gebhart/patrepeval huggingface dataset:
Subcellular distribution of clathrin in cultured hypothalamic neurons (1991)

The subcellular distribution of clathrin has been examined in developing hypothalamic neurons cultured in a chemically defined medium up to synapse formation (12-13 days in vitro) and exposed, or not, to a depolarizing concentration of KCl (60 mM for 3 min) followed, or not, by a return to control KCl concentration (3 mM KCl for 3 min). Previous studies have shown that such treatments induce in synaptic boutons a rapid vesicle depletion followed by massive restoration. Using an enzyme immunoassay, we have compared the relative proportion of assembled and unassembled pools of clathrin as a function of exposure to depolarizing or repolarizing concentrations of KCl. In parallel we have localized clathrin at the electron microscopic level using immunoperoxidase. Clathrin concentration in culture is lower (0.36 vs 0.75%) and the proportion of unassembled clathrin is much higher than in the adult brain (82 vs 14%). These proportions were not affected by depolarizing or repolarizing treatments. Morphologically clathrin was exclusively detected in two neuron compartments: perikarya and synaptic boutons. In perikarya clathrin was localized as a thick coat on plasma membrane coated pits and in the Golgi zone on coated buds and vesicles, presumably located in a trans compartment. In synaptic boutons clathrin immunoreaction was found as an irregular thin rim around synaptic vesicles, whatever the polarization state of the cells, but coated vesicles were extremely rare. Taken together these findings raise the problem of the functional meaning and localization of the large unassembled pool of clathrin in such neurons and question its role in vesicular traffic in synaptic boutons.
Identification of Histone Demethylases in Saccharomyces cerevisiae (2007)

Based on the prediction that histone lysine demethylases may contain the JmjC domain, we examined the methylation patterns of five knock-out strains (ecm5Delta, gis1Delta, rph1Delta, jhd1Delta, and jhd2Delta (yjr119cDelta)) of Saccharomyces cerevisiae. Mass spectrometry (MS) analyses of histone H3 showed increased modifications in all mutants except ecm5Delta. High-resolution MS was used to unequivocally differentiate trimethylation from acetylation in various tryptic fragments. The relative abundance of specific fragments indicated that histones K36me3 and K4me3 accumulate in rph1Delta and jhd2Delta strains, respectively, whereas both histone K36me2 and K36me accumulate in gis1Delta and jhd1Delta strains. Analyses performed with strains overexpressing the JmjC proteins yielded changes in methylation patterns that were the reverse of those obtained in the complementary knock-out strains. In vitro enzymatic assays confirmed that the JmjC domain of Rph1 specifically demethylates K36me3 primarily and K36me2 secondarily. Overexpression of RPH1 generated a growth defect in response to UV irradiation. The demethylase activity of Rph1 is responsible for the phenotype. Collectively, in addition to Jhd1, our results identified three novel JmjC domain-containing histone demethylases and their sites of action in budding yeast S. cerevisiae. Furthermore, the methodology described here will be useful for identifying histone demethylases and their target sites in other organisms.
Tyrosine kinase gene expression in the mouse small intestine. (1994)

To identify tyrosine kinases that may regulate regeneration of the mammalian intestinal epithelium, we amplified portions of the catalytic domains of protein kinases expressed in intestinal crypt cells, using the polymerase chain reaction technique with primers directed against two invariant amino acid sequence motifs found in all kinases. These fragments were cloned and a library of kinase catalytic domains was generated. Sequence analysis of unique clones resulted in the identification of the catalytic domains of several characterized tyrosine kinases, including lyn, hck, c-fgr, tec, JAK2, itk, and the putative receptor kinase ryk, and expression of these kinases has not previously been described in the intestine. We compared the levels of mRNA encoding these kinases in multiple tissues using RNase protection assays, and we localized the expression of hck, lyn, and JAK2 in the intestine using in situ hybridization. In addition, we identified two novel putative catalytic domain sequences. One of these, which we have named sik (src-related intestinal kinase), is expressed at high levels in the gastrointestinal tract and may play a specific role in signal transduction in epithelial tissues.
Neural selectivity, efficiency, and dose equivalence in deep brain stimulation through pulse width tuning and segmented electrodes (2020)

We find agreement with classic studies and predict that long pulse widths may focus the stimulation effect on small, nearby fibers and improve power consumption. While future pre-clinical and clinical work is necessary regarding pulse width tuning, it is clear that future studies must ensure dose equivalence, noting that energy- and charge-equivalent amplitudes do not result in equivalent spread of neural activation when changing pulse width.
Interactive Depth of Field Using Simulated Diffusion on a GPU (2006)

Accurate computation of depth-of-field effects in computer graphics rendering is generally very time consuming, creating a problematic workflow for film authoring. The computation is particularly challenging because it depends on large-scale spatially-varying filtering that must accurately respect complex boundaries. A variety of real-time algorithms have been proposed for games, but the compromises required to achieve the necessary frame rates have made them them unsuitable for film. Here we introduce an approximatedepth-of-field computation that is good enough for film preview, yet can be computed interactively on a GPU. The computation creates depth-of-field blurs by simulating the heat equation for a nonuniform medium. Our alternating direction implicit solution gives rise to separable spatially varying recursive filters that can compute large-kernel convolutions in constant time per pixel while respecting the boundaries between in-focus and out-of-focus objects. Recursive filters have traditionally been viewed as problematic for GPUs, but using the well-established method of cyclic reduction of tridiagonal systems, we are able to vectorize the computation and achieve interactive frame rates.
Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2 (2020)

Reverse transcription (RT)-PCR, the principal diagnostic method applied in the worldwide struggle against COVID-19, is capable of detecting a single molecule of a viral genome. Correctly designed and practiced RT-PCR assays for SARS-CoV-2 should not cross-react with similar but distinct viral pathogens, such as the coronaviruses associated with the common cold, and should perform with very high analytical sensitivity. This analytical performance is predicated on the ability of the method to detect the presence of the selected nucleic acid target, without detection of a false positive signal.
Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production (2011)

Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic Acid Bacteria (LAB) used for cheese and yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial strain mainly used for yogurt production, was completely sequenced and compared against the other two ATCC collection strains of the same subspecies. Specific physiological properties of strain 2038, such as lysine biosynthesis, formate production, aspartate-related carbon-skeleton intermediate metabolism, unique EPS synthesis and efficient DNA restriction/modification systems, are all different from those of the collection strains that might benefit the industrial production of yogurt. Other common features shared by Lb. bulgaricus strains, such as efficient protocooperation with Streptococcus thermophilus and lactate production as well as well-equipped stress tolerance mechanisms may account for it being selected originally for yogurt fermentation industry. Multiple lines of evidence suggested that Lb. bulgaricus 2038 was genetically closer to the common ancestor of the subspecies than the other two sequenced collection strains, probably due to a strict industrial maintenance process for strain 2038 that might have halted its genome decay and sustained a gene network suitable for large scale yogurt production.
The Antibiotic Pipeline — Challenges, Costs, and Values (2004)

In 1941, Skinner and Keefer vividly chronicled an astonishing 82 percent mortality among 122 consecutive patients who had been treated for Staphylococcus aureus bacteremia in the preantibiotic era.1 Of the 41 patients older than 50 years of age, only 1 (2 percent) survived. Imagine the elation a few years later over the availability of penicillin, the prototype of a new therapeutic class of drugs (see page 524). In the next few decades, well-intentioned academic leaders predicted the demise of bacterial infections.(Figure)Such irrational exuberance over the sustained benefits of antibiotics should have been tempered by at least two . . .
Health Heritage<sup>©</sup>, a Web-Based Tool for the Collection and Assessment of Family Health History: Initial User Experience and Analytic Validity (2010)

A detailed family health history is currently the most potentially useful tool for diagnosis and risk assessment in clinical genetics. We developed and evaluated the usability and analytic validity of a patient-driven web-based family health history collection and analysis tool. Health Heritage(©) guides users through the collection of their family health history by relative, generates a pedigree, completes risk assessment, stratification, and recommendations for 89 conditions. We compared the performance of Health Heritage to that of Usual Care using a nonrandomized cohort trial of 109 volunteers. We contrasted the completeness and sensitivity of family health history collection and risk assessments derived from Health Heritage and Usual Care to those obtained by genetic counselors and genetic assessment teams. Nearly half (42%) of the Health Heritage participants reported discovery of health risks; 63% found the information easy to understand and 56% indicated it would change their health behavior. Health Heritage consistently outperformed Usual Care in the completeness and accuracy of family health history collection, identifying 60% of the elevated risk conditions specified by the genetic team versus 24% identified by Usual Care. Health Heritage also had greater sensitivity than Usual Care when comparing the identification of risks. These results suggest a strong role for automated family health history collection and risk assessment and underscore the potential of these data to serve as the foundation for comprehensive, cost-effective personalized genomic medicine.
Towards an assessment of African scales (1958)

It would appear from the evidence of certain writers on African music that there still remains much confusion about the subject of African scales and modes. A tenacious misconception continually occurs, namely that African scales or modal systems are but an imperfect imitation of, or striving towards, the western system. Nothing, of course, could be further from the truth. It is with the intention of opening the subject for discussion by members of the Society and others interested in this aspect of musicology throughout the African world that this short article is now written. In order to avoid a confusion of terms which would take too long to enumerate here it might be as well for the reader who is interested to refer to the references to Scales and Modes in the Oxford Companion to Music, by Percy Scholes or to Grove’s Dictionary of Music and Musicians, and elsewhere. Scholes, for example, remarks of scales that “Apparently any combination of notes whatever may be adopted as the material from which a peasantry, or a composer, or a group of composers may make their tunes, and there exists not even one interval common to all the scales of the world”.
- Extraction of DNA from Forensic Biological Samples for Genotyping (2013)

Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms.
Nano‐hydroxyapatite‐coated PEEK implants: A pilot study in rabbit bone (2012)

Osseointegration of surface-modified polyetheretherketone (PEEK) implants was studied in vivo. A total of 18 cylinder-shaped PEEK implants were inserted in the femurs of nine New Zealand rabbits; half were coated with nanocrystalline hydroxyapatite (nanoHA) and half were uncoated controls. Healing time was 6 weeks. Samples were retrieved with the implant and surrounding tissue, processed to cut and ground sections, and analyzed histomorphometrically. The implant surfaces were analyzed with optical interferometry, scanning electron microscopy (SEM), atomic force microscopy, and X-ray photoelectron spectroscopy (XPS). NanoHA-coated PEEK surfaces had lower height deviation (Sa) than controls [mean ± SD: 0.41 μm (± 0.14) vs. 0.96 μm (± 0.28)]. SEM images showed the nanoHA crystals as a thin layer on the polymer surface. XPS analysis of the coated implants showed a Ca/P ratio of 1.67. Histomorphometry indicated that the nanoHA-coated implants had more bone-to-implant contact [16% (± 4.7) vs. 13% (± 9.3)] and more bone area [52% (± 9.5) vs. 45% (± 11.9)]. We found no difference between smooth nanoHA-coated cylinder-shaped PEEK implants and uncoated controls. However, higher mean bone-to-implant contact indicated better osseointegration in the coated implants than in the uncoated controls. The large number of lost implants was interpreted as a lack of primary stability due to implant design.
“Green” Ammonia: Impact of Renewable Energy Intermittency on Plant Sizing and Levelized Cost of Ammonia (2018)

Ammonia production currently contributes almost 11% of global industrial carbon dioxide emissions, or 1.3% of global emissions. In the context of global emission targets and growing demand, decarbonization of this process is highly desirable. We present a method to calculate a first estimate for the optimum size of an ammonia production plant (at the process level), the required renewable energy (RE) supply, and the levelized cost of ammonia (LCOA) for islanded operation with a hydrogen buffer. A model was developed to quantitatively identify the key variables that impact the LCOA (relative to a ±10 GBP/tonne change in LCOA): levelized cost of electricity (±0.89 GBP/MWh), electrolyzer capital expenditure (±65 GBP/kW), minimum Haber–Bosch (HB) load (±12% of rated power), maximum rate of HB load ramping, and RE supply mix. Using 2025/2030 estimates results in a LCOA of 588 GBP/tonne for Lerwick, Scotland. The application of the model will facilitate and improve the production of carbon-free ammonia in the future.
A generalization of isolated word recognition using vector quantization (2005)

The use of vector quantization (VQ) for isolated-word speech recognition of a 20-word vocabulary was shown in previous work to achieve more than 99% accuracy for speaker-dependent recognition and 87% accuracy for speaker-independent recognition. Separate VQ codebooks were designed for each word in the recognition vocabulary, and input words were classified by performing VQ and finding the codebook that achieves the smallest average distortion. The method obviates time-normalization and makes no use of time-sequence information. This paper presents results for a generalization that incorporates time-sequence information. The generalization, which was motivated by work of Martinez, Riveria, and Buzo, is more accurate and faster than the previous method. Words in the training and input sequences are normalized linearly to the same length and then divided into sections. Separate VQ codebooks are designed for each section of each vocabulary word. Each vocabulary word is then represented by a "multisection" codebook - a time-dependent sequence of section-codebooks. New words are classified by performing VQ and finding the multi-section codebook that achieves the smallest average distortion. Initial tests on a twenty-word vocabulary resulted in accuracies greater than 97% for speaker-independent recognition.
MEP pathway-mediated isopentenol production in metabolically engineered Escherichia coli (2014)

The isopentenol production was successfully increased through multi-step optimization of the MEP and its upstream glycolysis pathways. It demonstrated that the total fluxes and their balance of the precursors of the MEP pathway are of critical importance in isopentenol production. In the future, an elucidation of the contribution of PPP and ED to MEP is needed for further optimization of isopentenol production.
Ultrasound monitoring of temperature change in liver tissue during laser thermotherapy: 10°C intervals (2007)

In thermal tissue ablation, it is very important to control the increase in the temperature for having an efficient ablation therapy. We conducted this study to determine the efficacy of measuring pixel shift of ultrasound B-mode images as a function of change in tissue temperature. By fixing some micro thermocouples in liver tissues, temperature at different points was monitored invasively in vitro during laser-induced thermotherapy. According to our results optimum power and exposure time were determined for ultrasound temperature monitoring. Simultaneously, noninvasive temperature monitoring was performed with ultrasound B-mode images. These images were saved on computer from 25 degrees C to 95 degrees C with 10 degrees C steps. The speed of sound changes with each 10 degrees C temperature change that produce virtual shifts in the scatter positions. Using an image processing method, the pixel shift due to 10 degrees C temperature change was extracted by motion detection. The cubic regression function between the mean pixel shifts on ultrasound B-mode images caused by the change in speed of sound which in turn was a function of the mean change in temperature was evaluated. When temperature increased, pixel shift occurs in ultrasound images. The maximum pixel shift was observed between 60 to 70 degrees C. After 70 degrees C, the local pixel shift due to change in the speed of sound in liver tissue had an irregular decreasing. Pearson correlation coefficient between invasive and non-invasive measurements for 10 degrees C temperature changes was 0.93 and the non-linear function was suitable for monitoring of temperature. Monitoring of changes in temperature based on pixel shifts observed in ultrasound B-mode images in interstitial laser thermotherapy of liver seems a good modality.
Functiona l Analysis of Eubacterial Diterpene Cyclases Responsible for Biosynthesis of a Diterpene Antibiotic, Terpentecin (2002)

Eubacterial diterpene cyclase genes had previously been cloned from a diterpenoid antibiotic terpentecin producer (Dairi, T., Hamano, Y., Kuzuyama, T., Itoh, N., Furihata, K., and Seto, H. (2001) J. Bacteriol. 183, 6085-6094). Their products, open reading frame 11 (ORF11) and ORF12, were essential for the conversion of geranylgeranyl diphosphate (GGDP) into terpentetriene (TTE) that had the same basic skeleton as terpentecin. In this study, functional analyses of these two enzymes were performed by using purified recombinant enzymes. The ORF11 product converted GGDP into a cyclized intermediate, terpentedienol diphosphate (TDP), which was then transformed into TTE by the ORF12 product. Interestingly, the ORF12 product directly catalyzed the conversion of GGDP into three olefinic compounds. Moreover, the ORF12 product utilized farnesyl diphosphate as a substrate to give three olefinic compounds, which had the same structures as those formed from GGDP with the exception of the chain lengths. These results suggested that the ORF11 product with a DXDD motif converted GGDP into TDP by a protonation-initiated cyclization and that the ORF12 product with a DDXXD motif completed the transformation of TDP to the olefin, terpentetriene by an ionization-initiated reaction followed by deprotonation. The kinetics of the ORF12 product indicated that the affinity for TDP and GGDP were higher than that of farnesyl diphosphate and that the relative activity of the reaction converting TDP into TTE was highest among the reactions using TDP, GGDP, or farnesyl diphosphate as the substrate. These results suggested that an actual reaction catalyzed by the ORF12 was the conversion of TDP into TTE in vivo.
Efficient modeling of thyristor static characteristics from device fabrication data (1979)

A method for determination of the dc characteristics of an n-p-n-p structure is described. Each of the three diffused regions is first of all characterized by computer analysis using the variable boundary regional approach at one low-bias value (mobility variation with doping level and high doping bandgap reduction effects are included in this program). A set of constants thus obtained is used to define a set of simplified analytic <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I-V</tex> relations for each of the four regions. These analytic relations are solved using an elementary program to predict the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I-V</tex> characteristics. Experimental and computed results are included for normal and gold-doped devices and explanations for operation with extreme (low- and high-) lifetime values are given.
Synthesis of 5-(Aminoacylamido)-3-methylisothiazole Derivatives and Their Analgesic Action (1963)

5-(2-Haloacylamido)-3-methylisothiazoles were prepared by treatment of 5-amino-3-methylisothiazole with 2-haloacyl halides and afforded with dimethylamine, diethyl-amine, piperidine, morpholine, and pyre rolidine the corresponding 5-(2-alkylamino-acylamido)-3-methylisothiazoles respectively. Interreaction of 5-amino-3-methylthiazole and p-nitrobenzoyl chloride gave 5-(p-nitrobenzamino)-3-methylisothiazole which was reduced with iron in acetic acid to afford 5-(p-aminobenzamido)-3-methyliso thiazole. Analgesic action and toxicity of these compounds were tested and most of them especially compounds V, VI, X, and XI were found to be more effective than aminopyrine.