bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid Centrifugation in the Routine Hemostasis Laboratory
Authors: Wolfensberger Nathan , Georgiou Georgios , Giabbani Evelyne , Reusser Marianne , Njue Linet M. , Fiedler Martin , Leichtle Alexander B. , Nagler Michael
Published: October 2019

Background The use of short and uniform centrifugation schemes contributes significantly to the successful automation of laboratory procedures. It is however unclear if this is applicable to the hemostasis laboratory.

Objectives This article assesses the accuracy of measurements obtained with a rapid, high-speed centrifugation scheme in a large set of hemostasis tests, covering the full spectrum of values obtained in clinical practice, and using meaningful statistical measures.

Methods Two citrated plasma samples were obtained from consecutive patients of a tertiary hospital with suspected abnormal hemostasis tests and processed with two centrifugation schemes in parallel: 1,500 × g for 10 minutes and 3,137 × g for 7 minutes. The following tests were conducted: prothrombin time (n = 125), international normalized ratio (n = 146), activated partial thromboplastin time (n = 119), thrombin time (n = 105), fibrinogen (n = 125), factor (F)II (n = 69), FV (n = 64), FVII (n = 64), FX (n = 67), FVIII (n = 55), FIX (n = 37), FXI (n = 35), and FXIII (n = 20), D-dimer (n = 34), antithrombin (n = 31), anti-Xa activity (n = 30), von Willebrand antigen (n = 25), and von Willebrand activity (VWF:GPIbM; n = 27).

Results A wide range of results were obtained in all tests. Spearman's rank correlation coefficient was at least 0.95 for all tests except FV, FIX, and FXI. The coverage probability π at a given deviation index κ of 15% was above 0.9 for all tests except FV, FVII, FX, FVIII, FIX, FXI, and VWF:GPIbM, suggesting a lack of agreement.

Conclusion Our results suggest that high-speed centrifugation is applicable to the majority of routine hemostasis parameters. The coverage probability was more sensitive than Spearman's rank correlation to detect disagreement among centrifugation schemes.
The Contribution of an Infectious Workup in Understanding Stillbirth
Authors: Fouks Yuval , Many Ariel , Shulman Yael , Bak Stella , Shinar Shiri
Published: October 2019

Objective This study was aimed to assess the utility of diagnostic tests of maternal and fetal infection in the evaluation of stillbirth.

Study Design A single-center retrospective study from January 2011 to December 2016 of all women presenting to the hospital with intrauterine fetal death at or after 20 weeks of gestation. Standard evaluation included review of medical records, clinical and laboratory inflammatory workup, maternal serologies, fetal autopsy, placental pathology, and fetal and placental cultures. A suspected infectious etiology was defined as meeting at least two diagnostic criteria, and only after exclusion of any other identifiable stillbirth cause.

Results During the 7-year study period, 228 cases of stillbirth were diagnosed at our center. An infectious etiology was the suspected cause of stillbirth in 35 cases (15.3%). The mean gestational age of infection-related stillbirth was 28 1/7 (range: 22–37) weeks, while for a noninfectious etiology, it was 34 0/7 (range: 25–38) weeks (p = 0.005). Placental histological findings diagnostic of overt chorioamnionitis and funisitis were observed in 31 (88.5%) cases. In 16 (45.7%) cases the placental and fetal cultures were positive for the same pathogen. Serology of acute infection was positive in three (8.5%) of the cases.

Conclusion Maternal and fetal infectious workup is valuable in the investigation of stillbirth, particularly before 30 weeks of gestation and should be considered a part of standard evaluation.
Clinical Research on Delayed Cure after Microvascular Decompression for Hemifacial Spasm
Authors: Li Ming-Wu , Jiang Xiao-Feng , Wu Min , He Fang , Niu Chaoshi
Published: October 2019

Objective The clinical data of patients with hemifacial spasm (HFS) were analyzed statistically to identify factors leading to delayed cure after microvascular decompression (MVD).

Methods A retrospective analysis of the clinical data of 600 patients with HFS subjected to MVD from March 2016 to May 2018 was performed. Student t test, chi-square test, logistic regression analysis, and multivariate analysis of variance were used to analyze the correlation between delayed cure and its related factors.

Results Among the 600 patients enrolled, 117 had delayed cure after MVD. The shortest duration of delayed cure was 4 days, and the longest was 540 days, with an average of 108 days. The frequency of delayed improvement in these patients was not associated with sex, age, or offending vessel type (p > 0.05); however, delayed cure was positively correlated with the course of the disease, grade of HFS severity, and disappearance of abnormal muscle responses during the operation (p < 0.05). Moreover, a longer disease course was associated with more severe related symptoms and a longer duration of postoperative delayed cure.

Conclusion MVD is an effective treatment for HFS. Given that postoperative delayed cure was unavoidable, even with accurate identification of the offending vessel and sufficient decompression of the root exit zone, delayed cure should be considered in patients undergoing reoperation due to lack of remission or relapse after the operation. Additionally, the timing of efficacy assessments should be delayed.
Roadmap on material-function mapping for photonic-electronic hybrid neural networks
Authors: Miscuglio Mario , Adam Gina C. , Kuzum Duygu , Sorger Volker J.
Published: October 2019

The state-of-the-art hardware in artificial neural networks is still affected by the same capacitive challenges known from electronic integrated circuits. Unlike other emerging electronic technologies, photonics provides low-delay interconnectivity suitable for node-distributed non-von Neumann architectures, relying on dense node-to-node communication. Here, we provide a roadmap to pave the way for emerging hybridized photonic-electronic neural networks by taking a detailed look into a single node perceptron. We discuss how it can be realized in hybrid photonic-electronic heterogeneous technologies. Furthermore, we assess that electro-optic devices based on phase change or strong carrier dispersive effects could provide a viable path for both the perceptron “weights” and the nonlinear activation function in trained neural networks, while simultaneously being foundry process-near materials. This study also assesses the advantages of using nonlinear optical materials as efficient and instantaneous activation functions. We finally identify several challenges that, if solved, could accelerate the adoption of such heterogeneous integration strategies of emerging memory materials into integrated photonics platforms for near real-time responsive neural networks.
Wind turbine blade surface inspection based on deep learning and UAV-taken images
Authors: Xu Donghua , Wen Chuanbo , Liu Jihui
Published: October 2019

As a key component of wind turbines (WTs), the blade conditions are related to the WT normal operation and the WT blade inspection is a significant task. Most studies of WT blade inspection focus attention on acquired sensor signal processing; however, there exist problems of stability, sensor installation, and data storage and processing. Onsite visual surface inspection is still the most common inspection method, but it is inefficient and requires a long downtime. Aimed at solving the above issues, a novel blade inspection method based on deep learning and unmanned aerial vehicles is proposed. Since common defect types are visible, the inspection problem is regarded as an image recognition problem. Three convolutional neural networks are trained by using the constructed dataset for image recognition, and the F1-score is applied to evaluate the models. The VGG-11 model is chosen for the final model due to its best performance. Then, the alternating direction method of multipliers algorithm is employed to compress the model to reduce the requirements on hardware devices. The blind area of the WT can be reduced, the efficiency of subsequent maintenance can be improved, maintenance costs can be reduced, and the economic performance can be increased. Finally, a comparison experiment of different inspection methods is carried out to demonstrate the proposed advantages.
Effects of upstream pipe length on pipe-cavity jet noise
Authors: Baskaran Kabilan , Srinivasan K.
Published: October 2019

An experimental study is carried out to quantify the acoustic radiation of underexpanded pipe-cavity jet noise. Pipe-cavity configurations with different upstream pipe lengths are studied over a range of Mach numbers. Detailed acoustic measurements such as frequency analysis, sound pressure levels, directivity, and acoustic power analysis are carried out to show the effect of upstream pipe length. Finite element simulations are carried to predict the resonance frequencies of the pipe-cavity. Results of simulation with zero mean flow condition match well with theoretical results and the present experiments. The far-field acoustic spectrum exhibits strong cavity tones and shock associated noise. The results show that the pipe-cavity resonates close to the combined tangential-longitudinal mode. The increase in shear layer thickness tends to attenuate the cavity tones, with a small increase in screech tonal noise. An increase in upstream pipe length leads to a decrease in overall sound pressure levels and acoustic power.
Iterative multireference configuration interaction
Authors: Zhang Wen-yan , Chen Fei-wu
Published: October 2019

Iterative multireference configuration interaction (IMRCI) is proposed. It is exploited to compute the electronic energies of H2O and CH2 (singlet and triplet states) at equilibrium and non-equilibrium geometries. The potential energy curves of H2O, CH2 (singlet and triplet states) and N2 have also been calculated with IMRCI as well as the Møller Plesset perturbation theory (MP2, MP3, and MP4), the coupled cluster method with single and double substitutions (CCSD), and CCSD with perturbative triples correction (CCSD(T)). These calculations demonstrate that IMRCI results are independent of the initial guess of configuration functions in the reference space and converge quickly to the results of the full configuration interaction. The IMRCI errors relative to the full configuration interaction results are at the order of magnitude of 10−5 hartree within just 2–4 iterations. Further, IMRCI provides an efficient way to find on the potential energy surface the leading electron configurations which, as correct reference states, will be very helpful for the single-reference and multireference theoretical models to obtain accurate results.
HSC70 regulates cold-induced caspase-1 hyperactivation by an autoinflammation-causing mutant of cytoplasmic immune receptor NLRC4
Authors: Raghawan Akhouri Kishore , Ramaswamy Rajashree , Radha Vegesna , Swarup Ghanshyam
Published: October 2019

Significance

Immune receptor NLRC4 mediates caspase-1 activation upon stimulation. Mutations of NLRC4 and other cytoplasmic immune receptors cause familial cold autoinflammatory syndrome (FCAS). Individuals carrying the NLRC4-H443P mutation show exacerbated inflammation upon exposure to a cold environment due to caspase-1 hyperactivation. The mechanism of cold-induced hyperactivation of caspase-1 by none of the FCAS-causing mutants is known. We identified heat shock cognate protein 70 (HSC70) as an interacting partner of NLRC4-H443P that negatively regulates caspase-1 activation. Exposure to subnormal temperature reduces interaction of H443P with HSC70, causing caspase-1 hyperactivation. We provide a molecular mechanism for exacerbation of inflammation induced by cold temperature in individuals carrying the NLRC4-H443P mutation, which might have broader implications for temperature regulation of FCAS-causing mutations of other receptors.
Electronic structure of dense solid oxygen from insulator to metal investigated with X-ray Raman scattering
Authors: Fukui Hiroshi , Anh Le The , Wada Masahiro , Hiraoka Nozomu , Iitaka Toshiaki , Hirao Naohisa , Akahama Yuichi , Irifune Tetsuo
Published: October 2019

Significance

Oxygen diatomic molecules have lone-pair electrons and magnetic moments. A high-pressure phase called epsilon oxygen is considered stable in a wide pressure range. This material exhibits the transition to metal at ∼100 GPa (1,000,000× atmospheric pressure). The change in the electronic structure involved in the transition under pressure is difficult to measure using conventional methods. In this study, the electronic structures of oxygen have been successfully measured with oxygen
K
-edge X-ray Raman scattering spectroscopy. We found a change in the spectra related to the metallization of oxygen. Another change in the electronic structure was also observed at ∼40 GPa. This is likely related to the semimetallic transition.
Battery-free, lightweight, injectable microsystem for in vivo wireless pharmacology and optogenetics
Authors: Zhang Yi , Castro Daniel C. , Han Yuan , Wu Yixin , Guo Hexia , Weng Zhengyan , Xue Yeguang , Ausra Jokubas , Wang Xueju , Li Rui , Wu Guangfu , Vázquez-Guardado Abraham , Xie Yiwen , Xie Zhaoqian , Ostojich Diana , Peng Dongsheng , Sun Rujie , Wang Binbin , Yu Yongjoon , Leshock John P. , Qu Subing , Su Chun-Ju , Shen Wen , Hang Tao , Banks Anthony , Huang Yonggang , Radulovic Jelena , Gutruf Philipp , Bruchas Michael R. , Rogers John A.
Published: October 2019

Significance

Neuroscience studies using optogenetics have greatly improved our understanding of brain circuits. Advances in the combined use of optogenetics and pharmacology to further probe important neurochemical signals has lagged, however, in large part due to the inconvenience of conventional cannulated approaches, as well as the difficulty in controlling, powering, and manufacturing optofluidic devices that are reliable and scalable for distribution to the neuroscience community. Here, we present a battery-free, wireless, lightweight optofluidic device that allows adjustable infusion rates, hands-free operation, and unlimited power supply, and is compatible with existing near-field communication (NFC) technology. We show that this device not only reproduces optogenetic and pharmacological experiments in vivo but, additionally, allows far greater freedom of movement in small animal models compared to existing, comparable platforms.
Centromere repositioning causes inversion of meiosis and generates a reproductive barrier
Authors: Lu Min , He Xiangwei
Published: October 2019

The chromosomal position of each centromere is determined epigenetically and is highly stable, whereas incremental cases have supported the occurrence of centromere repositioning on an evolutionary time scale (evolutionary new centromeres, ENCs), which is thought to be important in speciation. The mechanisms underlying the high stability of centromeres and its functional significance largely remain an enigma. Here, in the fission yeast
Schizosaccharomyces pombe
, we identify a feedback mechanism: The kinetochore, whose assembly is guided by the centromere, in turn, enforces centromere stability. Upon going through meiosis, specific inner kinetochore mutations induce centromere repositioning—inactivation of the original centromere and formation of a new centromere elsewhere—in 1 of the 3 chromosomes at random. Repositioned centromeres reside asymmetrically in the pericentromeric regions and cells carrying them are competent in mitosis and homozygotic meiosis. However, when cells carrying a repositioned centromere are crossed with those carrying the original centromere, the progeny suffer severe lethality due to defects in meiotic chromosome segregation. Thus, repositioned centromeres constitute a reproductive barrier that could initiate genetic divergence between 2 populations with mismatched centromeres, documenting a functional role of ENCs in speciation. Surprisingly, homozygotic repositioned centromeres tend to undergo meiosis in an inverted order—that is, sister chromatids segregate first, and homologous chromosomes separate second—whereas the original centromeres on other chromosomes in the same cell undergo meiosis in the canonical order, revealing hidden flexibility in the perceived rigid process of meiosis.
Trichomonas vaginalis
extracellular vesicles are internalized by host cells using proteoglycans and caveolin-dependent endocytosis
Authors: Rai Anand Kumar , Johnson Patricia J.
Published: October 2019

Significance

Extracellular vesicles (EVs) produced by one cell and internalized by a different cell are widely used for cellular communication and protein and RNA exchange between cells. Cancer metabolism and immune and neuronal responses are modulated by mammalian EVs. The uptake of parasite EVs by host cells also modifies host:pathogen interactions. Our research identifies surface components of both the host cell and EVs produced by the parasite
Trichomonas vaginalis
and defines cellular mechanisms critical for EV internalization and cross-talk between different cell types. Our findings reveal mechanisms that a pathogen can use to communicate with its host. This study is also instructive in guiding medical therapeutics aimed at exploiting EVs for drug and vaccine delivery.
Directional coupling of slow and fast hippocampal gamma with neocortical alpha/beta oscillations in human episodic memory
Authors: Griffiths Benjamin J. , Parish George , Roux Frederic , Michelmann Sebastian , van der Plas Mircea , Kolibius Luca D. , Chelvarajah Ramesh , Rollings David T. , Sawlani Vijay , Hamer Hajo , Gollwitzer Stephanie , Kreiselmeyer Gernot , Staresina Bernhard , Wimber Maria , Hanslmayr Simon
Published: October 2019

Significance

Episodic memories detail our personally experienced past. The formation and retrieval of these memories have long been thought to be supported by a division of labor between the neocortex and the hippocampus, where the former processes event-related information and the latter binds this information together. However, it remains unclear how the 2 regions interact. We uncover directional coupling between these regions, with power decreases in the neocortex that precede and predict power increases in the hippocampus during memory formation. Fascinatingly, this process reverses during memory retrieval, with hippocampal power increases preceding and predicting neocortical power decreases. These results suggest a bidirectional flow of information between the neocortex and hippocampus is fundamental to the formation and retrieval of episodic memories.
Microstructure and mechanical properties of laser metal deposited AlSi10Mg alloys
Authors: Wang Xian , Li Liqun , Qu Jingyu , Tao Wang
Published: October 2019

Thin-walled specimens with more than 150 layers were deposited by laser metal deposition without cracks and concaving deformation. The microstructure in each layer could be divided into three zones according to the morphology. The homogeneity deteriorated with the rising of the input. The tensile strength dropped 29.7% when the porosity increased from 0.53% to 1.88%. Controlling the oxygen under 0.5% and optimising the heat input, the as-built tensile strength reached 360 MPa. The fracture elongation was enhanced from 3.9% to 12.7% when the heat input was increased from 480 to 1200 W. The decrease of the secondary dendrite arm spacing and the change of fracture mechanism is the main reason leading to the strengthening of the mechanical properties.
Conjugate hemispheric response of earth’s ionosphere due to geomagnetic storms occurred during two equinox periods
Authors: Patari Arup , De Barin Kumar , Guha Anirban , Paul Bapan
Published: October 2019

The ionospheric response of two geomagnetic storms of 2016 occurred during spring equinox (5-8 March, 2016) and autumn equinox (12-15 October, 2016) is investigated using the total electron content (TEC) data derived from Global Positioning System (GPS) receivers located in the equatorial ionization anomaly (EIA) crest regions at northern hemisphere (Tripura University, Agartala, India) and southern hemisphere (Karratha, Australia). While in southern EIA station ionospheric responses for the two storms are found to be symmetric but in northern EIA station the responses are completely asymmetric. The observations are explained by the contribution of storm-time prompt penetration electric fields (PPEFs), disturb dynamo electric fields (DDEFs), disturbed meridional (equatorward) winds as well as the neutral compositional changes over low latitudes.
Response of the Earth’s equatorial ionosphere during the severe G4-class geomagnetic storm of 8th September 2017
Authors: Paul Bapan , Patari Arup , De Barin Kumar , Guha Anirban
Published: October 2019

Equatorial and low latitude ionospheric response of the 8th September 2017 severe G4-class geomagnetic storm is investigated using the total electron content (TEC) data from a longitudinal chain of global positioning system (GPS) receivers over Asian, African and American sectors. During the main phase, a positive storm effect is observed over Asian sector, a complete negative storm effect over African sector and both are observed over American sector. A sharp increase in peak TEC is observed over the complete longitudinal chain during the recovery phase. The results show the decisive contribution of prompt penetration electric fields (PPEFs) and disturbance dynamo electric fields (DDEFs), storm time disturbed meridional (equatorward) wind as well as the neutral compositional changes over equatorial and low latitudes in the observed ionospheric storm effects.
Nature friendly cleaning: the detergency of hamburger seed
Authors: Tongbram Asha , Bhattacharyya Amitabha
Published: October 2019

Detergents or surfactants are surface active agents, active at surfaces and interfaces. A surfactant molecule consists of two parts. One is water liking or hydrophilic and the other is water hating or hydrophobic. When added to water, they arrange themselves at the surface and reduce the surface tension. This surface tension reduction gives the wetting ability and hence the cleaning ability of any solution. On further increasing the concentration, the surface becomes saturated with molecules. Molecules added now go to the bulk of the liquid and form closed structures called micelles, where the hydrophilic parts surround the hydrophobic parts. This concentration is called critical micelle concentration. Surfactants are widely used in homes and industry for cleaning and other purposes. Commercially prepared chemical detergents are toxic and harmful to the environment, while bio-chemical detergents, obtained from plants are less toxic. We report our work on the surface activity and cleaning ability of the seeds of Mucuna gigantea, commonly known as hamburger seed. The extract of the insides of the seeds show good surface tension reduction and foaming. We have also studied the dirt dispersion and other relevant properties of the extract. Our studies show that the seeds can probably supply a good natural detergent, bio-degradable and environment friendly.
Electron life time (τ) in trap levels of Dy3+ activated calcium aluminate: Implications in TL dosimetry
Authors: Moirangthem Nara Singh , Lisham Paris Chanu , Barua Anurup Gohain , Gartia R K
Published: October 2019

RE3+ (Rare Earth) activated calcium aluminates (CaAl2O4) form an excellent class of phosphors for various applications. The multi-functionality of this class of phosphor is tailored by optimising the relative concentration of the trap-levels within the large band gap (Eg=7.4eV). In this paper we determine the trap-levels in Dy3+ activated nanocrystalline calcium aluminate (CaAl2O4: Dy3+) phosphor by rigorous analysis of the complex TL curves by computerised-glow-curve-deconvolution (CGCD) technique. We assume the kinetics to be the general order kinetic (1≤ b ≤ 2). Six trap levels have been identified with a lifetime ranging from 8 hours to 108 years at room temperature. The ones with τ300 = 6.46×1005 years, 1.02×1007 years and 9.02×1008 years in principle can be the candidates for TL dosimetric application.
Polydiacetylene and imidazole mixed self-standing films for colorimetric detection of various volatile organic analytes
Authors: Suklabaidya Sudip , Chakraborty S , Sarkar S , Bhattacharjee D , Hussain Syed Arshad
Published: October 2019

Polydiacetylens (PDAs) have attracted great attention for application in sensing field due to their unique fluorescence and colorimetric properties. Polydiacetylenes (PDAs) are important class of polymer that exists in two distinct phases namely metastable, non-fluorescent blue phase and stable, auto-fluorescent red phase under specific conditions. PDA is obtained through polymerization of diacetylene (DA) monomers, typically using UV irradiation that leads to photopolymerization of the diacetylene lipids. Herein, the diacetylene monomer 10, 12-tricosadiynoic acid (TCDA) and N-1-hexadecyl Imidazole have been used to prepare mixed films onto a filter paper surface using the self-standing technique and then polymerizes the mixed films to get blue phase by UV irradiation. The PDA and N-1-hexadecyl Imidazole mixed films in the blue phase exhibit rapid colorimetric/fluorescence response upon exposure to various volatile organic analytes. The colorimetric and fluorogenic responses of TCDA and N-1-hexadecyl Imidazole mixed films were investigated by UV-vis absorption spectroscopy, inverting fluorescence microscopy and RGB analysis. This study demonstrates that PDA and N-1-hexadecyl Imidazole mixed films can be a used for detection of various volatile organic analytes even in naked eye.
A study of asynchronous noise in indoor power line with applications to power line communication
Authors: Baishya R , Tiru B , Sarma U
Published: October 2019

Power line channels do not have standard models for noise simulation. As such, study and analysis of different types of noise is imperative to developing channel simulator where communication systems can be tested and optimized for maximum efficiency. This is an indispensable part in developing power line communication systems that uses the available power line as a communication channel. This paper analyzes the asynchronous impulsive noise in indoor power line channels. The experimental setup for noise acquisition is described in detail. It is found that the impulse amplitude and the impulse durations follow the t-location scale and the log-logistic distribution better than other distribution tested. Such a distribution is easier to handle in terms of random number generation using the inverse cumulative distribution method. This can be used in the random noise simulation of impulsive noise in the generation of overall power line noise for system testing and optimization.
Phenomenological study of texture zeros of fermion mass matrices in minimal extended seesaw mechanism
Authors: Kumar P , Patgiri M
Published: October 2019

We study the two-zero textures in

M
v

4
×
4

in minimal extended type-I seesaw (MES) mechanism with incorporating one extra gauge singlet field ‘S’.

M
v

4
×
4

has (3×3)Dirac neutrino mass matrix MD
, (3×3) right-handed Majorana mass matrix MR
and (1×3) row matrix MS
. For our study we consider 5 zeros in MD
and 4 zeros in MR
, (5+4) scheme, along with one-zero textures of MS
to arrive at the two-zero textures of

M
v

4
×
4

. We find that out of 15 allowed two-zero textures, only 9 textures can be realized under (5+4) scheme. We also find that different textures of MD
, MR
and MS
are related to each other through S3
permutation group which leads to only a few basic combinations of MD
, MR
and MS
. We present all the combinations of MD
, MR
and MS
and show their interconvertability nature due to S
3 symmetry between them.
Study of small x behaviour of unintegrated gluon distribution constraining gluon evolution in MD-BFKL equation
Authors: Phukan P , Lalung M , Sarma J K
Published: October 2019

In this work we have proposed a modified form of MD-BFKL nonlinear evolution equation imposing a kinematic constraint on the gluon evolution in multi-Regge kinematics. Later we have suggested an analytical solution to our KC imposed MD-BFKL equation and studied nonlinear effect of the transverse momentum dependent (TMD) gluon distribution function at small x (10−6 ≤ x ≤ 10−2). Our results have been compared to various TMDlibuPDF datasets viz. PB-NLO-HERA I+II 2018, ccfm set A0.
Ag NP enhanced photoluminescence study of Sm3+ ions in solgel silica glasses
Authors: Dehingia Nibedita , Dutta Pankaj , Kakoti Dibyajyoti , Boruah Arindam , Rajkonwar Navaneeta , Gogoi Purabi
Published: October 2019

Sm3+ ions singly doped and Ag NPs co-doped with Sm3+ ions for fixed concentrations of both Ag and Sm3+ ions in sol-gel silica glasses were fabricated and their spectroscopic behaviour studied. Phenomenological Judd-Ofelt (JO) theory has been utilized for the spectroscopic characterization of the studied samples. Significant enhancement in the Sm3+ ion emissions were observed with the addition of Ag NPs. The enhancement is attributed to the local surface plasmon resonance effect of the Ag NPs.
Comparative study of oscillator strengths in dye and metal doped silica glasses
Authors: Dihingia S , Bora D , Singha R , Saikia P
Published: October 2019

In the present study sol gel silica glasses doped with rhodamine dye (Rh6G) and transition metals like silver, copper and iron were prepared at room temperature through sol gel route. The molar concentrations of dye and metal are varied and synthesized to get a uniform dye and metal doped clusters in silica matrices. Structural characterization is performed by SEM and XRD on doped silica glasses. SEM micrographs reveal the size of particles to be 10-50μm. The amorphous structures of the glasses are confirmed by XRD. The absorption spectra are monitored and analyzed. The absorption spectra of fluorescent dye doped sol gel silica glasses are found within the limit of 400-600 nm and the absorption spectra of different metal doped glasses are in the range of 250-350nm. Oscillator strengths of dye doped and metal doped glasses are calculated and compared. Oscillator strength of rhodamine dye doped silica glasses is comparatively higher than the other doped glasses. Silver is seen to have high oscillator strength among the metal doped silica glasses.
Phosphorylation of nephrin induces phase separated domains that move through actomyosin contraction
Authors: Kim Soyeon , Kalappurakkal Joseph M. , Mayor Satyajit , Rosen Michael K.
Published: October 2019

The plasma membrane of eukaryotic cells is organized into lipid and protein microdomains, whose assembly mechanisms and functions are incompletely understood. We demonstrate that proteins in the nephrin/Nck/N-WASP actin-regulatory pathway cluster into micron-scale domains at the basal plasma membrane upon triggered phosphorylation of transmembrane protein nephrin. The domains are persistent but readily exchange components with their surroundings, and their formation is dependent on the number of Nck SH3 domains, suggesting they are phase separated polymers assembled through multivalent interactions among the three proteins. The domains form independent of the actin cytoskeleton, but acto-myosin contractility induces their rapid lateral movement. Nephrin phosphorylation induces larger clusters at the cell periphery, which are associated with extensive actin assembly and dense filopodia. Our studies illustrate how multivalent interactions between proteins at the plasma membrane can produce micron-scale organization of signaling molecules, and how the resulting clusters can both respond to and control the actin cytoskeleton.
Fungal and bacterial community dynamics in substrates during the cultivation of morels (Morchella rufobrunnea) indoors
Authors: Longley Reid , Benucci Gian Maria Niccoló , Mills Gary , Bonito Gregory
Published: October 2019

Morel mushrooms (Morchella, Pezizales) are highly prized edible fungi. Approaches to cultivate morels indoors in pasteurized composted substrates have been successful for Morchella rufobrunnea. We used DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) ribosomal DNA and 16S rRNA gene to follow bacterial and fungal communities in substrates during indoor morel cultivation. Our goal was to determine changes in microbial communities at key stages of morel cultivation, which included primordia development, fundament initiation, differentiation and maturation. Additionally, we compared microbial communities between trays that successfully fruited to those that produced conidia and primordia but aborted before ascocarp formation (non-fruiting). The prokaryotic community was dominated by Firmicutes belonging to Bacillus and Paenibacillus with a lower abundance of Flavobacteria. At earlier stages, the fungal community was dominated by Pezizomycetes including Morchella and other species, whereas, later in the cropping cycle Sordariomycetes dominated. Additionally, differences were observed between trays with successful fruiting, which were dominated by Gilmaniella; compared to trays that did not fruit, which were dominated by Cephalotrichum. Our findings inform understanding of microbial community dynamics during morel cultivation, and show that fungal genera, such as Gilmaniella, and prokaryotic genera, such as Bacillus, are abundant in substrates that support M. rufobrunnea fruiting.
Democratic Openings and Country Visibility: Media Attention and the Allocation of US Democracy Aid, 1975–2010
Authors: Scott James M , Rowling Charles M , Jones Timothy M
Published: October 2019

Late in the twentieth century, the United States embraced democracy promotion as a foreign policy priority, a central component of which involved allocating democracy aid to governments, political parties, and nongovernmental organizations around the world to support and encourage democratization. Nonetheless, as a scarce resource, democracy assistance is allocated selectively: some states receive substantial commitments while others receive none. As previous studies have concluded, democracy aid allocations are, in part, strategic bets placed on the likelihood of progress toward and consolidation of democracy, as donors consider cues that identify situations where democracy aid is likely to be most successful. We introduce the role of media coverage as a key factor in democracy aid allocations and argue that a shift toward democracy within a potential recipient state interacts with media attention to that state to generate cues for aid allocators. To gauge the agenda-setting and cueing effects of media coverage on democracy aid allocations, we examine US democracy assistance from 1975 to 2010, weighing the impact of media attention, democratic openings, and other factors related to recipient characteristics and US political, strategic, economic, and ideational interests on democracy assistance. We conclude with a discussion of the implications of these findings.
PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
Authors: Bayliss Sion C , Thorpe Harry A , Coyle Nicola M , Sheppard Samuel K , Feil Edward J
Published: October 2019

Background

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets.

Results

Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family.

Conclusions

We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.
How Speculative Fiction Can Teach about Gender and Power in International Politics: A Pedagogical Overview
Authors: Boaz Cynthia
Published: October 2019

Fictional universes can be treated as discrete units of analysis in which we see the operation of international relations theory. This article discusses insights gleaned from a course created at Sonoma State University called “Gender and Geopolitics in Science Fiction and Fantasy,” in which feminist theory and international relations approaches are integrated, and science fiction and fantasy texts serve as the mechanism through which to examine the key themes and questions. This article provides an overview of the pedagogy to highlight the usefulness of speculative fiction in teaching. Each of the fictional universes is treated as a separate system where gender and political dynamics manifest in ways that observers of international relations will recognize. The core texts are Battlestar Galactica, Game of Thrones, Jessica Jones, Star Trek, Misfits, and Watchmen. The major theories and approaches explored here have implications for gender studies and feminist theory, the concepts of metaphor and allegory, and game theory.
The Etest for antimicrobial susceptibility testing of Bartonella henselae
Authors: Wolfson Candice , Branley James , Gottlieb Thomas
Published: October 2019

The in-vitro susceptibility of 10 isolates of Bartonella henselae was assessed using the Etest. The organisms, one reference human strain and nine feline isolates, were grown on chocolate agar and the Etests read at days 5, 8 and 11. Six antibiotics, erythromycin, azithromycin, doxycycline, ciprofloxacin, rifampicin and vancomycin were evaluated. The results correlated well with published results using agar dilution. The results confirmed the high in-vitro susceptibility of B. henselae to erythromycin, azithromycin, doxycycline and rifampicin and to a lesser extent ciprofloxacin. The majority of isolates were resistant to vancomycin. Although in-vitro results of B. henselae susceptibility testing may not necessarily correlate with clinical response, the Etest may be a simpler way for laboratories to monitor for the development of resistance particularly in the setting of relapsing infection.
Do Top Managers’ Individual Characteristics Affect Accounting Manipulation in the Public Sector?
Authors: Anessi-Pessina Eugenio , Sicilia Mariafrancesca
Published: October 2019

Drawing on upper echelons theory, the article investigates the potential impact of top managers’ background and demographic characteristics and personality traits on organizational decisions in the public sector. The top-management figure being investigated is the municipal chief financial officer (CFO) and the specific organizational decision under analysis is the extent of revenue misrepresentation during both budget formulation and execution. The empirical setting is provided by the CFOs of Italian municipalities with populations above 15,000 over a 3-year period (2012–14). Financial data are drawn from existing databases. Non-financial data are collected through an online survey. The results show that top managers’ individual characteristics and traits do influence the extent of accounting manipulation. In particular, revenue misrepresentation was found to be smaller in the presence of female managers, managers with degrees in business administration, and managers describing themselves as “conscientious”. These effects on accounting manipulation were moderated by auditors’ and opposition councilors’ oversight, managers’ experience, and the presence of local elections. The article extends upper echelons theory and its applications in several directions: from the private to the public context, from CEOs to CFOs, from managerial decisions in general to accounting choices, and from background and demographic variables to personality traits.
Reassembling Disabled Identities: Employment, Ex-servicemen and the Poppy Factory
Authors: Bartlett Emily
Published: October 2019

This article explores popular understandings of disability, work, and gender in the context of charitable employment schemes for disabled ex-servicemen after the First World War. It offers a case study of the British Legion–funded poppy factories in Richmond and Edinburgh, which employed war-disabled men to manufacture artificial flowers from 1922 onward. In so doing, this article demonstrates that press reports and charitable publications surrounding the schemes rhetorically incorporated the factories into wider twentieth-century understandings of Taylorist/Fordist productivity and manufacturing and reimagined the sites as sprawling production lines that churned out millions of flowers per year. This discourse positioned flower making as a highly skilled, masculine occupation, and relatedly constructed war-disabled flower makers as successful, productive, and physically capable workers. As one of the most publicly visible employment schemes—which catered to the most severely disabled ex-servicemen—the factories symbolized the potential of all war-disabled men for employment and went some way to challenge widespread perceptions of disabled people as idle, dependent, and useless. Moreover, this discourse represented modern, scientific methods of manufacturing as a way to make disabled bodies efficient and useful. Charitable reports positioned Taylorist/Fordist production as a solution to the problem of mass disability and ultimately countered widespread British discontent with American manufacturing ideals.
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
Authors: Rodchenkov Igor , Babur Ozgun , Luna Augustin , Aksoy Bulent Arman , Wong Jeffrey V , Fong Dylan , Franz Max , Siper Metin Can , Cheung Manfred , Wrana Michael , Mistry Harsh , Mosier Logan , Dlin Jonah , Wen Qizhi , O’Callaghan Caitlin , Li Wanxin , Elder Geoffrey , Smith Peter T , Dallago Christian , Cerami Ethan , Gross Benjamin , Dogrusoz Ugur , Demir Emek , Bader Gary D , Sander Chris
Published: October 2019

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.
Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing
Authors: Plangger Raphael , Juen Michael Andreas , Hoernes Thomas Philipp , Nußbaumer Felix , Kremser Johannes , Strebitzer Elisabeth , Klingler David , Erharter Kevin , Tollinger Martin , Erlacher Matthias David , Kreutz Christoph
Published: October 2019

Although group II intron ribozymes are intensively studied the question how structural dynamics affects splicing catalysis has remained elusive. We report for the first time that the group II intron domain 6 exists in a secondary structure equilibrium between a single- and a two-nucleotide bulge conformation, which is directly linked to a switch between sugar puckers of the branch site adenosine. Our study determined a functional sugar pucker equilibrium between the transesterification active C2′-endo conformation of the branch site adenosine in the 1nt bulge and an inactive C3′-endo state in the 2nt bulge fold, allowing the group II intron to switch its activity from the branching to the exon ligation step. Our detailed NMR spectroscopic investigation identified magnesium (II) ions and the branching reaction as regulators of the equilibrium populations. The tuneable secondary structure/sugar pucker equilibrium supports a conformational selection mechanism to up- and downregulate catalytically active and inactive states of the branch site adenosine to orchestrate the multi-step splicing process. The conformational dynamics of group II intron domain 6 is also proposed to be a key aspect for the directionality selection in reversible splicing.
The ethics of psychedelic research in disorders of consciousness
Authors: Peterson Andrew , Tagliazucchi Enzo , Weijer Charles
Published: October 2019

This article provides an ethical analysis of psychedelic research involving disorders of consciousness patients. We apply two internationally accepted approaches for analyzing the ethics of human research, the Value-Validity Framework and Component Analysis, to a research program recently proposed by Scott and Carhart-Harris. We focus on Scott and Carhart-Harris’s proposal, but the ethical frameworks outlined are applicable to other novel research protocols in the science of consciousness.
Fiscal consolidations and distributional effects: which form of fiscal austerity is least harmful?
Authors: McManus Richard , Ozkan F Gulcin , Trzeciakiewicz Dawid
Published: October 2019

Distributional consequences of fiscal austerity, while being increasingly recognized in the policy debate, have received little attention in the existing formal work. This paper proposes a medium-scale New Keynesian dynamic stochastic general equilibrium model incorporating an appropriate dimension of household heterogeneity and a well-specified fiscal structure, allowing for a comprehensive analysis of losers and winners from austerity. We find, first, that cutting transfers and public employment, and raising labour income taxes are the most regressive forms of austerity, greatly raising income inequality. In contrast, raising capital income taxes is progressive—the only such policy in our analysis—and entails the smallest output losses in the short term. Second, the speed of austerity emerges as a potential tool in fiscal adjustment. Indeed, speedy austerity yields the worst distributive and output effects irrespective of its composition. Finally, fiscal consolidation is particularly damaging in downturns where distributional effects are substantially more unfavourable than in normal times.