gebhart/patrepeval huggingface dataset:
A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language (2011)

Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.
Topological Polymer Chemistry:Progress of Cyclic Polymers in Syntheses, Properties and Functions (2012)

There are examples aplenty in the macroscopic world that demonstrate the form of objects directing their functions and properties. On the other hand, the fabrication of extremely small objects having precisely defined structures has only recently become an attractive challenge, which is now opening the door to nanoscience and nanotechnology. In the field of synthetic polymer chemistry, a number of critical breakthroughs have been achieved during the first decade of this century to produce an important class of polymers having a variety of cyclic and multicyclic topologies. These developments now offer unique opportunities in polymer materials design to create unprecedented properties and functions simply based on the form, i.e. topology, of polymer molecules. In this book on topological polymer chemistry, the important developments in this growing area will be collected for the first time, with particular emphasis on new conceptual insights for polymer chemistry and polymer materials. The book will systematically review topological polymer chemistry from basic aspects to practice, and give a broad overview of cyclic polymers covering new synthesis, structure characterization, basic properties/functions and the eventual applications
Tannins and related compounds. XLI. Isolation and characterization of novel ellagitannins, punicacorteins A, B, C and D, and punigluconin from the bark of Punica granatum L. (1986)

A chemical examination of the bark of Punica granatum L. (Punicaceae) has led to the isolation of five new ellagitannins, punicacorteins A, B, C and D, and punigluconin, together with the known ellagitannins, casuariin (6) and casuarinin (7). Based on chemical and spectroscopic evidence, the structures of punicacorteins A, B, C and D were established as novel C-glycosideic ellagitannins, the former two possessing a unique tetraphenyl (gallagyl) ester group (1 and 2), and the latter two containing a galloyl group in place of the gallagyl group (3 and 4), while punigluconin was characterized as 2, 3-di-O-galloyl-4, 6-(S)-hexahydroxydiphenoylgluconic acid (5).
Hunting with Traps: Genome-Wide Strategies for Gene Discovery and Functional Analysis (1999)

With sequence analysis of the human genome well underway, there is an increasingly urgent challenge to understand the fundamental function and interplay of genes that build and maintain an organism. Several approaches will be critical for interpreting gene function, including random cDNA sequencing, expression profiling in different tissues, genetic analysis of human or model organism phenotypes, and creation of transgenic or "knockout" animals. Traditional gene-trapping approaches, in which genes are randomly disrupted with DNA elements inserted throughout the genome, have been used to generate large numbers of mutant organisms for genetic analysis. Recent modifications of gene-trapping methods and their increased use in mammalian systems are likely to result in a wealth of new information on gene function. Various trapping strategies allow genes to be segregated based on criteria like the specific subcellular location of an encoded protein, the tissue expression profile, or responsiveness to specific stimuli. Genome-wide gene-trapping strategies, which integrate gene discovery and expression profiling, can be applied in a massively parallel format to produce living assays for drug discovery.
Harrison's Principles of internal medicine: Pretest self-assessment and review (1983)

Linked to the 14th edition of Harrison's Principles of Internal Medicine, this review text contains over 800 multiple choice questions that reflect the form and content of the medical board exam. Answers and detailed explanations are provided at the end of each section. Also provided are thorough references by chapter to the main text and to appropriate journal articles.
What is the pathological significance of tau oligomers? (2012)

Insoluble aggregates of the microtubule-associated protein tau characterize a number of neurodegenerative diseases collectively termed tauopathies. These aggregates comprise abnormally hyperphosphorylated and misfolded tau proteins. Research in this field has traditionally focused on understanding how hyperphosphorylated and aggregated tau mediates dysfunction and toxicity in tauopathies. Recent findings from both Drosophila and rodent models of tauopathy suggest that large insoluble aggregates such as tau filaments and tangles may not be the key toxic species in these diseases. Thus some investigators have shifted their focus to study pre-filament tau species such as tau oligomers and hyperphosphorylated tau monomers. Interestingly, tau oligomers can exist in a variety of states including hyperphosphorylated and unphosphorylated forms, which can be both soluble and insoluble. It remains to be determined which of these oligomeric states of tau are causally involved in neurodegeneration and which signal the beginning of the formation of inert/protective filaments. It will be important to better understand this so that tau-based therapeutic interventions can target the most toxic tau species.
Chemical Analysis by X-Ray Diffraction: Classification and Use of X-Ray Diffraction Patterns (1986)

Editor's Note: As part of our plan to reprint previously published papers of great historical interest, the editorial board is pleased to reproduce the following paper by Hanawalt, Frevel and Rinn. This paper was originally published in Volume 10 (1938) of the Analytical Ediction of “Industrial and Engineering Chemistry” and is considered by most diffractionists to be the classic work in qualitative identification of multiphase polycrystalline material. The original publication carried a foreword written by the editor of Industrial and Engineering Chemistry. This foreword ended with this prophetic statement : “There is reason to believe that this publication, which is made possible in this form by the generous financial assistance of the Dow Chemical Company, will serve to bring this method of analysis into general use in industrial and consulting analytical laboratories.”
The primary sequence of Ricinus communis agglutinin. Comparison with ricin. (1985)

A mixture of synthetic oligonucleotides representing all possible sequences of a peptide present in the ricin B chain has been used to screen a cDNA library constructed using ripening castor bean seed poly(A+) RNA. The eight largest recombinant plasmids selected, by hybridization, a single mRNA species whose translational product was identified as preprolectin by immunoprecipitation. Restriction enzyme analysis of these clones demonstrated that two classes were present representing sequences complementary to two distinct but closely related preprolectin mRNA species. The nucleotide sequence of the cloned cDNA from one of these classes encodes preproricin and has been presented elsewhere (Lamb, F. I., Roberts, L. M., and Lord, J. M., (1985) Eur. J. Biochem. 148, 265-270). The nucleotide sequence of the second class is presented here and shown to represent prepro-Ricinus communis agglutinin. The entire coding sequence was deduced from two overlapping cDNA clones having inserts of 1668 and 1151 base pairs. The coding region defines a preproprotein with a 24-amino acid N-terminal signal sequence preceding the A chain (266 amino acids) which is joined to the B chain (262 amino acids) by a 12-amino acid linking peptide. The protein was confirmed as R. communis agglutinin since the deduced B chain N-terminal sequence corresponds exactly with that determined for purified R. communis agglutinin B chain over a region where several residue differences occur in the ricin B chain. The nucleotide and deduced amino acid sequences of the R. communis agglutinin precursor are compared with those of the ricin precursor.
Post-CMOS-Compatible Aluminum Nitride Resonant MEMS Accelerometers (2009)

This paper describes the development of aluminum nitride (AlN) resonant accelerometers that can be integrated directly over foundry CMOS circuitry. Acceleration is measured by a change in resonant frequency of AlN double-ended tuning-fork (DETF) resonators. The DETF resonators and an attached proof mass are composed of a 1-mum-thick piezoelectric AlN layer. Utilizing piezoelectric coupling for the resonator drive and sense, DETFs at 890 kHz have been realized with quality factors ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> ) of 5090 and a maximum power handling of 1 muW. The linear drive of the piezoelectric coupling reduces upconversion of 1/ <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> amplifier noise into 1/ <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> phase noise close to the oscillator carrier. This results in lower oscillator phase noise, -96 dBc/Hz at 100-Hz offset from the carrier, and improved sensor resolution when the DETF resonators are oscillated by the readout electronics. Attached to a 110-ng proof mass, the accelerometer microsystem has a measured sensitivity of 3.4 Hz/G and a resolution of 0.9 mG/radicHz from 10 to 200 Hz, where the accelerometer bandwidth is limited by the measurement setup. Theoretical calculations predict an upper limit on the accelerometer bandwidth of 1.4 kHz.
Medicine in the 1950s in South Sudan: amputation for a puff adder (Bitis arietans) envenomation in a child - 1954. (2014)

IntroduconDiaries spanning three decades (1943-1964) have been discovered that tell the story of the life of missionary nurses, doctors and surgeons working at the Lui and Leer Hospitals in South Sudan (then known as Southern Sudan). The medical facility at Leer during this period covered a 300 miles radius serving approximately 60,000 of the Nilotic Western Nuer tribe [1]. It was among these records that the following case description was found. The puff adder (Bitis arietans) is one of the commonest African snakes, causing more bites in animals and humans than all other species of snake put together in sub-Saharan regions. It commonly inhabits the banks of the Nile [2]. The venom of the puff adder causes speciﬁc cytotoxic, ﬁbrinolytic, platelet-inhibiting, pro-thrombotic, vasodilating, cardiodepressant, and neurotoxic effects [3-8]. When envenomation occurs in a human tissue necrosis, coagulopathy, hypotension, thrombocytopenia and spontaneous bleeding have all been reported [9].
Synergistic effect between IL10 and bcl2 genotypes in determining susceptibility to systemic lupus erythematosus (1998)

Objective To determine whether genes participating in programmed cell death, including bcl-2, IL-10, Fas-L, and CTLA-4, may contribute to the genetic predisposition to systemic lupus erythematosus (SLE). Methods First, intragenic markers for the bcl-2, IL-10, Fas-L, and CTLA-4 genes were characterized and their extent of polymorphism in normal populations was determined. The allelic distribution of these gene markers in a large Mexican American SLE cohort of 158 patients and 223 ethnically matched controls was determined using fluorescent-labeled primers and semiautomated genotyping. Results The bcl-2, Fas-L, and IL-10 loci showed significantly different allelic distribution in SLE patients compared with controls, indicating an association between these genes and SLE. No association was found between SLE and the CTLA-4 gene. Further analysis revealed a synergistic effect between susceptibility alleles of the bcl-2 and IL-10 genes in determining disease susceptibility. Alone, the presence of each of these alleles was associated with a moderate increase in SLE risk, while the occurrence of these alleles together increased the odds of developing SLE by more than 40-fold. Conclusion The results suggest that individuals carrying specific genotypes of both bcl-2 and IL-10 are at significant risk of developing SLE.
Image analysis and processing of an imperfect two‐dimensional crystal: the surface layer of the archaebacterium Sulfolobus acidocaldarius re‐investigated (1991)

SUMMARY The surface layer of the archaebacterium Sulfolobus acidocaldarius has been re‐investigated exploring various image analysis and image processing strategies. Straightforward correlation averaging correcting for translational disorder only, and lattice unbending in conjunction with filtration in the Fourier domain gave equivalent results. Careful examination of cross‐correlation functions as well as multivariate statistical analysis of individual unit cells revealed the existence of interpenetrating domains with intrinsic p3 symmetry but rotated with respect to each other by 60° and separated by twin boundaries. Non‐discriminative averaging over twinned crystal patches generates a higher (p6) class of symmetry emphasizing the importance of selective averaging.
Variants of 3T3 cells lacking mitogenic response to epidermal growth factor. (1977)

We have previously demonstrated that epidermal growth factor (EGF) can serve as a potent mitogen for 3T3 cells. We have now selected variant 3T3 cell lines unable to respond to EGF, in order to define cellular events unique to the EGF response and to distinguish which of these events are necessary and which are merely correlative to mitogenesis. By simultaneously treating cells with EGF and colchicine, we eliminated those cells stimulated by EGF to enter mitosis. Of the eight clonal EGF nonresponder variants selected by this procedure, none retains a functional EGF receptor. The EGF nonresponsive va-riant lines still retain the ability to respond to other mitogens.
Machining of Reactive Metals (1989)

Abstract This article focuses on the machining of reactive metals which refer collectively to the elements titanium, hafnium, and zirconium. It provides guidelines for machining titanium and titanium alloys and describes machining operations, such as turning, milling, drilling, tapping, reaming, grinding, and sawing, performed on titanium and its alloys. The article also provides information on electrochemical machining (ECM), chemical milling (CHM), and laser beam machining (LBM) for titanium and titanium alloys. Guidelines for machining zirconium alloys and hafnium are also provided. The article provides a short description of turning, milling, and drilling operations performed on zirconium alloys and hafnium. It also discusses health and safety considerations related to zirconium and hafnium.
N‐Substituted 4,5‐dihydro‐1,2‐benzothiazepin‐3‐one 1,1‐dioxide (1980)

Abstract The reaction of 2‐carboethoxyethyl‐4,5‐dimethoxybenzene sulfochloride with substituted pyridines leads to the corresponding sulfonamides. The latter were hydrolysed to the acids, on which a general method for preparing a new ring system was based.
The gene encoding interleukin-13: a susceptibility locus for asthma and related traits (2000)

Asthma is a complex inflammatory disorder controlled by both genetic and environmental influences. Multiple genetic analyses have identified the T helper type 2 (Th2) cytokine gene cluster on chromosome 5q as a susceptibility locus for asthma. Recently, the Th2 cytokine interleukin-13 has been shown to be a critical mediator of the asthma phenotype in murine models. In this commentary we discuss several recent studies that have identified polymorphisms in the gene encoding interleukin-13. The consistent genetic associations of interleukin-13 with asthma and related traits across diverse ethnic populations in these studies provides strong support for the candidacy of this cytokine as a susceptibility locus for asthma and atopy on chromosome 5q31.
Chemical and biological studies of a new cigarette that primarily heats tobacco. Part 1. Chemical composition of mainstream smoke. (1998)

A new-technology cigarette has been developed. While the new cigarette burns some tobacco, it does not use tobacco as the fuel to sustain combustion and provide heat to the cigarette. Rather, the new cigarette primarily heats tobacco thereby reducing products of smoke formation mechanisms such as tobacco combustion, tobacco pyrolysis and pyrosynthesis. The mainstream smoke composition from a cigarette based on the new design (TOB-HT) has been characterized in comparative chemical testing with two reference cigarettes using the FTC puffing regimen. Thermal properties, UV absorption characteristics, elemental composition and materials balance studies all suggest a simplified smoke aerosol. Twenty-five smoke constituents ("target compounds") identified by the scientific community as compounds that may contribute to the diseases statistically associated with smoking have also been measured. Mainstream smoke concentrations of most target compounds are significantly lower with the TOB-HT cigarette when compared with reference cigarettes in the ultra-light "tar" and light "tar" categories. Taken together, chemical analysis results suggest simplified TOB-HT smoke chemistry with marked reductions in specific chemicals reported to be biologically active.
Behavioral models of Parkinson's disease in rodents: A new look at an old problem (2006)

The circuitry important for voluntary movement is influenced by dopamine from the substantia nigra and regulated by the nigrostriatal system. The basal ganglia influence the pyramidal tract and other motor systems, such as the mesopontine nuclei and the rubrospinal tract. Although the neuroanatomical substrates underlying motor control are similar for humans and rodents, the behavioral repertoire mediated by those circuits is not. The principal aim of this review is to evaluate how injury to dopamine-mediated pathways in rodents gives rise to motor dysfunction that mimics human Parkinsonism. We will examine the behavioral tests in common use with rodent models of Parkinson's disease and critically evaluate the appropriateness of each test for detecting motor impairment. We will show how tests of motor performance must be guided by a thorough understanding of the clinical symptoms accompanying the disease, the circuitry mediating dopamine deficits in rodents, and familiarity with the rodent behavioral repertoire. We will explain how investigations in rodents of skilled forepaw actions, including placing, grooming, or foot faults, have clear correlates in Parkinson's disease, and are, therefore, the most sensitive ways of detecting motor impairment following dopamine loss from the basal ganglia of rodents.
Tumour promoting and suppressing roles of the atypical MAP kinase signalling pathway ERK3/4-MK5 (2012)

Perturbed action of signal transduction pathways, including the mitogen-activated protein (MAP) kinase pathways, is one of the hallmarks of many cancers. While the implication of the typical MAP kinase pathways ERK1/2-MEK1/2, p38MAPK and JNK is well established, recent findings illustrate that the atypical MAP kinase ERK3/4-MK5 may also be involved in tumorigenic processes. Remarkably, the ERK3/4-MK5 pathway seems to possess anti-oncogenic as well as pro-oncogenic properties in cell culture and aninal models. This review summarizes the mutations in the genes encoding ERK3, ERK4 and MK5 that have been detected in different cancers, reports aberrant expression levels of these proteins in human tumours, and discusses the mechanisms by which this pathway can induce senescence, stimulate angiogenesis and invasiveness.
Ground Station Tracking of Dual Linearly Polarized Satellites (1975)

A new generation of communication satellites carry traffic in both planes of linear polarization within the common carrier band. The tracking of these satellites puts a minor additional burden on the tracking system of the attending ground station inasmuch as communication signals at the beacon frequency, but in the orthogonal plane of polarization, form an additional noise source for the tracking ing system. This paper analyzes a dual channel monopulse tracking system using a simplified monopulse feed intended for tracking of dual polarized domestic satellites. In addition, trade-offs for the selection of system parameters are presented.
Microsystem Technologies for Biomedical Applications (2011)

Microsystems, also often known as microelectromechanical systems (MEMS), areminiaturized devices fabricated using techniques called “micromachining”, and thatare common in different application areas, such as automotive, consumer electronics,industrial measurements, and recently biomedical too Dean & Luque (2009). The typicaldeﬁnition states that a microsystem is any device which has at least one feature size in theorder of micrometers (1:1000 of a mm).Historically, silicon has been used as the material of choice for fabricating microsystems, dueto the processing equipment which was already available in microelectronics foundries, andthe thorough understanding of the properties that the impressive development of electronicsin the 1950s and 60s made possible. Another advantage derived from microelectronics isthe low cost associated when fabricating devices at very large production volume. It wasthen natural to try to integrate other devices with the microelectronic chips, and so the ﬁrstmicrosystems were born. Initially, the market was driven by automotive applications, andaccelerometers for stability control and airbag deployment were one of the ﬁrst commercialsuccesses of microsystems technology. Other typical examples from this age are pressuresensors and inkjet printer nozzles. Since then, the global MEMS market has not ceased togrow, and their applications are more diverse now. It is expected that by 2010 more than 8000million MEMS devices will be sold yearly
A Stereocontrolled Route to (-)-Epibatidine Using a Chiral cis-Cyclohexadiene-1,4-diol Equivalent (1999)

A concise diastereo- and enantio-controlled synthesis of (-)-epibatidine, the potent analgesic alkaloid from an Ecuadoran poison frog, Epipedobates tricolor, has been developed starting with a synthetic equivalent of chiral cis-cyclohexadiene-1,4-diol.