gebhart/patrepeval huggingface dataset:
Design, synthesis and biological evaluation of 4′-demethyl-4-deoxypodophyllotoxin derivatives as novel tubulin and histone deacetylase dual inhibitors (2014)

In this study, we have designed and synthesized a class of 4′-demethyl-4-deoxypodophyllotoxin derivatives as tubulin–HDAC dual inhibitors.
Hydrogen bonding basicity of amidines (1988)

The hydrogen bonding basicity of amidines (1)–(20) has been measured by means of the frequency shift Δν(OH) of methanol hydrogen bonded to amidines and of the formation constant K of their complexes with 4-fluorophenol. The electronic and steric effects of substituents on the imino nitrogen have been studied. Hydrogen bonding occurs at the imino nitrogen atom except for acetylformamidine (16) for which it occurs on the carbonyl group. For compounds 4-XC6H4NCHNMe2, with X = NO2, COMe, or CN, hydrogen bonding also takes place on the NO2, COMe, or CN groups. From the logK/Δν(OH) correlation, two subsets, phenylformamidines and alkylformamidines, can be distinguished for the family of formamidines. For formamidines, Brönsted basicities correlate with Δν(OH) as for the pyridines.
Message Disposition Notification (MDN) profile for Internet Message Access Protocol (IMAP) (2003)

The Message Disposition Notification (MDN) facility defined in RFC 2298 provides a means by which a message can request that message processing by the recipient be acknowledged as well as a format to be used for such acknowledgements. However, it doesn't describe how multiple Mail User Agents (MUAs) should handle the generation of MDNs in an Internet Message Access Protocol (IMAP4) environment.
Vibrio cholerae O139 synonym bengal is closely related to Vibrio cholerae El Tor but has important differences (1994)

Although Vibrio cholerae O139 synonym Bengal strains, from the current epidemics in India and Bangladesh, are closely related to seventh-pandemic strains, as shown by multilocus enzyme electrophoresis, Bengal strains are encapsulated and portions of the O1 antigen biosynthetic complex genes found in O1 strains are altered or lacking. Encapsulated Bengal strains showed resistance to killing by normal human serum. The presence of the capsule suggests the potential for bloodstream invasion in susceptible hosts and has profound implications for vaccine development.
Physics of biological evolution (2014)

Part I: A remarkable feature of life on Earth is that despite the apparent observed diversity, the underlying chemistry that powers it is highly conserved. From the level of the nucleobases, through the amino acids and proteins they encode, to the metabolic pathways of chemical reactions catalyzed by these proteins, biology often utilizes identical solutions in vastly disparate organisms. This universality is intriguing as it raises the question of whether these recurring features exist because they represent some truly optimal solution to a given problem in biology, or whether they simply exist by chance, having arisen very early in life's history. In this project we consider the universality of metabolism { the set of chemical reactions providing the energy and building blocks for cells to grow and divide. We develop an algorithm to construct the complete network of all possible biochemically feasible compounds and reactions, including many that could have been utilized by life but never were. Using this network we investigate the most highly conserved piece of metabolism in all of biology, the trunk pathway of glycolysis. We design a method which allows a comparison between the large number of alternatives to this pathway and which takes into account both thermodynamic and biophysical constraints, finding evidence that the existing version of this pathway produces optimal metabolic fluxes under physiologically relevant intracellular conditions. We then extend our method to include an evolutionary simulation so as to more fully explore the biochemical space. Part II: Studies of population dynamics have a long history and have been used to understand the properties of complex networks of ecological interactions, extinction events, biological diversity and the transmission of infectious disease. One aspect of these models that is known to be of great importance, but one which nonetheless is often neglected, is spatial structure. Various classes of models have been proposed with each allowing different insights into the role space plays. Here we use a lattice-based approach. Motivated by gene transfer and parasite dynamics, we extend the well-studied contact process of statistical physics to include multiple levels. Doing so generates a simple model which captures in a general way the most important features of such biological systems: spatial structure and the inclusion of both vertical as well as horizontal transmission. We show that spatial structure can produce a qualitatively new effect: a coupling between the dynamics of the infection and of the underlying host population, even when the infection does not affect the fitness of the host. Extending the model to an arbitrary number of levels, we find a transition between regimes where both a finite and infinite number of parasite levels are sustainable, and conjecture that this transition is related to the roughening transition of related surface growth models.
what the journals say (2007)

Lead cancer nurse roles have evolved following the publication of the Calman−Hine Report in 1995 as well as other subsequent government publications. The authors recognize that the lead cancer nurse works in collaboration with the lead cancer clinician and cancer services manager to make an effective contribution to the planning and delivery of cancer care services. However, the authors recognize a significant variation in the role across the country. This led them to explore the complex and often ill-defined remit of the lead cancer nurse role and compares this with nurse consultants and advanced nurse practitioner roles. This article sets out to explore the challenges facing both postholders and organizations and aims to focus on strategies that will offer support and education.
<i>Response</i> : Immuno-PCR with a Commercially Available Avidin System (1993)

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Carbon Nanotubes Promote Growth and Spontaneous Electrical Activity in Cultured Cardiac Myocytes (2012)

Nanoscale manipulations of the extracellular microenvironment are increasingly attracting attention in tissue engineering. Here, combining microscopy, biological, and single-cell electrophysiological methodologies, we demonstrate that neonatal rat ventricular myocytes cultured on substrates of multiwall carbon nanotubes interact with carbon nanotubes by forming tight contacts and show increased viability and proliferation. Furthermore, we observed changes in the electrophysiological properties of cardiomyocytes, suggesting that carbon nanotubes are able to promote cardiomyocyte maturation.
Gene Therapy for Sensorineural Hearing Loss (2014)

Gene therapy is a promising treatment modality that is being explored for several inherited disorders. Multiple human gene therapy clinical trials are currently ongoing, but few are directed at hearing loss. Hearing loss is one of the most prevalent sensory disabilities in the world, and genetics play an important role in the pathophysiology of hearing loss. Gene therapy offers the possibility of restoring hearing by overcoming the functional deficits created by the underlying genetic mutations. In addition, gene therapy could potentially be used to induce hair cell regeneration by delivering genes that are critical to hair cell differentiation into the cochlea. In this review, we examine the promises and challenges of applying gene therapy to the cochlea. We also summarize recent studies that have applied gene therapy to animal models of hearing loss.
A single-amino acid substitution in a gamma-aminobutyric acid subtype A receptor locus is associated with cyclodiene insecticide resistance in Drosophila populations. (1993)

Resistance to cyclodiene insecticides, documented in at least 277 species, is perhaps the most common kind of resistance to any pesticide. By using cyclodiene resistance to localize the responsible gene, a gamma-aminobutyric acid type A receptor/chloride ion-channel gene was previously cloned and sequenced from an insecticide-susceptible Drosophila melanogaster strain. We now describe the molecular genetics of the resistance allele. A single-base-pair mutation, causing a single-amino acid substitution (Ala-->Ser) within the second membrane-spanning region of the channel, was found to be the only consistent difference between resistant and susceptible strains of D. melanogaster. Some resistant strains of Drosophila simulans show the same mutation, whereas others show an alternative single-base-pair mutation in the same codon, resulting in the substitution of a different amino acid (glycine). These constitute single-box-pair mutations in insects that confer high levels of resistance to insecticides. The presence of the resistance mutations was then tested in a much larger set of strains by the PCR and subsequent digestion with a diagnostic restriction endonuclease. Both resistance-associated mutations cause the loss of a Hae II site. This site was invariably present in 122 susceptible strains but absent in 58 resistant lines of the two species sampled from five continents. PCR/restriction endonuclease treatment was also used to examine linkage of an EcoRI polymorphism in a neighboring intron in D. melanogaster, which was found associated with resistance in all but 3 of 48 strains examined. These PCR-based techniques are widely applicable to examination of the uniqueness of different resistance alleles in widespread populations, the identification of resistance mechanisms in different species, and the determination of resistance frequencies in monitoring.
Why looking at the whole hippocampus is not enoughâ€”a critical role for anteroposterior axis, subfield and activation analyses to enhance predictive value of hippocampal changes for Alzheimerâ€™s disease diagnosis (2014)

The hippocampus is one of the earliest affected brain regions in Alzheimer's disease (AD) and its dysfunction is believed to underlie the core feature of the disease-memory impairment. Given that hippocampal volume is one of the best AD biomarkers, our review focuses on distinct subfields within the hippocampus, pinpointing regions that might enhance the predictive value of current diagnostic methods. Our review presents how changes in hippocampal volume, shape, symmetry and activation are reflected by cognitive impairment and how they are linked with neurogenesis alterations. Moreover, we revisit the functional differentiation along the anteroposterior longitudinal axis of the hippocampus and discuss its relevance for AD diagnosis. Finally, we indicate that apart from hippocampal subfield volumetry, the characteristic pattern of hippocampal hyperactivation associated with seizures and neurogenesis changes is another promising candidate for an early AD biomarker that could become also a target for early interventions.
A Reconfigurable Multichannel Capacitive Sensor Array Interface (2011)

The design of a reconfigurable capacitive sensor array interface comprised of a subsystem able to read an array of capacitive-type sensors and an embedded processor is described. Each sensor is connected to a ring oscillator, which translates capacitive changes into a variable-frequency pulse train. An in-depth analysis of the oscillator behavior including all parasitic elements has been performed, and the use of a Schmitt trigger at the inverter chain is proposed to assure oscillation for capacitance values ranging from 1 to 1500 pF. The oscillation frequency is estimated by using a 16-b counter and the appropriate user-defined counting interval ranging from a few microseconds to several seconds in order to achieve maximum accuracy within the entire capacitance range. The 2-B word thus produced can be sent to a host computer through a serial or parallel interface for further processing. To demonstrate the concept, a 16-channel interface has been described in a hardware description language and implemented on a complex programmable logic device. Measurement of two different capacitive pressure sensors developed in-house reveals frequency sensitivity values of -252.1 and -9.54 Hz/fF, which are in good agreement with the expected values derived by the analytic relations.
Erythropoietin in Sports (2005)

Erythropoietin (EPO) is found naturally in the human body and has been commercially available as recombinant human EPO (rEPO) for almost 20 years. Although the positive benefits of rEPO cannot be denied for those who suffer from anemia, athletes have also used the drug as an ergogenic aid. It has replaced conventional “blood doping” as the drug of choice to improve performance in contests requiring aerobic potential. Testing for the drug in the past has proven difficult due to several factors. The similarities in structure and metabolism of EPO and rEPO allow those who choose to abuse rEPO to avoid detection. Due to the inherent danger of abusing rEPO and its analogues, the various governing bodies of international sports continue to improve testing methods for this illegal substance.
The BDGP Gene Disruption Project (2004)

The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in >30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7140 lines. It now includes individual lines predicted to disrupt 5362 of the 13,666 currently annotated Drosophila genes (39%). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene misexpression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.
A 90nm CMOS 13.56MHz NFC transceiver (2009)

This paper presents the design of a 90 nm 13.56 MHz NFC transceiver. The concept of near field communication is introduced while discussing how a combination of both initiator and target functions are required. The initiator circuitry used to generate the required magnetic field and demodulate the received back-scatter is explained and the passive and active target circuitry used to receive a magnetic field whilst demodulating and load-modulating is presented. Finally there is a short description of the evaluation module (EVM) containing the 90 nm NFC, an antenna and interface to a host processor or PC.
Effect of colesevelam on faecal bile acids and bowel functions in diarrhoea‐predominant irritable bowel syndrome (2015)

Colesevelam increases delivery of bile acids to stool while improving stool consistency, and increases hepatic bile acid synthesis, avoiding steatorrhoea in patients with IBS-D. Overall effects are consistent with luminal bile acid sequestration by colesevelam.
Strength of U-Shaped Bellows : Supplement, Design Formulas and Charts for the Case of Axial Loading (1967)

In this paper, the design formulas and charts indicating the relation between displacement and maximum stress values of U-shaped bellows for the case of axial loading are given, and simple and practical design formulas are derived from the design charts in the 2nd report. Also the simple design formulas and charts for C-and Ω-shaped bellows are presented. On the other hand authors' results, part of which have been already published, are compared with M. W. Kellogg's formulas which are nowadays widely employed for practical design.
Nuclear magnetic resonance monitoring of sodium in biological tissues (1989)

In recent year, the 23Na nuclear magnetic resonance (NMR) technique has been applied to the study of biological tissues. The advantages of this method are noninvasiveness and good sensitivity. The resonances of the intra- and extra-cellular sodium can be separated by the addition of shift reagents to the extracellular compartment. The method has been mostly applied to cell suspensions, kidney tubules, glands, and small organs. Owing to line-broadening effects, the NMR visibility of the intracellular sodium is reduced to 40% in most cases but can be lower or higher. Time-dependent measurements are possible with adequate life-supporting equipment, allowing the determination of transport parameters. 23Na relaxation times are short in tissues (below 50 ms) and highly dependent on the medium composition. The application of the 23Na NMR technique to intact organs can be hampered by the difficulty of getting a good distribution of the shift reagent in the extracellular milieu. A summary of the studies performed is presented with specific examples to illustrate typical applications.
Liver‐specific protein 2: a <scp>P</scp>lasmodium protein exported to the hepatocyte cytoplasm and required for merozoite formation (2012)

The liver stage is the first stage of the malaria parasite that replicates in the vertebrate host. However, little is known about the interplay between the parasite liver stage and its host cell, the hepatocyte. In this study, we identified an exported protein that has a critical role in parasite development in host hepatocytes. Expressed sequence tag analysis of Plasmodium berghei liver-stage parasites indicated that transcripts encoding a protein with an N-terminal signal peptide, designated liver-specific protein 2 (LISP2), are highly expressed in this stage. Expression of LISP2 was first observed 24 h after infection and rapidly increased during the liver-stage schizogony. Immunofluorescent staining with anti-LSP2 antibodies showed that LISP2 was carried to the parasitophorous vacuole and subsequently transported to the cytoplasm and nucleus of host hepatocytes. Gene targeting experiments demonstrated that majority of the LISP2-mutant liver-stage parasites arrested their development during formation of merozoites. These results indicate that exported LISP2 is involved in parasite-host interactions required for the development of liver-stage parasites inside hepatocytes. This study demonstrated that mid-to-late liver-stage malarial parasites have a system for exporting proteins to the host cell as intraerythrocytic stages do and presumably to use the proteins to modify the host cell and improve the environment.
Highly Thermostable L-Threonine Dehydrogenase from the Hyperthermophilic Archaeon Thermococcus kodakaraensis (2009)

l-Threonine dehydrogenase, a key enzyme in the l-threonine metabolism, catalyses the NAD(+)-dependent conversion of l-threonine to 2-amino-3-ketobutyrate, that non-enzymically decarboxylates to aminoacetone. A search of the genome sequence of hyperthermophilic archaeon, Thermococcus kodakaraensis revealed the presence of a closely related orthologue (TK0916) of archaeal and bacterial l-threonine dehydrogenase genes. Expression in Escherichia coli, purification and characterization of the TK0916 gene product revealed that this gene actually coded for a protein with high levels of l-threonine dehydrogenase activity (7.26 U mg(-1)). The enzyme exhibited highest activity at pH 12 and 90 degrees C. The K(m) values for l-threonine and NAD(+) at 50 degrees C were 1.6 mM and 0.028 mM, respectively. The enzyme activity was dependent on divalent cations. The half-life of the enzyme was more than 2 h at 85 degrees C and 24 min in boiling water. This is the most thermostable threonine dehydrogenase exhibiting optimal activity at the highest pH (12) reported to date. This is the first report on the characterization of a TDH from genus Thermococcus.
Detecting nonlinearity in multivariate time series (1995)

We propose an extension to time series with several simultaneously measured variables of the nonlinearity test, which combines the redundancy -- linear redundancy approach with the surrogate data technique. For several variables various types of the redundancies can be defined, in order to test specific dependence structures between/among (groups of) variables. The null hypothesis of a multivariate linear stochastic process is tested using the multivariate surrogate data. The linear redundancies are used in order to avoid spurious results due to imperfect surrogates. The method is demonstrated using two types of numerically generated multivariate series (linear and nonlinear) and experimental multivariate data from meteorology and physiology.
Effect of high‐fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock (2017)

The 6-month cattle and female parents shared similar intestinal bacteria; the community structure of fecal microbiota was significantly affected by high-fat diet in older cattle. © 2017 Society of Chemical Industry.
Diagnosis and treatment of halitosis. (1996)

Diagnostic and treatment services for patient complaints of "bad breath" are currently being offered in many dental offices. There are no accepted standards of care for these services, and clinical protocols for the diagnosis and treatment of breath malodor vary widely. This article attempts to review the biological and psychological bases of patients' complaints of bad breath and to describe a clinical protocol for the evaluation and treatment of such complaints. This protocol resulted in a 99% success rate in eliminating objectively measured breath malodor. However, 24% of patients continued to believe that at least some of their bad breath persisted after treatment. The merits of various diagnostic procedures are discussed in light of the psychogenic component of the symptomatology of halitosis sufferers.