gebhart/patrepeval huggingface dataset:
Heterotrimeric Coiled Coils with Core Residue Urea Side Chains (2008)

We report several coiled coil heterotrimers with varying core residue buried polar groups, all with T(m) values >43 degrees C. Introduction of new synthetic side chain structures, including some terminating in monosubstituted ureas, diversifies the pool of viable core residue candidates. A study of core charge pairings demonstrates that, unlike dimeric systems, trimeric coiled coils do not tolerate guanidine-guanidine contacts, even in the presence of a compensating carboxylate. Overall, the roster of feasible coiled coil designs is significantly expanded.
Natural Language–based Machine Learning Models for the Annotation of Clinical Radiology Reports (2018)

Purpose To compare different methods for generating features from radiology reports and to develop a method to automatically identify findings in these reports. Materials and Methods In this study, 96 303 head computed tomography (CT) reports were obtained. The linguistic complexity of these reports was compared with that of alternative corpora. Head CT reports were preprocessed, and machine-analyzable features were constructed by using bag-of-words (BOW), word embedding, and Latent Dirichlet allocation-based approaches. Ultimately, 1004 head CT reports were manually labeled for findings of interest by physicians, and a subset of these were deemed critical findings. Lasso logistic regression was used to train models for physician-assigned labels on 602 of 1004 head CT reports (60%) using the constructed features, and the performance of these models was validated on a held-out 402 of 1004 reports (40%). Models were scored by area under the receiver operating characteristic curve (AUC), and aggregate AUC statistics were reported for (a) all labels, (b) critical labels, and (c) the presence of any critical finding in a report. Sensitivity, specificity, accuracy, and F1 score were reported for the best performing model's (a) predictions of all labels and (b) identification of reports containing critical findings. Results The best-performing model (BOW with unigrams, bigrams, and trigrams plus average word embeddings vector) had a held-out AUC of 0.966 for identifying the presence of any critical head CT finding and an average 0.957 AUC across all head CT findings. Sensitivity and specificity for identifying the presence of any critical finding were 92.59% (175 of 189) and 89.67% (191 of 213), respectively. Average sensitivity and specificity across all findings were 90.25% (1898 of 2103) and 91.72% (18 351 of 20 007), respectively. Simpler BOW methods achieved results competitive with those of more sophisticated approaches, with an average AUC for presence of any critical finding of 0.951 for unigram BOW versus 0.966 for the best-performing model. The Yule I of the head CT corpus was 34, markedly lower than that of the Reuters corpus (at 103) or I2B2 discharge summaries (at 271), indicating lower linguistic complexity. Conclusion Automated methods can be used to identify findings in radiology reports. The success of this approach benefits from the standardized language of these reports. With this method, a large labeled corpus can be generated for applications such as deep learning. <sup>©</sup> RSNA, 2018 Online supplemental material is available for this article.
Exercise and Amino Acid Anabolic Cell Signaling and the Regulation of Skeletal Muscle Mass (2012)

A series of complex intracellular networks influence the regulation of skeletal muscle protein turnover. In recent years, studies have examined how cellular regulators of muscle protein turnover modulate metabolic mechanisms contributing to the loss, gain, or conservation of skeletal muscle mass. Exercise and amino acids both stimulate anabolic signaling potentially through several intracellular pathways including the mammalian target of rapamycin complex 1 and the mitogen activated protein kinase cell signaling cascades. As novel molecular regulators of muscle integrity continue to be explored, a contemporary analysis of the literature is required to understand the metabolic mechanisms by which contractile forces and amino acids affect cellular process that contribute to long-term adaptations and preservation of muscle mass. This article reviews the literature related to how exercise and amino acid availability affect cellular regulators of skeletal muscle mass, especially highlighting recent investigations that have identified mechanisms by which contractile forces and amino acids modulate muscle health. Furthermore, this review will explore integrated exercise and nutrition strategies that promote the maintenance of muscle health by optimizing exercise, and amino acid-induced cell signaling in aging adults susceptible to muscle loss.
ESR: No Longer in the Margins of Engineering (1994)

The key aspects and features of Engineering for Social Responsibility (ESR) are discussed. The aim of ESR was to encourage engineers to think more deeply about the social implications of their work and attitudes.
Validation and Practical Procedure for Vibrational Evaluation of Tendons (2008)

Vibrational testing of tension to identify potentially distressed external tendons of post-tensioned segments and columns has been successfully used in major Florida Department of Transportation (FDOT) bridges. This investigation provided validation of basic assumptions and verification of tension obtained by the vibration method against independent load cell measurements with tendon segments of size, length, and tension levels comparable to those used in actual structures. Measurements were conducted in a specially built tendon test facility with 12-strand tendons up to nearly 10 m (400 in.) long, some including a deviation block. Tension estimated from vibration tests was on average within ~6% of load cell measurements, after correction for the effect of metal pipe ends in some cases. Upon simulated strand failures at the anchorage area there was tension loss that was tracked adequately in nearly all cases by the vibration tests. Advanced data processing methods were developed to perform rapid evaluation of data from large populations (thousands) of tendons in actual bridges. Vibration test field equipment was developed for simplified operation and analysis procedures. A portable field equipment prototype was designed and constructed to permit testing by a single operator. Extensive vibration tests of tendons were conducted in the segmental approaches of the Sunshine Skyway Bridge, revealing generally normal tension levels but flagging specific tendons with fringe performance for subsequent inspection. A user-oriented summary of findings and applications is provided.
Hydroformylation of oct-1-ene with extremely high rates using rhodium catalysts containing bulky phosphites (1991)

A rhodium complex containing tris(o-tert-butyl-p-methylphenyl) phosphite as a ligand catalyses the hydroformylation of oct-1-ene with good selectivity and extremely high rates; the rate constant, which is pseudo first-order in [H2] and 1/[CO], shows that the reaction of hydrogen is the rate determining step.
Surfactant-Free Preparation of Biodegradable Hydrogel Microspheres for Protein Release (1999)

The preparation of biodegradable hydrogel microspheres in the absence of surfactants was carried out by a two-step procedure which involved the formation of non-crosslinked microspheres from gelatin based on its inherent gelation nature at low temperatures and the subsequent glutaraldehyde (GA) crosslinking. The size of the microspheres was controlled in the range of 3 to 100 μm by changing the concentration of gelatin or GA, the emulsification method, and the crosslinking time. Neutral aqueous solutions of proteins with different isoelectric points (IEPs) and molecular weights (Mws) were infused into freeze-dried hydrogel microspheres to produce protein-incorporated gelatin microspheres. In vitro protein release from the microspheres depended on the protein's IEP but not on the Mw. The incorporated basic proteins with IEPs > 7.0 were released initially from the acidic gelatin microspheres, followed by no substantial release, whereas a larger initial release of the incorporated acidic proteins with IEPs < 7.0 was observed. The basic gelatin microspheres exhibited an opposite relationship between proteins IEP and protein release. Noncharged dextran rapidly diffused out of acidic gelatin microspheres, irrespective of the Mw. These findings indicate that an ionic interaction with gelatin constituted hydrogel microspheres prevented oppositely charged protein from being released from gelatin under in vitro non-degradation conditions.
Revascularization of ischemic limbs after transplantation of human bone marrow cells with high aldehyde dehydrogenase activity (2009)

The development of cell therapies to treat peripheral vascular disease has proven difficult because of the contribution of multiple cell types that coordinate revascularization. We characterized the vascular regenerative potential of transplanted human bone marrow (BM) cells purified by high aldehyde dehydrogenase (ALDH(hi)) activity, a progenitor cell function conserved between several lineages. BM ALDH(hi) cells were enriched for myelo-erythroid progenitors that produced multipotent hematopoietic reconstitution after transplantation and contained nonhematopoietic precursors that established colonies in mesenchymal-stromal and endothelial culture conditions. The regenerative capacity of human ALDH(hi) cells was assessed by intravenous transplantation into immune-deficient mice with limb ischemia induced by femoral artery ligation/transection. Compared with recipients injected with unpurified nucleated cells containing the equivalent of 2- to 4-fold more ALDH(hi) cells, mice transplanted with purified ALDH(hi) cells showed augmented recovery of perfusion and increased blood vessel density in ischemic limbs. ALDH(hi) cells transiently recruited to ischemic regions but did not significantly integrate into ischemic tissue, suggesting that transient ALDH(hi) cell engraftment stimulated endogenous revascularization. Thus, human BM ALDH(hi) cells represent a progenitor-enriched population of several cell lineages that improves perfusion in ischemic limbs after transplantation. These clinically relevant cells may prove useful in the treatment of critical ischemia in humans.
A New Artificial Immune Approach to Hardware Test Based on the Principle of Antibody Diversity (2003)

This paper proposes a new artificial immune approach to hardware test. A novel algorithm of generating tolerance conditions is suggested based on the principle of the antibody diversity. Tolerance conditions in artificial immune system correspond to the antibody in biological immune system. The suggested method is applied to the on-line monitoring of a typical FSM (a decade counter) and its effectiveness is demonstrated by the computer simulation.
Incorporation of Agouti-Related Protein (AgRP) Human Single Nucleotide Polymorphisms (SNPs) in the AgRP-Derived Macrocyclic Scaffold c[Pro-Arg-Phe-Phe-Asn-Ala-Phe-<scp>d</scp>Pro] Decreases Melanocortin-4 Receptor Antagonist Potency and Results in the Discovery of Melanocortin-5 Receptor Antagonists (2019)

While the melanocortin receptors (MCRs) are known to be involved in numerous biological pathways, the potential roles of the MC5R have not been clearly elucidated in humans. Agouti-related protein (AgRP), an MC3R/MC4R antagonist and MC4R inverse agonist, contains an exposed β-hairpin loop composed of six residues (Arg-Phe-Phe-Asn-Ala-Phe) that is imperative for binding and function. Within this active loop of AgRP, four human missense polymorphisms were deposited into the NIH Variation Viewer database. These polymorphisms, Arg111Cys, Arg111His, Phe112Tyr, and Ala115Val (AgRP full-length numbering), were incorporated into the peptide macrocycles c[Pro<sup>1</sup>-Arg<sup>2</sup>-Phe<sup>3</sup>-Phe<sup>4</sup>-Xaa<sup>5</sup>-Ala<sup>6</sup>-Phe<sup>7</sup>-dPro<sup>8</sup>], where Xaa was Dap<sup>5</sup> or Asn<sup>5</sup>, to explore the functional effects of these naturally occurring substitutions in a simplified AgRP scaffold. All peptides lowered potency at least 10-fold in a cAMP accumulation assay compared to the parent sequences at the MC4Rs. Compounds MDE 6-82-3c, ZMK 2-82, MDE 6-82-1c, ZMK 2-85, and ZMK 2-112 are also the first AgRP-based chemotypes that antagonize the MC5R.
Multi-media extensions in super-pipelined micro-architectures. A new case for SIMD processing? (2002)

General purpose microprocessors have long been considered a computing platform unsuited to image processing and vision tasks. The so-called Von-Neumann paradigm and the associated memory bottleneck have motivated the research into various forms of parallel processing and of special processors for vision. The SIMD approach, adopted in massively parallel processors, has been introduced in a minimal format in the multimedia extensions to instruction set architectures of standard microprocessors. This paper examines the characteristics of SIMD processing that have been mapped into these extensions.
Image-Quality Assessment for Several Positron Emitters Using the NEMA NU 4-2008 Standards in the Siemens Inveon Small-Animal PET Scanner (2010)

With the intrinsic spatial resolution (approximately 1.5 mm) of this latest-generation small-animal PET scanner, the finite positron range has become the limiting factor for the overall spatial resolution and activity recovery in small structures imaged with (124)I and (68)Ga. The presence of single photons had only a limited effect on the image noise. MAP, as compared with the other reconstruction algorithms, increased RC and decreased %SD and SOR.
Dual Quaternions for Rigid Transformation Blending (2006)

Figure 1: A comparison of different rigid transformation blending algorithms applied in skinning shows that blending based on dual quaternions not only eliminates artifacts, but is also much easier to implement and more than twice as fast as previous methods. Quaternions have been a popular tool in 3D computer graphics for more than 20 years. However, classical quaternions are restricted to the representation of rotations, whereas in graphical applications we typically work with rotation composed with translation (i.e., a rigid transformation). Dual quaternions represent rigid transformations in the same way as classical quaternions represent rotations. In this paper we show how to generalize established techniques for blending of rotations to include all rigid transformations. Algorithms based on dual quaternions are computationally more efficient than previous solutions and have better properties (constant speed, shortest path and coordinate invariance). For the specific example of skinning, we demonstrate that problems which required considerable research effort recently are trivial to solve using our dual quaternion formulation. However, skinning is only one application of dual quaternions, so several further promising research directions are suggested in the paper.
Veterinary Medicine and Professionalism (1973)

Throughout the past four years, rumbles in the distance could be heard proclaiming veterinary medicine and its sense of professionalism. But lately some people have started to actually wonder about why they ever wanted to start the uphill battle towards that professional degree.
Persistence of benzo(a)pyrene metabolite:DNA adducts in lung and liver of mice. (1984)

The persistence of benzo(a)pyrene (BP) metabolite:DNA adducts has been studied in lung and liver of A/HeJ and C57BL/6J mice after a dose of BP (6 mg/mouse) which induces pulmonary adenomas in A/HeJ mice but not in C57BL/6J mice. BP is not a hepatic carcinogen in either strain. Following p.o. administration of [3H]BP, animals were killed at times ranging from 10 hr to 28 days, and BP metabolite:DNA adducts were analyzed by high-pressure liquid chromatography. The major adduct identified in each tissue was the (+)-7 beta-8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene:deoxyguanosine adduct. A 7 beta, 8 alpha-dihydroxy-9 beta,10 beta,epoxy-7,8,9, 10-tetrahydrobenzo(a)pyrene:deoxyguanosine adduct, a (-)-7 beta, 8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene:deoxyguanosine adduct, and an unidentified adduct were also observed. The disappearance of (+)-7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydro-BP adduct in A/HeJ mice followed first-order kinetics over the time period examined, with a half-life of 18 and 9 days in lung and liver, respectively. The decay of this adduct in C57BL/6J mice was biphasic in both tissues. Our data on cell turnover suggest that there is active removal of adducts in liver, but that normal DNA turnover can account for the partial or possibly total observed disappearance of adducts in lung. These results suggest that the tissue specificity for BP-induced neoplasia in A/HeJ mice may be related to the relative persistence of adducts and high cell turnover rates in lung. In contrast, the results on formation and persistence of adducts and cell turnover do not provide an explanation for the strain difference in susceptibility to BP-induced pulmonary adenomas. It was also shown that the rates of removal of BP metabolite:DNA adducts in A/HeJ mice are not significantly different at a 500-fold lower BP dose.
Spin-Rotation Interaction of Noble-Gas Alkali-Metal Atom Pairs (1985)

Recent experimental data show that the spin-rotation coupling for alkali-metal-noble-gas van der Waals molecules is mainly due to the spin-orbit interaction of the alkali-metal valence electron within the core of the noble gas. We present a simple formula which accounts very well for the systematic variation of the spin-rotation interaction with different noble-gas or alkali-metal atoms.
Determining Individual Particle Magnetizations in Assemblages of Micrograins (2018)

Abstract Obtaining reliable information from even the most challenging paleomagnetic recorders, such as the oldest igneous rocks and meteorites, is paramount to open new windows into Earth's history. Currently, such information is acquired by simultaneously sensing millions of particles in small samples or single crystals using superconducting quantum interference device magnetometers. The obtained rock‐magnetic signal is a statistical ensemble of grains potentially differing in reliability as paleomagnetic recorder due to variations in physical dimensions, chemistry, and magnetic behavior. Here we go beyond bulk magnetic measurements and combine computed tomography and scanning magnetometry to uniquely invert for the magnetic moments of individual grains. This enables us to select and consider contributions of subsets of grains as a function of particle‐specific selection criteria and avoid contributions that arise from particles that are altered or contain unreliable magnetic carriers. This new, nondestructive, method unlocks information from complex paleomagnetic recorders that until now goes obscured.
PHENOL-HALO-PHTHALEINS. PRELIMINARY PAPER<sup>1</sup> (1929)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPHENOL-HALO-PHTHALEINS. PRELIMINARY PAPER1F. F. Blicke and F. D. SmithCite this: J. Am. Chem. Soc. 1929, 51, 6, 1865–1875Publication Date (Print):June 1, 1929Publication History Published online1 May 2002Published inissue 1 June 1929https://pubs.acs.org/doi/10.1021/ja01381a038https://doi.org/10.1021/ja01381a038research-articleACS PublicationsRequest reuse permissionsArticle Views191Altmetric-Citations10LEARN 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
Gaseous disinfection of Cryptosporidium parvum oocysts (1996)

Purified oocysts of Cryptosporidium parvum suspended in approximately 400 microliters of phosphate-buffered saline or deionized water in microcentrifuge tubes were exposed at 21 to 23 degrees C for 24 h to a saturated atmosphere of ammonia, carbon monoxide, ethylene oxide, formaldehyde, or methyl bromide gas. Controls were exposed to air. Oocysts in each tube were then rinsed and resuspended in fresh, deionized water, and 1 million oocysts exposed to each gas were orally administered to each of three to six neonatal BALB/c mice in replicate groups. Histologic sections of ileum, cecum, and colon tissues taken from each mouse 72 h after oral administration of oocysts were examined microscopically to determine if infection had been established. All 15 mice given oocysts exposed to carbon monoxide had numerous developmental stages of cryptosporidium in all three intestinal segments. Of 10 mice given oocysts exposed to formaldehyde, 6 had a few developmental stages of cryptosporidium in the ileum. No mice given oocysts exposed to ammonia, ethylene oxide, or methyl bromide were found to be infected. These findings indicate the efficacy of these low-molecular-weight gases (ammonia, ethylene oxide, and methyl bromide) as potential disinfectants for C. parvum oocysts where soil, rooms, buildings, tools, or instruments might be contaminated.
A time-of arrival location algorithm for maneuvering target on two-dimensional surface (2002)

A time-of-arrival location and tracking method for a maneuvering target is discussed in this paper. The rapid location and tracking of a target in two-dimensional space is realized by using nonlinear weighted least square (WLS) estimation and a self-adapting Kalman filter based on the acceleration time correlation model. Computer simulations indicate that this method is very efficient. The algorithm is of great importance to the practicability of passive location and tracking systems.
Effect of 4‐Aminopyridine on Upbeat and Downbeat Nystagmus Elucidates the Mechanism of Downbeat Nystagmus (2005)

The potassium channel blocker 4-aminopyridine (4-AP) restored vertical smooth pursuit and gaze holding in light in one patient with upbeat (UBN) and in one with downbeat nystagmus (DBN). Without a visible target, however, 4-AP had no effect on UBN, but DBN vanished. We hypothesize that this difference in the effects of 4-AP, which is known to increase the excitability of cerebellar Purkinje cells, can be attributed to the different lesion sites involved in UBN and DBN.