gebhart/patrepeval huggingface dataset:
Synthesis of β‐pyrazinyl‐L‐alanine (Paa) and of peptide derivatives (1983)

Abstract The title compound was prepared via a malonic ester synthesis starting with α‐chloromethylpyrazine [2], and ending, after an asymmetric enzymatic hydrolysis of the racemic N ‐acetyl‐β‐2‐pyrazinylalanine to the L ‐form of the new amino acid. The optical purity was ascertained by 1 H‐NMR analysis at 360 MHz of the diastereoisomeric dipeptides L ‐pyrazinylalanine‐ L ‐leucine and D ‐pyrazinylalanine‐ L ‐leucine. Hydrophobic, steric and electronic parameters for its side chain were also estimated, which can be useful for the quantitative study of structure‐activity relationships of biologically active peptide derivatives. The new amino acid could be introduced in the place of phenylalanine in the enkephalin‐like pentapeptide [ D ‐alanyl 2 , leucine 5 ]enkephalin, thus showing good stability towards the classical methods of peptide synthesis.
Avian influenza: A review (2007)

Avian influenza virus A/H5N1 is a public health threat that has the potential to cause serious illness and death in humans. Understanding its pathology, transmission, clinical features, and pharmacologic treatments and preparing for the prevention and management of its outbreak will help avoid its potentially devastating consequences.
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture (2019)

DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.
MicroRNAs in Nonalcoholic Fatty Liver Disease (2015)

Nonalcoholic fatty liver disease (NAFLD) has become the most common liver disorder. Strongly linked to obesity and diabetes, NAFLD has the characteristics of complex diseases with substantial heterogeneity. Accordingly, our ability to predict the risk of advanced NAFLD and provide efficient treatment may improve by a better understanding of the relationship between genotype and phenotype. MicroRNAs (miRNAs) play a major role in the fine-tuning of gene expression and they have recently emerged as novel biomarkers and therapeutic tools in the management of NAFLD. These short non-coding RNA sequences act by partial repression or degradation of targeted mRNAs. Deregulation of miRNAs has been associated with different stages of NAFLD, while their biological role in the pathogenesis remains to be fully understood. Systems biology analyses based on predicted target genes have associated hepatic miRNAs with molecular pathways involved in NAFLD progression such as cholesterol and lipid metabolism, insulin signaling, oxidative stress, inflammation, and pathways of cell survival and proliferation. Moreover, circulating miRNAs have been identified as promising noninvasive biomarkers of NAFLD and linked to disease severity. This rapidly growing field is likely to result in major advances in the pathomechanism, prognostication, and treatment of NAFLD.
Use of Vacuum-Assisted Wound Closure in Three Chronic Wounds (1998)

Vacuum-assisted wound closure has been reported to promote the healing of chronic wounds by increasing the vascularity and oxygenation of the wound bed, maintaining a moist environment, and removing exudate through negative pressure. The results of vacuum-assisted wound closure for 3 patients with chronic wounds are presented.
Variable-Bin-Rate CABAC Engine for H.264/AVC High Definition Real-Time Decoding (2009)

This paper presents an efficient VLSI architecture for H.264/AVC content-adaptive binary arithmetic code (CABAC) decoding. We introduce several new techniques to maximize the parallelism of the decoding process, including variable-bin-rate strategy, multiple-bin arithmetic decoding, and efficient probability propagation scheme. The CABAC engine can ensure the real-time decoding for H.264/AVC main profile HD level 4.0. Synthesis results show that the multi-bin decoder can be operated up to 45 MHz, and the total logic area is only 42 K gates when targeted at TSMC's 0.18-mum process.
Transient loss of consciousness 2: patient pathways and the nurse's role. (2009)

This second article of a two-part unit explores the assessment and treatment of patients with transient loss of consciousness. It explains the importance of taking a thorough medical history, nurses' role in treating these patients, and the various diagnostic tests and management options.
Tau Oligomers as Potential Drug Target for Alzheimer Disease (AD) Treatment (2011)

The microtubule-associated protein tau is required for microtubule assembly, axonal transport, neurite outgrowth, and stability of microtubules (Binder et al. 1985). Tau selfassembly, aggregation, and accumulation in neurofibrillary tangles (NFTs) are major pathological hallmarks of Alzheimer disease (AD) and other neurodegenerative diseases (Lee et al. 2001, Alonso et al. 2008). Although the importance of tau in AD and other tauopathies is well established (Iqbal et al. 2009, Ballatore et al. 2007, Haroutunian et al. 2007) still unanswered is whether NFTs are the primary neurotoxic factor (Brunden et al. 2008, Marx 2007, Kayed & Jackson 2009). Despite the poor correlation between NFTs and disease progression, and evidence showing, that neuronal loss in AD actually precedes NFTs formation research until recently focused on them and other large meta-stable inclusions composed of aggregated hyperphosphorylated tau protein. Lately, the significance and toxicity of NFTs have been challenged and new aggregated tau entity has emerged as the true pathogenic species in tauopathies and a possible mediator of A┚ toxicity in AD. Tau intermediate aggregate (tau oligomers; aggregates of an intermediate that is between monomers and NFTs in size) can cause neurodegeneration and memory impairment in the absence of A┚. This exciting body of evidence includes results from human brain samples, transgenic mouse and cell-based studies, thus tau oligomers present a new and novel drug target for AD treatment. In this chapter, we summarize the characterization and toxicity of tau oligomers; discuss the evidence supporting their critical role in AD pathogenesis, and the potential and challenges for targeting them by immunotherapy and drug discovery as a novel approach for AD treatment
Chelating, film‐forming, and coagulating ability of the chitosan–glucan complex from Aspergillus niger industrial wastes (1980)

Waste mycelia of Aspergillus niger from a citric acid production plant are simply treated with boiling 30-40% NaOH aqueous solutions for 4-6 hr to obtain the insoluble chitosan-glucan complex whose infrared, ESR, and x-ray diffraction spectra are reported. A number of transition- and post-transition-metal ions are chelated and collected by chitosan-glucan with higher yields than by animal chitosan. Immediate flocculation occurs upon mixing chitosan-glucan dispersions with alginate and polymolybdate solutions. Membranes are also obtained from chitosan-glucan dispersions in acetic acid or in chloral and dimethyl formamide mixtures.
Real-time scheduling rules for demand responsive transit systems (2002)

The scheduling of vehicles for demand responsive transportation systems is a classic combinatorial optimization problem. With the passage of the Americans with Disabilities Act, which requires that transit agencies provide para-transit or on demand service for the disabled, there has been renewed interest in demand responsive transit. In this paper, we review the state-of-the-art in the literature on scheduling demand responsive systems and present a new heuristic for real-time scheduling of such systems. We evaluate the heuristics using data provided by para-transit service providers in Los Angeles County.
Electromagnetic simulation of terahertz frequency range filters for genetic sensing (2006)

We report on a numerical study of the sensitivity of electrical terahertz (THz) frequency range passive filters under conditions of dielectric loading. We investigate band-pass filters, ring resonators, and band-stop filters, all of which have been proposed as devices capable of measuring the hybridization state of overlaid DNA films, thereby acting as genetic sensors. The transmission characteristics of these filters are examined when loaded with samples of different relative permittivities and thicknesses, and these results are discussed in the context of recent experimental works. A comparative analysis of the three filter types is performed, and conclusions are drawn on the suitability of the various filters for the analysis of DNA films during genetic testing and other dielectric materials.
Using Simulation to Model an Iron Ore Logistics Chain (2008)

Simulation is a proven way of analysing the transport process in iron are projects, and is used to optimise operations and size fleets and equipment. It is a quantitative technique that has supported the strategic decision making of mining companies for over twenty years, both in greenfield projects and when considering expansion plans on existing projects. Major projects now use modelling as an integral part of their wider engineering studies. A number of major iron ore mines are proposed in the mid-west region of Western Australia, connected by rail to a proposed new port at Oakajee. As part of the Feasibility Studies for Oakajee Port & Rail, Maunsell modelled the logistics process from the Jack Hills and Weld Range mines to Oakajee Port. Detailed railway operations of a new 500km heavy haul railway were modelled, together with the stockyard and shipping operations at the proposed Oakajee Port. This paper provides a case study on the use of rail simulation and its relationship to the wider engineering study.
Physically based principles of cell adhesion mechanosensitivity in tissues (2012)

The minimal structural unit that defines living organisms is a single cell. By proliferating and mechanically interacting with each other, cells can build complex organization such as tissues that ultimately organize into even more complex multicellular living organisms, such as mammals, composed of billions of single cells interacting with each other. As opposed to passive materials, living cells actively respond to the mechanical perturbations occurring in their environment. Tissue cell adhesion to its surrounding extracellular matrix or to neighbors is an example of a biological process that adapts to physical cues. The adhesion of tissue cells to their surrounding medium induces the generation of intracellular contraction forces whose amplitude adapts to the mechanical properties of the environment. In turn, solicitation of adhering cells with physical forces, such as blood flow shearing the layer of endothelial cells in the lumen of arteries, reinforces cell adhesion and impacts cell contractility. In biological terms, the sensing of physical signals is transduced into biochemical signaling events that guide cellular responses such as cell differentiation, cell growth and cell death. Regarding the biological and developmental consequences of cell adaptation to mechanical perturbations, understanding mechanotransduction in tissue cell adhesion appears as an important step in numerous fields of biology, such as cancer, regenerative medicine or tissue bioengineering for instance. Physicists were first tempted to view cell adhesion as the wetting transition of a soft bag having a complex, adhesive interaction with the surface. But surprising responses of tissue cell adhesion to mechanical cues challenged this view. This, however, did not exclude that cell adhesion could be understood in physical terms. It meant that new models and descriptions had to be created specifically for these biological issues, and could not straightforwardly be adapted from dead matter. In this review, we present physical concepts of tissue cell adhesion and the unexpected cellular responses to mechanical cues such as external forces and stiffness sensing. We show how biophysical approaches, both experimentally and theoretically, have contributed to our understanding of the regulation of cellular functions through physical force sensing mechanisms. Finally, we discuss the different physical models that could explain how tissue cell adhesion and force sensing can be coupled to internal mechanosensitive processes within the cell body.
Data-streams and histograms (2001)

Histograms have been used widely to capture data distribution, to represent the data by a small number of step functions. Dynamic programming algorithms which provide optimal construction of these histograms exist, albeit running in quadratic time and linear space. In this paper we provide linear time construction of 1 + ε approximation of optimal histograms, running in polylogarithmic space.
Adaptive and reliable parallel computing on networks of workstations (1997)

In this paper, we present the design of Cilk-NOW, a runtime system that adaptively and reliably executes functional Cilk programs in parallel on a network of UNIX workstations. Cilk (pronounced “silk”) is a parallel multithreaded extension of the C language, and all Cilk runtime systems employ a provably efficient threadscheduling algorithm. Cilk-NOW is such a runtime system, and in addition, Cilk-NOW automatically delivers adaptive and reliable execution for a functional subset of Cilk programs. By adaptive execution, we mean that each Cilk program dynamically utilizes a changing set of otherwise-idle workstations. By reliable execution, we mean that the Cilk-NOW system as a whole and each executing Cilk program are able to tolerate machine and network faults. Cilk-NOW provides these features while programs remain fault oblivious, meaning that Cilk programmers need not code for fault tolerance. Throughout this paper, we focus on end-to-end design decisions, and we show how these decisions allow the design to exploit high-level algorithmic properties of the Cilk programming model in order to simplify and streamline the implementation. 1
Chitin-based Embolic Materials in the Renal Artery of Rabbits: Pathologic Evaluation of an Absorbable Particulate Agent (2005)

Chitosan microspheres have great potential as a new embolic material since they block blood vessels more compactly with a lower rate of capillary formation. This material is biocompatible, and it is absorbed 24 weeks after embolization.
Influence of temperature and relative humidity on the survival of Chlamydia pneumoniae in aerosols (1993)

The survival of Chlamydia pneumoniae in aerosols was investigated by using a chamber with a capacity of 114.5 liters. We injected 5 x 10(7) inclusion-forming units (IFU) of C. pneumoniae in aerosols with a droplet size of 3 to 5 microns. Samples were taken after 30 s and every 1 min thereafter. The survival of C. pneumoniae was measured at four temperatures (8.5, 15, 25, and 35 degrees C) and at three different relative humidities (RH) of 5, 50, and 95% for each temperature. The survival rates of Streptococcus pneumoniae, Streptococcus faecalis, Klebsiella pneumoniae, Chlamydia trachomatis LGV2, and cytomegalovirus were also determined at 25 degrees C and 95% RH and compared with that of C. pneumoniae. At the mentioned temperatures and RH, a rapid decrease of C. pneumoniae IFU was observed in the first 30 s. After this the decrease in the number of IFU was more gradual. The survival of C. pneumoniae in aerosols were optimal at 15 to 25 degrees C and 95% RH; it was good compared with those of other microorganisms. A lower death rate was observed only in S. faecalis. In C. trachomatis, the death rate during the first 30 s was higher than that in C. pneumoniae (85 and 53.3%, respectively). After the first 30 s, the death rates in the two organisms were identical. It was concluded that transmission of C. pneumoniae via aerosols was possible. There is probably a direct transmission from person to person, taking into account the relatively short survival period of C. pneumoniae in aerosols.
Leukocyte Interferon Conjugated to β-D-Galactosidase for Receptor Studies: A Preliminary Report (1985)

In this report, we describe a simple procedure for labeling leukocyte interferon (IFN) with the enzyme β-D-galactosidase β-gal), through a low-molecular-weight linking agent. The labeling procedure did not appear to alter the properties of the enzyme, the antiviral activity of the recombinant DNA-derived human clone A leukocyte IFN (rIFNαA), or the ability of the IFN to bind to Daudi cells. The binding of the putative IFN-enzyme complex to Daudi cells could be blocked by excess unlabeled IFN or by monoclonal antibody to IFN receptors. Our preliminary results indicate that enzyme labeling of IFN can result in a biologically active agent that has potential for use in the quantitation of circulating IFN and specific receptor proteins. In addition, this labeling procedure may be potentially useful with other immunomodulatory proteins.
Nitrite Infusions to Prevent Delayed Cerebral Vasospasm in a Primate Model of Subarachnoid Hemorrhage (2005)

Subacute sodium nitrite infusions prevented delayed cerebral vasospasm in a primate model of subarachnoid hemorrhage.
In-Liquid Quality Factor Improvement for Film Bulk Acoustic Resonators by Integration of Microfluidic Channels (2009)

We demonstrate a significant improvement in the quality factor ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> ) of film bulk acoustic resonators (FBARs) in liquid environments via the integration of microfluidic channels. Our device consists of a longitudinal-mode excited zinc oxide (ZnO) FBAR and parylene-encapsulated microfluidic channels. Considerable enhancement in the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> of the resonant system is obtained by confining the liquid in the microfluidic channels of thickness comparable to the acoustic wavelength. The improved FBAR achieves <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> values of up to 120, which represents an improvement of a factor of eight over those of current state-of-the-art devices.
Single-wall carbon nanotube/conjugated polymer photovoltaic devices (2002)

We report the optoelectronic properties occurring in single-walled carbon nanotubes (SWNTs)—conjugated polymer, poly(3-octylthiophene) composites. Composite films were drop or spin cast from a solution on indium–tin oxide (ITO) and quartz substrates and studied using absorption spectroscopy and electrical characterization methods. Diodes (Al/polymer-nanotube composite/ITO) with a low nanotube concentration (&amp;lt;1%) show photovoltaic behavior, with an open circuit voltage of 0.7–0.9 V. The short circuit current is increased by two orders of magnitude compared with the pristine polymer diodes and the fill factor also increases from 0.3 to 0.4 for the nanotube/polymer cells. It is proposed that the main reason for this increase is the photoinduced electron transfer at the polymer/nanotube interface. The results show that the conjugated polymer-SWNTs composite represents an alternative class of organic semiconducting material that is promising for organic photovoltaic cells with improved performance.
Robust real-time corner location measurement (2002)

In this paper, a new computationally efficient method for the tracking and measurement of center location is presented. This algorithm is well suited to real-time focus-of-attention applications in which regions-of-interest, or windows, are used to reduce image data rates. These techniques can be used in robot guidance applications, where high speed image processing is required for real-time position control, such as robot assembly operations in flexible manufacturing. The method is applied in a system based on a 200 frames/s digital camera, programmable gate array technology, and a network of TMS320C40 digital signal processor modules. A real-time motion tracking experiment that uses this corner detection technique is described to demonstrate the advantages of this approach. Experimental results show that the center location of an object in a gray scale image can be determined at 114 Hz.
Thalidomide in the Management of Multiple Myeloma (2002)

The discovery that multiple myeloma is associated with new vessel formation and is correlated with survival and proliferation led initially to the use of thalidomide for patients with relapsed or refractory disease. The outcome with conventional chemotherapy in this setting has historically been very poor. New insights into the biology of the disease suggests that thalidomide may work via a number of other mechanisms and the advent of the thalidomide analogues with their differential effects on survival and proliferation pathways has opened up a new era in the understanding and treatment of the disease. The encouraging results from phase I/II trials of these agents has meant that for the first time in 50 years there is the opportunity to improve outcome. Further work is in progress to define how best to use these drugs and their role in treatment at different stages of the disease.
Follistatin Is a Modulator of Gonadal Tumor Progression and the Activin-Induced Wasting Syndrome in Inhibin-Deficient Mice1 (2000)

Inhibins and activins are dimeric proteins belonging to the transforming growth factor-beta superfamily. Follistatin is an activin-binding protein that antagonizes the function of activin via binding to its beta-subunits. Previously, we demonstrated that mice deficient in inhibin develop ovarian and testicular sex cord-stromal tumors of granulosa and Sertoli cell origin, with 100% penetrance as early as 4 weeks of age. Overproduction of activins in the serum directly causes a cachexia-like wasting syndrome that results in lethality of these mice at an early stage after the onset of the tumors. In an independent set of studies, overexpression of mouse follistatin using the mouse metallothionein I promoter in transgenic mice led to gonadal defects and eventual infertility, primarily due to local effects of follistatin in these tissues. Activin has a positive growth effect on gonadal tumor cells in culture and directly causes the cancer cachexia-like syndrome in inhibin-deficient mice via interaction with activin receptor type IIA in livers and stomachs. We therefore hypothesized that an activin antagonist such as follistatin can act as a physiological modifier, either locally or via the serum, to block the activin-mediated cancer cachexia-like syndrome in inhibin-deficient mice and/or slow the progression of gonadal cancers in these mice. To test this hypothesis, we generated mice that are homozygous mutant for the inhibin alpha null allele (i.e. inham1/inham1) and carry the mouse metallothionein I follistatin (MT-FS) transgene. Our results show that gonadal tumors that are histologically similar in most, but not all, cases to the tumors in inhibin-deficient mice develop in these inham1/inham1, MT-FS+ mice. However, inham1/inham1, MT-FS+ mice exhibit a less severe wasting syndrome, lower serum activin levels, and a statistically significant prolonged survival in a number of cases compared with mice deficient in inhibin alone. Thus, follistatin can act as a modulator of tumor growth and the activin-induced cancer cachexia-like syndrome in inhibin-deficient mice.