for example, carbon nanotubes, may prove to be especially interesting.
Review on Reactor Configurations for Adsorption-Based CO2 Capture (2021)

Adsorption-based CO2 capture has enjoyed considerable research attention in recent years. Most of the research efforts focused on sorbent development to reduce the energy penalty. However, the use of suitable gas–solid contacting systems is key for extracting the full potential from the sorbent to minimize operating and capital costs and accelerate the commercial deployment of the technology. This paper reviews several reactor configurations that were proposed for adsorption-based CO2 capture. The fundamental behavior of adsorption in different gas–solid contactors (fixed, fluidized, moving, or rotating beds) and regeneration under different modes (pressure, temperature, or combined swings) is discussed, highlighting the strengths and limitations of different combinations of gas–solid contactor and regeneration mode. In addition, the estimated energy duties in published studies and current technology readiness level of the different reactor configurations are reported. Other aspects, such as the reactor footprint, the operation strategy, suitability to retrofits, and the ability to operate under flexible loads are also discussed. In terms of future work, the key research need is a standardized techno-economic benchmarking study to calculate CO2 avoidance costs for different adsorption technologies under standardized assumptions. Qualitatively, each technology presents several strengths and weaknesses that make it impossible to identify a clear optimal solution. Such a standardized quantitative comparison is therefore needed to focus on future technology development efforts.
Infusion devices: risks, functions and management (2000)

The use of infusion devices to administer intravenous solutions and drugs is common practice throughout a variety of healthcare settings. The risks associated with such practice are wide and varied. Training, maintenance, clinical need and availability of infusion devices are key areas that need to be addressed when managing associated risks. Nurses have a key role to play in addressing these risks.