gebhart/patrepeval huggingface dataset:
Role of Arginine 439 in Substrate Binding of 5-Aminolevulinate Synthase (1998)

5-Aminolevulinate synthase (EC 2.3.1.37) catalyzes the first reaction in the heme biosynthetic pathway in nonplant eukaryotes and some prokaryotes. Homology sequence modeling between 5-aminolevulinate synthase and some other alpha-family pyridoxal 5'-phosphate-dependent enzymes indicated that the residue corresponding to the Arg-439 of murine erythroid 5-aminolevulinate synthase is a conserved residue in this family of pyridoxal 5'-phosphate-dependent enzymes. Further, this conserved arginine residue in several enzymes, e.g., aspartate aminotransferase, for which the three-dimensional structure is known, has been shown to interact with the substrate carboxyl group. To test whether Arg-439 is involved in substrate binding in murine erythroid 5-aminolevulinate synthase, Arg-439 and Arg-433 of murine erythroid 5-aminolevulinate synthase were each replaced by Lys and Leu using site-directed mutagenesis. The R439K mutant retained 77% of the wild-type activity; its K(m) values for both substrates increased 9-13-fold, while the activity of R433K increased 2-fold and the K(m) values for both substrates remained unchanged. R439L had no measurable activity as determined using a standard 5-aminolevulinate synthase enzyme-coupled activity assay. In contrast, the kinetic parameters for R433L were comparable to those of the wild-type. Dissociation constants (Kd) for glycine increased 5-fold for R439K and at least 30-fold for R439L, while Kd values for glycine for both R433K and R433L mutants were similar to those of the wild-type. However, there was not much difference in methylamine binding among the mutants and the wild-type, excepting of a 10-fold increase in K(d)methylamine for R439L. R439K proved much less thermostable than the wild-type enzyme, with the thermotransition temperature, T1/2, determined to be 8.3 degrees C lower than that of the wild-type enzyme. In addition, in vivo complementation analysis demonstrated that in the active site of murine erythroid 5-aminolevulinate synthase, R439 is contributed from the same subunit as K313 (which is involved in the Schiff base linkage of the pyridoxal 5'-phosphate cofactor) and D279 (which interacts electrostatically with the ring nitrogen of the cofactor), while another subunit provides R149. Taken together, these findings suggest that Arg-439 plays an important role in substrate binding of murine erythroid 5-aminolevulinate synthase.
Perfused Organs and Intact Tissues in SITU * (2018)

31P nuclear magnetic resonance (NMR) is proving to be extremely usefui in the investigation of energy metabolism in perfused and superfused isolated organ systems. It has the advantage of being nondestructive, so that in certain systems energy metabolism may be observed as an ongoing process in living tissue. 31P NMR spectra of slow and fast skeletal muscle should be considered separately. In fast skeletal muscles, ATP and PCr are usually the only appreciable peaks. Most literature on 31P NMR studies of the heart centers on ischemia/recovery, a subject of vital importance to cardiologic management. The potential benefit of a sensitive and specific test of cardiac ischemia and infarction is enormous. Most of the 31P NMR studies of intact liver to date involved monitoring of ATP and P1 levels under conditions of ischemia, starvation, and fructose infusion. In 1979, McLaughlin et al.21 were able to obtain usable 31P spectra in only 1 min from isolated perfused mouse livers.
Bayesian tests for matched proportions (1981)

A sample of n subjects is observed in each of two states, S1-and S2. In each state, a subject is in one of two conditions, X or Y. Thus, a subject may be recorded as showing a change if its condition in the two states is ‘Y,X’ or ‘X,Y’ and, otherwise, the condition is unchanged. We consider a Bayesian test of the null hypothesis that the probability of an ‘X,Y’ change exceeds that of a ‘Y,X’ change by amount kO. That is, we develop the posterior distribution of kO, the difference between the two probabilities and reject the null hypothesis if k lies outside the appropriate posterior probability interval. The performance of the method is assessed by Monte Carlo and other numerical studies and brief tables of exact critical values are presented
Chemical Imaging with a Solid-State near Infrared Spectrometer Based on a Digital Micro-Mirror Array Device Coupled with Hadamard Transform Spectroscopy (2012)

Chemical imaging is demonstrated by using an innovative near infrared spectrometer that uses a digital micro-mirror array device (DMD) to provide both spatial and spectral resolution. Hadamard transform spectroscopy is used to enhance the signal-to-noise ratio of the measurement compared to single point raster scanning. The concept is demonstrated by collecting a spectral image of a polymer sample composed of separate regions of polystyrene and polypropylene. The resulting image is composed of 63 spectral resolution elements across the first overtone region of the near infrared spectrum (1538–1818 nm), as well as 65 spatial resolution elements across the longitudinal direction of the DMD (11.3 mm).
Amino Acids for the Sustainable Production of Cu2O Materials: Effects on Morphology and Photocatalytic Reactivity (2019)

Photocatalytic technologies represent intriguing approaches for long-term environmental remediation strategies; however, approaches to sustainably generate the catalytic materials remain limited. Many methods require the use of toxic surfactants and potentially harsh conditions. As an alternative, bioinspired approaches present pathways toward the production of functional structures under ambient conditions. In this contribution, the effects of amino acids in the low-temperature production of Cu2O-based materials is examined, providing first principle information for the eventual de novo design of peptides that can control the structure/function relationship of these inorganic materials. These studies demonstrate that only a fraction of the 20 canonical amino acids (Arg, Cys, Glu, His, Lys, and Trp) possess specific control over the morphology and size of Cu2O materials during the synthetic process. This level of control is shown to directly affect the photocatalytic activity of the materials for the degradation of model organic pollutants. Taken together, these results provide intriguing new directions for the rational design of sustainable synthetic approaches for the production of catalytically important semiconductor metal oxide materials applied to long-term environmental remediation capabilities.
Low Earth Orbit Communication Satellites: A Positively Disruptive Technology That Could Change the Delivery of Health Care in Rural and Northern Canada (Preprint) (2023)

<sec> <title>UNSTRUCTURED</title> Canada is a progressive nation that endeavors to provide comprehensive, universal, and portable health care to all its citizens. This is a challenge for a country with a population of 40 million living within a land expanse of 10 million km2 and where 18% live in rural or highly remote locations. The combined population of Yukon, Northwest Territories, and Nunavut is only 128,959 (0.32% of the population), living within 3.92 million km2, and many of these citizens live in isolated communities with unique health needs and social issues. The current solution to providing health care in the most remote locations has been to transport the patient to the health care provider or vice versa, which incurs considerable financial strain on our health care system and personal stress to the patient and provider. The recent global deployment of low Earth orbit communication satellites (LEO-ComSats) will change the practice and availability of online medicine everywhere, especially in northern Canada. The deployment of LEO-ComSats could result in disruptive but positive changes in medical care for underserved communities in remote geographic locations across Canada. LEO-ComSats can be used to demonstrate online medical encounters between a patient and a doctor in Canada, separated by thousands of kilometers. Most certainly, the academic medical centers in lower Canada could perform online telementored medical care to our northern communities like the remote care provided to many Canadians during the COVID-19 pandemic. An online health care model requires effective design, testing, and validation of the policies, standards, requirements, procedures, and protocols. Although the COVID-19 pandemic was the initial prime mover across all of Canada in the use of online medical encounters and creating rapidly devised reimbursement models, it was nonetheless created reactively, using real-time managerial fiat and poorly defined procedures based on minimal pedagogical experience, which made it “difficult to prove it was universally safe.” It is essential to proactively derive the medical policies, standards, and procedures for telementored medicine and “prove it is safe” before LEO-ComSat technology is ubiquitously deployed in northern Canada. This viewpoint was written by subject matter experts who have researched online and internet-based medicine for many years, sometimes 3 decades. In many cases, a literature review was not necessary since they already had the articles in the bibliography or knowledge in their possession. In many cases, internet search engines (ie, Google or PubMed) and Canadian government documents were used to provide corroborating evidence. </sec>
Combined-harmonic Analysis of Seismic Data Acquired with Two Vibrators Driven at Different Frequencies (2012)

The presence of hydrocarbons cannot be verified directly with current linear seismic relection methods. However, several studies suggest that third-order elastic moduli in reservoir rocks are anomalously large. This presents an opportunity to directly detect hydrocarbons by investigating nonlinear seismic responses. Although the existence of nonlinear seismic signals is well established, their generating mechanism is not known. Nonlinear seismic experiments are difficult to interpret. Vibrators are nonlinear targets and under the influence of a vibration at a different frequency, they may also emit combined harmonics. Hence, the observation of combined harmonics alone doesnot prove nonlinear generation in the subsurface. However, the presence of growing nonlinear responses is a characteristic signature of intrinsic nonlinearities in the medium. By observing this growth, medium nonlinearity can be discriminated from nonlinearities introduced by the source. We theoretically estimate the growth of nonlinear harmonic. Next we discuss an experiment in which two vibrators were driven at different frequencies in order to understand the source and propagation characteristics of nonlinear harmonics. We observe nonlinear harmonics. Comparing their amplitude decay with the theoretically estimated behaviour of nonlinear harmonics, we conclude that they are most likely generated by the sources and not in the medium.
Growth Hormone Has Dual Stage-Specific Effects on the Differentiation of 3T3-L1 Preadipocytes (2002)

Reports vary on the role of growth hormone (GH) in adipocyte differentiation. In this study, we showed that GH exerted dual effects depending on the stage of differentiation, using a serum-free culture of 3T3-L1 preadipocytes. GH promoted the differentiation when added to the medium during differentiation-inducing treatment with a hormone cocktail, but apparently suppressed it when added after the treatment. Only the suppressive effect was observed in the presence of 10% fetal bovine serum (FBS). Immunodepletion study showed that GH contributes to the differentiation-promoting activity of FBS. Insulin-like growth factor-1 could not replicate either the stimulative or the suppressive effect of GH. Stimulation of differentiation by GH involved the enhanced expression of mRNA of middle to late adipocyte markers. Among the key regulators of adipogenesis, peroxisome proliferator-activated receptor (PPAR) gamma and CCAAT/enhancer binding protein (C/EBP) alpha, but not C/EBPbeta, were stimulated for mRNA expression by GH added during the treatment with hormone cocktail. The stimulation of adipogenesis by GH was indeed due to the increase in the ratio of differentiated cells, though GH also promoted cell growth.
Research and implementation of hot topic detection system based on web (2017)

To alleviate the problem of “topic drift” in hot topic on web, the hot topic detection system is implemented. Our system contains the parts as follow. First, news data are collected from Web and cut into the Chinese word segmentation; second, the word weight is calculated by the improved word frequency-inverse document frequency formula (TF-IDF); at last, the Single-Pass clustering algorithm is used for text clustering. The TF-IDF formula is improved, which contains the position information of the word. Experiments show that the hot topic can be effectively identified by this system.
Whole Genome Doubling mitigates Muller’s Ratchet in Cancer Evolution (2019)

Abstract Whole genome doubling (WGD) is a prevalent macro-evolutionary event in cancer, involving a doubling of the entire chromosome complement. However, despite its prevalence and clinical prognostic relevance, the evolutionary selection pressures for WGD have not been investigated. Here, we explored whether WGD may act to mitigate the irreversible, inexorable ratchet-like, accumulation of deleterious mutations in essential genes. Utilizing 1050 tumor regions from 816 non-small cell lung cancers (NSCLC), we temporally dissect mutations to determine their temporal acquisition in relation to WGD. We find evidence for strong negative selection against homozygous loss of essential cancer genes prior to WGD. However, mutations in essential genes occurring after duplication were not subject to significant negative selection, consistent with WGD providing a buffering effect, decreasing the likelihood of homozygous loss. Finally, we demonstrate that loss of heterozygosity and temporal dissection of mutations can be exploited to identify signals of positive selection in lung, breast, colorectal cancer and other cancer types, enabling the elucidation of novel tumour suppressor genes and a deeper characterization of known cancer genes.
Visually lossless image compression extension for JPEG based on just-noticeable distortion evaluation (2015)

A visually lossless image encoding extension for JPEG is presented. Such extension enables an efficient implementation of perceptual coding by reusing existing widespread software libraries and hardware IP cores for JPEG. For any pixel in a decoded image, the proposed algorithm guarantees a maximum distortion bounded by the just-noticeable distortion (JND) threshold measured based on the input image. Perceptual coding is performed in three steps: (1) standard transform domain coding, (2) spatial domain distortion visibility analysis by JND model and (3) spatial domain residual coding. Such scheme has been implemented in this work as an extension for JPEG based on a low complexity JND model. The encoder determines if a pixel block in a standard JPEG output image contains distortions beyond the visibility threshold given by the JND model. If it is true then the locations and the values of such distortions are encoded as side information. Quantization step size for the distortion values, i.e. perceptual residuals, are chosen based on the visibility threshold. Experimental results show that in terms of compression efficiency, the proposed perceptual encoding extension outperforms the standard JPEG encoder by 50% for a visually lossless compression of images.
Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae (2020)

High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism.
Insulin-like growth factor I is a dual effector of multiple myeloma cell growth (2000)

Multiple myeloma (MM) is an invariably fatal disease that accounts for approximately 1% to 2% of all human cancers. Surprisingly little is known about the cellular pathways contributing to growth of these tumors. Although the cytokine interleukin-6 has been suggested to be the major stimulus for myeloma cell growth, the role of a second potential growth factor, insulin-like growth factor I (IGF-I), has been less clearly defined. The IGF-I signaling cascade in 8 MM cell lines was examined. In 7 of these, the IGF-I receptor (IGF-IR) was expressed and autophosphorylated in response to ligand. Downstream of IGF-IR, insulin receptor substrate 1 was phosphorylated, leading to the activation of phosphatidylinositol-3'-kinase (PI-3K). PI-3K, in turn, regulated 2 distinct pathways. The first included Akt and Bad, leading to an inhibition of apoptosis; the second included the mitogen-activated protein kinase (MAPK), resulting in proliferation. Biologic relevance of this pathway was demonstrated because in vitro IGF-I induced both an antiapoptotic and a proliferative effect. Importantly, in vivo administration of IGF-I in SCID mice inoculated with the OPM-2 line led to approximately twice the growth rate of tumor cells as in controls. These results suggest that IGF-I activates at least 2 pathways effecting myeloma cell growth and contributes significantly to expansion of these cells in vivo. (Blood. 2000;96:2856-2861)
Development of an automatic reading method and software for pointer instruments (2017)

To effectively resolve the automatic recognition of analog pointer measuring instruments, a reading recognition method based on Hough transform is proposed. In order to simplify the following procedure, image graying and binary, mathematical morphology, including dilation and thinning, edge recognition was applied to the system. We proposed the recognition principle for reading recognition of the pointer's angle by using Hough transform. And the reading of the pointer is decided by the linear relationship between the panel's scale and the angle of the instrument's dial revolutionary. Considering that in most practical cases, the panel cannot be horizontal, so the procedure of tilt correction is employed in this paper. Finally, the software is written in MATLAB. The recognition system is achieved in LabVIEW, where the front panel of the reading system is developed. The experimental results demonstrate that our method is feasible for pointer instrument recognition.
Influence of vestibular input on spatial and nonspatial memory and on hippocampal NMDA receptors (2011)

It has recently been shown that a lack of vestibular sensory information decreases spatial memory performance and induces biochemical changes in the hippocampus in rodents. After vestibular neurectomy, patients display spatial memory deficit and hippocampal atrophy. Our objectives were to explore: (a) spatial (Y maze, radial-arm maze), and non-spatial (object recognition) memory performance, (b) modulation of NMDA receptors within the hippocampus using radioligand binding, and (c) hippocampal atrophy, using MRI, in a rat model of bilateral labyrinthectomy realized in two operations. Chemical vestibular lesions (VLs) were induced in 24 animals by transtympanic injections of sodium arsanilate (30 mg/0.1 ml/ear), one side being lesioned 3 weeks after the other. The control group received transtympanic saline solution (0.1 ml/ear) (n = 24). Spatial memory performance (Y maze and radial maze) decreased after VL. Conversely, non-spatial memory performance (object recognition) was not affected by VL. No hippocampal atrophy was observed with MRI, but density of NMDA receptors were increased in the hippocampus after VL. These findings show that the lack of vestibular information induced specific deficits in spatial memory. Additionally, quantitative autoradiographic data suggest the involvement of the glutamatergic system in spatial memory processes related to vestibular information. When studying spatial memory performances in the presence of vestibular syndrome, two-step labyrinthectomy is a suitable procedure for distinguishing between the roles of the specific components of vestibular input loss and those of impaired locomotor activity.
Thermal architecture for the SPIDER flight cryostat (2010)

We describe the cryogenic system for SPIDER, a balloon-borne microwave polarimeter that will map 8% of the sky with degree-scale angular resolution. The system consists of a 1284 L liquid helium cryostat and a 16 L capillary-filled superfluid helium tank, which provide base operating temperatures of 4 K and 1.5 K, respectively. Closed-cycle <sup>3</sup>He adsorption refrigerators supply sub-Kelvin cooling power to multiple focal planes, which are housed in monochromatic telescope inserts. The main helium tank is suspended inside the vacuum vessel with thermally insulating fiberglass flexures, and shielded from thermal radiation by a combination of two vapor cooled shields and multi-layer insulation. This system allows for an extremely low instrumental background and a hold time in excess of 25 days. The total mass of the cryogenic system, including cryogens, is approximately 1000 kg. This enables conventional long duration balloon flights. We will discuss the design, thermal analysis, and qualification of the cryogenic system.
MONITORING DIAPREPES ABBREVIATUS WITH TEDDERS TRAPS IN SOUTHWEST FLORIDA CITRUS (1997)

A pyramid trap known as the Tedders trap was used to monitor emergence patterns of the root weevil, Diaprepes abbreviatus (L.) in two citrus groves in Hendry County (southwest Florida) during 1996 and 1997. Two sizes (1 ft and 2 ft base) and colors (red and black) were compared with no significant differences. A well defined peak of weevil captures was seen in mid-April both years, as was a more poorly defined fall peak which continued into early winter. While the traps failed to detect treatment effects in single row plots, they did provide useful information for management planning. Soon after peak emergence in mid-April would seem to be an optimal time for foliar sprays directed against adults. Applications of nematodes against larvae might best be made to coincide with the first summer rains in June, when most of the current year's crop of eggs would have hatched and soil conditions would be favorable to nematode movement and survival.
Variation of Functional Neurological Symptoms and Emotion Regulation with Time (2018)

Over the investigated time interval, augmented habitual cognitive emotion regulation suggests an alleviation of emotion processing deficits, but no significant symptom decrease. More controlled and prolonged treatment studies would be needed to determine whether and how a specific contribution of treatment-related changes of emotion regulation and FNS might be inferred.