gebhart/patrepeval huggingface dataset:
Crystal Structures of Fission Yeast Histone Chaperone Asf1 Complexed with the Hip1 B-domain or the Cac2 C Terminus (2008)

The assembly of core histones onto eukaryotic DNA is modulated by several histone chaperone complexes, including Asf1, CAF-1, and HIRA. Asf1 is a unique histone chaperone that participates in both the replication-dependent and replication-independent pathways. Here we report the crystal structures of the apo-form of fission yeast Asf1/Cia1 (SpAsf1N; residues 1-161) as well as its complexes with the B-domain of the fission yeast HIRA orthologue Hip1 (Hip1B) and the C-terminal region of the Cac2 subunit of CAF-1 (Cac2C). The mode of the fission yeast Asf1N-Hip1B recognition is similar to that of the human Asf1-HIRA recognition, suggesting that Asf1N recognition of Hip1B/HIRA is conserved from yeast to mammals. Interestingly, Hip1B and Cac2C show remarkably similar interaction modes with Asf1. The binding between Asf1N and Hip1B was almost completely abolished by the D37A and L60A/V62A mutations in Asf1N, indicating the critical role of salt bridge and van der Waals contacts in the complex formation. Consistently, both of the aforementioned Asf1 mutations also drastically reduced the binding to Cac2C. These results provide a structural basis for a mutually exclusive Asf1-binding model of CAF-1 and HIRA/Hip1, in which Asf1 and CAF-1 assemble histones H3/H4 (H3.1/H4 in vertebrates) in a replication-dependent pathway, whereas Asf1 and HIRA/Hip1 assemble histones H3/H4 (H3.3/H4 in vertebrates) in a replication-independent pathway.
Cytoskeletal actin patterns shape mast cell activation (2019)

Activation of immune cells relies on a dynamic actin cytoskeleton. Despite detailed knowledge of molecular actin assembly, the exact processes governing actin organization during activation remain elusive. Using advanced microscopy, we here show that Rat Basophilic Leukemia (RBL) cells, a model mast cell line, employ an orchestrated series of reorganization events within the cortical actin network during activation. In response to IgE antigen-stimulation of FCε receptors (FCεR) at the RBL cell surface, we observed symmetry breaking of the F-actin network and subsequent rapid disassembly of the actin cortex. This was followed by a reassembly process that may be driven by the coordinated transformation of distinct nanoscale F-actin architectures, reminiscent of self-organizing actin patterns. Actin patterns co-localized with zones of Arp2/3 nucleation, while network reassembly was accompanied by myosin-II activity. Strikingly, cortical actin disassembly coincided with zones of granule secretion, suggesting that cytoskeletal actin patterns contribute to orchestrate RBL cell activation.
Bortezomib Treatment to Potentiate the Anti-tumor Immunity of Ex-vivo Expanded Adoptively Infused Autologous Natural Killer Cells (2011)

Our results show that using an EBV-LCL feeder cell line, large numbers of pure populations of highly activated NK cells can be expanded ex vivo under GMP conditions. With the exception of thyroiditis and constitutional symptoms related to IL-2 therapy, infusions of up to 1 x 10(8) cells/kg of ex vivo expanded NK have been well tolerated and have provided preliminary clinical evidence for mediating anti-tumor immunity in patients with advanced cancer.
Binucleating Ligands:  Synthesis of Acyclic Achiral and Chiral Schiff Base−Pyridine and Schiff Base−Phosphine Ligands (1996)

5-tert-Butyl-3-(2‘-pyridyl)salicyaldehyde and 5-tert-butyl-3-(diphenylphosphino)salicyaldehyde were synthesized from 4-tert-butylphenol in good overall yields. Condensation of the salicyaldehydes with 2,3-diamino-2,3-dimethylbutane afforded the desired dinucleating Schiff base−pyridine and Schiff base−phosphine ligands, respectively. 5-tert-Butyl-3-(2‘-pyridyl)salicyaldehyde reacted with optically active 1,2-diaminocyclohexanes to give chiral dinucleating Schiff base−pyridine ligands.
A Connectomic Atlas of the Human Cerebrum—Chapter 6: The Temporal Lobe (2018)

In this supplement, we build on work previously published under the Human Connectome Project. Specifically, we show a comprehensive anatomic atlas of the human cerebrum demonstrating all 180 distinct regions comprising the cerebral cortex. The location, functional connectivity, and structural connectivity of these regions are outlined, and where possible a discussion is included of the functional significance of these areas. In part 6, we specifically address regions relevant to the temporal lobe.
Amping up HIV antibodies (2021)

High serum titers of neutralizing antibody can protect humans against HIV
Distribution of Furamidine Analogues in Tumor Cells:  Influence of the Number of Positive Charges (2002)

Fluorescence microscopy has been used to study the cellular distribution properties of a series of DNA binding cationic compounds related to the potent antiparasitic drug furamidine (DB75). The compounds tested bear a diphenylfuran or a phenylfuranbenzimidazole unfused aromatic core substituted with one or two amidine or imidazoline groups. The synthesis of five new compounds is reported. The B16 melanoma cell line was used to compare the capacities of mono-, bis-, and tetracations to enter the cell and nuclei. The high-resolution fluorescence pictures show that in the furamidine series, the compounds with two or four positive charges selectively accumulate in the cell nuclei whereas, in most cases, those bearing only one positive charge show reduced cell uptake capacities. One of the monocationic compounds, DB607, distributes in the cytoplasm, possibly in mitochondria, with no distinct nuclear accumulation. In sharp contrast, furamidine and benzimidazole analogues, including the drug DB293 that forms DNA minor groove dimers, efficiently accumulate in the cell nuclei and the intranuclear distribution of these DNA minor groove binders is significantly different from that seen with the DNA intercalating drug propidium iodide. The results suggest that the presence of two amidine terminal groups plays a role in facilitating nuclear accumulation into cells, probably as a result of nucleic acid binding. The determination of DNA melting temperature increases on addition of these compounds supports the importance of DNA binding in nuclear uptake.
Removal, Recovery, and Recycling of Triarylphosphonium-Supported Tin Reagents for Various Organic Transformations (2007)

Phosphonium-supported tin reagents and catalysts were prepared and were shown to be effective in Stille couplings, radical dehalogenations, radical cyclizations, and carbonyl allylations. Not only could the tin residues be removed from the crude reaction mixture through a phase separation process but also they could be recovered and recycled.
Genetic and Virulence Profiles of Enteroaggregative Escherichia coli (EAEC) Isolated From Deployed Military Personnel (DMP) With Travelers' Diarrhea (2020)

To discern if there was a particular genotype associated with clinical enteroaggregative <i>Escherichia coli</i> (EAEC) strains isolated from deployed military personnel (DMP) with travelers' diarrhea (TD), we characterized a collection of EAEC from DMP deployed to Afghanistan, Djibouti, Kenya, or Honduras. Although we did not identify a specific EAEC genotype associated with TD in DMP, we found that EAEC isolated at the first clinic visit were more likely to encode the dispersin gene <i>aap</i> than EAEC collected at follow-up visits. A majority of the EAEC isolates were typical EAEC that adhered to HEp-2 cells, formed biofilms, and harbored genes for aggregative adherence fimbriae (AAF), AggR, and serine protease autotransporters of <i>Enterobacteriaceae</i> (SPATEs). A separate subset of the EAEC had <i>aggR</i> and genes for SPATEs but encoded a gene highly homologous to that for CS22, a fimbriae more commonly found in enterotoxigenic <i>E. coli</i>. None of these CS22-encoding EAEC formed biofilms <i>in vitro</i> or adhered to HEp-2 cells. Whole genome sequence and single nucleotide polymorphism analyses demonstrated that most of the strains were genetically diverse, but that a few were closely related. Isolation of these related strains occurred within days to more than a year apart, a finding that suggests a persistent source and genomic stability. In an ampicillin-treated mouse model we found that an <i>agg4A</i>+ <i>aar</i>- isolate formed a biofilm in the intestine and caused reduced weight gain in mice, whereas a strain that did not form an <i>in vivo</i> biofilm caused no morbidity. Our diverse strain collection from DMP displays the heterogeneity of EAEC strains isolated from human patients, and our mouse model of infection indicated the genotype <i>agg4A</i>+ <i>aar</i>- and/or capacity to form biofilm <i>in vivo</i> may correlate to disease severity.
Chromatographic strategies for the analytical characterization of adeno-associated virus vector-based gene therapy products (2023)

In recent years, the biopharmaceutical industry's interest in gene therapy modalities has increased dramatically. To warrant their quality during manufacturing and upstream/downstream process, fit-for-purpose analytical methods play a crucial role in the overall control strategy. However, characterization of gene therapy products remains challenging due to their large size, structural complexity, heterogeneity, potential instability, and limited sample availability. In addressing some of these challenges with innovative approaches, liquid chromatography (LC) based methods have become an integral part of the currently used analytical toolbox. This review focuses on both established methods and emerging trends in the LC analysis of adeno-associated virus (AVV) vector-based gene therapy products. Each method is discussed to highlight their advantages, drawbacks, and unique capabilities in the analysis of AAV gene transfer vehicles and their corresponding impurities. Taken together, this review provides guidance on the selection of LC-based methods for routine testing and extended characterization of gene therapy products.
Al(OTf)3 Catalysed Friedel-Crafts Michael Type Addition of Indoles to a,ß-Unsaturated Ketones with PEG-200 as Recyclable Solvent (2013)

An Al(OTf)3 catalysed efficient Friedel–Crafts Michael type addition of indoles to a,ß-unsaturated ketones using recyclable PEG-200 as an alternative reaction solvent is disclosed. The reaction under microwave irradiation is clean, leads to excellent yields in minutes and reduces the use of volatile organic compounds.
Protein conformations in cellular membranes. (1966)

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.
The Persistent Mullerian Duct Syndrome: A Molecular Approach* (1989)

A rare form of male pseudohermaphroditism is characterized by the persistence of Müllerian derivatives in phenotypic males. To determine the etiology of this syndrome, we studied the expression of anti-Müllerian hormone (AMH) in six boys, including three brothers, with the persistent Müllerian duct syndrome. All except one presented with an inguinal hernia containing the Müllerian derivatives, and in two boys the hernial sac contained the contralateral testis. AMH was normally expressed in the testicular tissue of two patients, as shown by bioassay of anti-Müllerian activity and immunocytochemistry. The testicular tissue of the other patients had no detectable bioactive or immunoreactive AMH, yet they expressed AMH mRNA with a normal transcription initiation site and in the amount expected for their age. These results prove the heterogeneity of the persistent Müllerian duct syndrome and suggest that it may sometimes involve peripheral insensitivity to AMH.
Dispersion Characteristics of Holographic Grating (1997)

The results of the theoretical and experimental study of the dispersion characteristics of thick reflection holographic grating are presented. The analysis of the diffracted beam intensity is made for the conditions when both the wavelength and angle of the reconstructing wave differ considerably from those used at the recording. The magnitude of the diffracted signal can be described through the joint function of the angular-spectrum selectivity. This is of special interest when the color holographic image is reconstructed with a spectrally wideband light source. In this case the character of the angular-spectrum selectivity function should be taken into consideration for true color holographic image reconstruction.
Biomarker-Based Models Outperform Patient-Reported Scores in Predicting Endoscopic Inflammatory Disease Activity (2018)

The inclusion of biomarkers significantly improved predictive accuracy for endoscopic disease activity compared with PRO-exclusive models.
Ritodrine-induced rhabdomyolysis and psychiatric symptoms: a case report and literature review (2023)

Our results suggest that we should pay more attention to the risk of rhabdomyolysis and psychiatric symptoms induced by intravenous ritodrine hydrochloride, especially in patients with a history of neuromuscular disorder, or concomitant use of magnesium sulfate.
Cooperative Resolvability and Secrecy in the Cribbing Multiple-Access Channel (2020)

We study channel resolvability for the discrete memoryless multiple-access channel with cribbing, i.e., the characterization of the amount of randomness required at the inputs to approximately produce a chosen i.i.d. output distribution according to Kullback-Leibler divergence. We analyze resolvability rates when one encoder cribs (i) the input of the other encoder; or the output of the other encoder, (ii) non-causally, (iii) causally, or (iv) strictly-causally. For scenarios (i)-(iii), we exactly characterize the channel resolvability region. For (iv), we provide inner and outer bounds for the channel resolvability region; the crux of our achievability result is to handle the strict causality constraint with a block-Markov coding scheme in which dependencies across blocks are suitably hidden. Finally, we leverage the channel resolvability results to derive achievable secrecy rate regions for each of the cribbing scenarios under strong secrecy constraints.
Dynamic domain motion of thermal-magnetically formed marks on CoNi∕Pt multilayers (2006)

We characterized a method of heat-assisted magnetic recording, which is potentially suitable for probe-based storage systems. The field emission current from a scanning tunneling microscope tip was used as the heating source. Various pulse voltages were applied to two types of CoNi∕Pt multilayered films: one is strongly coupled with low coercivity, and the other is weakly coupled with high coercivity. Experimental results show that marks achieved in strongly coupled medium are larger than that in granular one. An external magnetic field was then applied to those marks. For weak fields (lower than the coercivity of the medium) the size of marks changes distinctly in the strongly coupled medium but not in the granular one. A model of magnetic domain dynamics is built to quantitatively explain the experimental results. It agrees with experiments. Based on this model, we will be able to figure out the proposals to achieve small marks for ultrahigh recording density.
Microstructure and Giant Magnetoresistance in Fe–Cu Thin Films Prepared by Cluster-Beam Deposition (1997)

Giant magnetoresistive Fe x Cu 100- x granular thin films have been prepared by cluster-beam deposition. The magnetoresistance (MR) ratio of the as-deposited films decreases monotonically with increasing Fe content. High resolution transmission electron microscopy of a low Fe content ( x =12) sample shows chemically-homogeneous, fine grains having a fcc structure. The film with x =28 exhibits, however, distinct chemical heterogeneity, where bcc Fe clusters are formed in the Cu matrix. The film with a higher Fe content ( x =53) consists mostly of the bcc phase with a small amount of the fcc phase. Mössbauer spectroscopy indicated that this MR behavior can be ascribed to the change in the magnetic state of Fe clusters with increasing the Fe content of the films: from cluster-glass to antiferromagnetic, and then to ferromagnetic states. After annealing, phase separation occurs in all specimens, and the grain size increases markedly, resulting in the suppression of the MR ratio in the low Fe content region.
2-Dimensional cross-shaped tetrathienonaphthalene-based ladder-type acceptor for high-efficiency organic solar cells (2020)

Development of 2-dimensional cross-shaped ladder-type TC is promising for achieving high-performance n-type materials and the device using PBDB-T:TC-FIC:PC<sub>71</sub>BM ternary blend achieves a high efficiency of 13.5%.
Collaborative filtering to locate, comprehend, and organize collections of Web sites (1998)

Finding information is a common and fundamental task for Internet users. Search engines such as AltaVista and indices such as Yahoo! are the tools commonly used for this task. Users type in queries using keywords to indicate their interest or navigate through hierarchical directories of topics, eventually obtaining (usually quite large) collections of Web pages.
Template-assembled synthetic proteins designed to adopt a globular, four-helix bundle conformation form ionic channels in lipid bilayers (1993)

Template-assembled synthetic proteins (TASPs) designed to adopt globular, four-helix bundle structures form ion channels in lipid bilayers. The rationale behind this work is that a bundle of amphiphilic alpha-helices may constitute a functional pore-forming motif in a lipid environment. TASPs designated T4(4alpha11), T4(4alpha15), and T4(4alpha18) contain four identical, amphiphilic, helical modules of 11, 15, or 18 residues, respectively; secondary structure modules are attached to the lysine epsilon-amino groups of a cyclic template, Ac-CysLysAlaLysProGlyLysAlaLysCys-NH2, which directs the intramolecular folding. T4(4alpha15) and T4(4alpha18) form cation selective channels with single channel conductances in 500 mM NaCl of 10 and 50 pS for T4(4alpha15) and 9 and 25 pS for T4(4alpha18). In contrast, T4(4alpha11) does not produce discrete conductance events. Notably, channel activity is observed only for molecules that display well-defined alpha-helical structure in solution; K(alpha15), Which contains a single peptide module attached to the epsilon-amino group of Ac-Lys-NH2, does not elicit single channels and displays low alpha-helical content. By contrast, K(alpha18) displays spectral features associated with alpha-helical structure and forms channels with primary conductances of 3 and 9 pS. The occurrence of multiple conductances suggests that molecules aggregate and form heterogeneous conductive oligomers. The minimum length of helical modules required to span a lipid bilayer is established by investigating the channel activity of T4(4alpha15) in bilayers of increasing width. Taken together, results suggest that the relative orientation of amphiphilic segments depends on the hydrophobicity of surrounding media; accordingly, TASP molecules may form ionic channels through a reorientation of template-assembled helical modules to expose charged residues to a central hydrophilic pore.
Erratum to: Risk and safety requirements for diagnostic and therapeutic procedures in allergology: World Allergy Organization Statement (2017)

This article was originally published online on 11 January 2017 Unfortunately, the original version of this article [1.Kowalski ML Ansotegui I Aberer W Al-Ahmad M Akdis M Ballmer-Weber BK et al.World Allergy Organ J. 2016; 9: 33Abstract Full Text Full Text PDF PubMed Scopus (72) Google Scholar] contained an error. The spelling of author name Vera van Kempen was incorrect. The correct spelling can be found below. Vera van Kampen Risk and safety requirements for diagnostic and therapeutic procedures in allergology: World Allergy Organization StatementWorld Allergy Organization JournalVol. 9PreviewOne of the major concerns in the practice of allergy is related to the safety of procedures for the diagnosis and treatment of allergic disease. Management (diagnosis and treatment) of hypersensitivity disorders involves often intentional exposure to potentially allergenic substances (during skin testing), deliberate induction in the office of allergic symptoms to offending compounds (provocation tests) or intentional application of potentially dangerous substances (allergy vaccine) to sensitized patients. Full-Text PDF Open Access
Dependence of electromigration failure modes on EM-induced and thermally-induced mechanical stress in interconnect lines (1996)

Experimental verification of electromigration failure modes on the mechanical stress state of interconnects line during accelerated EM tests is presented in this paper. The electromigration failure mode and failure rate during accelerated electromigration testing is expected to be strongly affected by the mechanical stress state of Al lines, since tensile stress and compressive stress states favor void growth and hillock formations, respectively. During electromigration testing, the mechanical stress state or evolution of mechanical stress of an interconnect is a function of current density and temperature, the two principal variables in electromigration testing. In our experiments, we have observed two different electromigration failure modes by varying the current density and temperatures where (i) the passivated Al lines tested at high current density and high temperatures failed by hillock type failure and (ii) the interconnect lines tested at low current density and moderate temperatures failed by voiding. A mechanical stress model which incorporates both electromigration-induced mechanical stress and thermally generated mechanical stress is invoked to explain the electromigration failure mode selection observed in our experiments.
Biochemical Mechanisms for the Inotropic Effect of the Cardiotonic Drug Milrinone (1987)

Milrinone is a new inotropic agent for the treatment of refractory congestive heart failure. Our understanding of the mechanisms(s) of action of this synthetic cardiotonic drug is incomplete. We examined the effects of milrinone and the parent compound amrinone on sarcoplasmic reticulum function (45Ca-uptake and Ca-ATPase); radioligand binding to adenosine, beta-adrenergic, and cholinergic muscarinic receptors; cyclic AMP accumulation; and inhibition of various forms of cyclic AMP phosphodiesterases. Comparisons were made to observe how these effects correlate with the inotropic response of heart. Milrinone was shown to be a potent phosphodiesterase inhibitor that was 40 times more potent than amrinone and 10 times more potent at inhibiting the high-affinity (Km = 0.23 microM) form (Ki = 22 microM) than the low-affinity (Km = 140 microM) form (Ki = 225 microM) of cyclic AMP phosphodiesterase in heart. The potency of milrinone as a phosphodiesterase inhibitor was the same in the presence and absence of calcium. Concentrations of milrinone that increased cyclic AMP accumulation also produced positive inotropy. A comparison of milrinone with amrinone and methylxanthines revealed the order of potency to be isobutylmethylxanthine greater than milrinone greater than theophylline greater than caffeine greater than amrinone. Milrinone and amrinone had no effect on 45Ca-uptake or Ca-ATPase activity in myocyte sarcoplasmic reticulum. However, milrinone did bind weakly to adenosine receptors (KD = 466 microM) but not to cholinergic muscarinic or beta-adrenergic receptors. Also, in combination with isoproterenol high concentrations of milrinone blocked the negative inotropic response to the adenosine agonist phenylisopropyladenosine.(ABSTRACT TRUNCATED AT 250 WORDS)