gebhart/patrepeval huggingface dataset:
The possible role of stress in the induction of pneumonic pasteurellosis. (1984)

Five groups of range bred calves (four calves per group) were used to investigate the effect of stress on susceptibility to aerosol exposures with bovine herpesvirus-1 or Pasteurella haemolytica. Twelve calves were weaned, transported, processed at a commercial feedlot and transported to isolation facilities three days later. An aerosol challenge of either 10 colony forming units of P. haemolytica or 10 plaque forming units of bovine herpesvirus-1 virus was given to two groups of calves and the third group was not challenged. The fourth group was transported directly to the isolation facilities after weaning and aerosol challenged with P. haemolytica. The fifth group remained at the farm after weaning and was not challenged. All transported animals had elevated plasma cortisol levels which remained above normal for at least three days postchallenge. The blastogenic response of all calves was depressed after leaving the farm and remained depressed throughout the experiment. The suppression correlated well with elevated serum cortisol levels. Calves processed through the feedlot encountered bovine herpesvirus-1 because eight out of 12 animals seroconverted to this antigen. Most calves seroconverted to P. haemolytica whether they were experimentally challenged or not. Where the unchallenged calves encountered P. haemolytica is unknown. Calves challenged with bovine herpesvirus-1 but not with P. haemolytica, had significant clinical signs of pneumonia and two animals died due to bovine herpesvirus-1 infection.(ABSTRACT TRUNCATED AT 250 WORDS)
Adversarial Purification with the Manifold Hypothesis (2022)

In this work, we formulate a novel framework for adversarial robustness using the manifold hypothesis. This framework provides sufficient conditions for defending against adversarial examples. We develop an adversarial purification method with this framework. Our method combines manifold learning with variational inference to provide adversarial robustness without the need for expensive adversarial training. Experimentally, our approach can provide adversarial robustness even if attackers are aware of the existence of the defense. In addition, our method can also serve as a test-time defense mechanism for variational autoencoders.
One-Year Anatomical and Functional Outcomes of the Argus II Implantation in Korean Patients with Late-Stage Retinitis Pigmentosa: A Prospective Case Series Study (2020)

Along with good anatomical outcomes and specialized rehabilitation practices, recipients of the Argus II implant showed profound improvements in functional vision and mobility.
Small Reorganization Energy of Intramolecular Electron Transfer in Fullerene-Based Dyads with Short Linkage (2002)

A bacteriochlorin-C60 dyad (H2BCh-C60) and a zinc chlorin dyad (ZnCh-C60) with the same short spacer have been synthesized. The rate constants for the charge-separation (CS) processes in these dyads were determined by fluorescence lifetime measurements of the dyads. The charge-recombination (CR) rate constants of the dyads were determined using laser flash photolysis. The photoexcitation of the zinc chlorin-C60 dyad results in formation of the long-lived radical ion pair, which has absorption maxima at 790 and 1000 nm due to the zinc chlorin radical cation and the C60 radical anion, respectively. Photoexcitation of the free-base bacteriochlorin-C60 dyad with the same short linkage leads to formation of the radical ion pair, which decays quickly to the triplet excited state of the bacteriochlorin moiety. The driving force dependence of the electron-transfer rate constants of these dyads with a short spacer affords a small reorganization energy (λ = 0.51 eV) as compared with the λ value (0.66 eV) of zinc porphyrin-C60 dyads with a longer spacer.
Corrigendum to &quot;Evaluated kinetic and photochemical data for atmospheric chemistry: Volume V – heterogeneous reactions on solid substrates&quot; published in Atmos. Chem. Phys. 10, 9059–9223, 2010 (2013)

ISSN:1680-7324
Impression Estimation for Deformed Portraits With a Landmark-Based Ranking Network (2019)

In recent years, it has become a trend for people to manipulate their own portraits before posting them on a social networking service. However, it is difficult to get a desired portrait after manipulation without sufficient experience or skill. To obtain a simpler and more effective portrait manipulation technique, we consider an automated portrait manipulation method based on the five impression words: clear, sweet, elegant, modern, and dynamic. In the first part of this work, we analyzed the relationship between deformed portrait (only facial features) and the five impression words over a huge data which we collected by crowd-sourcing. In the next part, we leveraged the knowledge from the results of the analysis to develop a ranking network trained on the collected data for estimating the impression associated with a portrait. Our network demonstrates superior performance in impression estimation when compared to other state-of-the-art methods.
At the Root of T2R Gene Evolution: Recognition Profiles of Coelacanth and Zebrafish Bitter Receptors (2020)

The careful evaluation of food is important for survival throughout the animal kingdom, and specialized chemoreceptors have evolved to recognize nutrients, minerals, acids, and many toxins. Vertebrate bitter taste, mediated by the taste receptor type 2 (T2R) family, warns against potentially toxic compounds. During evolution T2R receptors appear first in bony fish, but the functional properties of bony fish T2R receptors are mostly unknown. We performed a phylogenetic analysis showing the "living fossil" coelacanth (Latimeria chalumnae) and zebrafish (Danio rerio) to possess T2R repertoires typical for early-diverged species in the lobe-finned and the ray-finned clade, respectively. Receptors from these two species were selected for heterologous expression assays using a diverse panel of bitter substances. Remarkably, the ligand profile of the most basal coelacanth receptor, T2R01, is identical to that of its ortholog in zebrafish, consistent with functional conservation across >400 Myr of separate evolution. The second coelacanth receptor deorphaned, T2R02, is activated by steroid hormones and bile acids, evolutionary old molecules that are potentially endogenously synthesized agonists for extraoral T2Rs. For zebrafish, we report the presence of both specialized and promiscuous T2R receptors. Moreover, we identified an antagonist for one of the zebrafish receptors suggesting that bitter antagonism contributed to shape this receptor family throughout evolution.
Stereospecificity in the Pictet-Spengler Reaction. Enantiospecific Synthesis of (6S,10S)-(-)-5-Methyl-9-oxo-12-benzyl-6,7,8,9,10,11-hexahydro-6,10-imino-5H-cyclooct[b]indole, a Template for Preparation of Macroline/Sarpagine Alkaloids (1992)

The synthesis [from D(+)-tryptophan] of the tetracyclic ketone [(-)-lb] was carried out in enantiospecific fashion (>98% ee) via the 1,341ansfer of chirality from Na-methyl, Nb-benzyl tryptophan methyl ester [(+)-I41 to the t m diastereomer [(-)4b] in the Pictet-Spengler reaction.Although the condensation of 14 with aldehyde (15) in refluxing benzene generated the tetrahydro Dcarbolines (4b/5b) in a kinetic ratio (72:28), epimerization (C-1) of the cir diastereomer [(+)-5b] into the tmm isomer [(-)4b] occurred stereospecifically under acidic conditions.Dieckmann cyclization of either the Na-methyl, Nbbenzylcir-(+)-5b or m-(-)-4b diastereomer provided the cir-bicyclo[3.3.1]azanonanesystem at approximately the same rate, although the D-keto esters were antipodal, in contrast to results reported in the Na-benzyl series by Magnus.Over fifty indole alkaloids isolated from Alstonia rnue~leriana,~ Alstonia rnacrophylla2 and other Alstonia species possess the basic tetracyclic skeleton (1) depicted in Scheme I.During studies directed toward the total synthesis of suaveoline ( z ) ~ and (-)-alstonerine (3)4 the need arose for an enantiospecific synthesis of
Action‐at‐a‐distance interactions enhance protein binding affinity (2005)

The identification of protein mutations that enhance binding affinity may be achieved by computational or experimental means, or by a combination of the two. Sources of affinity enhancement may include improvements to the net balance of binding interactions of residues forming intermolecular contacts at the binding interface, such as packing and hydrogen-bonding interactions. Here we identify noncontacting residues that make substantial contributions to binding affinity and that also provide opportunities for mutations that increase binding affinity of the TEM1 beta-lactamase (TEM1) to the beta-lactamase inhibitor protein (BLIP). A region of BLIP not on the direct TEM1-binding surface was identified for which changes in net charge result in particularly large increases in computed binding affinity. Some mutations to the region have previously been characterized, and our results are in good correspondence with this results of that study. In addition, we propose novel mutations to BLIP that were computed to improve binding significantly without contacting TEM1 directly. This class of noncontacting electrostatic interactions could have general utility in the design and tuning of binding interactions.
Keynote Address—Adjuvant Chemotherapy and Cancer Cure (1982)

No AccessJournal of Urology1 Dec 1982Keynote Address—Adjuvant Chemotherapy and Cancer Cure J.R. Bertino J.R. BertinoJ.R. Bertino More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)53551-XAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Keynote Address—Adjuvant Chemotherapy and Cancer Cure." The Journal of Urology, 128(6), p. 1420 © 1982 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 128Issue 6December 1982Page: 1420 Advertisement Copyright & Permissions© 1982 by The American Urological Association Education and Research, Inc.MetricsAuthor Information J.R. Bertino More articles by this author Expand All Advertisement PDF downloadLoading ...
Clinical evaluation of the Keeler PULSAIR 2000 tonometer. (1992)

Intraocular pressures (IOPs) were obtained from 380 eyes of 190 normal subjects using hand-held Keeler PULSAIR 2000 and slit lamp-mounted Goldmann tonometers. IOPs obtained with the PULSAIR were in close agreement with Goldmann pressures over the range of IOPs represented in the subject population (9-27 mmHg). This agreement is better than that found in a previous study comparing the original PULSAIR model to the Goldmann, and suggests that the model 2000 represents a significant improvement over the original unit.
Understanding crystallization processes of NiO/Ce0.9Gd0.1O2−δ sol–gel processed thin films for the design of efficient electrodes: an in situ thermal ellipsometry analysis (2012)

We describe a simple, non-destructive method, in situ thermal ellipsometry analysis (TEA), for understanding the different processes (decomposition of organics, crystallization, and sintering) occurring upon heating hybrid organic–inorganic films. According to these studies, a thermal treatment was tailored in order to obtain robust, nanocrystalline inorganic mesoporous 100–150 nm thick films with efficiently connected porosity surrounded by a crystalline inorganic network. Polymodal porous, nanocrystalline NiO/Gd-doped Ceria composites or Ni/Gd-doped Ceria films, interconnected network of open pores ranging from macro- to micro-pores, have been synthesized. The inorganic network is built from connected crystalline nanoparticles with mean diameters of 12 ± 3 nm, whose small size is still preserved even at 800 °C. We also show that the thermal ellipsometry analysis is readily extendable to MO/Gd-doped Ceria with M = Cu, Ni, Co, etc., therefore demonstrating the interest of this technique in understanding thermal phenomena in complex ceramic and composite systems. This is trivial for designing electrodes with efficient microstructure.
Broadening the scope of binding free energy calculations using a Separated Topologies approach (2023)

Binding free energy calculations predict the potency of compounds to protein binding sites in a physically rigorous manner and see broad application in prioritizing the synthesis of novel drug candidates. Relative binding free energy calculations (RBFE) have emerged as an industry standard approach to achieve highly accurate rank-order predictions of the potency of related compounds; however, this approach requires that the ligands share a common scaffold and a common binding mode, restricting the methods' domain of applicability. This is a critical limitation, since complex modifications to the ligands, especially core hopping, are very common in drug design. Absolute Binding Free Energy calculations (ABFE) are an alternate method, which can be used for ligands that are not congeneric. However, ABFE suffer from a known problem of long convergence times, due to the need to sample additional degrees of freedom within each system, such as sampling rearrangements necessary to open and close the binding site. Here, we report on an alternative method for RBFE, called Separated Topologies (SepTop), which overcomes the issues in both of the aforementioned methods, by enabling large scaffold changes between ligands with a convergence time comparable to traditional RBFE. Instead of only mutating atoms that vary between two ligands, this approach performs two absolute free energy calculations at the same time in opposite directions, one for each ligand. Defining the two ligands independently allows the comparison of binding of diverse ligands without the artificial constraints of identical poses or a suitable atom-atom mapping. This approach also avoids the need to sample the unbound state of the protein, making it more efficient than absolute binding free energy calculations. Here, we introduce an implementation of SepTop. We developed a general and efficient protocol for running SepTop, and we demonstrated the method on four diverse, pharmaceutically relevant systems. Here we report the performance of the method, as well as our practical insights into strengths, weaknesses, and challenges of applying this method in an industrial drug design setting. We find that the accuracy of the approach is sufficiently high to rank order ligands with an accuracy comparable to traditional RBFE calculations, while maintaining the additional flexibility of SepTop.
A scanning tunneling microscopy study of an insect lipoprotein ice nucleator (1991)

A scanning tunneling microscopy (STM) study of the lipoprotein ice nucleator (LPIN) from hemolymph of the cranefly, Tipula trivittata, showed strong organization of the individual LPINs into chain structures. Each strand of the chain is two lipoproteins wide with the lipoproteins arranged in aligned conformation. The size of the spherical LPINs within the strands (diameter of 90–120 Å) agrees with the value of 135±29 Å obtained from transmission electron microscopy (TEM). A non-ice-nucleating lipoprotein from Manduca sexta was used as a control. The Manduca lipoprotein does not exhibit any organizational tendency, but sometimes forms large aggregates. The two apolipoproteins of the LPIN, Apo-I (MW=265 000) and Apo-II (MW=82 000) were also imaged. The apolipoproteins exist as isolated individuals with platelike morphology, indicating the possibility of protein unfolding.
Long-term clinical outcome of atrial fibrillation ablation in patients with history of mitral valve surgery (2022)

Long-term freedom of atrial arrhythmias after atrial fibrillation catheter ablation is achievable and safe in patients with a history of mitral valve surgery. In AF patients without a history of mitral valve surgery, repeated procedures are needed to maintain sinus rhythm.
Regulation of plasma lipid levels by plasma viscosity in nephrotic rats (1985)

The viscosity of the extracellular medium of cultured hepatocytes has been shown to be a regulator of the secretion and synthesis of very low-density lipoproteins (Yedgar et al., J. Biol. Chem. 257: 2188-2192, 1982). At present, the role of plasma viscosity in regulation of plasma lipoprotein levels was examined in vivo using nephrotic hyperlipidemic rats. Plasma viscosity was increased by injection of macromolecules: simultaneously with induction of nephrosis by aminonucleoside; and after the lipid level had reached its maximum. In experiment 1 the elevation of plasma viscosity (which persisted for at least 2 days) delayed the development of the hyperlipidemia by at least 2 days. In experiment 2 increasing the plasma viscosity reduced plasma triglyceride and cholesterol levels by 70 and 40%, respectively, within 2 days. The hyperlipidemia was accompanied by increased plasma viscosity. The contribution of lipoproteins to plasma viscosity was 27% in the nephrotic-hyperlipidemic rats, compared with 4% in normal rats. It is suggested that plasma viscosity regulates lipoprotein levels in vivo concordant with the observation in cultured hepatocytes.
Eukaryotic GST fusion vector for the study of protein-protein associations in vivo: application to interaction of ATFa with Jun and Fos. (1995)

We describe a multipurpose eukaryotic expression vector that incorporates the following features: restriction sites for in-frame insertion of cDNAs of interest between sequences encoding the glutathione-S-transferase (GST) and an oligohistidine element, allowing expression of the corresponding fusion proteins; a phosphorylation site for protein kinase A for in vitro labeling of the fusion protein; a T7 promoter for in vitro transcription and subsequent translation; and signals for single-stranded DNA production in bacteria. We have used this vector to demonstrate the formation in vivo of complexes between the transcription factor ATFa, a member of the family of ATF/CRE binding proteins, and the c-Jun or c-Fos proteins. Such interactions could be detected in crude extracts from cells transfected with vectors expressing the GST-ATFa fusion protein, as well as the c-Jun or c-Fos proteins. Complexes containing both ATFa and either c-Jun or c-Fos were specifically retained on glutathione (GSH)-agarose beads as revealed by immunoblot analyses. We also show that the leucine zipper domain of ATFa is essential for this interaction.
Cerebral Protection by Barbiturates and Loop Diuretics in Head Trauma (1981)

Departments of Anesthesiology and Neurosurgery, New York University Medical Center, New York, New York
Position-tolerant differential microphones for noisy environments (1994)

Directional microphones are best noted for their noise reduction properties in communication systems. Close-talking differential microphones are particularly useful when the noise environment disturbs the ability to communicate without error, such as in public and cellular telephony, aircraft communications, etc. These differential microphones work best when they are placed within 1 cm from the lips of the talker where the sound field has a large gradient. For a plane-wave sound field the sensitivity rises proportional to ωn, where n is the order of the difference. Users of differential microphones do not always correctly position the sensor at the proper distance from the mouth and therefore the sensitivity of the microphone may also rise proportional to ωn especially at high frequencies. A method is described of correcting for this high-frequency gain without significantly degrading the noise canceling properties of first- and second-order differential microphones.
Multi-objective optimization of mimo antenna systems (2009)

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Apelin modulates pathological remodeling of lymphatic endothelium after myocardial infarction (2017)

Lymphatic endothelium serves as a barrier to control fluid balance and immune cell trafficking to maintain tissue homeostasis. Long-term alteration of lymphatic vasculature promotes edema and fibrosis, which is an aggravating factor in the onset of cardiovascular diseases such as myocardial infarction. Apelin is a bioactive peptide that plays a central role in angiogenesis and cardiac contractility. Despite an established role of apelin in lymphangiogenesis, little is known about its function in the cardiac lymphatic endothelium. Here, we show that apelin and its receptor APJ were exclusively expressed on newly formed lymphatic vasculature in a pathological model of myocardial infarction. Using an apelin-knockout mouse model, we identified morphological and functional defects in lymphatic vasculature associated with a proinflammatory status. Surprisingly, apelin deficiency increased the expression of lymphangiogenic growth factors VEGF-C and VEGF-D and exacerbated lymphangiogenesis after myocardial infarction. Conversely, the overexpression of apelin in ischemic heart was sufficient to restore a functional lymphatic vasculature and to reduce matrix remodeling and inflammation. In vitro, the expression of apelin prevented the alteration of cellular junctions in lymphatic endothelial cells induced by hypoxia. In addition, we demonstrated that apelin controls the secretion of the lipid mediator sphingosine-1-phosphate in lymphatic endothelial cells by regulating the level of expression of sphingosine kinase 2 and the transporter SPNS2. Taken together, our results show that apelin plays a key role in lymphatic vessel maturation and stability in pathological settings. Thus, apelin may represent a novel candidate to prevent pathological lymphatic remodeling in diseases.
Genome-wide Association Study of Smoking Initiation and Current Smoking (2020)

For the identification of genes associated with smoking initiation and current smoking, genome-wide association analyses were carried out in 3497 subjects. Significant genes that replicated in three independent samples (n = 405, 5810, and 1648) were visualized into a biologically meaningful network showing cellular location and direct interaction of their proteins. Several interesting groups of proteins stood out, including glutamate receptors (e.g., GRIN2B, GRIN2A, GRIK2, GRM8), proteins involved in tyrosine kinase receptor signaling (e.g., NTRK2, GRB14), transporters (e.g., SLC1A2, SLC9A9) and cell-adhesion molecules (e.g., CDH23). We conclude that a network-based genome-wide association approach can identify genes influencing smoking behavior.
Dissolution Kinetics in Chemically Amplified EUV Resist (2011)

Polymer structure effects on the dissolution kinetics and deprotection reaction were investigated to understand inherent extreme ultraviolet (EUV) resist characteristics. The effect of protecting groups and protecting ratio on activation energy were observed. Also, the protecting ratio effect on dissolution kinetics was observed. The speed of TMAH penetration into each resist film was different for each resist as the concept of the ″penetration zone″. This indicated that the dominant rate-determining step in resists is TMAH penetration into the resist film. Thus, the dissolution rates were affected by changing the protection ratio of polymer. Moreover, the preliminary evaluation of resist profile for EUV chemically amplified resists was performed by using PROLITH and parameters obtained with EUV exposure tool. Furthermore, the resist patterns were produced by electron beam and the SEM observation results were compared with the PROLITH simulation results. It is important for EUV lithography to select appropriate protecting group and protecting ratio.