bluuebunny/crossref_metadata_2025 huggingface dataset:
Phospholipid ebb and flow makes mitochondria go
Authors: Acoba Michelle Grace , Senoo Nanami , Claypool Steven M.
Published: July 2020

Mitochondria, so much more than just being energy factories, also have the capacity to synthesize macromolecules including phospholipids, particularly cardiolipin (CL) and phosphatidylethanolamine (PE). Phospholipids are vital constituents of mitochondrial membranes, impacting the plethora of functions performed by this organelle. Hence, the orchestrated movement of phospholipids to and from the mitochondrion is essential for cellular integrity. In this review, we capture recent advances in the field of mitochondrial phospholipid biosynthesis and trafficking, highlighting the significance of interorganellar communication, intramitochondrial contact sites, and lipid transfer proteins in maintaining membrane homeostasis. We then discuss the physiological functions of CL and PE, specifically how they associate with protein complexes in mitochondrial membranes to support bioenergetics and maintain mitochondrial architecture.
Cbl and Cbl-b control the germinal center reaction by facilitating naive B cell antigen processing
Authors: Li Xin , Gong Liying , Meli Alexandre P. , Karo-Atar Danielle , Sun Weili , Zou Yongrui , King Irah L. , Gu Hua
Published: July 2020

Antigen uptake and presentation by naive and germinal center (GC) B cells are different, with the former expressing even low-affinity BCRs efficiently capture and present sufficient antigen to T cells, whereas the latter do so more efficiently after acquiring high-affinity BCRs. We show here that antigen uptake and processing by naive but not GC B cells depend on Cbl and Cbl-b (Cbls), which consequently control naive B and cognate T follicular helper (Tfh) cell interaction and initiation of the GC reaction. Cbls mediate CD79A and CD79B ubiquitination, which is required for BCR-mediated antigen endocytosis and postendocytic sorting to lysosomes, respectively. Blockade of CD79A or CD79B ubiquitination or Cbls ligase activity is sufficient to impede BCR-mediated antigen processing and GC development. Thus, Cbls act at the entry checkpoint of the GC reaction by promoting naive B cell antigen presentation. This regulation may facilitate recruitment of naive B cells with a low-affinity BCR into GCs to initiate the process of affinity maturation.
Circulating tumor cells: Ready for translation?
Authors: Diamantopoulou Zoi , Castro-Giner Francesc , Aceto Nicola
Published: July 2020

Circulating tumor cells are tumor-derived pioneers responsible for the metastatic spread of cancer. Here, we outline recent discoveries, challenges, and future trends for circulating tumor cell investigations, arguing that the time is coming for translation of this work into clinical practice.
ZBP1: A STARGᐰTE to decode the biology of Z-nucleic acids in disease
Authors: Kesavardhana Sannula , Kanneganti Thirumala-Devi
Published: July 2020

ZBP1 triggers NLRP3 inflammasome activation/pyroptosis, apoptosis, and necroptosis; the specific ligand for ZBP1 activation remains ambiguous. Recent studies, including Devos et al. in this issue of JEM (https://doi.org/10.1084/jem.20191913), collectively suggest that ZBP1 sensing Z-nucleic acids is critical for cell death/inflammatory disease.
Carbon monoxide interacting with free-electron-laser pulses
Authors: Banks H I B , Hadjipittas A , Emmanouilidou A
Published: July 2020

We study the interaction of a heteronuclear diatomic molecule, carbon monoxide, with a free-electron laser (FEL) pulse. We compute the ion yields and the intermediate states by which the ion yields are populated. We do so using rate equations, computing all relevant molecular and atomic photo-ionisation cross-sections and Auger rates. We find that the charge distribution of the carbon and oxygen ion yields differ. By varying the photon energy, we demonstrate how to control higher-charged states being populated mostly by carbon or oxygen. Moreover, we identify the differences in the resulting ion yields and pathways populating these yields between a homonuclear molecule, molecular nitrogen, and a heteronuclear molecule, carbon monoxide, interacting with an FEL pulse. These two molecules have similar electronic structure. We also identify the proportion of each ion yield which accesses a two-site double-core-hole state and tailor pulse parameters to maximise this proportion.
Round robin test for height valuation methods, LEL and W/3, in China
Authors: Liu Jian , You Xiaoyu , Shi Yushu , Zhang Shu , Wang Yuhang , Yu Xixi , Li Yuan , Wang Yunxiang , Fang Dan , Hao Yanbin , Bian Wei , Zhang Xinyu , Wang Min , Guo Xin , Guo Jiping , Li Ameng , Yan Jiewen , Wei Chun , Guo Tong , Wang Jiuhong , Wang Chenying , Liu Xiaojun , Lei Zili , Chen Yuanliu
Published: July 2020

In the field of optical microscopy, height valuations, or calibrations, are critical to ensure accuracy and traceability. Height assessment, however, may be controversial, particularly for measurements on large steps or narrow grooves. Thus, standard setting and instrument operations are essential. In this paper, the limited energy lost (LEL) method, which is a Chinese solution, and the well-known ISO W/3 method were both applied in a two-year round robin test to verify their theoretical compatibility and promote their corresponding applications throughout China. The results show that the LEL method successfully predicted outlier growth for progressively narrowing grooves. In addition, compared with the W/3 method, 71% of the results from 24 measurements showed improved repeatability when applying the LEL method. This paper supports the LEL method with evidence from a large sample, after its original publishing in 2016 and the subsequent publication, as a key part of China’s standard on confocal microscopy, in 2017. These results indicate that dynamic model-based valuation might be the future trend for 3D optical micro-nano metrology.
Non-invasive analysis of motor neurons controlling the intrinsic and extrinsic muscles of the hand
Authors: Tanzarella Simone , Muceli Silvia , Del Vecchio Alessandro , Casolo Andrea , Farina Dario
Published: July 2020

Objective. We present a non-invasive framework for investigating efferent commands to 14 extrinsic and intrinsic hand muscles. We extend previous studies (limited to a few muscles) on common synaptic input among pools of motor neurons in a large number of muscles. Approach. Seven subjects performed sinusoidal isometric contractions to complete seven types of grasps, with each finger and with three combinations of fingers in opposition with the thumb. High-density surface EMG (HD-sEMG) signals (384 channels in total) recorded from the 14 muscles were decomposed into the constituent motor unit action potentials. This provided a non-invasive framework for the investigation of motor neuron discharge patterns, muscle coordination and efferent commands of the hand muscles during grasping. Moreover, during grasping tasks, it was possible to identify common neural information among pools of motor neurons innervating the investigated muscles. For this purpose, principal component analysis (PCA) was applied to the smoothed discharge rates of the decoded motor units. Main results. We found that the first principal component (PC1) of the ensemble of decoded motor neuron spike trains explained a variance of (53.0 ± 10.9) % and was positively correlated with force (R = 0.67 ± 0.10 across all subjects and tasks). By grouping the pools of motor neurons from extrinsic or intrinsic muscles, the PC1 explained a proportion of variance of (57.1 ± 11.3) % and (56.9 ± 11.8) %, respectively, and was correlated with force with R = 0.63 ± 0.13 and 0.63 ± 0.13, respectively. Significance. These observations demonstrate a low dimensional control of motor neurons across multiple muscles that can be exploited for extracting control signals in neural interfacing. The proposed framework was designed for hand rehabilitation perspectives, such as post-stroke rehabilitation and hand-exoskeleton control.
DNA as a semiconductor: Analysis of charge localization
Authors: Mesa L. G. , Garcia-Castro A.C. , Páez C. J.
Published: July 2020

In this work, we analyze the charge localization in DNA molecules using an effective tight-binding approach that includes the backbone onsite energies. The localization length and participation number are examined as a function of energy dependence. We see that for specific energy ranges, the electronic states spread out into all sites, while in other energy ranges, the probability density is highly concentrated on either the backbone sites or the nucleotide like sites.
Synthesis and characterization of starch stabilized Ag nanoparticles. Effect of the crystalline structure of starch.
Authors: Paola Sanchez-Castañeda M. , Cañon-Ibarra Andres F. , Cruz-Posada Andres F. , Sanchez Leidy T. , Pinzon Magda I. , Villa Cristian C.
Published: July 2020

Silver nanoparticles (AgNps) are known for their antimicrobial activity and other physicochemical properties that can be applied in several fields. Most of their synthesis methods include chemical reduction and the use of stabilizing agents such as starch. In recent years, several green methods have been developed such as using carbohydrates as reducing agents. On the other hand, starch is a semi crystalline structure formed by mixtures of the linear glucan, amylose and the branched glucan amylopectin. In this work we studied the effect of the semi crystalline structure on the physicochemical properties (particle size and surface plasmon resonance). Three types of starch were selected (corn, potato and banana) representing the three types of semi crystalline structures of the starch granule (A, B and C). Results showed that banana starch allowed larger particle sizes and broader size distribution, while there was not significant difference between nanoparticles stabilized with A and B type starches.
Influence of the variation of the experimental conditions when obtaining the TiO2 antireflective thin film
Authors: Montes-Monsalve J.I. , Florez L. A. , Mósquera L. M. , Dorantes-Rodriguez R. , Cruz-Muñoz B.
Published: July 2020

The formation of thin films based on TiO2 plays a fundamental role in research involving solar energy (solar cell and solar thermal collectors) and from the part environmental (photocatalysis-artificial photosynthesis as a source of clean energy). In this sense, our work has focused on the experimental details directed towards the method of obtaining, for which as a precursor salt Titanium Oxyacetylacetonate (IV) (Sigma Aldrich with 90 % purity) it has been used dissolved in methyl alcohol (Fisher Chemical with 99.8% purity) in 0.05 M molar concentration. The effect on deposited films was studied by varying airflow (2 L/min - 6 L/min) and substrate temperature (150 °C - 450 °C). For the Optical and structural characterization was used UV-VIS spectroscopy and X-ray diffraction techniques. From the analysis of the results was determined the energy band gap with values around 3.5 eV for all films. The Anatase phase with tetragonal structure was find it, refined using the Rietveld method that determined network parameters of a = 3.807617 Å, b = 3.807617 Å, c = 9.547797 Å, the thickness of the films ranged in a range between 70 nm - 150 nm whose values depended on the deposit conditions. The previous evidence allows concluding that this material can be used as an anti-reflective layer to be implemented in solar collectors.
An Analysis and Comparison Performance of DNA and Chaotic Method Combination for Image Encryption
Authors: Saputra V , Setiadi D R I M , Rachmawanto E H
Published: July 2020

There is a variety of important and personal information stored in an image that is often shared via the internet. Cryptography is one way to protect these image files, so that private information cannot be read by malicious third parties. The DNA and Chaos methods are one of the cryptographic methods that are widely proposed and combined. Some previous research proposes a combination of these two methods with a sequence of different methods and different testing techniques where all the research claims the results are very good. This research aims to analyze and compare the performance of two methods namely DNA-Chaos and Chaos-DNA with more complete measurement tools such as PSNR and SSIM to measure results visually, there is also entropy to measure the probability of encryption results can be solved, NPCR and UACI to find out encryption strength from differential attacks and image histogram analysis. From the test results, it appears that both methods have their own strengths and weaknesses. Chaos-DNA is superior in entropy, and UACI, while DNA-Chaos is superior in PSNR, SSIM and NPCR values, but the difference is not significant, so it can be said that the performance of the two methods is quite identical. The results of the histogram analysis also showed that the shape of the histogram generated from the encrypted image was also quite similar.
Identification the Maturity Level of Carica Papaya Using the K-Nearest Neighbor
Authors: Suban I B , Paramartha A , Fortwonatus M , Santoso A J
Published: July 2020

The agricultural sector plays an essential role in economic growth in Indonesia. It can see from the grouping of economic activities. In the grouping of economic activities, the agricultural sector is classified in the primary sector. Determination of proper maturity at harvest is essential to get good quality fruit. Overripe fruits tend to be softer and more chewy and produce a bland taste. This research aims to assist papaya farmers in recognizing the maturity level of papaya so that they can effectively determine the maturity level of the papaya fruit. The method used in this research is the K-Nearest Neighbor method. The success rate of identification of papaya fruit maturity obtained using the K-Nearest Neighbor learning method with a success rate of 100%. From the identification results obtained, produce two outputs that are 100% unripe and 100% ripe.
Comparison of EMD, VMD and EEMD Methods in Respiration Wave Extraction Based on PPG Waves
Authors: Hadiyoso S , Dewi E M , Wijayanto I
Published: July 2020

Plethysmographic (PPG) wave analysis can provide interesting information including heart rate and oxygen saturation. Since PPG signals are modulated by breathing waves, further analysis can provide additional information that is the respiration rate (RR). This is a way to simplify sensor devices. This paper discusses a respiration wave extraction mechanism to calculate RR using the signal decomposition approach. Decomposition methods which are applied in this study include empirical mode decomposition (EMD), variational mode decomposition (VMD) and ensemble empirical mode decomposition (EEMD). This paper specifically addresses the performance of EEMD to EMD and VMD. This proposed method has been tested on an open PPG dataset (containing PPG and RR wave signals). Test results on 20 PPG signals, each of which had a duration of 1 minute showed that the EEMD was able to estimate the RR with an accuracy of more than 90% with an average error rate of 1 rate/minute.
IT Governance Audit and Determination of Work Priorities Using Analytical Hierarchy Process: Case Study the Government of North Maluku, Indonesia
Authors: Arief A , Natsir D , Khairan A , Sensuse D I
Published: July 2020

In the planning stage of IT Governance, there are problems that are found, namely, how to recommend an order of improvement for given work priorities so that it matches the needs of the existing conditions. The goal to be achieved is to be able to provide recommendations in order of work priority, using Analytical Hierarchy Process (AHP). The results of the study are work priority recommendations that can be used as material for consideration at the ICT Department in the Government North Maluku, Indonesia. The results of the analysis give the 1st recommendation is the optimization of information technology utilization ranks highest with AHP score of 0.172, 2nd for improving the quality of apparatus resources with AHP score of 0.147, office administration services with a score of 0.119, third-order, improvement of communication and information and the use of mass media with a score of 0.117, and the last one is increasing the quality of public services with a score of 0.116. So that the recommendations for improvement in the order of work priorities can be an IT governance guide in the Government of North Maluku to move forward.
Optimal energy management of Ice thermal energy storage-based air conditioning system for commercial buildings in real-time – A review based on POET framework
Authors: Odufuwa O Y , Kusakana K , Numbi B P
Published: July 2020

This paper applied the POET framework to analyze and identify possible energy efficiency activities that may reduce energy costs in HVAC cooling systems with Ice Thermal Energy Storage (ITES) in order to achieve maximum potential cost-savings, particularly for cooling loads in commercial buildings. Significant cost savings may be realized by the optimal shifting of the energy usage profile to the least costly regions of the Time-of-Use (TOU) using the ITES system. Moreover, a further reduction of energy costs may be achieved by introducing renewable energy (RE) sourced systems. A potential reduction of approximately 50% in energy cost savings could be achieved with the application of the POET framework. Improvement in operational efficiency may be achieved if systems were optimally sized and controlled. Studies conducted on control methods have shown that Model Predictive Control (MPC) offers significant benefits of achieving reasonable operational efficiency compared to other methods, particularly on HVAC systems. Combined ITES and hybrid energy systems allow an additional advantage in demand-side management, per the TOU tariff and peak demand. This may ultimately result in minimal energy usage during the costly regions of the TOU tariff, which would minimize energy costs and technology and equipment efficiency may be improved.
Reverse Engineering Website Navigation Using an Information Architecture Approach (Case Study: Kanal Pengetahuan Universitas Gadjah Mada)
Authors: Fikri M , Kusumawardani S S , Ferdiana R
Published: July 2020

In its development, the website of Kanal Pengetahuan UGM is built through a practical approach, so there are many shortcomings in defining the need and strategy information for the needs of the service business. As for the current problem, i.e., poor navigation related to the definition of primary content and links in the navigation menu. This is causing the granularity of information that makes users difficult to understand and find the information they need. This research aims to do reverse engineering of website navigation using the information architecture method to investigate the way how users to find and interact with information content from the website. The main contribution of this research is the analysis of the result of card sorting has directed the research to gain insight into how the users in categorizing information on the website. As a result, in the current system, there are only 3 categories that have not yet represented all the information provided by the website, so that research conducted with 102 participants produced a new navigation proposal with 4 new categories that fit the user’s mental model.
Intensified burn severity in California’s northern coastal mountains by drier climatic condition
Authors: Huang Yuhan , Jin Yufang , Schwartz Mark W , Thorne James H
Published: July 2020

The severity of wildfire burns in interior lands of western US ecosystems has been increasing. However, less is known about its coastal mountain ecosystems, especially under extreme weather conditions, raising concerns about the vulnerability of these populated areas to catastrophic fires. Here we examine the fine-scale association between burn severity and a suite of environmental drivers including explicit fuel information, weather, climate, and topography, for diverse ecosystems in California’s northern coastal mountains. Burn severity was quantified using Relative difference Normalized Burn Ratio from Landsat multispectral imagery during 1984–2017. We found a significant increasing trend in burned areas and severity. During low-precipitation years, areas that burned had much lower fuel moisture and higher climatic water deficit than in wetter years, and the percentage of high-severity areas doubled, especially during the most recent 2012–2016 drought. The random forest (RF) machine learning model achieved overall accuracy of 79% in classifying categories of burn severity. Aspect, slope, fuel type and availability, and temperature were the most important drivers, based on both classification and regression RF models. We further examined the importance of drivers under four climatic conditions: dry vs. wet years, and during two extended drought periods (the 2012–2016 warmer drought vs. the 1987–1992 drought). During warm and dry years, the spatial variability of burn severity was a mixed effect of slope, long-term minimum temperature, fuel amount, and fuel moisture. In contrast, climatic water deficit and short-term weather became dominant factors for fires during wetter years. These results suggest that relative importance of drivers for burn severity in the broader domain of California’s northern coastal mountains varied with weather scenarios, especially when exacerbated by warm and extended drought. Our findings highlight the importance of targeting areas with high burn severity risk for fire adaptation and mitigation strategies in a changing climate and intensifying extremes.
A systematical ab-initio review of promising 2D MXene monolayers towards Li-ion battery applications
Authors: Yorulmaz Uğur , Demiroğlu İlker , Çakir Deniz , Gülseren Oğuz , Sevik Cem
Published: July 2020

Two-dimensional materials have been attracting increasing interests because of their outstanding properties for Lithium-ion battery applications. In particular, a material family called MXenes (Mn+1Cn, where n = 1, 2, 3) have been recently attracted immense interest in this respect due to their incomparable fast-charging properties and high capacity promises. In this article, we review the state-of-the-art computational progress on Li-ion battery applications of MXene materials in accordance with our systematical DFT calculations. Structural, mechanical, dynamical, and electrical properties of 20 distinct MXene (M: Sc, Ti, V, Cr, Nb, Mo, Hf, Ta, W, and Zr) have been discussed. The battery performances of these MXene monolayers are further investigated by Li-ion binding energies, open circuit voltage values, and Li migration energy barriers. The experimental and theoretical progress up to date demonstrates particularly the potential of non-terminated or pristine MXene materials in Li ion-storage applications. Stability analyses show most of the pristine MXenes should be achievable, however susceptible to the development progress on the experimental growth procedures. Among pristine MXenes, Ti2C, V2C, Sc2C, and Zr2C compounds excel with their high charge/discharge rate prospect due to their extremely low Li diffusion energy barriers. Considering also their higher predicted gravimetric capacities, Sc, Ti, V, and Zr containing MXenes are more promising for their utilization in energy storage applications.
Preanalytical Challenges During Capillary Fingerstick Sampling Preclude Its Widespread Use in Adult Hospitalized Patients
Authors: Jankowski Christopher A , Casapao Anthony M , Siller Sandra , Isache Carmen , Cani Kelia V , Claudio Alyssa M , Brown Megan , Milstid Bryan , Feldhammer Matthew
Published: July 2020

Objectives

Patient compliance with laboratory testing is one of the most underrecognized challenges in developing a treatment plan for acute and chronically ill patients. The ability to offer alternatives to standard venipuncture blood draws would greatly increase a laboratory’s ability to provide testing to patients and health care providers.

Methods

We performed a prospective observational study on paired venous and fingerstick capillary blood samples from admitted patients undergoing vancomycin therapy. Paired specimens were analyzed for vancomycin and a basic metabolic panel (BMP: calcium, carbon dioxide, chloride, potassium, sodium, creatinine, glucose, serum urea nitrogen) on the core laboratory’s automated chemistry and immunochemistry platforms.

Results

A total of 59 paired fingerstick and venous blood specimens from 56 unique inpatients were analyzed. Paired samples were comparable for all the analytes tested with the exception of bicarbonate and potassium, which were significantly different among the capillary sample group. Patients required multiple fingers be lanced in 15% of cases to obtain sufficient blood to carry out the testing. Capillary sample rejection rates due to insufficient volumes were as high as 30% in the initial 30 patients enrolled in the study.

Conclusions

Vancomycin and the BMP, with the exception of potassium and bicarbonate, were determined to be analytically comparable. However, significant preanalytical issues should preclude laboratories and providers from more widespread adoption of fingerstick-derived capillary blood as an alternative sampling method except in the most extenuating of circumstances.
Retinoic acid receptor antagonists for male contraception: current status†
Authors: Noman Md Abdullah Al , Kyzer Jillian L , Chung Sanny S W , Wolgemuth Debra J , Georg Gunda I
Published: July 2020

Retinoic acid receptor alpha (RARA), a nuclear receptor protein, has been validated as a target for male contraception by gene knockout studies and also pharmacologically using a pan-retinoic acid receptor antagonist. Retinoic acid receptor alpha activity is indispensable for the spermatogenic process, and therefore its antagonists have potential as male contraceptive agents. This review discusses the effects of systematic dosing regimen modifications of the orally bioavailable and reversible pan-antagonist BMS-189453 as well as studies with the alpha-selective antagonists BMS-189532 and BMS-189614 in a murine model. We also provide an overview of structure–activity studies of retinoic acid receptor alpha antagonists that provide insight for the design of novel alpha-selective ligands.
Hypokalaemic periodic paralysis with a charge-retaining substitution in the voltage sensor
Authors: Kubota Tomoya , Wu Fenfen , Vicart Savine , Nakaza Maki , Sternberg Damien , Watanabe Daisuke , Furuta Mitsuru , Kokunai Yosuke , Abe Tatsuya , Kokubun Norito , Fontaine Bertrand , Cannon Stephen C , Takahashi Masanori P
Published: July 2020

Familial hypokalaemic periodic paralysis is a rare skeletal muscle disease caused by the dysregulation of sarcolemmal excitability. Hypokalaemic periodic paralysis is characterized by repeated episodes of paralytic attacks with hypokalaemia, and several variants in CACNA1S coding for CaV1.1 and SCN4A coding for NaV1.4 have been established as causative mutations. Most of the mutations are substitutions to a non-charged residue, from the positively charged arginine (R) in transmembrane segment 4 (S4) of a voltage sensor in either CaV1.1 or NaV1.4. Mutant channels have aberrant leak currents called ‘gating pore currents’, and the widely accepted consensus is that this current is the essential pathological mechanism that produces susceptibility to anomalous depolarization and failure of muscle excitability during a paralytic attack. Here, we have identified five hypokalaemic periodic paralysis cases from two different ethnic backgrounds, Japanese and French, with charge-preserving substitutions in S4 from arginine, R, to lysine, K. An R to K substitution has not previously been reported for any other hypokalaemic periodic paralysis families. One case is R219K in NaV1.4, which is located at the first charge in S4 of Domain I. The other four cases all have R897K in CaV1.1, which is located at the first charge in S4 of Domain III. Gating pore currents were not detected in expression studies of CaV1.1-R897K. NaV1.4-R219K mutant channels revealed a distinct, but small, gating pore current. Simulation studies indicated that the small-amplitude gating pore current conducted by NaV1.4-R219K is not likely to be sufficient to be a risk factor for depolarization-induced paralytic attacks. Our rare cases with typical hypokalaemic periodic paralysis phenotypes do not fit the canonical view that the essential defect in hypokalaemic periodic paralysis mutant channels is the gating pore current and raise the possibility that hypokalaemic periodic paralysis pathogenesis might be heterogeneous and diverse.
Tumor somatic mutations also existing as germline polymorphisms may help to identify functional SNPs from genome-wide association studies
Authors: Gorlov Ivan P , Xia Xiangjun , Tsavachidis Spiridon , Gorlova Olga Y , Amos Christopher I
Published: July 2020

We hypothesized that a joint analysis of cancer risk-associated single-nucleotide polymorphism (SNP) and somatic mutations in tumor samples can predict functional and potentially causal SNPs from GWASs. We used mutations reported in the Catalog of Somatic Mutations in Cancer (COSMIC). Confirmed somatic mutations were subdivided into two groups: (1) mutations reported as SNPs, which we call mutational/SNPs and (2) somatic mutations that are not reported as SNPs, which we call mutational/noSNPs. It is generally accepted that the number of times a somatic mutation is reported in COSMIC correlates with its selective advantage to tumors, with more frequently reported mutations being more functional and providing a stronger selective advantage to the tumor cell. We found that mutations reported ≥10 times in COSMIC—frequent mutational/SNPs (fmSNPs) are likely to be functional. We identified 12 cancer risk-associated SNPs reported in the Catalog of published GWASs at least 10 times as confirmed somatic mutations and therefore deemed to be functional. Additionally, we have identified 42 SNPs that are tightly linked (R2 ≥ 0.8) to SNPs reported in the Catalog of published GWASs as cancer risk associated and that are also reported as fmSNPs. As a result, 54 candidate functional/potentially causal cancer risk associated SNPs were identified. We found that fmSNPs are more likely to be located in evolutionarily conserved regions compared with cancer risk associated SNPs that are not fmSNPs. We also found that fmSNPs also underwent positive selection, which can explain why they exist as population polymorphisms.
Mitigation of a Coronavirus Disease 2019 Outbreak in a Nursing Home Through Serial Testing of Residents and Staff
Authors: Escobar Daniel J , Lanzi Maria , Saberi Pouné , Love Ruby , Linkin Darren R , Kelly John J , Jhala Darshana , Amorosa Valerianna , Hofmann Mary , Doyon Jeffrey B
Published: July 2020

Nursing homes and long-term care facilities represent highly vulnerable environments for respiratory disease outbreaks, such as coronavirus disease 2019 (COVID-19). We describe a COVID-19 outbreak in a nursing home that was rapidly contained by using a universal testing strategy of all residents and nursing home staff.
Utility of a Fifth-Generation Ultrasensitive Prostate-Specific Antigen Assay for Monitoring Prostate Cancer Patients after Radical Prostatectomy with 3 Years of Follow-Up
Authors: Ren Annie H , Soosaipillai Antoninus , Mathew Anu , Nikolenko Galina , Sardesai Laukik , Stengelin Martin , Diamandis Eleftherios P
Published: July 2020

Background

We investigated an ultrasensitive prostate-specific antigen (uPSA) immunoassay (MesoScale; lower limit of detection (LLD) of 0.0035 pg/mL) to monitor patients with prostate cancer (PCa) following radical prostatectomy (RP) and to examine whether changes in PSA in the conventionally undetectable range (<1 pg/mL) can predict biochemical relapse (BCR).

Methods

We measured uPSA in serial serum samples (N = 100) collected from 20 RP cases with a third-generation ELISA (LLD of 1 pg/mL) and the fifth-generation MesoScale assay. We analyzed the PSA nadir changes to classify patients into BCR or non-BCR groups, observed the trends in PSA kinetics, and associated BCR status with clinicohistopathological features.

Results

The ELISA could quantify PSA in only 38% of the RP samples, detecting BCR in 7 of 20 patients with PCa. The MesoScale assay quantified PSA in all samples, showing 8 of 20 patients with BCR. However, there was no significant difference between the median time to BCR detection based on ELISA (1016 days) compared with MesoScale data (949 days). Gleason scores were higher in the BCR groups compared with non-BCR. There was no significant difference for other clinicohistopathological parameters.

Conclusions

The uPSA MesoScale technology could track miniscule changes in serum PSA in the range of 0.003–1 pg/mL in all RP cases. However, PSA kinetics and nadir at concentrations <2 pg/mL fluctuated, and increases below this range could not reliably suggest signs of BCR. Instead, ultrasensitive fifth-generation PSA assays may hold clinical potential for measuring the low concentrations of PSA in women for various medical contexts.
Identifying and estimating the effects of unconventional monetary policy: How to do it and what have we learned?
Authors: Rossi Barbara
Published: July 2020

The recent financial crisis led central banks to lower their interest rates in order to stimulate the economy until they hit the zero lower bound. How should one identify monetary policy shocks in unconventional times? Are unconventional monetary policies as effective as conventional ones? And has the monetary policy transmission mechanism changed in the zero lower bound era? This article aims to provide an overview of the econometric challenges of and the solutions to the identification of monetary policy shocks in unconventional times as well as a survey of their empirical effects on the economy.
A complexity-driven framework for waveform tomography with discrete adjoints
Authors: Szenicer Alexandre , Leng Kuangdai , Nissen-Meyer Tarje
Published: July 2020

We develop a new approach for computing Fréchet sensitivity kernels in full waveform inversion by using the discrete adjoint approach in addition to the widely used continuous adjoint approach for seismic waveform inversion. This method is particularly well suited for the forward solver AxiSEM3D, a combination of the spectral-element method (SEM) and a Fourier pseudo-spectral method, which allows for a sparse azimuthal wavefield parametrization adaptive to wavefield complexity, leading to lower computational costs and better frequency scaling than conventional 3-D solvers. We implement the continuous adjoint method to serve as a benchmark, additionally allowing for simulating off-axis sources in axisymmetric or 3-D models. The kernels generated by both methods are compared to each other, and benchmarked against theoretical predictions based on linearized Born theory, providing an excellent fit to this independent reference solution. Our verification benchmarks show that the discrete adjoint method can produce exact kernels, largely identical to continuous kernels. While using the continuous adjoint method we lose the computational advantage and fall back on a full-3-D frequency scaling, using the discrete adjoint retains the speedup offered by AxiSEM3D. We also discuss the creation of a data-coverage based mesh to run the simulations on during the inversion process, which would allow to exploit the flexibility of the Fourier parametrization and thus the speedup offered by our method.
Is it a possibility to achieve energy plus prefabricated building worldwide?
Authors: Alkhalidi Ammar , Abuothman Abeer , AlDweik Abdallah , Al-Bazaz Al-Hamza
Published: July 2020

Prefabricated buildings constructed to be used in a specific region cannot be assumed to work unconditionally in different climates around the world. It is important to develop passive house solutions for each location, suitable for the actual climate and geographic conditions. Shelters could be used in different applications such as refugee housing or telecommunication stations. Photovoltaic energy could cover the electricity consumption of these shelters. Shelters for different applications should be usable in all weather conditions, and because of that different climate zones were chosen. A full study about three climate zones was done to study the different factors that play a significant rule in choosing the location of the shelter. In this study, prefabricated housing was designed to ensure thermal comfort by doing structure design changes and using solar energy as an energy source. Three different locations have been chosen to be able to perform the best structure and components design for every location, taking into consideration the assumptions taken in each place. The total photovoltaic system was designed with a capacity of hot, moderate and cold climate zones with 2.0, 1.8 and 3.45 kWp, respectively, along with energy plus the production of 38% in the hot, 47% in the moderate and 28% in the cold climate.
Affine Equivalence and Saddle Connection Graphs of Half-Translation Surfaces
Authors: Pan Huiping
Published: July 2020

To every half-translation surface, we associate a saddle connection graph, which is a subgraph of the arc graph. We prove that every isomorphism between two saddle connection graphs is induced by an affine homeomorphism between the underlying half-translation surfaces. We also investigate the automorphism group of the saddle connection graph and the corresponding quotient graph.
Higher genus theory
Authors: Koymans Peter , Pagano Carlo
Published: July 2020

In $1801$, Gauss found an explicit description, in the language of binary quadratic forms, for the $2$-torsion of the narrow class group and dual narrow class group of a quadratic number field. This is now known as Gauss’s genus theory. In this paper, we extend Gauss’s work to the setting of multi-quadratic number fields. To this end, we introduce and parametrize the categories of expansion groups and expansion Lie algebras, giving an explicit description for the universal objects of these categories. This description is inspired by the ideas of Smith [ 16] in his recent breakthrough on Goldfeld’s conjecture and the Cohen–Lenstra conjectures. Our main result shows that the maximal unramified multi-quadratic extension $L$ of a multi-quadratic number field $K$ can be reconstructed from the set of generalized governing expansions supported in the set of primes that ramify in $K$. This provides a recursive description for the group $\textrm{Gal}(L/\mathbb{Q})$ and a systematic procedure to construct the field $L$. A special case of our main result gives an upper bound for the size of $\textrm{Cl}^{+}(K)[2]$.
The Registry of Senior Australians outcome monitoring system: quality and safety indicators for residential aged care
Authors: Inacio Maria C , Lang Catherine , Caughey Gillian E , Bray Sarah C E , Harrison Stephanie L , Whitehead Craig , Visvanathan Renuka , Evans Keith , Corlis Megan , Cornell Victoria , Wesselingh Steve
Published: July 2020

Objectives

To introduce the Registry of Senior Australians (ROSA) Outcome Monitoring System, which can monitor the quality and safety of care provided to individuals accessing residential aged care. Development and examination of 12 quality and safety indicators of care and their 2016 prevalence estimates are presented.

Design

Retrospective.

Setting

2690 national and 254 South Australian (SA) aged care facilities.

Participants

208 355 unique residents nationally and 18 956 in SA.

Main Outcome Measures

Risk-adjusted prevalence of high sedative load, antipsychotic use, chronic opioid use, antibiotic use, premature mortality, falls, fractures, medication-related adverse events, weight loss/malnutrition, delirium and/or dementia hospitalisations, emergency department presentations, and pressure injuries.

Results

Five indicators were estimated nationally; antibiotic use (67.5%, 95% confidence interval (CI): 67.3–67.7%) had the highest prevalence, followed by high sedative load (48.1%, 95% CI: 47.9–48.3%), chronic opioid use (26.8%, 95% CI: 26.6–26.9%), antipsychotic use (23.5%, 95% CI: 23.4–23.7%) and premature mortality (0.6%, 95% CI: 0.6–0.7%). Seven indicators were estimated in SA; emergency department presentations (19.1%, 95% CI: 18.3–20.0%) had the highest prevalence, followed by falls (10.1%, 95% CI: 9.7–10.4%), fractures (4.8%, 95% CI: 4.6–5.1%), pressure injuries (2.9%, 95% CI: 2.7–3.1%), delirium and/or dementia related hospitalisations (2.3%, 95% CI: 2.1–2.6%), weight loss/malnutrition (0.7%, 95% CI: 0.6–0.8%) and medication-related events (0.6%, 95% CI: 0.5–0.7%).

Conclusions

Twelve quality and safety indicators were developed to monitor aged care provided to older Australians based on the synthesis of existing literature and expert advisory input. These indicators rely on existing data within the aged care and healthcare sectors, therefore creating a pragmatic tool to examine quality and unwarranted care variation.
Thermomechanical and enzyme-facilitated processing of soybean meal enhanced in vitro kinetics of protein digestion and protein and amino acid digestibility in weaned pigs
Authors: Ton Nu Mai Anh , Lupatsch Ingrid , Zannatta Joaquin S , Schulze Hagen , Zijlstra Ruurd T
Published: July 2020

Soybean meal (SBM) contains anti-nutritional factors (ANF) that may limit kinetics and total extent of protein digestion in pigs. This study evaluated the effects of thermomechanical and enzyme-facilitated (TE) processing on in vitro kinetics of crude protein (CP) digestion and CP and amino acid (AA) digestibility in weaned pigs. Each batch of SBM (48% CP) was divided into two parts: non-processed SBM as control vs. thermomechanical and enzyme-facilitated processed soybean meal (TES) as the experimental group. For digestion kinetics, samples (three batches of non-processed SBM vs. TES) were incubated in triplicate sequentially with pepsin at pH 3.5 for 1.5 h (stomach phase) and subsequently with pancreatin and bile extract at pH 6.8 for 0, 0.5, 1, 2, 4, or 6 h (small intestine phase). Protein was classified into CPfast, CPslow, and CPresistant corresponding to CP digested within the first 0.5 h, from 0.5 to 4 h, and after 4 h plus undigested CP, respectively. Eight weaned barrows (Large White × Duroc, 9.43 ± 0.40 kg) were surgically fitted with a T-cannula at the terminal ileum. Pigs were randomly assigned to a Youden square with three diets over four periods. The three diets were an N-free diet and two diets using 40% SBM or TES as the sole source of AA with Cr2O3 as an indigestible marker. Each period included sequentially a 5-d adaptation, 2-d collection of feces, and 2-d collection of ileal digesta. The TE processing reduced ANF content in TES by 91% for lectin, 22% for trypsin inhibitor activity, 75% for β-conglycinin, and 62% for glycinin compared with SBM. In vitro, TE processing increased (P < 0.05) digested CP by 5.6% and enhanced the kinetics of CP digestion by tending to increase (P = 0.056) CPfast by 25% and reducing (P < 0.05) CPslow and CPresistant by 48% and 11%, respectively. In pigs, TE processing increased (P < 0.05) apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of CP in TES by 2.3% and 2.1%, respectively. The TE processing increased (P < 0.05) AID and SID of all AA up to 3.3%, except for AID of Pro and SID of Pro, Gly, and Cys. The TE processing did not change reactive Lys or Lys:CP but increased (P < 0.05) SID of Lys and reactive Lys by 3%. Combined, the greater in vitro digestion kinetics matched the greater in vivo AID and SID of CP in TES and lower ANF compared with SBM. Thus, TE processing created a protein source that is digested faster and to a greater extent than SBM, thereby lowering the chance of protein fermentation.
Identification of Edible Short- and Long-Horned Grasshoppers and Their Host Plants in East Africa
Authors: Leonard Alfonce , Khamis Fathiya M , Egonyu James P , Kyamanywa Samuel , Ekesi Sunday , Tanga Chrysantus M , Copeland Robert S , Subramanian Sevgan
Published: July 2020

There is a paucity of information on the edible grasshoppers and their host plants in East Africa. This study adopted morphological and molecular analysis to identify edible grasshoppers in Kenya and Uganda. The associated host plants were identified through molecular analysis of the gut contents of the grasshoppers. The cytochrome b and 16s gene primers were used for grasshopper DNA analysis; while matK gene primers were used for plant DNA analysis. All long-horned grasshoppers sampled were identified as Ruspolia differens (Serville) (Orthoptera: Tettigonidae); whereas short-horned grasshoppers were identified as Acanthacris ruficornis (Fabricius) (Orthoptera: Acrididae) and Cyrtacanthacris tatarica (L.) (Orthoptera: Acrididae). Host plants of A. ruficornis were Achyranthes aspera (L.), Centella virgata L.f. Drude, Digitaria gayana (Kunth), Galinsoga quadriradiata Ruiz and Pavon, and Triumfetta pilosa Roth; whereas those of C. tatarica were Alysicarpus rugosus (Willd.) DC and Teramnus uncinatus (L.) SW. Host plants of R. differens were Ageratum conyzoides (L.), Citrus depressa Hayata, Cynodon dactylon (L.), D. gayana, Eragrostis mexicana Hornem, Eucalyptus saligna SM., Indigofera arrecta Hochst. ex A. Rich., Persicaria nepalensis (L.), and Sorghum halepense (L.). Information on the host plants of edible grasshoppers can help in the development of their mass rearing protocols.
Summer roosts of “The revenant” flat-headed myotis, Myotis planiceps
Authors: Núñez-Rojo María Paulina , Arroyo-Cabrales Joaquín , Rivera-Téllez Emmanuel , Medellín Rodrigo A
Published: July 2020

The flat-headed myotis (Myotis planiceps) was declared extinct in 1996 but rediscovered in 2004, thus the reference to a revenant, one who came back from the dead, as it was declared extinct in 1996 but rediscovered in 2004. However, the species still faces serious extinction risk. To aid in the strategic planning and priorities for conservation, we studied roosting ecology. These bats inhabit the Chihuahuan Desert in one of the smallest distributional ranges of any mammal. Using radiotelemetry, we located 25 summer roosts, all in the skirts of dry leaves of yucca trees (Yucca carnerosana). We conclude that to roost, these bats search for clumps of tall yucca trees with a mean height of 3.93 m and mean width of skirts of 1.35 m.
Formation of planetary populations – III. Core composition and atmospheric evaporation
Authors: Alessi Matthew , Inglis Julie , Pudritz Ralph E
Published: July 2020

The exoplanet mass–radius diagram reveals that super-Earths display a wide range of radii, and therefore mean densities, at a given mass. Using planet population synthesis models, we explore the key physical factors that shape this distribution: planets’ solid core compositions, and their atmospheric structure. For the former, we use equilibrium disc chemistry models to track accreted minerals on to planetary cores throughout the formation. For the latter, we track gas accretion during the formation and consider photoevaporation-driven atmospheric mass-loss to determine what portion of accreted gas escapes after the disc phase. We find that atmospheric stripping of Neptunes and sub-Saturns at small orbital radii (≲0.1 au) plays a key role in the formation of short-period super-Earths. Core compositions are strongly influenced by the trap in which they formed. We also find a separation between Earth-like planet compositions at small orbital radii ≲0.5 au and ice-rich planets (up to 50 per cent by mass) at larger orbits ∼1 au. This corresponds well with the Earth-like mean densities inferred from the observed position of the low-mass planet radius valley at small orbital periods. Our model produces planet radii comparable to observations at masses ∼1–3 M⊕. At larger masses, planets’ accreted gas significantly increases their radii to be larger than most of the observed data. While photoevaporation, affecting planets at small orbital radii ≲0.1 au, reduces a subset of these planets’ radii and improves our comparison, most planets in our computed populations are unaffected due to low-far ultraviolet fluxes as they form at larger separations.