gebhart/patrepeval huggingface dataset:
Focal Adhesion Kinase Is Activated and Mediates the Early Hypertrophic Response to Stretch in Cardiac Myocytes (2003)

Previously we reported that the rapid activation of the Fak/Src multicomponent signaling complex mediates load-induced activation of growth and survival signaling pathways in adult rat heart. In this study, we report that 5% to 20% (10-minute) cyclic stretch (1 Hz) of neonatal rat ventricular myocytes (NRVMs) was paralleled by increases of Fak phosphorylation at Tyr-397 (from 1.5- to 2.8-fold), as detected by anti-Fak-pY397 phosphospecific antibody. Moreover, 15% cyclic stretch lasting from 10 to 120 minutes increased Fak phosphorylation at Tyr-397 by 2.5- to 3.5-fold. This activation was accompanied by a dramatic change in Fak localization in NRVMs from densely concentrated in the perinuclear regions in nonstretched cells to aggregates regularly distributed along the myofilaments in stretched cells. Furthermore, a 4-hour cyclic stretch enhanced the activity of an atrial natriuretic factor (ANF) promoter-luciferase reporter gene by 2.7-fold. Disrupting endogenous Fak/Src signaling either by expression of a dominant-negative Fak mutant with phenylalanine substituted for Tyr-397 or by treatment with a c-Src pharmacological inhibitor (PP-2) markedly attenuated stretch-induced Fak activation and clustering at myofilaments and inhibited stretch-induced ANF gene activation. On the other hand, overexpression of wild-type Fak potentiated the stretch-induced Fak phosphorylation but did not enhance either baseline or stretch-induced ANF promoter-luciferase reporter gene activity compared with the responses of nontransfected NRVMs. These findings identify Fak as an important element in the early responses induced by stretch in cardiac myocytes, indicating that it may coordinate the cellular signaling machinery that controls gene expression program associated with load-induced cardiac myocyte hypertrophy.
Cerebellar neurons lacking complex gangliosides degenerate in the presence of depolarizing levels of potassium (2000)

Mice engineered to lack GM2/GD2 synthase (GalNAc-T), with resultant deficit of GM2, GD2, and all gangliotetraose gangliosides, were originally described as showing a relatively normal phenotype with only a slight reduction in nerve conduction. However, a subsequent study showed that similar animals suffer axonal degeneration, myelination defects, and impaired motor coordination. We have examined the behavior of cerebellar granule neurons from these neonatal knockouts in culture and have found evidence of impaired capacity for Ca2+ regulation. These cells showed relatively normal behavior when grown in the presence of physiological or moderately elevated K+ but gradually degenerated in the presence of high K+. This degeneration in depolarizing medium was accompanied by progressive elevation of intracellular calcium and onset of apoptosis, phenomena not observed with normal cells. No differences were detected in cells from normal vs. heterozygous mice. These findings suggest that neurons from GalNAc-T knockout mice are lacking a calcium regulatory mechanism that is modulated by one or more of the deleted gangliosides, and they support the hypothesis that maintenance of calcium homeostasis is one function of complex gangliosides during, and perhaps subsequent to, neuronal development.
C-terminal truncated forms of Met, the hepatocyte growth factor receptor. (1991)

The MET proto-oncogene encodes a transmembrane tyrosine kinase of 190 kDa (p190MET), which has recently been identified as the receptor for hepatocyte growth factor/scatter factor. p190MET is a heterodimer composed of two disulfide-linked chains of 50 kDa (p50 alpha) and 145 kDa (p145 beta). We have produced four different monoclonal antibodies that are specific for the extracellular domain of the Met receptor. These antibodies immunoprecipitate with p190MET two additional Met proteins of 140 and 130 kDa. The first protein (p140MET) is membrane bound and is composed of an alpha chain (p50 alpha) and an 85-kDa C-terminal truncated beta chain (p85 beta). The second protein (p130MET) is released in the culture supernatant and consists of an alpha chain (p50 alpha) and a 75-kDa C-terminal truncated beta chain (p75 beta). Both truncated forms lack the tyrosine kinase domain. p140MET and p130MET are consistently detected in vivo, together with p190MET, in different cell lines or their culture supernatants. p140MET is preferentially localized at the cell surface, where it is present in roughly half the amount of p190MET. The two C-terminal truncated forms of the Met receptor are also found in stable transfectants expressing the full-length MET cDNA, thus showing that they originate from posttranslational proteolysis. This process is regulated by protein kinase C activation. Together, these data suggest that the production of the C-terminal truncated Met forms may have a physiological role in modulating the Met receptor function.
Rapid Context-Dependent Ligand Desolvation in Molecular Docking (2010)

In structure-based screens for new ligands, a molecular docking algorithm must rapidly score many molecules in multiple configurations, accounting for both the ligand's interactions with receptor and its competing interactions with solvent. Here we explore a context-dependent ligand desolvation scoring term for molecular docking. We relate the Generalized-Born effective Born radii for every ligand atom to a fractional desolvation and then use this fraction to scale an atom-by-atom decomposition of the full transfer free energy. The fractional desolvation is precomputed on a scoring grid by numerically integrating over the volume of receptor proximal to a ligand atom, weighted by distance. To test this method's performance, we dock ligands versus property-matched decoys over 40 DUD targets. Context-dependent desolvation better enriches ligands compared to both the raw full transfer free energy penalty and compared to ignoring desolvation altogether, though the improvement is modest. More compellingly, the new method improves docking performance across receptor types. Thus, whereas entirely ignoring desolvation works best for charged sites and overpenalizing with full desolvation works well for neutral sites, the physically more correct context-dependent ligand desolvation is competitive across both types of targets. The method also reliably discriminates ligands from highly charged molecules, where ignoring desolvation performs poorly. Since this context-dependent ligand desolvation may be precalculated, it improves docking reliability with minimal cost to calculation time and may be readily incorporated into any physics-based docking program.
Guillain-Barré syndrome associated with the Zika virus outbreak in Brazil (2016)

Zika virus (ZIKV) is now considered an emerging flavivirosis, with a first large outbreak registered in the Yap Islands in 2007. In 2013, a new outbreak was reported in the French Polynesia, with associated cases of neurological complications including Guillain-Barré syndrome (GBS). The incidence of GBS has increased in Brazil since 2015, what is speculated to be secondary to the ZIKV infection outbreak. The gold-standard test for detection of acute ZIKV infection is the polymerase-chain reaction technique, an essay largely unavailable in Brazil. The diagnosis of GBS is feasible even in resource-limited areas using the criteria proposed by the GBS Classification Group, which is based solely on clinical grounds. Further understanding on the relationship of ZIKV with neurological complications is a research urgency.
A Mechanism for Bitter Taste Sensibility in Peptides (1988)

Journal Article A Mechanism for Bitter Taste Sensibility in Peptides Get access Norio Ishibashi, Norio Ishibashi Morinaga Milk Industry Co., Ltd., Nutritional Science Laboratory, 4–22, Meguro 4-chome, Meguro-ku, Tokyo 153, Japan Search for other works by this author on: Oxford Academic Google Scholar Katsushige Kouge, Katsushige Kouge Department of Fermentation Technology, Faculty of Engineering, Hiroshima University, Shitami, Saijo-cho, Higashihiroshima 724, Japan Search for other works by this author on: Oxford Academic Google Scholar Ichizo Shinoda, Ichizo Shinoda Department of Fermentation Technology, Faculty of Engineering, Hiroshima University, Shitami, Saijo-cho, Higashihiroshima 724, Japan Search for other works by this author on: Oxford Academic Google Scholar Hidenori Kanehisa, Hidenori Kanehisa Department of Fermentation Technology, Faculty of Engineering, Hiroshima University, Shitami, Saijo-cho, Higashihiroshima 724, Japan Search for other works by this author on: Oxford Academic Google Scholar Hideo Okai Hideo Okai Department of Fermentation Technology, Faculty of Engineering, Hiroshima University, Shitami, Saijo-cho, Higashihiroshima 724, Japan To whom enquiries should be addressed. Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 52, Issue 3, 1 March 1988, Pages 819–827, https://doi.org/10.1080/00021369.1988.10868743 Published: 01 March 1988 Article history Received: 27 October 1987 Published: 01 March 1988
Location of spermine and other polyamines on DNA as revealed by photoaffinity cleavage with poly(amino)benzenediazonium salts (1991)

Although polyamines interact strongly with nucleic acids, X-ray and NMR studies have not revealed much structural information about spermine-DNA complexes. Therefore, it was of interest to look at the binding of polyamines to 32P-labeled DNA restriction fragments by sequencing gel electrophoresis of the photoaffinity cleavage products induced by polyaminobenzendiazonium salts. The shift of cleavage patterns observed on opposite strands as well as competition experiments with distamycin shows polyamines to be located in the minor groove of B-DNA and to depend on the nucleic acid polymorphism, jumping to the major groove in the A-form. The sequence selectivities of various polycations (spermine, putrescine, and cobalt (III) hexaammine) are similar and slightly favor A,T-rich regions. Taken together, these results show that polycations which are not point charges are guided by the electronegative potential along the nucleic acid and suggest fast crawling of the polyamine within the minor groove, due to individual NH2+ jumping between multiple equidistant and isoenergetic bidentate hydrogen-bonding sites. Such a picture could be the clue to the unexpected NMR and to the frequently silent X-ray behavior of polyamines when bound to DNA.
RNA enzyme-directed gene therapy. (1993)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Single transverse mode operation at 1345 nm wavelength of a diode-laser pumped neodymium:ZBLAN multimode fiber laser (1990)

A diode-laser pumped multitransverse-mode neodymium-doped fluoride fiber laser is shown to oscillate in the lowest-order transverse mode when the cavity conditions are optimized. The combination of good pump coupling efficiency, laser operating efficiency, and good overlap of the HE/sub 11/ mode to that of a single-mode fiber, allows up to 12 mW of continuous wave (CW) power to be coupled into a standard single-mode fiber at a 1345-nm wavelength. Improved lens design should significantly increase the power injected into the single-mode fiber from the multimode fiber laser.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Complete Primary Structures of Two Subunits of Purothionin A, a Lethal Protein for Brewer's Yeast from Wheat Flour (1977)

Purothionin (a lethal protein for brewer's yeast) obtained from wheat flour (Triticurm vulgare, Manitoba No. 3) was separated into two active fractions, A and B, by CM-cellulose column chromatography. The main component, purothionin A, was purified to a homogeneous state as shown by polyacrylamide gel disk electrophoresis and isoelectric focusing. The molecular weight of purothionin A was estimated by the sedimentation equilibrium method to be 11,300 in its native state, 5,500 in 6 M guanidine HCl and after its modification with succinic anhydride. Chemical studies including the determination of N- and C-terminal amino acid residues and amino acid sequence analyses using a combination of automatic Edman degradation and tryptic digestion of purothionin A revealed its dimeric structure composed of nonidentical and closely similar polypeptide chains. Two distinct polypeptides were isolated by DE-52 column chromatography after succinylation. Based on the amino acid composition of each polypeptide, it was possible to align all the tryptic peptides of purothionin A without any ambiguities, establishing the complete primary structures of the purothionin A subunits. The two polypeptides in purothionin A have very similar structures, differences occurring at the five positions enclosed by boxes.
Person-to-Person Transmission of Nipah Virus in a Bangladeshi Community (2007)

An encephalitis outbreak was investigated in Faridpur District, Bangladesh, in April-May 2004 to determine the cause of the outbreak and risk factors for disease. Biologic specimens were tested for Nipah virus. Surfaces were evaluated for Nipah virus contamination by using reverse transcription-PCR (RT-PCR). Thirty-six cases of Nipah virus illness were identified; 75% of case-patients died. Multiple peaks of illness occurred, and 33 case-patients had close contact with another Nipah virus patient before their illness. Results from a case-control study showed that contact with 1 patient carried the highest risk for infection (odds ratio 6.7, 95% confidence interval 2.9-16.8, p < 0.001). RT-PCR testing of environmental samples confirmed Nipah virus contamination of hospital surfaces. This investigation provides evidence for person-to-person transmission of Nipah virus. Capacity for person-to-person transmission increases the potential for wider spread of this highly lethal pathogen and highlights the need for infection control strategies for resource-poor settings.
Unsupervised Domain Adaptation by Backpropagation (2014)

Top-performing deep architectures are trained on massive amounts of labeled data. In the absence of labeled data for a certain task, domain adaptation often provides an attractive option given that labeled data of similar nature but from a different domain (e.g. synthetic images) are available. Here, we propose a new approach to domain adaptation in deep architectures that can be trained on large amount of labeled data from the source domain and large amount of unlabeled data from the target domain (no labeled target-domain data is necessary). As the training progresses, the approach promotes the emergence of "deep" features that are (i) discriminative for the main learning task on the source domain and (ii) invariant with respect to the shift between the domains. We show that this adaptation behaviour can be achieved in almost any feed-forward model by augmenting it with few standard layers and a simple new gradient reversal layer. The resulting augmented architecture can be trained using standard backpropagation. Overall, the approach can be implemented with little effort using any of the deep-learning packages. The method performs very well in a series of image classification experiments, achieving adaptation effect in the presence of big domain shifts and outperforming previous state-of-the-art on Office datasets.
The function of phytochrome A (1997)

ABSTRACT Knowledge of the photoperceptive function of phytochrome A has improved substantially thanks to the availability of mutants lacking phytochrome A and transgenic plants transformed with the PHYA gene in sense or anti‐sense orientation. In imbibed seeds, phytochrome A mediates very‐low‐fluence responses. In etiolated seedlings, phytochrome A mediates very‐low‐fluence responses, high‐irradiance responses under continuous far‐red light, responsivity amplification to phytochrome B and red‐light enhancement of the phototropic response to blue light. In light‐grown seedings, phytochrome A modulates the extent of response to reductions in red/far‐red ratio perceived by phytochrome B, perceives daylength extensions and night interruptions affecting flowering, and perceives light treatments resetting endogenous rhythms. Under natural radiation these abilities are manifested during seed germination and seedling de‐etiolation under dense canopies or extremely low light fluences, and during early neighbour detection, but other processes await experimental evaluation. Phytochrome A affects growth and development throughout the whole life cycle of angiosperms.
Air Stability of Alkanethiol Self-Assembled Monolayers on Silver and Gold Surfaces (1998)

Surface Raman spectroscopy, electrochemistry, and X-ray photoelectron spectroscopy have been used to study the effects of air exposure on the stability of self-assembled monolayers (SAMs) formed from alkanethiols on mechanically polished, smooth Ag and Au surfaces. Raman spectra exhibit oxidized sulfur modes after only hours of air exposure. X-ray photoelectron spectroscopy of the S 2p region provides additional evidence for sulfur oxidation. Cyclic voltammetry of Ru(NH3)63+ indicates that oxidized alkanethiol SAMs retain blocking characteristics toward electron transfer, even after exposure of the oxidized SAM-surface to a solubilizing solvent. Control experiments suggest ozone as the primary oxidant in ambient laboratory air which causes rapid oxidation of the thiolate moiety. These results have important ramifications for the general use of SAMs in many proposed applications.
EGFR-Targeted Magnetic Nanoparticle Heaters Kill Cancer Cells without a Perceptible Temperature Rise (2011)

It is currently believed that magnetic nanoparticle heaters (MNHs) can kill cancer cells only when the temperature is raised above 43 °C due to energy dissipation in an alternating magnetic field. On the other hand, simple heat conduction arguments indicate that in small tumors or single cells the relative rates of energy dissipation and heat conduction result in a negligible temperature rise, thus limiting the potential of MNHs in treating small tumors and metastatic cancer. Here we demonstrate that internalized MNHs conjugated to epidermal growth factor (EGF) and which target the epidermal growth factor receptor (EGFR) do result in a significant (up to 99.9%) reduction in cell viability and clonogenic survival in a thermal heat dose dependent manner, without the need for a perceptible temperature rise. The effect appears to be cell type specific and indicates that magnetic nanoparticles in alternating magnetic fields may effectively kill cancer cells under conditions previously considered as not possible.
Prevention and Management of Infections Associated With Combat-Related Extremity Injuries (2008)

Orthopedic injuries suffered by casualties during combat constitute approximately 65% of the total percentage of injuries and are evenly distributed between upper and lower extremities. The high-energy explosive injuries, environmental contamination, varying evacuation procedures, and progressive levels of medical care make managing combat-related injuries challenging. The goals of orthopedic injury management are to prevent infection, promote fracture healing, and restore function. It appears that 2% to 15% of combat-related extremity injuries develop osteomyelitis, although lower extremity injuries are at higher risk of infections than upper extremity. Management strategies of combat-related injuries primarily focus on early surgical debridement and stabilization, antibiotic administration, and delayed primary closure. Herein, we provide evidence-based recommendations from military and civilian data to the management of combat-related injuries of the extremity. Areas of emphasis include the utility of bacterial cultures, antimicrobial therapy, irrigation fluids and techniques, timing of surgical care, fixation, antibiotic impregnated beads, wound closure, and wound coverage with negative pressure wound therapy. Most of the recommendations are not supported by randomized controlled trials or adequate cohorts studies in a military population and further efforts are needed to answer best treatment strategies.
Synthetic routes to 2‐(2‐benzofuranyl)benzoic acids and their cyclization into benz[6]indeno[2,1‐d]furan‐10‐ones (1990)

Abstract The benz[6]indeno[2,1‐ d ]furan‐10‐ones 1 were prepared by the intramolecular cyclization of the 2‐(2‐benzofuranyl)benzoic acids, 2 , the unequivocal routes to which are described herein. Various synthetic methods to these acids were tested, as well as the methods to cyclize them.
The complex theory of gravitational lensing. Beltrami equation and cluster lensing. (1995)

Received date; accepted date Abstract. We introduce a new complex formalism to describe arclet elds in clusters of galaxies and derive the appropriate inversion techniques to nd the related mass distribution of the lensing cluster. Applying the complex formalism to the statistics of lensed background sources shows that the mean of the axial ratios of locally lensed isotropically distributed elliptical sources is not in uenced by the intrinsic ellipticity distribution, if the cluster is subcritical in that region.
Some newer aspects of organozirconium chemistry of relevance to organic synthesis. Zr-Catalyzed enantioselective carbometallation (2001)

Abstract The reaction of terminal alkenes with trialkylalanes in the presence of chiral (NMI) 2 ZrCl 2 has been shown to be 70-75% ee for methylalumination and 90-95% ee for ethyl- and higher alkylalumination. It must involve an acyclic bimetallic process. Its scope, limitations, and applications to some natural products syntheses are discussed.
Diversity among Police Officers as Represented in Non-fiction Children’s Literature (2014)

Gender/racial stereotyping and gender/racial bias in children's books have been the subjects of many research investigations over time. Hughes and Seta (2003) suggested stereotypes negatively impact how children perceive their educational, occupational, and social role options in life. Policing, a predominately white male occupation, was the targeted occupation to explore. This investigation examined the diversity of police officers as represented in 18 nonfiction children's books about policing. A content analysis was conducted on current picture books about policing and police officers. This investigation followed Charles' (1998) eight steps for content analysis and modified methodologies suggested by Martinez and Harmon (2012). Each book was analyzed quantitatively to examine the number of pictures of officers by gender and by race. Conclusions and implications were drawn from the results obtained.
StressCam (2005)

We present a novel methodology for monitoring the affective states of computer users. The method is based on thermal imaging of the face. To the user, the imaging system appears much like a video-conferencing camera. The method does not require contact with the subject and is passive; therefore, monitoring can be continuous and transparent to the computer user. We have found that user stress is correlated with increased blood flow in the frontal vessel of the forehead. This increased blood flow dissipates convective heat, which can be monitored through thermal imaging. The system has been evaluated on 12 subjects, and compared against real-time measurements of Energy Expenditure (EE). The new method is highly correlated with the established, but awkward EE methodology. The StressCam methodology is applicable to many instances where the real time measurement of users' emotional state is needed.