bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of ribotype on Clostridioides difficile diagnostics
Authors: Rizzardi Kristina , Åkerlund Thomas , Norén Torbjörn , Matussek Andreas
Published: December 2019

This study investigates the performance of diagnostic methods for detection of Clostridioides difficile infection in Sweden, including impact of PCR ribotype on diagnostic performance. Between 2011 and 2016, a total of 17,878 stool samples from 26 laboratories were tested by either well-type enzyme immunoassays (EIAs), membrane bound EIAs, cell cytotoxicity neutralization assay (CTA), or nucleic acid amplification tests (NAATs) and subsequently cultured for C. difficile. Roughly half of the samples (9454/17878) were subjected to diagnostic testing both on the fecal sample and on the 1323 isolated C. difficile strains. All C. difficile isolates were typed by PCR ribotyping, and the isolates were classified as toxigenic or non-toxigenic based on the empirical knowledge of the association between toxin-positivity and ribotype. The overall sensitivity, specificity, and positive and negative predictive values were highest for NAATs and membrane EIAs. Ribotype-specific sensitivity varied greatly between methods and ribotypes. All methods had 100% sensitivity against ribotype 027 and 013. For other types, the sensitivity ranged from 33 to 85% in fecal samples and from 78 to 100% on isolates. For the most prevalent ribotypes (014, 020, and 001), the sensitivity varied between 38 and 100% in the fecal samples, with the lowest sensitivity observed for well-type EIAs and CTA. The large variation in diagnostic sensitivity implies that type distribution significantly affects the outcome when evaluating diagnostic performance. Furthermore, performing comparative studies of diagnostic tests in settings with high prevalence of ribotype 027 will overestimate the general performance of diagnostic tests.
Evidence for the critical role of the PI3K signaling pathway in particulate matter-induced dysregulation of the inflammatory mediators COX-2/PGE2 and the associated epithelial barrier protein Filaggrin in the bronchial epithelium
Authors: Song Chenjian , Liu Lingjing , Chen Junjie , Hu Yiran , Li Jingli , Wang Beibei , Bellusci Saverio , Chen Chengshui , Dong Nian
Published: December 2019

Particulate matter (PM) is an environmental pollutant closely associated with human airway inflammation. However, the molecular mechanisms of PM-related airway inflammation remains to be fully elucidated. It is known that COX-2/PGE2 play key roles in the pathogenesis of airway inflammation. Filaggrin is a transmembrane protein contributing to tight junction barrier function. As such, Filaggrin prevents leakage of transported solutes and is therefore necessary for the maintenance of epithelial integrity. The objective of the present study was to investigate the regulatory mechanisms of COX-2/PGE2 and Filaggrin upon PM exposure both in vivo and in vitro. C57BL/6 mice received intratracheal instillation of PM for two consecutive days. In parallel, human bronchial epithelial cells (HBECs) were exposed to PM for 24 h. PM exposure resulted in airway inflammation together with upregulation of COX-2/PGE2 and downregulation of Filaggrin in mouse lungs. Corresponding dysregulation of COX-2/PGE2 and Filaggrin was also observed in HBECs subjected to PM. PM exposure led to the phosphorylation of ERK, JNK, and PI3K signaling pathways in a time-dependent manner, while blockade of PI3K with the specific molecular inhibitor LY294002 partially reversed the dysregulation of COX-2/PGE2 and Filaggrin. Moreover, pretreatment of HBECs with NS398, a specific molecular inhibitor of COX-2, and AH6809, a downstream PGE2 receptor inhibitor, reversed the downregulation of Filaggrin upon PM exposure. Taken together, these data demonstrated that the PI3K signaling pathway upregulated COX-2 as well as PGE2 and acted as a pivotal mediator in the downregulation of Filaggrin.
Risk Factors of Metabolic Syndrome Among Patients Receiving Antipsychotics: A Retrospective Study
Authors: Hammoudeh Samer , Al Lawati Hawra , Ghuloum Suhaila , Iram Huma , Yehya Arij , Becetti Imen , Al-fakhri Nora , Ghabrash Hany , Shehata Mena , Ajmal Nighat , Amro Iman , Safdar Hira , Eltorki Yassin , Al-Amin Hassen
Published: December 2019

This study aimed to assess the differential effects of first-generation (FGA) and second-generation antipsychotics (SGA) on the prevalence of risk factors for metabolic syndrome among mentally ill patients in Qatar. We also wanted to check if there is proper adherence with the guidelines for prescribing antipsychotics and the monitoring of metabolic effects in this population. We collected the available retrospective data (socio-demographic, psychiatric, anthropometric, and metabolic measures) from the records of 439 patients maintained on antipsychotics. The majority were males, married, employed, having a psychotic disorder, and receiving SGA. Patients on SGA showed more obesity, higher BP, and more elevated triglycerides compared to those on FGA. The prevalence of the abnormal metabolic measures was high in this sample, but those on SGA showed a significantly higher prevalence of abnormal body mass index and BP. Obesity and hypertension were common in patients maintained on antipsychotics, especially those on SGA. Polypharmacy was common, and many metabolic measures were not monitored properly in those maintained on antipsychotics. More prospective studies with guided monitoring of the patients' clinical status and metabolic changes are needed to serve better this population of patients.
The Eye of a Needle: Temporary Prison Leave in Ukraine
Authors: Symkovych Anton
Published: December 2019

Although temporary prison leave humanises custodial punishment, offsets its negative effects, and prepares prisoners for (re)integration into wider society, its use proves to be controversial and uneven across jurisdictions. Since the collapse of the USSR, the former Soviet countries have been pursuing different criminal justice policies, liberalising some penal practices whilst retaining many punitive Soviet legacies. Through analysis of the legal provisions regulating temporary prison leave and official statistics in Ukraine, I demonstrate the apparent strain between the official policies and practice. Whilst legally available, temporary leave for prisoners in closed prisons is almost never granted in this Eastern European country. I argue that for Ukraine to reconcile the official rhetoric of rehabilitation and social reintegration of offenders and actual implementation of penal policies, the country must reverse the underlying requirements governing temporary prison leave and expand its use.
An experimental scrutiny of visual design modelling: VCL up against UML+OCL
Authors: Amálio Nuno , Briand Lionel , Kelsen Pierre
Published: December 2019

The graphical nature of prominent modelling notations, such as the standards UML and SysML, enables them to tap into the cognitive benefits of diagrams. However, these notations hardly exploit the cognitive potential of diagrams and are only partially graphical with invariants and operations being expressed textually. The Visual Contract Language (VCL) aims at improving visual modelling; it tries to (a) maximise diagrammatic cognitive effectiveness, (b) increase visual expressivity, and (c) level of rigour and formality. It is an alternative to UML that does largely pictorially what is traditionally done textually. The paper presents the results of a controlled experiment carried out four times in different academic settings and involving 43 participants, which compares VCL against UML and OCL and whose goal is to provide insight on benefits and limitations of visual modelling. The paper’s hypotheses are evaluated using a crossover design with the following tasks: (i) modelling of state space, invariants and operations, (ii) comprehension of modelled problem, (iii) detection of model defects and (iv) comprehension of a given model. Although visual approaches have been used and advocated for decades, this is the first empirical investigation looking into the effects of graphical expression of invariants and operations on modelling and model usage tasks. Results suggest VCL benefits in defect detection, model comprehension, and modelling of operations, providing some empirical evidence on the benefits of graphical software design.
Relative Necessity and Propositional Quantification
Authors: Roberts Alexander
Published: December 2019

Following Smiley’s (The Journal of Symbolic Logic, 28, 113–134 1963) influential proposal, it has become standard practice to characterise notions of relative necessity in terms of simple strict conditionals. However, Humberstone (Reports on Mathematical Logic, 13, 33–42 1981) and others have highlighted various flaws with Smiley’s now standard account of relative necessity. In their recent article, Hale and Leech (Journal of Philosophical Logic, 46, 1–26 2017) propose a novel account of relative necessity designed to overcome the problems facing the standard account. Nevertheless, the current article argues that Hale & Leech’s account suffers from its own defects, some of which Hale & Leech are aware of but underplay. To supplement this criticism, the article offers an alternative account of relative necessity which overcomes these defects. This alternative account is developed in a quantified modal propositional logic and is shown model-theoretically to meet several desiderata of an account of relative necessity.
Modified biochar from Moringa seed powder for the removal of diclofenac from aqueous solution
Authors: Bagheri Afrouz , Abu-Danso Emmanuel , Iqbal Jibran , Bhatnagar Amit
Published: December 2019

In this study, Moringa seed powder (MSP) was pyrolyzed at 450 °C to synthesize Moringa seed powder biochar (MSPB) and treated with phosphoric acid (H3PO4) to synthesize phosphate-modified Moringa seed powder biochar (MSPB-HPO) as an adsorbent for the removal of diclofenac (Dfc) from aqueous solution. Fourier transform infrared (FTIR) analysis, energy dispersive X-ray spectroscopy (EDS), scanning electron microscopy (SEM), and pH point of zero charge (pHpzc) were conducted to give more insight into the adsorbent’s properties. The SEM analysis showed the transformations in the surface morphology from the parent material to the synthesized materials after the thermal and acid treatment. EDS analysis revealed the variation in the elemental composition of the materials prior to and after adsorption of Dfc ions. The FTIR analysis showed changes and peak intensities of functional groups involved in Dfc removal. The pHpzc showed the charge carried by MSPB-HPO in different pH conditions. Isotherm data best matched the Sips model, and the pseudo-second-order model best described the adsorption kinetics. The maximum adsorption capacity of MSPB-HPO by Sips model was found to be 100.876 mg g−1.
Financial crises and the attainment of the SDGs: an adjusted multidimensional poverty approach
Authors: Antoniades Andreas , Widiarto Indra , Antonarakis Alexander S.
Published: December 2019

This paper analyses the impact of financial crises on the Sustainable Development Goal of eradicating poverty. To do so, we develop an adjusted Multidimensional Poverty Framework (MPF) that includes 15 indicators that span across key poverty aspects related to income, basic needs, health, education and the environment. We then use an econometric model that allows us to examine the impact of financial crises on these indicators in 150 countries over the period 1980–2015. Our analysis produces new estimates on the impact of financial crises on poverty’s multiple social, economic and environmental aspects and equally important captures dynamic linkages between these aspects. Thus, we offer a better understanding of the potential impact of current debt dynamics on Multidimensional Poverty and demonstrate the need to move beyond the boundaries of SDG1, if we are to meet the target of eradicating poverty. Our results indicate that the current financial distress experienced by many low-income countries may reverse the progress that has been made hitherto in reducing poverty. We find that financial crises are associated with an approximately 10% increase of extreme poor in low-income countries. The impact is even stronger in some other poverty aspects. For instance, crises are associated with an average decrease of government spending in education by 17.72% in low-income countries. The dynamic linkages between most of the Multidimensional Poverty indicators, warn of a negative domino effect on a number of SDGs related to poverty, if there is a financial crisis shock. To pre-empt such a domino effect, the specific SDG target 17.4 on attaining long-term debt sustainability through coordinated policies plays a key role and requires urgent attention by the international community.
The function and regulation of OTU deubiquitinases
Authors: Du Jiansen , Fu Lin , Sui Yingli , Zhang Lingqiang
Published: December 2019

Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including cell division, immune responses, and apoptosis. Ubiquitin-mediated control over these processes can be reversed by deubiquitinases (DUBs), which remove ubiquitin from target proteins and depolymerize polyubiquitin chains. Recently, much progress has been made in the DUBs. In humans, the ovarian tumor protease (OTU) subfamily of DUBs includes 16 members, most of which mediate cell signaling cascades. These OTUs show great variation in structure and function, which display a series of mechanistic features. In this review, we provide a comprehensive analysis of current progress in character, structure and function of OTUs, such as the substrate specificity and catalytic activity regulation. Then we discuss the relationship between some diseases and OTUs. Finally, we summarize the structure of viral OTUs and their function in immune escape and viral survival. Despite the challenges, OTUs might provide new therapeutic targets, due to their involvement in key regulatory processes.
Effectiveness of Descriptions in Missing Children Appeals: Exploration of Length, Type of Content and Confidence on Recall Accuracy
Authors: Hunt Daniel , Ioannou Maria , Synnott John
Published: December 2019

When a child goes missing, it is commonplace to release details of the child in the hope that a member of the public can help to locate him or her. Despite their importance and daily usage, there remains a significant gap in understanding just how effective these appeals are in helping to locate missing children. This exploratory study utilized a two-stage approach and sought (1) to explore whether the length of the description and the type of content enclosed in the description influenced subsequent recall abilities, (2) to determine whether the length of time spent reading the mock appeal influences the subsequent recall ability, (3) to establish whether confidence in own recall ability is associated with overall recall ability, and (4) to determine whether descriptive length and content influences the subsequent recall ability following a 3-day break. Two hundred and twenty-three participants observed one of four mock missing children descriptions followed by a short word memory distraction task and a free-recall task. The second stage comprised of another free-recall task presented after a short 3-day delay. Two-way factorial ANOVAs found observing shorter descriptions have significantly greater recall accuracy than observing longer descriptions both immediately after observing the appeal and after a 3-day delay. Results also found that newsworthy descriptive content had a greater recall accuracy than non-newsworthy descriptive content after a 3-day delay. Additional analyses found that confidence in own accuracy and time spent observing the appeals was also significantly associated with recall accuracy. The findings demonstrate the necessity for improving missing children appeals.
Advanced Biotechnology for Cell Cryopreservation
Authors: Yang Jing , Gao Lei , Liu Min , Sui Xiaojie , Zhu Yingnan , Wen Chiyu , Zhang Lei
Published: December 2019

Cell cryopreservation has evolved as an important technology required for supporting various cell-based applications, such as stem cell therapy, tissue engineering, and assisted reproduction. Recent times have witnessed an increase in the clinical demand of these applications, requiring urgent improvements in cell cryopreservation. However, cryopreservation technology suffers from the issues of low cryopreservation efficiency and cryoprotectant (CPA) toxicity. Application of advanced biotechnology tools can significantly improve post-thaw cell survival and reduce or even eliminate the use of organic solvent CPAs, thus promoting the development of cryopreservation. Herein, based on the different cryopreservation mechanisms available, we provide an overview of the applications and achievements of various biotechnology tools used in cell cryopreservation, including trehalose delivery, hydrogel-based cell encapsulation technique, droplet-based cell printing, and nanowarming, and also discuss the associated challenges and perspectives for future development.
Right-Angle Shaped Elements as Dual-Band Metamaterial Absorber in Terahertz
Authors: Daniel Salman , Bawuah Prince
Published: December 2019

Metamaterial absorbers display potential applications in the field of photonics and have been investigated extensively during the last decade. We propose a dual-band resonant metamaterial absorber with right-angle shaped elements (RAEs) in the terahertz range based on numerical simulations. The absorber remains insensitive to a wide range of incidence angles (0°–70°) by showing a minimum absorbance of ~80% at 70°. Furthermore, the proposed absorber is highly independent on any state of polarization of the incidence electromagnetic wave due to the high absorbance, i.e., greater than 80%, recorded for the considered polarization states. To further comprehend the slight variations in absorbance as a function of change in the angle of incidence, the impedance of the structure has been critically examined. The metamaterial absorber is simple in design, and we provide a possible path of fabrication.
Coherent Random Lasing Realized in Polymer Vesicles
Authors: Li Yaxin , Xie Kang , Zhang Xiaojuan , Hu Zhijia , Ma Jiajun , Chen Xianxian , Zhang Junxi , Liu Zhenming , Chen Dong
Published: December 2019

We have demonstrated the realization of a coherent vesicle random lasing (VRL) from the dye doped azobenzene polymer vesicles self-assembled in the tetrahydrofuran-water system, which contains a double-walled structure: a hydrophilic and hydrophobic part. The effect of the dye and azobenzene polymer concentration on the threshold of random laser has been researched. The threshold of random laser decreases with an increase in the concentration of the pyrromethene 597 (PM597) laser and azobenzene polymer. Moreover, the scattering of small size group vesicles is attributed to providing a loop to boost the coherent random laser through the Fourier transform analysis. Due to the vesicles having the similar structure with the cell, the generation of coherent random lasers from vesicles expand random lasers to the biomedicine filed.
The influence of Bacillus subtilis 87Y isolated from Eisenia fetida on the growth of pathogenic and probiotic microorganisms
Authors: Szmigiel I. , Suchodolski J. , Łukaszewicz M. , Krasowska A.
Published: December 2019

Bacillus subtilis strain 87Y, isolated from the earthworm Eisenia fetida, decreases the growth of pathogenic Salmonella spp. and Staphylococcus aureus and promotes the growth of probiotic Lactococcus spp. Preserving viability in acidic conditions as well as in bile salts, B. subtilis 87Y meets two of the requirements of a probiotic strain. Thanks to the production of the biosurfactant surfactin, B. subtilis 87Y limits the growth of the Gram-positive bacterium S. aureus. In the presence of sucrose, B. subtilis produces levan, which contributes to promoting the growth of other probiotics. Our in vitro studies justify the continuation of enriching rapeseed meal waste from solid-state fermentation with B. subtilis 87Y, to produce high-value animal feed supplements.
Image-Based Inspection Technique of a Machined Metal Surface for an Unmanned Lapping Process
Authors: Ravimal Dinuka , Kim Hanul , Koh Daegwon , Hong Jin Hyuk , Lee Sun-Kyu
Published: December 2019

This paper presents a new machine vision framework for the efficient examination and classification of surface textures on medium- and large-sized mold products, such as used for automobiles, TVs, and refrigerators. Existing techniques, which are based on the hands and eyes of skilled workers, are inconsistent and time-consuming. Although there are many types of precise surface inspection and measurement methods, most are difficult to apply at industrial sites or by finishing robots due to problems such as speed, setup limitations, and robustness. This paper proposes two techniques based on image processing that aims to automate surface inspection during an unmanned lapping process that is mainly employed to eliminate milling tool marks. First, both the shape of the reflected light and the intensity of the captured near-field contrast image right after the reflected specular are used to determine the machined surface state, and the presence of tool marks as the line light source scans counter-clockwise. Second, the photometric stereo technique is used to detect surface scratches through the normal map that recovers the surface. The proposed techniques show localized machined patterns and classify them with high accuracy.
Building Safe Lithium-Ion Batteries for Electric Vehicles: A Review
Authors: Duan Jian , Tang Xuan , Dai Haifeng , Yang Ying , Wu Wangyan , Wei Xuezhe , Huang Yunhui
Published: December 2019

Lithium-ion batteries (LIBs), with relatively high energy density and power density, have been considered as a vital energy source in our daily life, especially in electric vehicles. However, energy density and safety related to thermal runaways are the main concerns for their further applications. In order to deeply understand the development of high energy density and safe LIBs, we comprehensively review the safety features of LIBs and the failure mechanisms of cathodes, anodes, separators and electrolyte. The corresponding solutions for designing safer components are systematically proposed. Additionally, the in situ or operando techniques, such as microscopy and spectrum analysis, the fiber Bragg grating sensor and the gas sensor, are summarized to monitor the internal conditions of LIBs in real time. The main purpose of this review is to provide some general guidelines for the design of safe and high energy density batteries from the views of both material and cell levels.

Graphic Abstract

Safety of lithium-ion batteries (LIBs) with high energy density becomes more and more important in the future for EVs development. The safety issues of the LIBs are complicated, related to both materials and the cell level. To ensure the safety of LIBs, in-depth understanding of the safety features, precise design of the battery materials and real-time monitoring/detection of the cells should be systematically considered. Here, we specifically summarize the safety features of the LIBs from the aspects of their voltage and temperature tolerance, the failure mechanism of the LIB materials and corresponding improved methods. We further review the in situ or operando techniques to real-time monitor the internal conditions of LIBs.
Vestibular stimulation with Indian hammock versus music intervention in the prevention of infantile colic in term infants
Authors: Ravikumar Senthikumaran , Srinivasaraghavan Rangan , Gunasekaran Dhandapany , Sundar Sumathy , Soundararajan Palanisamy
Published: December 2019

Background and Objectives:

To determine whether vestibular stimulation offered by Indian hammock and music intervention are useful in reducing the occurrence of infantile colic in term infants.

Methods:

This open-labelled randomized clinical trial was conducted among 465 term neonates who were randomly assigned to one of three groups: music group, hammock group and control group. The music intervention was given for a cumulative duration of at least 4 h a day with one stretch of at least 1 h. In the hammock group, babies were put to sleep inside the Indian hammock and were swung gently until they sleep, and were allowed to sleep in it, until they wake up. For the control group, routine predischarge counselling was given. All parents were provided a cry log and were instructed to record the log of cry events and duration. The primary outcome measure was occurrence of infantile colic episode as defined by ROME IV criteria. The infants were followed up from birth until the age of 3.5 months, and the cry log was collected during each follow-up visit.

Results:

Of the 435 term neonates who completed follow-up, 59 infants developed infantile colic (13.6%). The prevalence of infantile colic in the control group, music group and the Indian hammock group was 25.6%, 5.4% and 9.6% respectively; there was a significant reduction in the prevalence of infantile colic in the intervention groups as compared to the control group.

Conclusions:

Vestibular stimulation by Indian hammock and music intervention individually reduced the occurrence of infantile colic.
Convolution neural network–based Alzheimer's disease classification using hybrid enhanced independent component analysis based segmented gray matter of T2 weighted magnetic resonance imaging with clinical valuation
Authors: Basheera Shaik , Sai Ram M Satya
Published: December 2019

In recent times, accurate and early diagnosis of Alzheimer's disease (AD) plays a vital role in patient care and further treatment. Predicting AD from mild cognitive impairment (MCI) and cognitive normal (CN) has become popular. Neuroimaging and computer‐aided diagnosis techniques are used for classification of AD by physicians in the early stage. Most of the previous machine learning techniques work on handpicked features. In the recent days, deep learning has been applied for many medical image applications. Existing deep learning systems work on raw magnetic resonance imaging (MRI) images and cortical surface as an input to the convolution neural network (CNN) to perform classification of AD. AD affects the brain volume and changes the gray matter texture. In our work, we used 1820 T2‐weighted brain magnetic resonance volumes including 635 AD MRIs, 548 MCI MRIs, and 637 CN MRIs, sliced into 18,017 voxels. We proposed an approach to extract the gray matter from brain voxels and perform the classification using the CNN. A Gaussian filter is used to enhance the voxels, and skull stripping algorithm is used to remove the irrelevant tissues from enhanced voxels. Then, those voxels are segmented by hybrid enhanced independent component analysis. Segmented gray matter is used as an input to the CNN. We performed clinical valuation using our proposed approach and achieved 90.47% accuracy, 86.66% of recall, and 92.59% precision.
Temporal association of neuropsychological test performance using unsupervised learning reveals a distinct signature of Alzheimer's disease status
Authors: Joshi Prajakta S. , Heydari Megan , Kannan Shruti , Alvin Ang Ting Fang , Qin Qiuyuan , Liu Xue , Mez Jesse , Devine Sherral , Au Rhoda , Kolachalama Vijaya B.
Published: December 2019

Introduction

Subtle cognitive alterations that precede clinical evidence of cognitive impairment may help predict the progression to Alzheimer's disease (AD). Neuropsychological (NP) testing is an attractive modality for screening early evidence of AD.

Methods

Longitudinal NP and demographic data from the Framingham Heart Study (FHS; N = 1696) and the National Alzheimer's Coordinating Center (NACC; N = 689) were analyzed using an unsupervised machine learning framework. Features, including age, logical memory‐immediate and delayed recall, visual reproduction‐immediate and delayed recall, the Boston naming tests, and Trails B, were identified using feature selection, and processed further to predict the risk of development of AD.

Results

Our model yielded 83.07 ± 3.52% accuracy in FHS and 87.57 ± 1.19% accuracy in NACC, 80.52 ± 3.93%, 86.74 ± 1.63% sensitivity in FHS and NACC respectively, and 85.63 ± 4.71%, 88.41 ± 1.38% specificity in FHS and NACC, respectively.

Discussion

Our results suggest that a subset of NP tests, when analyzed using unsupervised machine learning, may help distinguish between high‐ and low‐risk individuals in the context of subsequent development of AD within 5 years. This approach could be a viable option for early AD screening in clinical practice and clinical trials.
Projected Changes to Extreme Precipitation Along North American West Coast From the CESM Large Ensemble
Authors: Ma Weiming , Norris Jesse , Chen Gang
Published: December 2019

Precipitation events along the North American (NA) west coast are strongly modulated by atmospheric rivers, yet the mechanisms of their influences on the probability distributions of precipitation events are not well studied. Simulations from the Community Earth System Model (CESM) large ensemble under global warming are investigated using a moisture budget conditioned onto precipitation events for the recurrence intervals ranging from 0.1 to 50 years. In the midlatitudes, the increases in precipitation intensity and accumulation for all events over the NA west coast are predominantly controlled by moisture increases. In contrast, changes in the subtropical precipitation distributions in southwestern NA are associated with moisture increases and duration decreases for all events, with additional dynamical amplification for the heaviest precipitation events. These interpretations from the conditional moisture budget are more consistent with future projection of atmospheric rivers than the conventional mean and transient decomposition of the moisture budget.
Multiharmonic Toroidal Standing Alfvén Waves in the Midnight Sector Observed During a Geomagnetically Quiet Period
Authors: Takahashi Kazue , Vellante Massimo , Del Corpo Alfredo , Claudepierre Seth G. , Kletzing Craig , Wygant John , Koga Kiyokazu
Published: December 2019

Excitation of toroidal mode standing Alfvén waves in the midnight sector of the inner magnetosphere in association with substorms is well documented, but studies are sparse on dayside sources for the waves. This paper reports observation of midnight toroidal waves by the Van Allen Probe B spacecraft during a geomagnetically quiet period on 12–13 May 2013. The spacecraft detected toroidal waves excited at odd harmonics below 30 mHz as it moved within the plasmasphere from
2100 magnetic local time to
0030 magnetic local time through midnight in the dipole
range 4.2–6.1. The frequencies and the relationship between the electric and magnetic field components of the waves are consistent with theoretical toroidal waves for a reflecting ionosphere. At the time of the nightside toroidal waves, compressional waves were observed by geostationary satellites located on the dayside, and the amplitudes of both types of waves varied with the cone angle of the interplanetary magnetic field. The nightside toroidal waves were likely driven by fast mode waves that resulted from transmission of upstream ultralow frequency waves into the magnetosphere. Ground magnetometers located near the footprint of the spacecraft did not detect toroidal waves.
Deformation of Granular Aggregates: Static and Dynamic Bulk Moduli
Authors: Muqtadir Arqam , Al‐Dughaimi Saud , Dvorkin Jack
Published: December 2019

Sand and glass bead samples were monotonically loaded from 0 to 50 MPa and then monotonically unloaded, all under hydrostatic stress conditions. Sand deformed irreversibly and its porosity loss was permanent. In contrast, the glass bead deformation was almost fully reversible with the initial porosity recovered. During loading, the static bulk modulus in all sand samples increased from 0 to about 0.5 GPa between 0‐ and 15‐MPa stress and remained constant for the remainder of the loading. Such behavior, somewhat unexpected in a granular system, means that sand deforms as a linear elastic body during loading from 15 to 50 MPa. The unloading behavior was very different—the static bulk modulus almost linearly decreased from about 4 GPa at 50 MPa to zero as the stress was reduced. Once again, this behavior was very different from that observed in glass beads, where the static bulk modulus during loading was essentially the same as during unloading and appeared to be a unique function of stress, independent of the direction of its variation. Moreover, the static and dynamic bulk moduli in glass beads, the latter computed from Vp, Vs, and density measured during the loading/unloading cycle, were very close to each other. In contrast, the dynamic bulk modulus in dry sand exceeded the static modulus during unloading by a factor of 1.5 to 2.0. We used a quantitative theory based on contact mechanics and the concept of stress heterogeneity in particulates to analytically match the observed results.
Larval Fish Habitats and Deoxygenation in the Northern Limit of the Oxygen Minimum Zone off Mexico
Authors: Sánchez‐Velasco Laura , Godínez Víctor M. , Ruvalcaba‐Aroche Erick D. , Márquez‐Artavia Amaru , Beier Emilio , Barton Eric D. , Jiménez‐Rosenberg S. Patricia A.
Published: December 2019

The present state of deoxygenation in the northern limits of the shallow oxygen minimum zone off Mexico is examined in order to detect its effects on larval fish habitats and consider the sensitivity of fish larvae to decreased dissolved oxygen. A series of cruises between 2000 and 2017 indicated a significant vertical expansion of low oxygen waters. The upper limit of suboxic conditions (<4.4 μmol/kg) has risen ~100 m at 19.5°N off Cabo Corrientes and ~50 m at 25°N in the mouth of the Gulf of California. The larval habitat distribution was related to the geographic variability of dissolved oxygen and water masses between these two latitudes. One recurrent larval habitat, with Bregmaceros bathymaster larvae as the indicator species, extended throughout the water column off Cabo Corrientes from Subtropical Subsurface Water (suboxic conditions) to the surface (220 μmol/kg). The second recurrent habitat was located between the oxycline (>44 μmol/kg) and the surface in association with the Gulf of California Water, with Benthosema panamense as the indicator species. During the warm El Niño event of 2015–2016, a tropical larval fish habitat (Auxis spp.) associated with Tropical Surface Water appeared to change the larval habitat distributions. These results indicate that some species are resilient to changes of dissolved oxygen and temperature generated by El Niño events and by continuing deoxygenation, although other species with more limited environmental windows could be affected by deoxygenation, probably leading to a change of the pelagic ecosystem over time.
Wave Period and Grain Size Controls on Short‐Wave Suspended Sediment Transport Under Shoaling and Breaking Waves
Authors: Christensen Drude F. , Hughes Michael G. , Aagaard Troels
Published: December 2019

Beach recovery is key to the continued existence of sandy beaches and is typically driven by the onshore‐directed transport of sediment by short waves during low‐moderate energy conditions. The physical processes governing beach recovery are not well understood, but the theoretically developed dimensionless fall velocity, Ω = H/wsT, was suggested to be important for separating onshore/offshore sediment motion (Dean, 1973). In this paper, the effect of wave period and sediment grain size on short‐wave suspended sediment flux was investigated based on field measurements obtained beneath shoaling and breaking waves at Durras and Vejers beaches. The efficiency of the breaking waves in transporting suspended sediment onshore was roughly the same for the two beaches, despite the wave periods being larger and the mean sediment grain size coarser at Durras beach. The flux efficiencies were, however, shown to be degraded by wave‐current interactions and long/short‐wave interactions at Durras beach, especially. Excluding time series of strong undertow velocities (< −0.1 m/s) and infragravity wave‐energy (>5 m2/s3) resulted in significantly larger flux efficiencies beneath breaking waves at Durras beach compared to Vejers beach. These results indicate that wave‐current interactions and long/short‐wave interactions should be taken into consideration along with the wave period and mean grain size when estimating short‐wave suspended sediment fluxes. The results also showed that plunging breakers were more efficient in suspending sediment and transporting it onshore compared to spilling breakers/surf bores. This finding suggests that wave breaker type also is an important parameter to incorporate when modeling beach recovery.
Two Improvements to Gardner's Method of Measuring the Hydraulic Conductivity of Non‐saturated Media: Accounting for Impedance Effects and Non‐constant Imposed Suction Increment
Authors: Stanić Filip , Delage Pierre , Cui Yu‐Jun , De Laure Emmanuel , Versini Pierre‐Antoine , Schertzer Daniel , Tchiguirinskaia Ioulia
Published: December 2019

Gardner's (1956, https://doi.org/10.2136/sssaj1956.03615995002000030006x) transient method of measuring the hydraulic conductivity function of unsaturated media has been largely used, together with the improved graphical method proposed by Kunze and Kirkham (1962, https://doi.org/10.2136/sssaj1962.03615995002600050006x) to account for the impedance effect resulting from using a low hydraulic conductivity ceramic disk in porous plate testing. These methods are nowadays seldom used, since they have been replaced by numerical back analysis and methods for parameter optimization. Based on tests carried out on a specific device allowing to determine the water retention and transport properties of water in a coarse granular media at low suctions (up to 50 kPa), it was found necessary to account (i) for impedance effects and (ii) for the effects of nonconstant suction increments, as is often the case when using the hanging column technique. A new method is proposed to account for impedance effects, based on an analytical solution of the equations governing water transfer. The validity of this method is tested by considering experimental data from three distinct materials: a coarse green roof volcanic substrate, poorly graded sand, and undisturbed silty clay. Compared to the graphical method Kunze and Kirkham's method, it is less operator‐dependent and hence more objective. It is also simpler than numerical back analysis methods, since it does not require any use of numerical code or parameter optimization algorithm, providing a more direct and reliable access to the hydraulic conductivity. An analytical solution is also proposed to solve the problem resulting from the application of a nonconstant suction increment.
Study of a catalyst supported on rice husk ash for NO reduction with carbon monoxide
Authors: Teng Zhaohui , Huang Shan , Fu Liang , Xu Heng , Li Na , Zhou Qulan
Published: December 2019

Fe–Cu catalysts supported on rice husk ash were used in CO-SCR of NO and this new combination was effective.
Current and future role of Haber–Bosch ammonia in a carbon-free energy landscape
Authors: Smith Collin , Hill Alfred K. , Torrente-Murciano Laura
Published: December 2019

The future of green ammonia as long-term energy storage relies on the replacement of the conventional CO2intensive methane-fed Haber–Bosch process by distributed and agile ones aligned to the geographically isolated and intermittent renewable energy.
Recent advances in solution-processed photodetectors based on inorganic and hybrid photo-active materials
Authors: Li Chao , Huang Weichun , Gao Lingfeng , Wang Huide , Hu Lanping , Chen Tingting , Zhang Han
Published: December 2019

In this review, the progress in photodetector devices focusing on inorganic and hybrid photo-active materials by low cost wet-chemistry methods, which will bring about the prospect of a new era, has been carefully summarized.
Poroelasticity of (bio)polymer networks during compression: theory and experiment
Authors: Punter Melle T. J. J. M. , Vos Bart E. , Mulder Bela M. , Koenderink Gijsje H.
Published: December 2019

The permeability and elasticity of (bio)polymer networks can be determined from a single compression test in a commercial rheometer using a novel poroelastic model.
Gender Surgery Beyond Chest and Genitals: Current Insurance Landscape
Authors: Ngaage Ledibabari M , McGlone Katie L , Xue Shan , Knighton Brooks J , Benzel Caroline A , Rada Erin M , Coon Devin , Berli Jens , Rasko Yvonne M
Published: December 2019

Background

Plastic surgery plays an essential role in the treatment of gender dysphoria. International standards of care currently consider genital and chest surgeries to be medically necessary. Ancillary procedures such as facial surgery, chondrolaryngoplasty, hair restoration/removal, and body contouring are considered cosmetic surgeries except in individual circumstances.

Objective

The authors sought to assess the frequency of coverage provision for ancillary transition-related surgeries through a cross-sectional analysis of US insurance policies.

Methods

The authors selected insurance companies based on state enrollment data and market share. Policies were identified through web-based search and telephone interviews. A list of eligible procedures was compiled and grouped into 5 categories: body masculinization, body feminization, facial procedures, hair restoration/removal, and chondrolaryngoplasty. Medical necessity criteria from publicly accessible policies were then abstracted.

Results

Sixty-one insurance companies held an established policy. One-third of these policies offered favorable coverage for at least 1 ancillary procedure. Chondrolaryngoplasty was the most covered category (26%, n = 16), whereas body masculinization was the least covered (8%, n = 5). Almost two-thirds of the companies with favorable policies listed coverage criteria. We identified 4 recurring requirements: age, hormone therapy, continuous living in a congruent gender role, and referral from a mental health professional.

Conclusions

There is a low prevalence of US insurance coverage for ancillary gender surgeries and wide variability in coverage criteria. Reevaluation of ancillary transition-related procedures from cosmetic to medically necessary based on clinical judgement or establishment of defined coverage criteria may augment coverage and better address the needs of transgender patients.
Bringing data from curated pathway resources to Cytoscape with OmniPath
Authors: Ceccarelli Francesco , Turei Denes , Gabor Attila , Saez-Rodriguez Julio
Published: December 2019

Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools.

Availability and implementation

The OmniPath App has been developed for Cytoscape 3 in the Java programing language. The latest source code and the plugin can be found at: https://github.com/saezlab/Omnipath_Cytoscape and http://apps.cytoscape.org/apps/omnipath, respectively.

Supplementary information

Supplementary data are available at Bioinformatics online.
Histological Markers of Clinical Relapse in Endoscopically Quiescent Ulcerative Colitis
Authors: Kevans David , Kirsch Richard , Dargavel Callum , Kabakchiev Boyko , Riddell Robert , Silverberg Mark S
Published: December 2019

Background

In ulcerative colitis (UC) patients who have achieved mucosal healing, active microscopic colonic mucosal inflammation is commonly observed. We aimed to assess the association between histological activity and disease relapse in endoscopically quiescent UC.

Methods

Ulcerative colitis patients with endoscopically quiescent disease and ≥12 months of follow-up were included. Biopsies were reviewed for the presence of basal plasmacytosis (BPC) and active histological inflammation, defined as a Geboes score (GS) ≥3.2. Primary outcome measures were disease relapse at 18 months and time to first relapse after index colonoscopy.

Results

Seventy-six UC patients (51% male; mean age, 38.6 years; median follow-up [range], 75.2 [2–118] months) were included. Sixty-two percent had an endoscopic Mayo score of 0 at index colonoscopy. Basal plasmacytosis was present in 46% and active histological inflammation in 30% of subjects. Presence of BPC was associated with a significantly shorter time to disease relapse (P = 0.01). Active histological inflammation was significantly associated with clinical relapse at 18 months (P = 0.0005) and shorter time to clinical relapse (P = 0.0006). Multivariate analysis demonstrated active histological inflammation to be independently associated with clinical relapse at 18 months and time to clinical relapse.

Conclusions

In endoscopically quiescent UC, active histological inflammation and the presence of BPC are adjunctive histological markers associated with increased likelihood of disease relapse. Although prospective studies are required, the presence of these histological markers should be a factor considered when making therapeutic decisions in UC.
Variation in Tick Load Among Bird Body Parts: Implications for Studying the Role of Birds in the Ecology and Epidemiology of Tick-Borne Diseases
Authors: Roselli Megan A , Cady Samantha M , Lao Sirena , Noden Bruce H , Loss Scott R
Published: December 2019

Wild birds play important roles in the maintenance and dispersal of tick populations and tick-borne pathogens, yet in field studies of tick-borne disease ecology and epidemiology there is limited standardization of how birds are searched for ticks. We conducted a qualitative literature review of 100 field studies where birds were searched for ticks to characterize which parts of a bird’s anatomy are typically sampled. To increase understanding of potential biases associated with different sampling approaches, we described variation in tick loads among bird body parts using field-collected data from 459 wild-caught birds that were searched across the entire body. The literature review illustrated a lack of clarity and consistency in tick-searching protocols: 57% of studies did not explicitly report whether entire birds or only particular body parts were searched, 34% reported concentrating searches on certain body parts (most frequently the head only), and only 9% explicitly reported searching the entire bird. Based on field-collected data, only 22% of ticks were found on the head, indicating that studies focusing on the head likely miss a large proportion of ticks. We provide tentative evidence that feeding locations may vary among tick species; 89% of Amblyomma americanum, 73% of Ambloyomma maculatum, and 56% of Haemaphysalis leporispalustris were on body parts other than the head. Our findings indicate a need for clear reporting and increased standardization of tick searching methodologies, including sampling the entire bird body, to provide an unbiased understanding of the role of birds in the maintenance and emergence of tick-borne pathogens.