bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient characteristics as effect modifiers for psoriasis biologic treatment response: an assessment using network meta-analysis subgroups
Authors: Wade Ros , Sharif-Hurst Sahar , Dias Sofia
Published: June 2020

Background

Network meta-analyses (NMAs) of psoriasis treatments, undertaken as part of the NICE Single Technology Appraisal (STA) process, have included heterogeneous studies. When there is inconsistency or heterogeneity across the different comparisons or trials within the network of studies, the results of the NMA may not be valid. We explored the impact of including studies with heterogeneous patient characteristics on the results of NMAs of psoriasis treatments.

Methods

All NMAs undertaken for psoriasis STAs were identified and the included studies tabulated, including patient characteristics that may influence relative treatment effects. In addition to the original network of all studies using licensed treatment doses, a range of smaller, less heterogeneous networks were mapped: ‘no previous biologic use’ (< 25% patients had prior biologic therapy exposure), ‘Psoriasis Area and Severity Index score ≤ 25’, ‘weight ≤ 90 kg’ and ‘white ethnicity’ (≥ 90% patients were white).

Results

Sixty-nine studies were included in our synthesis (34,924 participants). A random effects model with a log-normal prior distribution was chosen for each of the subgroup NMAs. Heterogeneity was reduced for the four smaller networks. There were no significant differences in the relative treatment effect (PASI 75 response) for each treatment across the five NMAs, with all credible intervals overlapping, although there were noticeable differences. Treatment rankings based on the median relative risks were also generally consistent across the networks. However, the NMA that included only studies in which < 25% patients had prior biologic therapy exposure had slightly different treatment rankings; the anti-TNF therapies certolizumab pegol and infliximab ranked higher in this network than any other network, although credible intervals were large.

Conclusions

This work has highlighted potential differences in treatment response for biologic-naïve patients. When conducting NMAs in any area, heterogeneity in patient characteristics of included trials should be carefully assessed and effect modification related to certain patient characteristics investigated through clinically relevant subgroup analyses.
Numerical simulation for a class of predator–prey system with homogeneous Neumann boundary condition based on a sinc function interpolation method
Authors: Dai Dandan , Lv Ximing , Wang Yulan
Published: June 2020

For the nonlinear predator–prey system (PPS), although a variety of numerical methods have been proposed, such as the difference method, the finite element method, and so on, but the efficient numerical method has always been the direction that scholars strive to pursue. Based on this question, a sinc function interpolation method is proposed for a class of PPS. Numerical simulations of a class of PPS with complex dynamical behaviors are performed. Time series plots and phase diagrams of a class of PPS without self-diffusion are shown. The pattern is obtained by setting up different initial conditions and the parameters in the system according to Turing bifurcation condition. The numerical simulation results have a good agreement with theoretical results. Simulation results show the effectiveness of the method.
On abundant new solutions of two fractional complex models
Authors: Khater Mostafa M. A. , Baleanu Dumitru
Published: June 2020

We use an analytical scheme to construct distinct novel solutions of two well-known fractional complex models (the fractional Korteweg–de Vries equation (KdV) equation and the fractional Zakharov–Kuznetsov–Benjamin–Bona–Mahony (ZKBBM) equation). A new fractional definition is used to covert the fractional formula of these equations into integer-order ordinary differential equations. We obtain solitons, rational functions, the trigonometric functions, the hyperbolic functions, and many other explicit wave solutions. We illustrate physical explanations of these solutions by different types of sketches.
Some problems related to the growth of $z(n)$
Authors: Trojovský Pavel
Published: June 2020

Let $(F_{n})_{n\geq 0}$(Fn)n≥0 be the Fibonacci sequence. The order of appearance $z(n)$z(n) of a positive integer n is defined as $z(n):= \min \{k\geq 1: n\mid F_{k}\}$z(n):=min{k≥1:n∣Fk}. In 2013, Marques proved that $\liminf_{n\to \infty }z(n)/n=0$lim infn→∞z(n)/n=0. Let ϵ be a positive real number. In this paper, in particular, we generalized this Marques’ result by proving that almost all positive integers satisfy $z(n)/n<\epsilon $z(n)/n<ϵ.
Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria
Authors: Tao Xuanyu , Feng Jiajie , Yang Yunfeng , Wang Gangsheng , Tian Renmao , Fan Fenliang , Ning Daliang , Bates Colin T. , Hale Lauren , Yuan Mengting M. , Wu Linwei , Gao Qun , Lei Jiesi , Schuur Edward A. G. , Yu Julian , Bracho Rosvel , Luo Yiqi , Konstantinidis Konstantinos T. , Johnston Eric R. , Cole James R. , Penton C. Ryan , Tiedje James M. , Zhou Jizhong
Published: June 2020

Background

In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.

Results

The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.

Conclusions

Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated.
Successful treatment of Aspergillus mural endocarditis in malignant lymphoma using a combined antifungal and surgical approach: a case report
Authors: Hiroshima Yuya , Kurumisawa Soki , Aizawa Kei , Fukushima Noriyoshi , Kawahito Koji
Published: June 2020

Background

Aspergillus endocarditis (AE) is a rare and lethal cardiac infection with a high rate of mortality. AE most commonly presents in immunocompromised patients and is associated with various co-morbidities. Herein, we present a case of AE associated with lung, brain, and cervical abscesses after chemotherapy for malignant lymphoma that was successfully treated by a combination of antifungal and surgical therapy.

Case presentation

A 29-year-old man was admitted to our hospital with an unidentified fever. He was diagnosed with malignant lymphoma (extra-nodal NK/T cell lymphoma nasal type), and chemotherapy was administered. After chemotherapy, nodular lung shadows along with new brain, cervical, and myocardial abscesses appeared, despite anti-bacterial/fungal therapy. Gene analysis of the cervical abscess biopsy revealed the presence of Aspergillus fumigatus species, and the transesophageal echocardiogram showed a mobile mural vegetation in the left ventricle (22 × 8 mm). He underwent surgical resection of this mural vegetation. His postoperative course was uneventful. He remains healthy at 28 months after surgery with continued oral antifungal therapy.

Conclusion

Although AE associated with immunosuppression is a fatal clinical presentation, combined treatment with surgical resection and antifungal therapy was effective.
Can automated item generation be used to develop high quality MCQs that assess application of knowledge?
Authors: Pugh Debra , De Champlain André , Gierl Mark , Lai Hollis , Touchie Claire
Published: June 2020

The purpose of this study was to compare the quality of multiple choice questions (MCQs) developed using automated item generation (AIG) versus traditional methods, as judged by a panel of experts. The quality of MCQs developed using two methods (i.e., AIG or traditional) was evaluated by a panel of content experts in a blinded study. Participants rated a total of 102 MCQs using six quality metrics and made a judgment regarding whether or not each item tested recall or application of knowledge. A Wilcoxon two-sample test evaluated differences in each of the six quality metrics rating scales as well as an overall cognitive domain judgment. No significant differences were found in terms of item quality or cognitive domain assessed when comparing the two item development methods. The vast majority of items (> 90%) developed using both methods were deemed to be assessing higher-order skills. When compared to traditionally developed items, MCQs developed using AIG demonstrated comparable quality. Both modalities can produce items that assess higher-order cognitive skills.
Biological control agents in the integrated nematode management of pepper in Egypt
Authors: Abd-Elgawad Mahfouz M. M.
Published: June 2020

Pepper is an important vegetable crop in Egypt and worldwide. Yet, it is usually attacked and damaged by numerous plant-parasitic nematodes (PPNs) especially root-knot nematodes in Egypt. This review summarizes ecology, biology, and economic value of such nematodes from the standpoint of pest management. The use of sound cultural practices and other phytosanitary measures against PPNs of pepper should be sought. Biological control agents (BCAs) rank high among other PPN management options on pepper plants given their outstanding role in sustainable agriculture. Therefore, BCAs especially those reviewed herein due to their usefulness in reducing PPN populations and increasing pepper yield should be incorporated into pepper management systems. Further aspects of BCA biology and ecology should better be understood to let them fit into existing or emerging integrated pest management strategies for growing pepper. Examples of commercially produced biocontrol agents that have become well established in several Egyptian markets and may be used against PPNs on pepper plants are shown.
Can diffusion tensor imaging lesion patterns predict the outcome of ischemic stroke?
Authors: Mostafa Mervat , Abdel Naseer Maged , Edward Ramy , Edrees Mohammad , Labib Dalia M.
Published: June 2020

Background

Stroke can affect any portion of the central nervous system leading to a wide variety of symptoms depending on the part that is involved. Diffusion tensor imaging (DTI) is an emerging neuroimaging technique that allows measuring the integrity of white matter tracts.

Objectives

The objective of this study is to find out if the diffusion tensor tractography technique can provide prognostic information regarding clinical outcome following ischemic stroke.

Subjects and methods

Forty patients with acute ischemic stroke were studied with DTI. Size of infraction, degree of reduction of fractional anisotropy (FA), and pattern of corticospinal tract (CST) affection were identified. We assessed our patients according to the National Institute of Health Stroke Scale (NIHSS) and Medical Research Council (MRC) scale at onset of stroke and 3 months later.

Results

FA reduction was correlated with MRC and NIHSS on admission (P < 0.001, 0.004 respectively) and after 3 months (P < 0.001, 0.013 respectively). The pattern of CST affection was associated with NIHSS and MRC after 3 months (P = 0.035, 0.001 respectively).

Conclusion

DTI may be an indirect indicator of the ischemic stroke outcome.
Assessment of noise pollution and its effect on patients undergoing surgeries under regional anesthesia, is it time to incorporate noise monitoring to anesthesia monitors: an observational cohort study
Authors: Mohammed Hany Mohammed El-Hadi Shoukat , Badawy Sahar Sayed Ismail , Hussien Ahmed Ibrahim Hussien , Gorgy Antony Adel Fahmy
Published: June 2020

Background

Operating rooms (OR) are noisy places, and proper control of intraoperative noise is advised by health care organizations to avoid its hazardous effects. Finding a smartphone application to measure and control intraoperative annoying sound is necessary.

Objective

To compare noise levels in Kasr Al Ainy Hospitals’ ORs with the World Health Organization (WHO) recommendations and to investigate their effects on patients.

Methods and material

Forty patients who underwent surgeries under regional anesthesia at six different theaters enrolled in this observational cohort study. Sound was recorded by TM-102 Sound Level Meter and NoiseCapture app simultaneously. They used to capture the maximum (Max) and minimum (Min) values of A-weighting and average (mean) values in decibel (dB). The 1ry outcome was a comparison of the equivalent sound pressure levels (Leq (A)) measured by TM-102 Sound Level Meter with WHO recommendation (i.e., 40 dB).

Results

Mean noise levels in different theaters were far away from the WHO recommendations. The mean (Leq (A)) level measured by TM-102 Sound Level Meter was 73.01 (± 5.74) compared to 72.15 (± 6.57) measured by NoiseCapture. These levels exceeded the WHO recommendation by around 1.8 times. Both tools showed a good correlation with no statistically significant differences in all readings. Four distressed patients (66.7%) reported the obstetric theater as the highest noisy OR (78 dB).

Conclusions

Intraoperative noise levels at Kasr Al Ainy Hospital reached critical values that exceeded the international recommendations. For intraoperative noise monitoring, NoiseCapture smartphone application appeared like a straightforward hand-held software appropriate for this purpose.
Small fiber neuropathy and related factors in patients with systemic lupus erythematosus; the results of cutaneous silent period and skin biopsy
Authors: Tekatas Aslan , Tekatas Demet Deniz , Solmaz Volkan , Karaca Turan , Pamuk Omer Nuri
Published: June 2020

Introduction

Evaluating small nerve fibers in patients with systemic lupus erythematosus (SLE) using cutaneous silent period (CSP) and skin biopsy and assesssing the relationship between clinical signs, autoantibodies and neuropathic pain score.

Objective – methods

Fifty one SLE patients and 46 healthy volunteers were included in this study. Nerve conduction studies and CSP were performed both on upper and lower limbs in subjects. Skin biopsy was performed and the number of epidermal nerve density and IL-6 staining were evaluated.

Results

In SLE patients, CSP latencies were significantly prolonged both in lower and upper limbs and lower and upper extremity CSP durations were significantly shorter when compared to controls (p < 0.001). The number of epidermal nerve was significantly lower in SLE patients when compared to healthy controls (p < 0.001).

Conclusion

We detected marked small nerve fiber damage in both lower and upper limbs in SLE patients using CSP. Decreased epidermal nerve density also supports this finding.
Marine transgression(s) to evaporite basin: The case of middle Miocene (Badenian) gypsum in the Central Paratethys, SE Poland
Authors: Peryt Danuta , Gedl Przemysław , Peryt Tadeusz Marek
Published: June 2020

The middle Miocene Badenian evaporite basin of the Carpathian Foredeep Basin was a saline lake, separated by a barrier from the sea and supplied with seawater seeping through the barrier or overflowing it occasionally in the form of short-lived marine transgressions. Such transgressions could leave behind marine microfossils in marly clay intercalations. One of them (2.3 m thick) occurs in the uppermost part of the sulphate sequence, in the unit ‘o’, in the Babczyn 2 borehole section. It contains marine palynomorphs (dinoflagellate cysts) and foraminiferal assemblages indicating a marine environment. The low-diversity benthic foraminiferal assemblages are dominated by opportunistic, shallow infaunally living species, preferring muddy or clayey substrate for thriving, brackish to normal marine salinity, and inner shelf environment. Dinoflagellate cyst assemblages, although taxonomically impoverished, consist of marine species; euryhaline forms that tolerate increased salinity are missing. Relatively common microfossils found in clay intercalations within gypsum have important palaeogeographical implications: they strongly suggest that there existed an additional inflow channel supplying the Polish Carpathian Basin from the south during the evaporite deposition and afterwards.
A parametric analysis of oilfield design factors affecting the detectability and characterization of electrically conductive hydrofracks
Authors: Didem Beskardes G. , Weiss Chester J.
Published: June 2020

Electrical responses in the vicinity of energized steel-cased well sources offer significant potential for monitoring induced fractures. However, the high complexity of well-fracture-host models spanning multiple length scales compels analysts to simplify their numerical models due to enormous computational costs. This consequently limits our understanding regarding monitoring capabilities and the limitations of electrical measurements on realistic hydraulically fracturing systems. Here, we use the hierarchical finite element approach to construct geoelectric models in which geometrically complex fractures and steel-cased wells are discretely represented in 3D conducting media without sacrificing the model realism and computation efficiency. We have discovered systematic numerical analyses of the electrical responses to evaluate the influences of borehole material conductivity and the source type as well as the effects of well geometry, conductivity contrast, source location, fracture growth, and fracture propagation. The numerical results indicate that the borehole material property has a strong control on the electrical potentials along the production and monitoring wells. The monopole source located at a steel-cased well results in a current density distribution that decays away from the source location throughout the well length, whereas the dipole source produces a current density that dominates mainly along the dipole length. Moreover, the conductivity contrast between the fractures and host does not change the overall pattern of the electrical potentials but varies its amplitude. The fracture models near different well systems indicate that the well geometry controls the entire distribution of potentials, whereas the characteristics of the voltage difference profiles along the wells before and after fracturing are insensitive to the well geometry and the well in which the source is located. Further, the hydraulic-fracturing models indicate that the voltage differences along the production well before and after fracturing have strong sensitivity to fracture growth and fracture set propagation.
Data-driven identification of stratigraphic units in 3D seismic data using hierarchical density-based clustering
Authors: Bugge Aina Juell , Lie Jan Erik , Evensen Andreas K. , Nilsen Espen H. , Kolbjørnsen Odd , Faleide Jan Inge
Published: June 2020

Seismic sequences are stratigraphic units of relatively conformable seismic reflections. These units are intervals of similar sedimentation conditions, governed by sediment supply and relative sea level, and they are key elements in understanding the evolution of sedimentary basins. Conventional seismic sequence analyses typically rely on human interpretation; consequently, they are time-consuming. We have developed a new data-driven method to identify first-order stratigraphic units based on the assumption that the seismic units honor a layer-cake earth model, with layers that can be discriminated by the differences in seismic reflection properties, such as amplitude, continuity, and density. To identify stratigraphic units in a seismic volume, we compute feature vectors that describe the distribution of amplitudes, texture, and two-way traveltime for small seismic subvolumes. Here, the seismic texture is described with a novel texture descriptor that quantifies a simplified 3D local binary pattern around each pixel in the seismic volume. The feature vectors are preprocessed and clustered using a hierarchical density-based cluster algorithm in which each cluster is assumed to represent one stratigraphic unit. Field examples from the Barents Sea and the North Sea demonstrate that the proposed data-driven method can identify major 3D stratigraphic units without the need for manual interpretation, labeling, or prior geologic knowledge.
Deep denoising autoencoder for seismic random noise attenuation
Authors: Saad Omar M. , Chen Yangkang
Published: June 2020

Attenuation of seismic random noise is considered an important processing step to enhance the signal-to-noise ratio of seismic data. A new approach is proposed to attenuate random noise based on a deep-denoising autoencoder (DDAE). In this approach, the time-series seismic data are used as an input for the DDAE. The DDAE encodes the input seismic data to multiple levels of abstraction, and then it decodes those levels to reconstruct the seismic signal without noise. The DDAE is pretrained in a supervised way using synthetic data; following this, the pretrained model is used to denoise the field data set in an unsupervised scheme using a new customized loss function. We have assessed the proposed algorithm based on four synthetic data sets and two field examples, and we compare the results with several benchmark algorithms, such as f- x deconvolution ( f- x deconv) and the f- x singular spectrum analysis ( f- x SSA). As a result, our algorithm succeeds in attenuating the random noise in an effective manner.
Petrophysical properties prediction from prestack seismic data using convolutional neural networks
Authors: Das Vishal , Mukerji Tapan
Published: June 2020

We have built convolutional neural networks (CNNs) to obtain petrophysical properties in the depth domain from prestack seismic data in the time domain. We compare two workflows — end-to-end and cascaded CNNs. An end-to-end CNN, referred to as PetroNet, directly predicts petrophysical properties from prestack seismic data. Cascaded CNNs consist of two CNN architectures. The first network, referred to as ElasticNet, predicts elastic properties from prestack seismic data followed by a second network, referred to as ElasticPetroNet, that predicts petrophysical properties from elastic properties. Cascaded CNNs with more than twice the number of trainable parameters as compared to end-to-end CNN demonstrate similar prediction performance for a synthetic data set. The average correlation coefficient for test data between the true and predicted clay volume (approximately 0.7) is higher than the average correlation coefficient between the true and predicted porosity (approximately 0.6) for both networks. The cascaded workflow depends on the availability of elastic properties and is three times more computationally expensive than the end-to-end workflow for training. Coherence plots between the true and predicted values for both cases show that maximum coherence occurs for values of the inverse wavenumber greater than 15 m, which is approximately equal to 1/4 the source wavelength or λ/4. The network predictions have some coherence with the true values even at a resolution of 10 m, which is half of the variogram range used in simulating the spatial correlation of the petrophysical properties. The Monte Carlo dropout technique is used for approximate quantification of the uncertainty of the network predictions. An application of the end-to-end network for prediction of petrophysical properties is made with the Stybarrow field located in offshore Western Australia. The network makes good predictions of petrophysical properties at the well locations. The network is particularly successful in identifying the reservoir facies of interest with high porosity and low clay volume.
Estimation of microfracture porosity in deep carbonate reservoirs based on 3D rock-physics templates
Authors: Pang Mengqiang , Ba Jing , Fu Li-Yun , Carcione José M. , Markus Uti I. , Zhang Lin
Published: June 2020

Carbonate reservoirs in the S area of the Tarim Basin (China) are ultradeep hydrocarbon resources, with low porosity, complex fracture systems, and dissolved pores. Microfracturing is a key factor of reservoir connectivity and storage space. We have performed measurements on limestone samples, under different confining pressures, and we used the self-consistent approximation model and the Biot-Rayleigh theory of double porosity to study the microfractures. We have computed the fluid properties (mainly oil) as a function of temperature and pressure. Using the dependence of seismic [Formula: see text] on the microfractures, a multiscale 3D rock-physics template (RPT) is built, based on the attenuation, P-wave impedance, and phase velocity ratio. We estimate the ultrasonic and seismic attenuation with the spectral-ratio method and the improved frequency-shift method, respectively. Then, calibration of the RPTs is performed at ultrasonic and seismic frequencies. We use the RPTs to estimate the total and microfracture porosities. The results indicate that the total porosity is low and the microfracture porosity is relatively high, which is consistent with the well log data and actual oil production reports. This work presents a method for identification of deep carbonate reservoirs by using the microfracture porosity estimated from the 3D RPT, which could be exploited in oil and gas exploration.
First-Trimester Prenatal Dexamethasone Treatment Is Associated With Alterations in Brain Structure at Adult Age
Authors: van’t Westeinde Annelies , Karlsson Leif , Nordenström Anna , Padilla Nelly , Lajic Svetlana
Published: June 2020

Context

Prenatal treatment of human disease is rare. Dexamethasone (DEX) is used in pregnancies at risk for congenital adrenal hyperplasia (CAH) to prevent virilization in an affected female fetus. The safety and long-term consequences of prenatal DEX exposure on the brain are largely unknown.

Objective

We investigate whether first-trimester prenatal DEX treatment is associated with alterations in brain structure at adult age, and if these alterations are associated with DNA methylation, mood, and cognitive abilities.

Design, Setting, and Participants

T1-weighted and diffusion-weighted imaging scans, from a single research institute, are compared between 19 (9 women) first-trimester DEX-treated individuals, at risk of CAH but not having CAH, and 43 (26 women) controls (age range, 16.0-26.4 years).

Results

DEX-treated participants showed bilateral enlargement of the amygdala, increased surface area and volume of the left superior frontal gyrus, and widespread increased radial, mean, and axial diffusivity of white matter, in particular in the superior longitudinal fasciculi and corticospinal tracts. In the DEX-treated group, increased mean and radial diffusivity correlated with increased methylation of the promotor region of the FKBP5 gene. There were no group differences in cognition or in scales assessing depression or anxiety, and the relationship between brain structure and cognition did not differ between DEX-treated and controls.

Conclusions

First-trimester prenatal DEX treatment is associated with structural alterations of the brain at adult age, with an accompanying change in gene methylation. The findings add to the safety concerns of prenatal DEX treatment in the context of CAH.
Trypanosomes have divergent kinesin-2 proteins that function differentially in flagellum biosynthesis and cell viability
Authors: Douglas Robert L. , Haltiwanger Brett M. , Albisetti Anna , Wu Haiming , Jeng Robert L. , Mancuso Joel , Cande W. Zacheus , Welch Matthew D.
Published: June 2020

Trypanosoma brucei, the causative agent of African sleeping sickness, has a flagellum that is crucial for motility, pathogenicity, and viability. In most eukaryotes, the intraflagellar transport (IFT) machinery drives flagellum biogenesis, and anterograde IFT requires kinesin-2 motor proteins. In this study, we investigated the function of the two T. brucei kinesin-2 proteins, TbKin2a and TbKin2b, in bloodstream form trypanosomes. We found that, compared to kinesin-2 proteins across other phyla, TbKin2a and TbKin2b show greater variation in neck, stalk and tail domain sequences. Both kinesins contributed additively to flagellar lengthening. Silencing TbKin2a inhibited cell proliferation, cytokinesis and motility, whereas silencing TbKin2b did not. TbKin2a was localized on the flagellum and colocalized with IFT components near the basal body, consistent with it performing a role in IFT. TbKin2a was also detected on the flagellar attachment zone, a specialized structure that connects the flagellum to the cell body. Our results indicate that kinesin-2 proteins in trypanosomes play conserved roles in flagellar biosynthesis and exhibit a specialized localization, emphasizing the evolutionary flexibility of motor protein function in an organism with a large complement of kinesins.
Ciliary proteins specify the cell inflammatory response by tuning NFκB signalling, independently of primary cilia
Authors: Mc Fie Megan , Koneva Lada , Collins Isabella , Coveney Clarissa R. , Clube Aisling M. , Chanalaris Anastasios , Vincent Tonia L. , Bezbradica Jelena S. , Sansom Stephen N. , Wann Angus K. T.
Published: June 2020

Complex inflammatory signalling cascades define the response to tissue injury but also control development and homeostasis, limiting the potential for these pathways to be targeted therapeutically. Primary cilia are subcellular regulators of cellular signalling, controlling how signalling is organized, encoded and, in some instances, driving or influencing pathogenesis. Our previous research revealed that disruption of ciliary intraflagellar transport (IFT), altered the cell response to IL-1β, supporting a putative link emerging between cilia and inflammation. Here, we show that IFT88 depletion affects specific cytokine-regulated behaviours, changing cytosolic NFκB translocation dynamics but leaving MAPK signalling unaffected. RNA-seq analysis indicates that IFT88 regulates one third of the genome-wide targets, including the pro-inflammatory genes Nos2, Il6 and Tnf. Through microscopy, we find altered NFκB dynamics are independent of assembly of a ciliary axoneme. Indeed, depletion of IFT88 inhibits inflammatory responses in the non-ciliated macrophage. We propose that ciliary proteins, including IFT88, KIF3A, TTBK2 and NPHP4, act outside of the ciliary axoneme to tune cytoplasmic NFκB signalling and specify the downstream cell response. This is thus a non-canonical function for ciliary proteins in shaping cellular inflammation.

This article has an associated First Person interview with the first author of the paper.
Cep57 and Cep57l1 function redundantly to recruit the Cep63–Cep152 complex for centriole biogenesis
Authors: Zhao Huijie , Yang Sen , Chen Qingxia , Duan Xiaomeng , Li Guoqing , Huang Qiongping , Zhu Xueliang , Yan Xiumin
Published: June 2020

The Cep63–Cep152 complex located at the mother centriole recruits Plk4 to initiate centriole biogenesis. How the complex is targeted to mother centrioles, however, is unclear. In this study, we show that Cep57 and its paralog, Cep57l1, colocalize with Cep63 and Cep152 at the proximal end of mother centrioles in both cycling cells and multiciliated cells undergoing centriole amplification. Both Cep57 and Cep57l1 bind to the centrosomal targeting region of Cep63. The depletion of both proteins, but not either one, blocks loading of the Cep63–Cep152 complex to mother centrioles and consequently prevents centriole duplication. We propose that Cep57 and Cep57l1 function redundantly to ensure recruitment of the Cep63–Cep152 complex to the mother centrioles for procentriole formation.
Drosophila Wash and the Wash regulatory complex function in nuclear envelope budding
Authors: Verboon Jeffrey M. , Nakamura Mitsutoshi , Davidson Kerri A. , Decker Jacob R. , Nandakumar Vivek , Parkhurst Susan M.
Published: June 2020

Nuclear envelope (NE) budding is a recently described phenomenon wherein large macromolecular complexes are packaged inside the nucleus and extruded through the nuclear membranes. Although a general outline of the cellular events occurring during NE budding is now in place, little is yet known about the molecular machinery and mechanisms underlying the physical aspects of NE bud formation. Using a multidisciplinary approach, we identify Wash, its regulatory complex (SHRC), capping protein and Arp2/3 as new molecular components involved in the physical aspects of NE bud formation in a Drosophila model system. Interestingly, Wash affects NE budding in two ways: indirectly through general nuclear lamina disruption via an SHRC-independent interaction with Lamin B leading to inefficient NE bud formation, and directly by blocking NE bud formation along with its SHRC, capping protein and Arp2/3. In addition to NE budding emerging as an important cellular process, it shares many similarities with herpesvirus nuclear egress mechanisms, suggesting new avenues for exploration in both normal and disease biology.
Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae
Authors: Zhu Mang , Kuechler Erich R. , Zhang Joyce , Matalon Or , Dubreuil Benjamin , Hofmann Analise , Loewen Chris , Levy Emmanuel D. , Gsponer Joerg , Mayor Thibault
Published: June 2020

Stress granules (SGs) are stress-induced membraneless condensates that store non-translating mRNA and stalled translation initiation complexes. Although metazoan SGs are dynamic compartments where proteins can rapidly exchange with their surroundings, yeast SGs seem largely static. To gain a better understanding of yeast SGs, we identified proteins that sediment after heat shock using mass spectrometry. Proteins that sediment upon heat shock are biased toward a subset of abundant proteins that are significantly enriched in intrinsically disordered regions (IDRs). Heat-induced SG localization of over 80 proteins were confirmed using microscopy, including 32 proteins not previously known to localize to SGs. We found that several IDRs were sufficient to mediate SG recruitment. Moreover, the dynamic exchange of IDRs can be observed using fluorescence recovery after photobleaching, whereas other components remain immobile. Lastly, we showed that the IDR of the Ubp3 deubiquitinase was critical for yeast SG formation. This work shows that IDRs can be sufficient for SG incorporation, can remain dynamic in vitrified SGs, and can play an important role in cellular compartmentalization upon stress.

This article has an associated First Person interview with the first author of the paper.
Effect of Catalyst Preparation Method on Ammonia Decomposition Reaction over Ru/MgO Catalyst
Authors: Fujitani Tadahiro , Nakamura Isao , Hashiguchi Yuta , Kanazawa Shoichi , Takahashi Atsushi
Published: June 2020

Ammonia decomposition on Ru/MgO was strongly affected by the pore structure of the MgO support. We found that highly active Ru/MgO catalysts were successfully prepared by using Ru hydroxide and hydromagnesite as catalyst precursors. The mesopores of MgO of about 3–5 nm and highly dispersed Ru species improved the catalytic performance.
Frame-shifted proteins of a given gene are unlikely to retain the same function
Authors: Mankin Alexander S.
Published: June 2020

In a recently published paper, Huang and coworkers claim that proteins translated in different reading frames from the same mRNA can have similar functions. This conclusion is possibly incorrect due to the possibility that the wild-type protein could still be expressed.
Impact of malaria on haematological parameters of urban, peri-urban and rural residents in the Ashanti region of Ghana: a cross-sectional study
Authors: Mutala Abdul-Hakim , Badu Kingsley , Owusu Christian , Agordzo Samuel Kekeli , Tweneboah Austine , Abbas Dawood Ackom , Addo Matthew Glover
Published: June 2020

Background: We aimed at investigating the impact of malaria on the haematological parameters of residents from different demographic settlements in the Ashanti Region of Ghana. Malaria parasites trigger changes in certain haematological parameters, which may result in a number of clinical manifestations. Differences in demographic settlements, such as rural, peri-urban and urban settlements may also influence these changes, but this has not been extensively studied in Ghana.

Methods: We conducted a hospital-based, cross-sectional study from January to December 2018 in three different settlements. A total of 598 participants were recruited. Blood smears were examined to detect and quantify malaria parasitaemia, while haematological parameters were measured using a haematology analyser.

Results: Participants from the rural settlement had the highest malaria prevalence (21.3%) compared to the urban (11.8%) and peri-urban areas (13.3%); however, the peri-urban area had the highest median parasite density (568; IQR=190.0-1312.0). Age was significantly associated with the odds of malaria positivity (OR: 0.97; CI:0.96 — 0.99). When haematological parameters of the malaria-infected study participants were compared to the parameters of uninfected participants, red blood cell count (p=0.017), haemoglobin (p=0.0165), haematocrit (p=0.0015), mean corpuscular volume (p=0.0014), plateletcrit (p<0.0001) and platelet count (p<0.0001) were all significantly lower in the malaria infected group. In addition to age, haemoglobin and plateletcrit levels were also inversely correlated with the odds of testing positive for malaria, suggesting that children who were anaemic and/or thrombocytopaenic were likely to be infected. After fitting the data to a logistic regression model comprising the three variables, the model correctly categorised 78% of uninfected study participants, but only 50% of the malaria-positive participants.

Conclusions: Study participants who were positive for malaria were younger and had low haemoglobin and plateletcrit levels compared to uninfected individuals. Further studies are needed to more precisely elucidate the relationship between malaria infection,demographic and haematological parameters.
Emerging therapies in acute ischemic stroke
Authors: Liaw Nicholas , Liebeskind David
Published: June 2020

Thrombolysis and mechanical thrombectomy have revolutionized the care of patients with acute ischemic stroke. The number of patients who can benefit from these treatments continues to increase as new studies demonstrate that not just time since stroke onset but also collateral circulation influences outcome. Technologies such as telestroke, mobile stroke units, and artificial intelligence are playing an increasing role in identifying and treating stroke. Stroke-systems-of-care models continue to streamline the delivery of definitive revascularization in the age of mechanical thrombectomy.
Melatonin Increasingly Used in Hospitalized Patients
Authors: MacMillan Thomas E , Lui Philip , Wu Robert C , Cavalcanti Rodrigo B
Published: June 2020

The frequency of melatonin use for insomnia in hospitalized patients is unknown. This study assessed temporal trends of melatonin use in the hospital and compared them with those of use of zopiclone and lorazepam. We performed a retrospective observational study over 6 years from January 2013 to December 2018 at two academic urban hospitals in Toronto, Canada. We abstracted pharmacy dispensing data and standardized rates of medication use by inpatient days. Melatonin use increased from almost none to more than 70 doses per 1,000 inpatient days during 2013‐2018, while zopiclone use decreased by 20 doses per 1,000 inpatient days. Melatonin use was twice as high at one hospital and was higher on internal medicine and critical care. Overall use of the three medications increased by 25.7%, which mainly reflects a marked increase in melatonin use. Melatonin is likely being used in a proportion of patients who would not otherwise have received a sleep medication.
Product-Line Design in the Presence of Consumers’ Anticipated Regret
Authors: Zou Tianxin , Zhou Bo , Jiang Baojun
Published: June 2020

Consumers are often uncertain about their valuations for product quality when choosing among different products and will learn their valuations only after buying and using a product. Some consumers may thus experience overpurchase or underpurchase regret, depending on whether they have purchased a higher- or lower-quality level than what they would have chosen had they known their true valuations. When consumers anticipate their potential postpurchase regret, their purchase decisions may be affected. Our analysis shows that overpurchase regret lowers the firm’s profit, but underpurchase regret can benefit the firm if consumers’ overpurchase regret is not strong. When the firm optimally designs its product line, the quality difference between its offerings will be larger (smaller) if consumers’ anticipated regret increases (reduces) its profit. Surprisingly, although anticipated regret tends to reduce consumers’ utility, in equilibrium, the presence of anticipated regret can increase consumers’ expected surplus. We further examine when the firm should allow consumers to return their products by paying a restocking fee and how the optimal restocking fee will change with consumers’ propensities for the two types of regret. We also experimentally show that consumers’ propensities of underpurchase and overpurchase regret are different and can be influenced by the firm’s messages.

This paper was accepted by Juanjuan Zhang, marketing.
Open repair with resection and reimplantation for popliteal artery aneurysm
Authors: Zenunaj G , Mucignat M , Gasbarro V
Published: June 2020

Popliteal artery aneurysms are the most frequent type of peripheral arterial aneurysm and can be repaired by either open or endovascular techniques. An 81-year-old man presented with leg swelling and during duplex ultrasound examination was diagnosed a popliteal aneurysm. The transverse diameter was 3.6 × 4.5cm, length 2.8cm, one run-off vessel patent. The popliteal aneurysm was asymptomatic for clinical signs of limb ischaemia. We opted for an open surgical repair through a posterior approach. During dissection of the popliteal artery above and below the aneurysm, the two non-diseased popliteal extremities appeared to be very close, leading to the decision to perform an end-to-end anastomosis between the two arterial extremities. The patient was discharged after three days with no adverse events. Follow-up consisted of duplex ultrasound examination at one, three and six months, and then annually. At the six-month follow-up there was no restenosis at the anastomosis.
Customization, extension and reuse of outdated hydrogeological software
Authors: Serrano-Juan A. , Criollo R. , Vázquez-Suñé E. , Alcaraz M. , Ayora C. , Velasco V. , Scheiber L.
Published: June 2020

Each scientist is specialized in his or her field of research and in the tools that he or she uses during the research in a specified site. Thus, he or she is the most suitable person for improving the tools by overcoming their limitations to realize faster and higher quality analysis. However, most scientists are not software developers. Hence, it is necessary to provide them with an easy approach that enables non-software developers to improve and customize their tools. This paper presents an approach for easily improving and customizing any hydrogeological software. It is the result of experiences with updating several interdisciplinary case studies. The main insights of this approachhave been demonstrated using four examples: MIX (FORTRAN-based), BrineMIX (C++-based), EasyQuim and EasyBal (both spreadsheet-based). The improved software has been proven to be a better tool for enhanced analysis by substantially reducing the computation time and the tedious processing of the input and output data files.
Comparison of probability density functions for aperture-averaged irradiance fluctuations of a Gaussian beam with beam wander
Authors: Beason Melissa , Gladysz Szymon , Andrews Larry
Published: June 2020

Over the years, there has been much interest in the use of optical wavelengths for communication because of the potential for high data rates. However, the performance of these systems can become significantly degraded due to turbulence-induced signal fluctuations. These fluctuations can be minimized by enlarging the receiving aperture, thereby averaging the fluctuations. There is extensive interest in developing probability density functions (PDFs) describing these intensity fluctuations so as to accurately predict system performance. This work examines several PDF models that have been suggested to represent fluctuations by comparing them to simulations of realistic propagation scenarios of a collimated Gaussian beam with centroid wander. Unlike with an infinite plane or spherical wave, the empirical PDF shape in these simulations changed significantly with increased aperture, going from a positively skewed to a negatively skewed distribution; therefore, the PDF model that describes it also must change. This change in skew can have serious consequences on the metrics of an optical communication system, e.g., number of fades and bit-error rate. In this work, we examine the evolution of the empirical PDF with aperture size and the fit of potential PDF models under various strengths of turbulence. We show that the change in skew with increasing aperture size occurred for all strengths of turbulence and that the currently used PDF models do not adequately characterize this for realistically sized apertures where beam wander is present.
Rotation velocity measurement based on a self-mixing grating interferometer
Authors: Dong Taiji , Gao Bingkun , Qing Chen , Geng Yuhan
Published: June 2020

A novel rotational velocity measurement method based on the self-mixing grating interferometer (SMGI) is explored and presented in this paper. In this method, the target object rotational velocity is measured by the Doppler frequency shift, which can be extracted through the power spectrum without measuring incident angles. The experimental results show that the relative errors are below 0.5%.
Fast 3D measurement based on improved optical flow for dynamic objects
Authors: Dai Mingyou , Peng Kuang , Zhao Jiang , Wan Meilin , Wang Wenfeng , Cao Yiping
Published: June 2020

High resolution, real-time three-dimensional (3D) measurement plays an important role in many fields. In this paper, a multi-directional dynamic real-time phase measurement profilometry based on improved optical flow is proposed. In a five-step phase shifting dynamic measurement, pixel matching is needed to make the pixels one-to-one corresponding in five patterns. However, in the frequently-used pixel matching method at present, it is necessary to calculate the correlation and traverse the whole deformed pattern for the motion information of the measured object. The huge amount of computation caused by correlation computation takes up most of the time in the process of the entire 3D reconstruction, so it can not meet the requirement of real-time dynamic measurement. In order to solve the problem, the improved optical flow algorithm is introduced to replace correlation calculation in pixel matching. In one measurement, five captured patterns need to be dealt with, and the optical flow between each two adjacent frames is calculated. Then four two-dimensional vector matrices can be obtained. The vector matrices contain the complete motion information of the measured object. Experiments and simulations prove that this method can improve the efficiency of pixel matching by 42 times and 3D reconstruction by 32 times on the premise of ensuring the accuracy.