gebhart/patrepeval huggingface dataset:
Ambient and Cryogenic Alignment Verification and Performance of the Infrared Multi-Object Spectrometer (2003)

The Infrared Multi-Object Spectrometer (IRMOS) is a facility instrument for the Kitt Peak National Observatory 4 and 2.1 meter telescopes. IRMOS is a near-IR (0.8 - 2.5 micron) spectrometer with low- to mid-resolving power (R = 300 - 3000). IRMOS produces simultaneous spectra of approximately 100 objects in its 2.8 x 2.0 arc-min field of view using a commercial Micro Electro-Mechanical Systems (MEMS) Digital Micro-mirror Device (DMD) from Texas Instruments. The IRMOS optical design consists of two imaging subsystems. The focal reducer images the focal plane of the telescope onto the DMD field stop, and the spectrograph images the DMD onto the detector. We describe ambient breadboard subsystem alignment and imaging performance of each stage independently, and the ambient and cryogenic imaging performance of the fully assembled instrument. Interferometric measurements of subsystem wavefront error serve to venfy alignment, and are accomplished using a commercial, modified Twyman-Green laser unequal path interferometer. Image testing provides further verification of the optomechanical alignment method and a measurement of near-angle scattered light due to mirror small-scale surface error. Image testing is performed at multiple field points. A mercury-argon pencil lamp provides spectral lines at 546.1 nm and 1550 nm, and a CCD camera and IR camera are used as detectors. We use commercial optical modeling software to predict the point-spread function and its effect on instrument slit transmission and resolution. Our breadboard test results validate this prediction. We conclude with an instrument performance prediction for first light.
Anthropometric deficits and the associated risk of death by age and sex in children aged 6–59 months: A meta‐analysis (2022)

Risk of death from undernutrition is thought to be higher in younger than in older children, but evidence is mixed. Research also demonstrates sex differences whereby boys have a higher prevalence of undernutrition than girls. This analysis described mortality risk associated with anthropometric deficits (wasting, underweight and stunting) in children 6-59 months by age and sex. We categorised children into younger (6-23 months) and older (24-59 months) age groups. Age and sex variations in near-term (within 6 months) mortality risk, associated with individual anthropometric deficits were assessed in a secondary analysis of multi-country cohort data. A random effects meta-analysis was performed. Data from seven low-or-middle-income-countries collected between 1977 and 2013 were analysed. One thousand twenty deaths were recorded for children with anthropometric deficits. Pooled meta-analysis estimates showed no differences by age in absolute mortality risk for wasting (RR 1.08, p = 0.826 for MUAC < 125 mm; RR 1.35, p = 0.272 for WHZ < -2). For underweight and stunting, absolute risk of death was higher in younger (RR 2.57, p < 0.001) compared with older children (RR 2.83, p < 0.001). For all deficits, there were no differences in mortality risk for girls compared with boys. There were no differences in the risk of mortality between younger and older wasted children, supporting continued inclusion of all children under-five in wasting treatment programmes. The risk of mortality associated with underweight and stunting was higher among younger children, suggesting that prevention programmes might be justified in focusing on younger children where resources are limited. There were no sex differences by age in mortality risk for all deficits.
Run-Time Analysis for Atomicity (2003)

Writing and debugging concurrent (shared-variable) programs is notoriously difficult. This motivated the development of numerous static analysis and run-time analysis techniques designed to (help) ensure that concurrent programs satisfy common correctness requirements for concurrent programs, such as absence of race conditions and absence of deadlocks. This paper focuses on another common correctness requirement for concurrent programs, namely, atomicity, which requires that any set of concurrent invocations of designated procedures is equivalent to performing those invocations serially in some order. Run-time analysis algorithms for detecting violations of atomicity are presented. The algorithms vary in cost and precision.
Increased responsiveness of hypoxic endothelial cells to FGF2 is mediated by HIF-1α-dependent regulation of enzymes involved in synthesis of heparan sulfate FGF2-binding sites (2002)

Binding of basic fibroblast growth factor (FGF2) to its high affinity receptors requires the presence of specific heparan sulfate (HS) moieties on the cell surface that act as coreceptors. To determine the contribution of cell-surface HS to modulation of FGF2-dependent cell growth, we studied the changes in the cell mass and FGF2 binding of endothelial cell HS under normoxic and hypoxic conditions in vitro. Both large vein and cardiac microvascular endothelial cells cultured under hypoxic conditions demonstrated an increase in the ratio of cell-surface HS to chondroitin sulfate (CS), as well as an increase in the number of low affinity (HS-associated) binding sites for FGF2 with no change in the apparent K(d). This increase in the number of HS-FGF2 binding sites, in the absence of a significant change in FGF receptor expression, resulted in enhanced responsiveness of hypoxic, compared with normoxic, endothelial cells to FGF2 stimulation. Gene expression studies demonstrated increased expression of the key regulatory enzyme responsible for HS chain synthesis, 1,4 GlcNAc transferase (GlcNAcT-I), as well as increased expression of 2-O sulfotransferase (HS2ST), the enzyme responsible for sulfation of IdoA, a crucial part of the HS-FGF2 binding site. Transduction of cells with an adenovirus encoding a HIF-1alpha expression construct resulted in a similar increase in GlcNAcT-I and HS2ST expression. We conclude that hypoxia increases endothelial cell responsiveness to FGF2 by promoting preferential synthesis of HS rather than CS chains and increasing the number of FGF2-binding sites on HS chains. Both of these events are mediated by a HIF-1alpha-dependent increase in expression of the enzymes GlnNAcT-I and HS2ST. This shift in cell-surface HS composition results in enhanced cell sensitivity to FGF2-induced growth stimulation.
A Minimally Invasive Device for the Monitoring of 24-hour Intraocular Pressure Patterns (2013)

Intraocular pressure (IOP) is the only modifiable risk factor for glaucoma, and lowering of IOP remains the mainstay of glaucoma treatment. IOP is a dynamic biologic parameter, nevertheless, current glaucoma management usually relies on single IOP measurements during clinic hours. However, a majority of glaucoma patients have their high, including their highest, IOP levels outside clinic hours. These undetected IOPs may explain why certain patients have progressive disease despite treatment. The interest in continuous 24-hour IOP monitoring started over half a century ago, but only recent technologic advances have provided clinicians with a practical device for continuous IOP monitoring. In this article, we discuss innovative approaches with permanent and temporary devices for 24-hour IOP monitoring, such as a contact lens sensor. Despite being in their infancy, these devices may soon enable clinicians to use 24-hour IOP data to improve glaucoma management and reduce the glaucoma-related burden of disease.
Pyrazines. I. Syntheses of 2,3-dihydroxypyrazines and their derivatives (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrazines. I. Syntheses of 2,3-dihydroxypyrazines and their derivativesJiro Adachi and Nobuhiro SatoCite this: J. Org. Chem. 1972, 37, 2, 221–225Publication Date (Print):January 1, 1972Publication History Published online1 May 2002Published inissue 1 January 1972https://pubs.acs.org/doi/10.1021/jo00967a010https://doi.org/10.1021/jo00967a010research-articleACS PublicationsRequest reuse permissionsArticle Views872Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Influence of thiol structure on neocarzinostatin activation and expression of DNA damage (1992)

Neocarzinostatin (NCS) is an enediyne antitumor antibiotic that cleaves DNA following a thiol-induced electronic rearrangement to a diradical form. Structure-function studies with 11 thiol-containing compounds were undertaken to clarify the role of the thiol in NCS-mediated DNA damage. The rates of activation of NCS in the presence of DNA with the various thiols approximated a Brønsted relation (beta = 0.43, r2 = 0.86), which suggests that the basicity/nucleophilicity of the thiol is important to NCS activation. However, an additional contribution to NCS activation may arise from the affinity of the thiol for DNA, since there is a correlation between the concentration of thiol producing maximal DNA damage, assessed by quantitating the topologic forms of plasmid pBR322 following treatment with NCS, and the apparent ability of the thiol to bind to DNA by hydrophobic or electrostatic interactions. The overall second-order rate constants for the activation of NCS were found to be inversely correlated with the thiol optima; a plot of the former versus the reciprocal of the optimal thiol concentration revealed a first-order rate constant of activation of 0.013 s-1 in the presence of DNA. This indicates that maximal DNA damage occurs when NCS is activated with a half-life of 52 s, a relatively slow rate of activation that suggests that NCS binds to DNA before undergoing activation by thiol. Finally, an analysis of strand breaks in pBR322 shows that thiols possessing a carboxylate moiety produce larger quantities of bistranded DNA lesions than their esterified or non-carboxylate-containing counterparts.
Second Generation Single-Round Infectious Particle (SRIP)-Producing Flavivirus Vaccine (2013)

The genus Flavivirus includes the important human arthropod-borne viral pathogens dengue virus (DENV), Japanese encephalitis virus (JEV), and West Nile virus (WNV). Vaccine research targeting these pathogenic flaviviruses has been driven by the need for inexpensive, efficacious, safe, and stable preparations applicable for use in the developing world. One promising vaccine strategy is to utilise flavivirus genomes which have large internal deletions within the capsid (C) gene, thus preventing packaging of the genome and formation of infectious particles. These dC vaccines lead to secretion of large amounts of immunogenic prM/E particles from self-replicating RNA but cannot form a spreading infection. Our laboratory has previously developed a DNA-based vaccine that trans-complements the deleted C within the same plasmid DNA and produces single-round infectious particles (SRIPs) in vivo, leading to an amplifying single round of infection in the vaccinee (1). The first generation SRIP-producing DNA, though protective against lethal WNV challenge, generated low amounts of both SRIPs and prM/E particles. In this project we aimed at increasing production of prM/E particles and SRIPs by generating smaller internal C deletions via the removal of specific alpha helices, by optimizing trans-C expression, and by investigating the benefits of envelope (E) protein glycosylation. New C-deletion constructs were investigated and assessment of E protein secretion and infectious assays demonstrated that removing alpha helices 1 and 2 led to secretion of relatively large amounts of prM/E particles while retaining the non-infectious phenotype. Trans-complementation of C-deleted Kunjin cDNA by addition of different forms of C protein under control of different promoters was investigated in regards to efficiency of SRIP production. The stronger EF1α promoter encoding a membrane-targeted extended form of C was demonstrated to lead to the formation of the highest titres of SRIPs. Additionally, SRIP titres further improved via the incorporation of a glycosylation motif in the E gene. Intradermal immunisation of mice with SRIP-producing vaccines led to recovery of infectious particles and induction of an immune response consistent with protection from virulent virus. As this optimised vaccine yields ≈ 2 log greater titres of SRIPs than the 1st generation vaccine, it appears to be a very promising candidate for further characterisation. 1. Chang DC, Liu WJ, Anraku I, Clark DC, Pollitt CC, Suhrbier A, Hall RA, Khromykh AA. 2008. Single-round infectious particles enhance immunogenicity of a DNA vaccine against West Nile virus. Nat Biotechnol 26:571-577.
The EM Algorithm and Extensions (1998)

The first unified account of the theory, methodology, and applications of the EM algorithm and its extensionsSince its inception in 1977, the Expectation-Maximization (EM) algorithm has been the subject of intense scrutiny, dozens of applications, numerous extensions, and thousands of publications. The algorithm and its extensions are now standard tools applied to incomplete data problems in virtually every field in which statistical methods are used. Until now, however, no single source offered a complete and unified treatment of the subject.The EM Algorithm and Extensions describes the formulation of the EM algorithm, details its methodology, discusses its implementation, and illustrates applications in many statistical contexts. Employing numerous examples, Geoffrey McLachlan and Thriyambakam Krishnan examine applications both in evidently incomplete data situations-where data are missing, distributions are truncated, or observations are censored or grouped-and in a broad variety of situations in which incompleteness is neither natural nor evident. They point out the algorithm's shortcomings and explain how these are addressed in the various extensions.Areas of application discussed include: Regression Medical imaging Categorical data analysis Finite mixture analysis Factor analysis Robust statistical modeling Variance-components estimation Survival analysis Repeated-measures designs For theoreticians, practitioners, and graduate students in statistics as well as researchers in the social and physical sciences, The EM Algorithm and Extensions opens the door to the tremendous potential of this remarkably versatile statistical tool.
Does the chromatic aberration of the eye vary with age? (1988)

The longitudinal chromatic aberration of the eye has been reported to decline with age. Using three different methods, we have measured the aberration in a group of young subjects (27-33 years old) and a group of older subjects (48-72 years old). In two of the methods we used a Badal optometer, either with or without an achromatizing lens incorporated, to examine the effect of wavelength on refractive error. In the third method we used a vernier-alignment apparatus to assess chromatic dispersion directly. None of the results of the experiments performed revealed any difference in aberration between the groups. Furthermore, a linear regression of aberration against age showed no relationship between these variables. We conclude that, for human adults, the magnitude of chromatic aberration is independent of age.
Gene delivery to embryonic stem cells (2005)

Since the establishment of embryonic stem (ES) cells and the identification of tissue-specific stem cells, researchers have made great strides in the analysis of the natural biology of such stem cells for the development of therapeutic applications. Specifically, ES cells are capable of differentiating into all of the cell types that constitute the whole body. Thus, ES cell research promises new type of treatments and possible cures for a variety of debilitating diseases and injuries. The potential medical benefits obtained from stem cell technology are compelling and stem cell research sees a bright future. Control of the growth and differentiation of stem cells is a critical tool in the fields of regenerative medicine, tissue engineering, drug discovery, and toxicity testing. Toward such a goal, we present here an overview of gene delivery in ES cells, covering the following topics: significance of gene delivery in ES cells, stable versus transient gene delivery, cytotoxicity, suspension versus adherent cells, expertise, time, cost, viral vectors for gene transduction (lentiviruses, adenoviruses, and adeno-associated viruses, chemical methods for gene delivery, and mechanical or physical gene delivery methods (electroporation, nucleofection, microinjection, and nuclear transfer).
Vein morphometry in end-stage kidney disease: Teasing out the contribution of age, comorbidities, and vintage to chronic wall remodeling (2022)

Age and diabetes are the most important risk factors for chronic development of venous IH and fibrosis independent of CKD status. Among kidney disease patients, longer dialysis vintage, and history of a previous AVF/AVG are strong predictors of IH.
Inorganic Materials Synthesis Planning with Literature-Trained Neural Networks (2020)

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated, unsupervised method for connecting scientific literature to inorganic synthesis insights. Starting from the natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for any inorganic materials of interest. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties and that the model's behavior complements the existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.
Design and Development of a Smart Variable Rate Sprayer Using Deep Learning (2020)

The uniform application (UA) of agrochemicals results in the over-application of harmful chemicals, increases crop input costs, and deteriorates the environment when compared with variable rate application (VA). A smart variable rate sprayer (SVRS) was designed, developed, and tested using deep learning (DL) for VA application of agrochemicals. Real-time testing of the SVRS took place for detecting and spraying and/or skipping lambsquarters weed and early blight infected and healthy potato plants. About 24,000 images were collected from potato fields in Prince Edward Island and New Brunswick under varying sunny, cloudy, and partly cloudy conditions and processed/trained using YOLOv3 and tiny-YOLOv3 models. Due to faster performance, the tiny-YOLOv3 was chosen to deploy in SVRS. A laboratory experiment was designed under factorial arrangements, where the two spraying techniques (UA and VA) and the three weather conditions (cloudy, partly cloudy, and sunny) were the two independent variables with spray volume consumption as a response variable. The experimental treatments had six repetitions in a 2 × 3 factorial design. Results of the two-way ANOVA showed a significant effect of spraying application techniques on volume consumption of spraying liquid (p-value &lt; 0.05). There was no significant effect of weather conditions and interactions between the two independent variables on volume consumption during weeds and simulated diseased plant detection experiments (p-value &gt; 0.05). The SVRS was able to save 42 and 43% spraying liquid during weeds and simulated diseased plant detection experiments, respectively. Water sensitive papers’ analysis showed the applicability of SVRS for VA with &gt;40% savings of spraying liquid by SVRS when compared with UA. Field applications of this technique would reduce the crop input costs and the environmental risks in conditions (weed and disease) like experimental testing.
N-Linked Glycosylation-Dependent and -Independent Mechanisms Regulating CTRP12 Cleavage, Secretion, and Stability (2018)

C1q/TNF-related protein 12 (CTRP12) is a secreted regulator of glucose and lipid metabolism. It circulates in plasma as a full-length protein or as a cleaved isoform generated by furin/PCSK3 cleavage. These isoforms preferentially activate different signaling pathways, and their ratio in plasma is altered in obesity and diabetes. Here, we show that three conserved asparagine residues (Asn-39, Asn-287, and Asn-297) play important roles in modulating CTRP12 cleavage, secretion, and stability. Mass spectrometry analysis provided direct evidence of Asn-39 glycosylation. When N-linked glycosylation was inhibited by tunicamycin or abolished by the N39Q, N39A, or T41A mutation, CTRP12 cleavage was enhanced. Complex-type N-glycans on CTRP12 blocked cleavage by the Golgi-localized furin. In N-acetylglucosaminyltransferase I (GnTI)-deficient cells that could not form hybrid and complex-type N-glycans in the Golgi, CTRP12 cleavage was enhanced, and re-expressing GnTI reduced cleavage. Replacing the nonglycosylated Asn-297 with glutamine or alanine also increased CTRP12 cleavage. Both Asn-39 and Asn-297 contributed independently to CTRP12 cleavage: maximum cleavage was observed in the double mutant. In addition, CTRP12 cleavage was abolished in furin-deficient cells and restored by furin re-expression. Replacing the nonglycosylated Asn-287 with glutamine or alanine resulted in protein misfolding and aggregation, leading to retention in the endoplasmic reticulum. Cycloheximide chase analyses indicated reduced protein stability for N39Q, T41A, and N297Q mutants. Lastly, we show that increasing the flux through the hexosamine biosynthesis pathway by exogenous glucosamine, known to disrupt protein glycosylation, also promoted CTRP12 cleavage. Combined, these data highlight glycosylation-dependent and -independent mechanisms regulating CTRP12 cleavage, secretion, and protein stability.