bluuebunny/crossref_metadata_2025_split huggingface dataset:
Myosin Light Chain–activating Phosphorylation Sites Are Required for Oogenesis in Drosophila
Authors: Jordan Pascale , Karess Roger 
Published: July 2002

The Drosophila spaghetti squash (sqh) gene encodes the regulatory myosin light chain (RMLC) of nonmuscle myosin II. Biochemical analysis of vertebrate nonmuscle and smooth muscle myosin II has established that phosphorylation of certain amino acids of the RMLC greatly increases the actin-dependent myosin ATPase and motor activity of myosin in vitro. We have assessed the in vivo importance of these sites, which in Drosophila correspond to serine-21 and threonine-20, by creating a series of transgenes in which these specific amino acids were altered. The phenotypes of the transgenes were examined in an otherwise null mutant background during oocyte development in Drosophila females.
Germ line cystoblasts entirely lacking a functional sqh gene show severe defects in proliferation and cytokinesis. The ring canals, cytoplasmic bridges linking the oocyte to the nurse cells in the egg chamber, are abnormal, suggesting a role of myosin II in their establishment or maintenance. In addition, numerous aggregates of myosin heavy chain accumulate in the sqh null cells. Mutant sqh transgene sqh-A20, A21 in which both serine-21 and threonine-20 have been replaced by alanines behaves in most respects identically to the null allele in this system, with the exception that no heavy chain aggregates are found. In contrast, expression of sqh-A21, in which only the primary phosphorylation target serine-21 site is altered, partially restores functionality to germ line myosin II, allowing cystoblast division and oocyte development, albeit with some cytokinesis failure, defects in the rapid cytoplasmic transport from nurse cells to cytoplasm characteristic of late stage oogenesis, and some damaged ring canals. Substituting a glutamate for the serine-21 (mutant sqh-E21) allows oogenesis to be completed with minimal defects, producing eggs that can develop normally to produce fertile adults. Flies expressing sqh-A20, in which only the secondary phosphorylation site is absent, appear to be entirely wild type. Taken together, this genetic evidence argues that phosphorylation at serine-21 is critical to RMLC function in activating myosin II in vivo, but that the function can be partially provided by phosphorylation at threonine-20.
Mouse Ten-m/Odz Is a New Family of Dimeric Type II Transmembrane Proteins Expressed in Many Tissues
Authors: Oohashi Toshitaka , Zhou Xiao-Hong , Feng Kang , Richter Brigitta , Mörgelin Matthias , Perez Maria Thereza , Su Wei-Dong , Chiquet-Ehrismann Ruth , Rauch Uwe , Fässler Reinhard 
Published: July 2002

The Drosophila gene ten-m/odz is the only pair rule gene identified to date which is not a transcription factor. In an attempt to analyze the structure and the function of ten-m/odz in mouse, we isolated four murine ten-m cDNAs which code for proteins of 2,700–2,800 amino acids. All four proteins (Ten-m1–4) lack signal peptides at the NH2 terminus, but contain a short hydrophobic domain characteristic of transmembrane proteins, 300–400 amino acids after the NH2 terminus. About 200 amino acids COOH-terminal to this hydrophobic region are eight consecutive EGF-like domains.
Cell transfection, biochemical, and electronmicroscopic studies suggest that Ten-m1 is a dimeric type II transmembrane protein. Expression of fusion proteins composed of the NH2-terminal and hydrophobic domain of ten-m1 attached to the alkaline phosphatase reporter gene resulted in membrane-associated staining of the alkaline phosphatase. Electronmicroscopic and electrophoretic analysis of a secreted form of the extracellular domain of Ten-m1 showed that Ten-m1 is a disulfide-linked dimer and that the dimerization is mediated by EGF-like modules 2 and 5 which contain an odd number of cysteines.
Northern blot and immunohistochemical analyses revealed widespread expression of mouse ten-m genes, with most prominent expression in brain. All four ten-m genes can be expressed in variously spliced mRNA isoforms. The extracellular domain of Ten-m1 fused to an alkaline phosphatase reporter bound to specific regions in many tissues which were partially overlapping with the Ten-m1 immunostaining. Far Western assays and electronmicroscopy demonstrated that Ten-m1 can bind to itself.
TOPAL 2.0: improved detection of mosaic sequences within
multiple alignments
Authors: McGuire Gráinne , Wright Frank 
Published: July 2002

Abstract
Motivation: The Dss statistic was proposed by (Mol. Biol. Evol., 14, 1125–1131, McGuire et al. (1997)) for scanning data sets for the presence of recombination, an important step in some phylogenetic analyses. The statistic, however, could not distinguish well between among-site rate variation and recombination, and had no statistical test for significant values. This paper addresses these shortfalls.
Results: A modification to the Dss statistic is proposed which accounts for rate variation to a large extent. A statistical test, based on parametric bootstrapping, is also suggested.
Availability: The TOPAL package (version 2) may be accessed from http://www.bioss.sari.ac.uk/~frank/Geneticsand by anonymous ftp from ftp://ftp.bioss.sari.ac.ukin the directory pub/phylogeny/topal.
Contact: frank@bioss.sari.ac.uk
Apoptosis is promoted by the dsRNA‐activated factor (DRAF1) during viral infection independent of the action of interferon or p53
Authors: WEAVER BRIAN K. , ANDO OSAMU , KUMAR K. PRASANNA , REICH NANCY C. 
Published: July 2002

ABSTRACTAn apoptotic cellular defense mechanism is triggered in response to viral dsRNA generated during the course of infection by many DNA and RNA viruses. We demonstrate that apoptosis induced by dsRNA or a paramyxovirus is independent of the action of interferon as it can proceed in a variety of cell lines and primary cells deficient in an interferon response. Initiation of apoptosis appears to be triggered by activation of a cellular transcription factor, the dsRNA‐activated factor (DRAF1). DRAF1 is composed of interferon regulatory factor 3 (IRF‐3) and the transcriptional coactivators CREB binding protein (CBP) or p300. We find that activation of IRF‐3 in the absence of viral infection stimulates apoptosis. In addition, a negative interfering mutant blocks both target gene induction and apoptosis, demonstrating a requirement for gene expression by IRF‐3/DRAF1 to promote apoptosis. IRF‐3/DRAF1 target gene expression is also induced in response to a distinct apoptotic stimulus, the DNA damaging agent etoposide. The activity of the p53 tumor suppressor does not appear to be required for IRF‐3/DRAF1‐mediated apoptosis.—Weaver, B. K., Ando, O., Kumar, K. P., Reich, N. C Apoptosis is promoted by the dsRNA‐activated factor (DRAF1) during viral infection independent of the action of interferon or p53. FASEB J. 15, 501‐514 (2001)
Cardiac contractile impairment associated with increased phosphorylation of troponin I in endotoxemic rats
Authors: Tavernier Benoît , Li Jian‐Mei , El‐Omar Magdi M. , Lanone Sophie , Yang Zhao‐Kang , Trayer Ian P , Mebazaa Alexandre , Shah Ajay M. 
Published: July 2002

ABSTRACTThe subcellular mechanisms underlying intrinsic myocardial depression during sepsis remain poorly defined, in particular the relative roles of altered intracellular Ca2+ transients versus changes in myofilament properties. We studied contractile function of cardiac myocytes isolated 12 h after induction of endotoxemia (5 mg/kg intravenous E. coli lipopolysaccharide [LPS]) in conscious rats. Cardiomyocytes from LPS‐injected rats had depressed twitch shortening compared with control cells (4.1±0.2% versus 7.8±0.3%; P<0.001; 0.5‐Hz stimulation), but similar Ca2+ transients (peak indo‐1 ratio 1.13±0.02 versus 1.12±0.02; P = NS). Contractile depression was unaffected by inhibitors of nitric oxide synthase. Steady‐state myofilament response to Ca2+, assessed by tetanization of intact cells over a range of [Ca2+], was reduced significantly in the LPS group (P<0.001). Intracellular pH (SNARF fluorescence) was similar in both groups, but the amount of phosphorylated troponin I present in endotoxemic myocardium was approximatel2y+ twofold greater than in control myocardium. In addition, steady‐state myofilament response to Ca2+ was unaffected by isoproterenol (3 nmol/L) in endotoxemic cells, whereas there was a rightward shift in control cells. A reduction in myofilament response to Ca2+ is the major determinant of intrinsic cardiac depression in systemic endotoxemia. This condition appears to be related to an increase in myocardial troponin I phosphorylation.
The structure of apo protein‐tyrosine phosphatase 1B C215S mutant: More than just an S → O change
Authors: Scapin Giovanna , Patel Sangita , Patel Vira , Kennedy Brian , Asante‐Appiah Ernest 
Published: July 2002

AbstractProtein‐tyrosine phosphatases catalyze the hydrolysis of phosphate monoesters via a two‐step mechanism involving a covalent phospho‐enzyme intermediate. Biochemical and site‐directed mutagenesis experiments show that the invariant Cys residue present in the PTPase signature motif (H/V)CX5R(S/T) (i.e., C215 in PTP1B) is absolutely required for activity. Mutation of the invariant Cys to Ser results in a catalytically inactive enzyme, which still is capable of binding substrates and inhibitors. Although it often is assumed that substrate‐trapping mutants such as the C215S retain, in solution, the structural and binding properties of wild‐type PTPases, significant differences have been found in the few studies that have addressed this issue, suggesting that the mutation may lead to structural/conformational alterations in or near the PTP1B binding site. Several crystal structures of apo‐WT PTP1B, and of WT‐ and C215S‐mutant PTP1B in complex with different ligands are available, but no structure of the apo‐PTP1B C215S has ever been reported. In all previously reported structures, residues of the PTPase signature motif have an identical conformation, while residues of the WPD loop (a surface loop which includes the catalytic Asp) assume a different conformation in the presence or absence of ligand. These observations led to the hypothesis that the different spectroscopic and thermodynamic properties of the mutant protein may be the result of a different conformation for the WPD loop. We report here the structure of the apo‐PTP1B C215S mutant, which reveals that, while the WPD loop is in the open conformation observed in the apo WT enzyme crystal structure, the residues of the PTPases signature motif are in a dramatically different conformation. These results provide a structural basis for the differences in spectroscopic properties and thermodynamic parameters in inhibitor binding observed for the wild‐type and mutant enzymes.
Unblocking Oxygen Charge Compensation for Stabilized High‐Voltage Structure in P2‐Type Sodium‐Ion Cathode
Authors: Zhu He , Yao Zhenpeng , Zhu Hekang , Huang Yalan , Zhang Jian , Li Cheng Chao , Wiaderek Kamila M. , Ren Yang , Sun Cheng‐Jun , Zhou Hua , Fan Longlong , Chen Yanan , Xia Hui , Gu Lin , Lan Si , Liu Qi 
Published: March 2022

AbstractLayered transition‐metal (TM) oxides are ideal hosts for Li+ charge carriers largely due to the occurrence of oxygen charge compensation that stabilizes the layered structure at high voltage. Hence, enabling charge compensation in sodium layered oxides is a fascinating task for extending the cycle life of sodium‐ion batteries. Herein a Ti/Mg co‐doping strategy for a model P2‐Na2/3Ni1/3Mn2/3O2 cathode material is put forward to activate charge compensation through highly hybridized O2pTM3d covalent bonds. In this way, the interlayer OO electrostatic repulsion is weakened upon deeply charging, which strongly affects the systematic total energy that transforms the striking P2–O2 interlayer contraction into a moderate solid‐solution‐type evolution. Accordingly, the cycling stability of the codoped cathode material is improved superiorly over the pristine sample. This study starts a perspective way of optimizing the sodium layered cathodes by rational structural design coupling electrochemical reactions, which can be extended to widespread battery researches.
Thickness‐Driven Morphotropic Phase Transition in Metastable Ferroelectric CaTiO3 Films
Authors: Lee Ji Hye , Kim Hong Joon , Ryoo Eunjo , Jang Jinhyuk , Kim Sanghyeon , Kim Jeong Rae , Park Se Young , Choi Si‐Young , Noh Tae Won , Lee Daesu 
Published: March 2022

AbstractThe intimate coexistence of multiple phases in ferroelectrics has been shown to result in exotic electromechanical properties, such as giant piezoelectricity. Here, via a thickness‐driven phase transition, the phase coexistence and enhanced piezoelectricity in a few tens of nanometers thick, Pb‐free CaTiO3 films are demonstrated. Due to the competition between interfacial and bulk energies, as film thickness increases, epitaxial CaTiO3 films exhibit a ferroelectric‐to‐paraelectric phase transition that is concomitant with the rhombohedral‐to‐orthorhombic structural transition. This so‐called thickness‐driven morphotropic phase transition (MPT) in nanoscale CaTiO3 films stems from the metastable nature of ferroelectricity. The resulting morphotropic phase boundary at the atomic scale in nanoscale CaTiO3 films is visualized. It is also shown that this thickness‐driven MPT can lead to reasonably good piezoelectricity at the nanoscale. This study highlights the rich phase evolution of complex ferroelectrics as a novel platform to control the functionality of nanoscale electromechanical devices.
Reduced Stochastic Resistive Switching in Organic‐Inorganic Hybrid Memristors by Vapor‐Phase Infiltration
Authors: Subramanian Ashwanth , Tiwale Nikhil , Kisslinger Kim , Nam Chang‐Yong 
Published: March 2022

AbstractResistive random‐access memory (RRAM) is promising for next‐generation data storage and non‐von Neumann computing hardware. However, tuning device switching characteristics and particularly, controlling their stochastic variation remain as critical challenges. Here, new organic‐inorganic hybrid RRAM media are reported whose bipolar switching characteristics and stochasticity can be controlled by vapor‐phase infiltration (VPI), an ex situ hybridization technique derived from atomic layer deposition. Hybrid RRAMs based on AlOx‐infiltrated SU‐8 feature facile tunability of device switching voltages, off‐state current, and on‐off ratio by adjusting the amount of infiltrated AlOx in the hybrid. Furthermore, a significant reduction in the stochastic, cycle‐to‐cycle variations of switching parameters is enabled by AlOx infiltration, driven by the infiltration‐induced changes in mechanical, dielectric, and chemical properties of organic medium and their influence on the dimension and formation characteristics of conductive filaments. Finally, multi‐level analog switching potentially useful for neuromorphic applications are demonstrated, along with direct, one‐step device patterning exploiting the negative‐tone resist feature of SU‐8. With the demonstrated control over switching characteristics and stochastic variation, combined with analog switching and one‐step patterning capabilities, the results not only present a novel hybrid medium for RRAM applications but also showcase the utility of VPI for developing new, high‐performance hybrid RRAM devices.
Mechanical properties of polyvinylpyrrolidone/polyvinyl alcohol‐based solid electrolytes
Authors: Orisekeh Kingsley , Anye Vitalis , Oyewole Oluwaseun , Ahmed Ridwan , Orisekeh David , Oyelade Omolara , Adeniji Sharafadeen , Umar Sadiq , Bello Abdulhakeem , Soboyejo Winston 
Published: March 2022

AbstractThe demand for flexible, lightweight, and long‐lasting energy devices has stimulated interest in solid polymer blends. The conventional lithium‐ion batteries use liquid electrolytes that are chemically unstable due to the presence of carbonates, which are highly volatile and flammable, creating a significant safety risk. Therefore, the need for the development of solid‐state electrolytes that are safe, environmentally friendly, with robust mechanical properties. In this work, the solid polymer blend is explored using a mixture of a polymer matrix of polyvinylpyrrolidone/polyvinyl alcohol and lithium perchlorate salt. The produced films are characterized using a scanning electron microscopy, X‐ray diffraction, and Fourier transform infrared. The mechanical properties of the flexible films are also measured using nanoindentation techniques, statistical deconvolution mapping, tensile tests, and fracture toughness measurements. (Young's modulus of 6.87 GPa, hardness of 1.3 GPa, tensile strength of 4.3 MPa, and fracture toughness of 0.81 MPa.m0.5) The implications of the results are then discussed for potential applications of robust solid polymer blends‐based electrolytes.
Surface modification of ZnO quantum dots coated polylactic acid knitted fabric for photocatalytic application
Authors: Cabral Rivaldo Leonn Bezerra , Galvão Felipe Mendonça Fontes , de Souto Silva Kesia Karina Oliveira , Felipe Brenno Henrique Silva , de Andrade Neto Nivaldo Freire , de Almeida Fechine Pierre Basílio , Zille Andrea , Kim Suyeon , do Nascimento José Heriberto Oliveira 
Published: March 2022

AbstractIn this work, ZnO quantum dots (ZnOQD) were synthesized by Sol–gel synthesis and impregnated on polylactic acid (PLA) knitted fabric through self‐assembly of different cycles from layer‐by‐layer (LBL) using cationic agent Poly(diallydimethylammonium chloride) (PDDA). Then, morphological, chemical and photocatalytic properties were studied. The results demonstrate that the synthesis provided 8 nm Wurtzite‐type ZnO nanoparticles. In addition, X‐ray photoelectron spectroscopy (XPS) spectra, X‐ray diffraction (XRD) and scanning electron microscopy (SEM) proved the inclusion of ZnOQD on the surface of PLA matrix, which allowed the evaluation of its photocatalytic properties, therefore, coated PLA with five cycles of ZnOQD obtained the best result for degrading 85% of the dye Rhodamine B (RhB) in 360 min under UV radiation, in addition to its reusability for another five cycles of photocatalytic activity.
An inversion‐based Feedback/Feedforward control for robust and precise payload positioning in gantry crane systems
Authors: Orsini Valentina 
Published: March 2022

AbstractThis paper deals with Feedback/Feedforward (FB/FF) control of a gantry crane system intended for the transport of payloads that take values over a known interval. It is also assumed that the crane is affected by unmeasurable disturbances. A new 2DoF control architecture is proposed whose purpose is to speed up the horizontal payload transition while minimizing its oscillations. The main features of the control design procedure are as follows: (1) The output FB controller is designed to ensure robust closed loop stability and steady‐state exact payload positioning; (2) the disturbance is estimated by means of an observer, and its transient effect is compensated through the FF action; and (3) the robust FF control action is given by the optimally weighted sum of the two contributions due to FF Plant Inversion (FFPI) and FF Closed Loop Inversion (FFCLI) control schemes.
Immersive In‐Person Field Courses during the Pandemic: Minimizing Risk while Maximizing Efficacy
Authors: McLaughlin John 
Published: March 2022

AbstractField courses can provide formative experiences that also reduce disparities in STEM education. Impacts of the ongoing COVID‐19 pandemic on‐field programs have been particularly severe, as many institutions shifted to online instruction. Some courses retained in‐person field experiences during the pandemic, and achieved high student learning outcomes. Here, I describe an approach to mitigating risk of COVID‐19 and other hazards during expedition‐based field courses, and student learning outcomes achieved using that approach. I applied comprehensive risk management to in‐person field expeditions that treated COVID‐19 as a hazard, requiring mitigation to maintain an acceptable low level of risk. Prior to broad availability of COVID‐19 vaccines, we applied a coronavirus‐free “bubble” strategy in which all participants passed a COVID‐19 PCR test immediately before departure and then avoided contact with people outside our bubble. In the future, vaccination can reduce risk further. We implemented additional safety factors to reduce risk of incidents that could require evacuation into medical facilities overloaded with COVID‐19 patients. The courses were successful: we had no infections or other serious incidents and student learning outcomes were transformative. The approach provides a model for conducting immersive field courses during the pandemic and beyond. Several field course networks are implementing similar approaches to restore valuable field education opportunities that have declined during the pandemic.
A quarter of a century biomechanical rupture risk assessment of abdominal aortic aneurysms. Achievements, clinical relevance, and ongoing developments
Authors: Gasser T. Christian , Miller Christopher , Polzer Stanislav , Roy Joy 
Published: March 2022

AbstractAbdominal aortic aneurysm (AAA) disease, the local enlargement of the infrarenal aorta, is a serious condition that causes many deaths, especially in men exceeding 65 years of age. Over the past quarter of a century, computational biomechanical models have been developed towards the assessment of AAA risk of rupture, technology that is now on the verge of being integrated within the clinical decision‐making process. The modeling of AAA requires a holistic understanding of the clinical problem, in order to set appropriate modeling assumptions and to draw sound conclusions from the simulation results. In this article we summarize and critically discuss the proposed modeling approaches and report the outcome of clinical validation studies for a number of biomechanics‐based rupture risk indices. Whilst most of the aspects concerning computational mechanics have already been settled, it is the exploration of the failure properties of the AAA wall and the acquisition of robust input data for simulations that has the greatest potential for the further improvement of this technology.
A model for predicting crimes using big data and neural‐fuzzy networks
Authors: Jaber Murtadha , Sheibani Reza , Shakeri Hassan 
Published: March 2022

AbstractBig data analytics is important for identifying and analyzing different patterns, relations, and trends within a large volume of data such as crime prediction. In this paper, we propose a new model for predicting crimes using neural‐fuzzy model. For this purpose, time of occurrence and longitude and latitude of the crime scene are used. We use k‐means algorithms to cluster crime records based on their locations. The crime pattern of each cluster was learnt by its own neural‐fuzzy network, in addition using shuffled frog leaping algorithm to determine the optimal cluster radius. The accuracy and Mean Absolute Error and Root Mean Squared Error of this method were compared with: Gaussian Process Regression, Classification and Regression Tree, and Artificial Neural Network. The experiment results showed that the proposed model was the most accurate model and had the least error to predict the occurrence of crimes so can be used as an effective tool in real‐world applications.